Ecology

@misc{elton1927animal29,
    author = "Elton, C. S",
    title = "Animal ecology",
    year = "1927",
    howpublished = "London, Sidgwick and Jackson, 209 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Elton, C. S., 1927, Animal ecology: London, Sidgwick and Jackson, 209 p.}"
}

@techreport{cowles1936a25,
    author = "Cowles, R. P. and Brambel, C. E",
    title = "A study of the environmental conditions in a bog pond with special reference to the diurnal vertical distribution of Gonyostomum semen",
    year = "1936",
    howpublished = "Biological Bulletin, Marine Biological Laboratory, Woods Hole, Mass., v. 71, p. 286-298",
    note = "talkorigins\_source = {true}; raw\_reference = {Cowles, R. P., and Brambel, C. E., 1936, A study of the environmental conditions in a bog pond with special reference to the diurnal vertical distribution of Gonyostomum semen: Biological Bulletin, Marine Biological Laboratory, Woods Hole, Mass., v. 71, p. 286-298.}"
}

@article{birch1948the6,
    author = "Birch, L. C",
    title = "The intrinsic rate of natural increase of an insect population",
    year = "1948",
    journal = "Journal of Animal Ecology, v. 16, p. 15-26",
    note = "talkorigins\_source = {true}; raw\_reference = {Birch, L. C., 1948, The intrinsic rate of natural increase of an insect population: Journal of Animal Ecology, v. 16, p. 15-26.}"
}

@misc{dammerman1948the27,
    author = "Dammerman, K. W",
    title = "The fauna of Krakatau",
    year = "1948",
    howpublished = "1883-1933: Verhandel. Kon-Inkl. Ned. Akad. Wetenschap. Afdel. Natuurk., v. 44, p. 1-594",
    note = "talkorigins\_source = {true}; raw\_reference = {Dammerman, K. W., 1948, The fauna of Krakatau: 1883-1933: Verhandel. Kon-Inkl. Ned. Akad. Wetenschap. Afdel. Natuurk., v. 44, p. 1-594.}"
}

@misc{allee1949principles1,
    author = "Allee, W. C. and Emerson, A. E. and Park, O. and Park, T. and Schmidt, K. P",
    title = "Principles of Animal Ecology",
    year = "1949",
    howpublished = "Philadelphia, Saunders, 837 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Allee, W. C., Emerson, A. E., Park, O., Park, T., and Schmidt, K. P., 1949, Principles of Animal Ecology: Philadelphia, Saunders, 837 p.}"
}

@misc{clements1949dynamics17,
    author = "Clements, F. E",
    title = "Dynamics of Vegetation",
    year = "1949",
    howpublished = "New York, Hafner, 296 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Clements, F. E., 1949, Dynamics of Vegetation: New York, Hafner, 296 p.}"
}

@book{clarke1954elements16,
    author = "Clarke, G",
    title = "Elements of Ecology",
    year = "1954",
    publisher = "New York, Wiley, 560 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Clarke, G., 1954, Elements of Ecology: New York, Wiley, 560 p.}"
}

@misc{elton1958the30,
    author = "Elton, C. S",
    title = "The ecology of invasions by animals and plants",
    year = "1958",
    howpublished = "London, England, Methuen, 181 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Elton, C. S., 1958, The ecology of invasions by animals and plants: London, England, Methuen, 181 p.}"
}

@misc{ladd1959ecology33,
    author = "Ladd, H. S",
    title = "Ecology, paleontology and stratigraphy",
    year = "1959",
    howpublished = "Science, v. 129, p. 69-78",
    note = "talkorigins\_source = {true}; raw\_reference = {Ladd, H. S., 1959, Ecology, paleontology and stratigraphy: Science, v. 129, p. 69-78.}"
}

@misc{bartlett1960stochastic4,
    author = "Bartlett, M. S",
    title = "Stochastic Population Models in Ecology and Epidemiology",
    year = "1960",
    howpublished = "London, Methuen, 90 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Bartlett, M. S., 1960, Stochastic Population Models in Ecology and Epidemiology: London, Methuen, 90 p.}"
}

@misc{carson1962silent11,
    author = "Carson, R",
    title = "Silent Spring",
    year = "1962",
    howpublished = "Boston, Houghton-Mifflin",
    note = "talkorigins\_source = {true}; raw\_reference = {Carson, R., 1962, Silent Spring: Boston, Houghton-Mifflin.}"
}

@book{doi104159harvard9780674865327,
    author = "Mayr, Ernst",
    title = "Animal Species and Evolution",
    year = "1963",
    booktitle = "Harvard University Press eBooks",
    url = "https://doi.org/10.4159/harvard.9780674865327",
    doi = "10.4159/harvard.9780674865327",
    openalex = "W2007993714"
}

@misc{caughley1966mortality14,
    author = "Caughley, G",
    title = "Mortality patterns in mammals",
    year = "1966",
    howpublished = "Ecology, v. 47, p. 906-918",
    note = "talkorigins\_source = {true}; raw\_reference = {Caughley, G., 1966, Mortality patterns in mammals: Ecology, v. 47, p. 906-918.}"
}

@misc{cody1966a18,
    author = "Cody, M. L",
    title = "A general theory of clutch size",
    year = "1966",
    howpublished = "Evolution, v. 20, p. 174- 184",
    note = "talkorigins\_source = {true}; raw\_reference = {Cody, M. L., 1966, A general theory of clutch size: Evolution, v. 20, p. 174- 184.}"
}

Adaptive radiation has been defined as the evolutionary divergence of members of a phyletic line into different niches or adaptive zones (Mayr, 1963:633). Although it has been customary to think of adaptive radiation solely in terms of species or races, a growing body of evidence indicates that some degree of radiation occurs also within populations, as individuals come to occupy different subniches or adaptive subzones, subdividing and, perhaps, expanding the total niche or zone utilized by the population. Probably all species show some degree of ecological variation, either polymorphic or continuous. But this phenomenon is being studied in only a few groups of organisms, notably in Drosophila, in which chromosomal polymorphism has been interpreted as a. means of adaptation of populations to heterogeneous environments (Dobzhansky, * 1961, 1963, 1965). Theoretical bases for research on ecological variation in animal populations have been provided by Ludwig (1950), Levene (1953)) da Cunha and Dobzhansky (1954), Dempster (1955), Li (1955), Carson (1959), and Levins (1962, 1963). In birds, as in other vertebrates, the sexes usually differ in size if not also in proportions of body parts, including those used in feeding (Amadon, 1959); and, especially where the degree of sexual dimorphism, which is a form of polymorphism (Ford, 1961: 12), is marked, it seems probable that the morphological divergence has ecological significance in adapting the sexes to different subniches. However, there is only an occasional reference in the literature to sexual dimorphism in relation to niche utilization (e.g., Pitelka, 1950; Rand, 19.52), and, in general, the whole problem of ecological variation in populations has been neglected by vertebrate ecologists. The primary purpose of this report is to present evidence of an adaptive function of sexual dimorphism in size in woodpeckers by relating degrees of morphological dimorphism and sexual divergence in foraging behavior in two melanerpine species, the strongly dimorphic Hispaniolan Woodpecker (Centurus striatus) of Haiti and the Dominican Republic and the moderately dimorphic Golden-fronted Woodpecker (Ce&zmus awifrons) of continental North and Central America. In addition, the paper surveys other evidence that sexual dimorphism in birds is related to differential niche utilization. Finally, some evolutionary aspects of sexual dimorphism and ecological variation are considered.

@article{doi1023071365712,
    author = "Selander, Robert K.",
    title = "Sexual Dimorphism and Differential Niche Utilization in Birds",
    year = "1966",
    journal = "Ornithological Applications",
    abstract = "Adaptive radiation has been defined as the evolutionary divergence of members of a phyletic line into different niches or adaptive zones (Mayr, 1963:633). Although it has been customary to think of adaptive radiation solely in terms of species or races, a growing body of evidence indicates that some degree of radiation occurs also within populations, as individuals come to occupy different subniches or adaptive subzones, subdividing and, perhaps, expanding the total niche or zone utilized by the population. Probably all species show some degree of ecological variation, either polymorphic or continuous. But this phenomenon is being studied in only a few groups of organisms, notably in Drosophila, in which chromosomal polymorphism has been interpreted as a. means of adaptation of populations to heterogeneous environments (Dobzhansky, * 1961, 1963, 1965). Theoretical bases for research on ecological variation in animal populations have been provided by Ludwig (1950), Levene (1953)) da Cunha and Dobzhansky (1954), Dempster (1955), Li (1955), Carson (1959), and Levins (1962, 1963). In birds, as in other vertebrates, the sexes usually differ in size if not also in proportions of body parts, including those used in feeding (Amadon, 1959); and, especially where the degree of sexual dimorphism, which is a form of polymorphism (Ford, 1961: 12), is marked, it seems probable that the morphological divergence has ecological significance in adapting the sexes to different subniches. However, there is only an occasional reference in the literature to sexual dimorphism in relation to niche utilization (e.g., Pitelka, 1950; Rand, 19.52), and, in general, the whole problem of ecological variation in populations has been neglected by vertebrate ecologists. The primary purpose of this report is to present evidence of an adaptive function of sexual dimorphism in size in woodpeckers by relating degrees of morphological dimorphism and sexual divergence in foraging behavior in two melanerpine species, the strongly dimorphic Hispaniolan Woodpecker (Centurus striatus) of Haiti and the Dominican Republic and the moderately dimorphic Golden-fronted Woodpecker (Ce\&zmus awifrons) of continental North and Central America. In addition, the paper surveys other evidence that sexual dimorphism in birds is related to differential niche utilization. Finally, some evolutionary aspects of sexual dimorphism and ecological variation are considered.",
    url = "https://doi.org/10.2307/1365712",
    doi = "10.2307/1365712",
    openalex = "W2084499670",
    references = "crowell1961the, crowell1962reduced, doi101086281792, doi101111j155856461963tb03295x, doi101111j155856461963tb03296x, doi101537ase188722495, doi1023071931600, doi1023071931976, doi1023071932042, doi1023072407089, doi1023072407090, doi104159harvard9780674865327, doi105962bhltitle110063, doi105962bhltitle27468, doi107312rens91062, openalexw1595343243, openalexw1973833797, openalexw2128666103"
}

@misc{clark1967the15,
    author = "Clark, L. R. and Geier, P. W. and Hughes, R. D. and Morris, R. F",
    title = "The Ecology of Insect Populations in Theory and Practice",
    year = "1967",
    howpublished = "London, Methuen, 232 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Clark, L. R., Geier, P. W., Hughes, R. D., and Morris, R. F., 1967, The Ecology of Insect Populations in Theory and Practice: London, Methuen, 232 p.}"
}

In the three lectures which give their title to this delightful collection of esays, the author of Enchanted Voyage and Itinerate Ivory Tower turns his attention to the influence of the environment on the course of evolution. The first lecture considers the nature of the terrestrial biosphere, both as a unique phenomenon on earth and as one of a class of possible spaces on other bodies; the second examines the nature of the ecological niche; and the third discusses some of the possible environmental interactions of a single species, emphasis being placed on the extremely recondite nature of the selective forces that act on man, as on other animals. Another of the pieces deals with the problem of the relation of natural beauty to works of art, particularly in the context of the similarities and differences apparent when natural history museums and art galleries are compared. The final essay, Cream in the Gooseberry Fool, is an account of the role of an English country clergyman and of the European magpie most in one of the most significant early discoveries of genetics.

@article{doi1023072401429,
    author = "Nelson, Jason and Hutchinson, Gillian",
    title = "The Ecological Theater and the Evolutionary Play.",
    year = "1967",
    journal = "Journal of Applied Ecology",
    abstract = "In the three lectures which give their title to this delightful collection of esays, the author of Enchanted Voyage and Itinerate Ivory Tower turns his attention to the influence of the environment on the course of evolution. The first lecture considers the nature of the terrestrial biosphere, both as a unique phenomenon on earth and as one of a class of possible spaces on other bodies; the second examines the nature of the ecological niche; and the third discusses some of the possible environmental interactions of a single species, emphasis being placed on the extremely recondite nature of the selective forces that act on man, as on other animals. Another of the pieces deals with the problem of the relation of natural beauty to works of art, particularly in the context of the similarities and differences apparent when natural history museums and art galleries are compared. The final essay, Cream in the Gooseberry Fool, is an account of the role of an English country clergyman and of the European magpie most in one of the most significant early discoveries of genetics.",
    url = "https://doi.org/10.2307/2401429",
    doi = "10.2307/2401429",
    openalex = "W2330647082"
}

@book{black1968soilplant7,
    author = "Black, C. A",
    title = "Soil-Plant Relationships [2nd ed.]",
    year = "1968",
    publisher = "New York, Wiley, 792 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Black, C. A., 1968, Soil-Plant Relationships [2nd ed.]: New York, Wiley, 792 p.}"
}

@misc{cody1968on19,
    author = "Cody, M. L",
    title = "On the methods of resource division in grassland bird communities",
    year = "1968",
    howpublished = "American Naturalist, v. 102, p. 107-147",
    note = "talkorigins\_source = {true}; raw\_reference = {Cody, M. L., 1968, On the methods of resource division in grassland bird communities: American Naturalist, v. 102, p. 107-147.}"
}

@misc{brown1970seeds8,
    author = "Brown, J. L",
    title = "Seeds of change. The green revolution and development in the 1970's",
    year = "1970",
    howpublished = "New York, Praeger",
    note = "talkorigins\_source = {true}; raw\_reference = {Brown, J. L., 1970, Seeds of change. The green revolution and development in the 1970's: New York, Praeger.}"
}

@misc{cody1970chilean20,
    author = "Cody, M. L",
    title = "Chilean bird distribution",
    year = "1970",
    howpublished = "Ecology, v. 51, p. 455-463",
    note = "talkorigins\_source = {true}; raw\_reference = {Cody, M. L., 1970, Chilean bird distribution: Ecology, v. 51, p. 455-463.}"
}

@misc{dale1970systems26,
    author = "Dale, M. B",
    title = "Systems analysis and ecology",
    year = "1970",
    howpublished = "Ecology, v. 51, p. 2-16",
    note = "talkorigins\_source = {true}; raw\_reference = {Dale, M. B., 1970, Systems analysis and ecology: Ecology, v. 51, p. 2-16.}"
}

@misc{bakker1971ecology3,
    author = "Bakker, R. T",
    title = "Ecology of the brontosaurs",
    year = "1971",
    howpublished = "Nature, v. 229, p. 172-174",
    note = "talkorigins\_source = {true}; raw\_reference = {Bakker, R. T., 1971, Ecology of the brontosaurs: Nature, v. 229, p. 172-174.}"
}

@misc{cailliet1971everymans9,
    author = "Cailliet, G. and Setzer, P. and Love, M",
    title = "Everyman's Guide to Ecological Living",
    year = "1971",
    howpublished = "New York, 119 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Cailliet, G., Setzer, P., and Love, M., 1971, Everyman's Guide to Ecological Living: New York, 119 p.}"
}

@misc{colwell1971on24,
    author = "Colwell, R. K. and Futuyma, D. J",
    title = "On the measurement of niche breadth and overlap",
    year = "1971",
    howpublished = "Ecology, v. 52, p. 567-576",
    note = "talkorigins\_source = {true}; raw\_reference = {Colwell, R. K., and Futuyma, D. J., 1971, On the measurement of niche breadth and overlap: Ecology, v. 52, p. 567-576.}"
}

Species distribution models (SDMs) are numerical tools that combine observations of species occurrence or abundance with environmental estimates. They are used to gain ecological and evolutionary insights and to predict distributions across landscapes,...Read More

@article{doi101146annureves02110171002341,
    author = "Janzen, Daniel H.",
    title = "Seed Predation by Animals",
    year = "1971",
    journal = "Annual Review of Ecology and Systematics",
    abstract = "Species distribution models (SDMs) are numerical tools that combine observations of species occurrence or abundance with environmental estimates. They are used to gain ecological and evolutionary insights and to predict distributions across landscapes,...Read More",
    url = "https://doi.org/10.1146/annurev.es.02.110171.002341",
    doi = "10.1146/annurev.es.02.110171.002341",
    openalex = "W2029894290",
    references = "doi101086282455, doi101111j155856461969tb03489x"
}

GoOD estimates of absolute population density as distinct from indices of relative abundance have been virtually unavailable for nonflocking land birds except in the breeding season when singing males, representing mated pairs, restrict themselves to more or less fixed territories where they or their nests can be counted. The lack of efficient and reasonably accurate census methods applicable at any season has seriously hampered the progress of quantitative studies of avian population ecology. This paper, after reviewing the potentialities and limitations of currently available methods, describes a new method that is, 1) applicable at all seasons, 2) more efficient in terms of area covered per unit of effort than the nest or territory count methods, and 3) comparable in accuracy. The method uses the lateral distribution pattern of all detection points for each species to derive coefficients of detectability with which trail counts may be converted directly to density values in units of birds per 100 acres. The method was developed over a period of 3 years while the author was gathering data on the ecological distribution of birds in mesquite grasslands in southern Texas, pine forests in Florida and the Bahamas, and mixed woodlands in Wisconsin and Michigan.

@article{doi1023074083883,
    author = "Emlen, John T.",
    title = "Population Densities of Birds Derived from Transect Counts",
    year = "1971",
    journal = "The Auk",
    abstract = "GoOD estimates of absolute population density as distinct from indices of relative abundance have been virtually unavailable for nonflocking land birds except in the breeding season when singing males, representing mated pairs, restrict themselves to more or less fixed territories where they or their nests can be counted. The lack of efficient and reasonably accurate census methods applicable at any season has seriously hampered the progress of quantitative studies of avian population ecology. This paper, after reviewing the potentialities and limitations of currently available methods, describes a new method that is, 1) applicable at all seasons, 2) more efficient in terms of area covered per unit of effort than the nest or territory count methods, and 3) comparable in accuracy. The method uses the lateral distribution pattern of all detection points for each species to derive coefficients of detectability with which trail counts may be converted directly to density values in units of birds per 100 acres. The method was developed over a period of 3 years while the author was gathering data on the ecological distribution of birds in mesquite grasslands in southern Texas, pine forests in Florida and the Bahamas, and mixed woodlands in Wisconsin and Michigan.",
    url = "https://doi.org/10.2307/4083883",
    doi = "10.2307/4083883",
    openalex = "W2326423025"
}

@inproceedings{tappen1971microplankton38,
    author = "Tappen, H",
    title = "Microplankton, ecological succession and evolution",
    year = "1971",
    booktitle = "North American Paleontological Convention, Proceedings, p. 1058-1103; Part H",
    note = "talkorigins\_source = {true}; raw\_reference = {Tappen, H., 1971, Microplankton, ecological succession and evolution: North American Paleontological Convention, Proceedings, p. 1058-1103; Part H.}"
}

@misc{campbell1972society10,
    author = "Campbell, R. R. and Wade, J. L",
    title = "Society and Environment",
    year = "1972",
    howpublished = "The Coming Collision: Boston, Allyn and Bacon, 375 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Campbell, R. R., and Wade, J. L., 1972, Society and Environment: The Coming Collision: Boston, Allyn and Bacon, 375 p.}"
}

@book{caswell1972an12,
    author = "Caswell, H. and Koenig, H. E. and Resh, J. A. and Ross, Q. E",
    title = "An Introduction to Systems Science for Ecologists, in Patten, B., ed., Systems Analysis and Simulation in Ecology",
    year = "1972",
    publisher = "New York, Academic Press, v. 2, p. 4-78; 592 pp",
    note = "talkorigins\_source = {true}; raw\_reference = {Caswell, H., Koenig, H. E., Resh, J. A., and Ross, Q. E., 1972, An Introduction to Systems Science for Ecologists, in Patten, B., ed., Systems Analysis and Simulation in Ecology: New York, Academic Press, v. 2, p. 4-78; 592 pp.}"
}

@phdthesis{caswell1973photosynthetic13,
    author = "Caswell, H. and Reed, F. and Stephenson, S. N. and Werner, P. A",
    title = "Photosynthetic pathways and selective herbivory",
    year = "1973",
    publisher = "a hypothesis: American Naturalist, v. 107, p. 465-480",
    note = "talkorigins\_source = {true}; raw\_reference = {Caswell, H., Reed, F., Stephenson, S. N., and Werner, P. A., 1973, Photosynthetic pathways and selective herbivory: a hypothesis: American Naturalist, v. 107, p. 465-480.}"
}

@book{cody1973competition21,
    author = "Cody, M. L",
    title = "Competition and Community Structure",
    year = "1973",
    publisher = "Princeton, New Jersey, Princeton University Press",
    note = "talkorigins\_source = {true}; raw\_reference = {Cody, M. L., 1973, Competition and Community Structure: Princeton, New Jersey, Princeton University Press.}"
}

@book{colinvaux1973introduction22,
    author = "Colinvaux, P. A",
    title = "Introduction to Ecology",
    year = "1973",
    publisher = "New York, Wiley, 621 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Colinvaux, P. A., 1973, Introduction to Ecology: New York, Wiley, 621 p.}"
}

@misc{collier1973dynamic23,
    author = "Collier, B. and Cox, G. W. and Johnson, A. W. and Miller, P. C",
    title = "Dynamic Ecology",
    year = "1973",
    howpublished = "Englewood Cliffs, New Jersey, Prentice-Hall, 563 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Collier, B., Cox, G. W., Johnson, A. W., and Miller, P. C., 1973, Dynamic Ecology: Englewood Cliffs, New Jersey, Prentice-Hall, 563 p.}"
}

The concepts by which MacArthur and Wilson have transformed the science of ecology in the past decade, and the results of ecological studies such as mine on New Guinea bird communities, have implications for conservation policies. For example, primary tropical rain forest, the most species-rich and ecologically complex habitat on earth, has for millions of years served as the ultimate evolutionary source of the world's dominant plant and animal groups. Throughout the tropics today, the rain forests are being destroyed at a rate such that little will be left in a few decades. When the rain forests have been reduced to isolated tracts separated by open country, the distribution of obligate rain forest species will come to resemble bird distributions on New Guinea land-bridge islands after severing of the land bridges. The smaller the tract, the more rapidly will forest species tend to disappear and be replaced by the widespread second-growth species that least need protection (13). This ominous process is illustrated by Barro Colorado Island, a former hill in Panama that became an island when construction of the Panama Canal flooded surrounding valleys to create Gatun Lake. In the succeeding 60 years several forest bird species have already disappeared from Barro Colorado and been unable to recolonize across the short intervening water gap from the forest on the nearby shore of Gatun Lake. The consequences of the species-area relation (Fig. 1) should be taken into consideration during the planning of tropical rain forest parks (13). In a geographical area that is relatively homogeneous with regard to the fauna, one large park would be preferable to an equivalent area in the form of several smaller parks. Continuous nonforest strips through the park (for example, wide highway swaths) would convert one rain forest "island" into two half-size islands and should be avoided. If other considerations require that an area be divided into several small parks, connecting them by forest corridors might significantly improve their conservation function at little further cost in land withdrawn from development. Modern ecological studies may also be relevant to the understanding of human populations. For instance, during a long period of human evolution there appear to have been not one but two coexistent hominid lines in Africa, the Australopithecus robustus-A. boisei ("Zinjanthropus") line, which became extinct, and the Australopithecus africanus-A. habilis line, which led to Homo sapiens (27). The need to maintain niche differences between these lines must have provided one of the most important selective pressures on the ancestors of modern man in the late Pliocene and early Pleistocene. Thus, any attempt to understand human evolution must confront the problem of what these ecological segregating mechanisms were. To what extent were contemporaneous species of the two lines separated by habitat, by diet, by size difference, or by foraging technique, and were their local spatial distributions broadly overlapping or else sharpened by behavioral interactions as in the case of the Crateroscelis warblers of Fig. 6? To take another example, there are striking parallels between the present distributions of human populations and of bird populations on the islands of Vitiaz and Dampier straits between New Guinea and New Britain. Some of these islands were sterilized by cataclysmic volcanic explosions within the last several centuries. The birds that recolonized these islands have been characterized as coastal and small-island specialists of high reproductive potential, high dispersal powers, and low competitive ability, unlike the geographically closer, competitively superior, slowly dispersing, and breeding birds of mainland New Guinea (10, 11, 13). It remains to be seen whether the people of the Vitiaz-Dampier islands, the Polynesians, and other human populations that colonize insular or unstable habitats also have distinctive population ecologies.

@article{doi101126science1794075759,
    author = "Diamond, Jared M.",
    title = "Distributional Ecology of New Guinea Birds",
    year = "1973",
    journal = "Science",
    abstract = {The concepts by which MacArthur and Wilson have transformed the science of ecology in the past decade, and the results of ecological studies such as mine on New Guinea bird communities, have implications for conservation policies. For example, primary tropical rain forest, the most species-rich and ecologically complex habitat on earth, has for millions of years served as the ultimate evolutionary source of the world's dominant plant and animal groups. Throughout the tropics today, the rain forests are being destroyed at a rate such that little will be left in a few decades. When the rain forests have been reduced to isolated tracts separated by open country, the distribution of obligate rain forest species will come to resemble bird distributions on New Guinea land-bridge islands after severing of the land bridges. The smaller the tract, the more rapidly will forest species tend to disappear and be replaced by the widespread second-growth species that least need protection (13). This ominous process is illustrated by Barro Colorado Island, a former hill in Panama that became an island when construction of the Panama Canal flooded surrounding valleys to create Gatun Lake. In the succeeding 60 years several forest bird species have already disappeared from Barro Colorado and been unable to recolonize across the short intervening water gap from the forest on the nearby shore of Gatun Lake. The consequences of the species-area relation (Fig. 1) should be taken into consideration during the planning of tropical rain forest parks (13). In a geographical area that is relatively homogeneous with regard to the fauna, one large park would be preferable to an equivalent area in the form of several smaller parks. Continuous nonforest strips through the park (for example, wide highway swaths) would convert one rain forest "island" into two half-size islands and should be avoided. If other considerations require that an area be divided into several small parks, connecting them by forest corridors might significantly improve their conservation function at little further cost in land withdrawn from development. Modern ecological studies may also be relevant to the understanding of human populations. For instance, during a long period of human evolution there appear to have been not one but two coexistent hominid lines in Africa, the Australopithecus robustus-A. boisei ("Zinjanthropus") line, which became extinct, and the Australopithecus africanus-A. habilis line, which led to Homo sapiens (27). The need to maintain niche differences between these lines must have provided one of the most important selective pressures on the ancestors of modern man in the late Pliocene and early Pleistocene. Thus, any attempt to understand human evolution must confront the problem of what these ecological segregating mechanisms were. To what extent were contemporaneous species of the two lines separated by habitat, by diet, by size difference, or by foraging technique, and were their local spatial distributions broadly overlapping or else sharpened by behavioral interactions as in the case of the Crateroscelis warblers of Fig. 6? To take another example, there are striking parallels between the present distributions of human populations and of bird populations on the islands of Vitiaz and Dampier straits between New Guinea and New Britain. Some of these islands were sterilized by cataclysmic volcanic explosions within the last several centuries. The birds that recolonized these islands have been characterized as coastal and small-island specialists of high reproductive potential, high dispersal powers, and low competitive ability, unlike the geographically closer, competitively superior, slowly dispersing, and breeding birds of mainland New Guinea (10, 11, 13). It remains to be seen whether the people of the Vitiaz-Dampier islands, the Polynesians, and other human populations that colonize insular or unstable habitats also have distinctive population ecologies.},
    url = "https://doi.org/10.1126/science.179.4075.759",
    doi = "10.1126/science.179.4075.759",
    openalex = "W2082049451",
    references = "doi101073pnas5161207, doi101073pnas6951109, doi101086282454, doi101086282738, doi101111j1469185x1965tb00815x, doi101111j155856461963tb03295x, doi101722611310, doi1023071931976, doi1023071934090, doi1023072407089, doi104159harvard9780674865327"
}

@inproceedings{stanley1973an37,
    author = "Stanley, S. M",
    title = "An ecological theory for the sudden origin of multicellular life in the Late Precambrian",
    year = "1973",
    booktitle = "Proceedings of the National Academy of Sciences, v. 70, p. 1486-1489",
    note = "talkorigins\_source = {true}; raw\_reference = {Stanley, S. M., 1973, An ecological theory for the sudden origin of multicellular life in the Late Precambrian: Proceedings of the National Academy of Sciences, v. 70, p. 1486-1489.}"
}

@misc{ellenberger1974le28,
    author = "Ellenberger, P",
    title = "Le Stormberg superior-I le biome de la zone B/1",
    year = "1974",
    howpublished = "Palaeovert., Mem. extraord. Montpellier, v. 5, p. 1-141",
    note = "talkorigins\_source = {true}; raw\_reference = {Ellenberger, P., 1974, Le Stormberg superior-I le biome de la zone B/1: Palaeovert., Mem. extraord. Montpellier, v. 5, p. 1-141.}"
}

@article{berry1975ecological5,
    author = "Berry, R. J. and Jakobson, M. E",
    title = "Ecological genetics of an island population of the house mouse (Mus musculus)",
    year = "1975",
    journal = "Journal of Zoology, v. 175, p. 532-540",
    note = "talkorigins\_source = {true}; raw\_reference = {Berry, R. J., and Jakobson, M. E., 1975, Ecological genetics of an island population of the house mouse (Mus musculus): Journal of Zoology, v. 175, p. 532-540.}"
}

@article{doi101038260204c0,
    author = "Cody, Martin L. and Diamond, Jared M.",
    title = "Ecology and Evolution of Communities",
    year = "1976",
    journal = "Nature",
    url = "https://doi.org/10.1038/260204c0",
    doi = "10.1038/260204c0",
    openalex = "W2321937847"
}

@misc{peters1976tautology36,
    author = "Peters, R. H",
    title = "Tautology in Evolution and Ecology",
    year = "1976",
    howpublished = "American Naturalist, v. 110, p. 1-12",
    note = "talkorigins\_source = {true}; raw\_reference = {Peters, R. H., 1976, Tautology in Evolution and Ecology: American Naturalist, v. 110, p. 1-12.}"
}

It is suggested that evolution in plants may be associated with the emergence of three primary strategies, each of which may be identified by reference to a number of characteristics including morphological features, resource allocation, phenology, and response to stress. The competitive strategy prevails in productive, relatively undisturbed vegetation, the stress-tolerant strategy is associated with continuously unproductive conditions, and the ruderal strategy is characteristic of severely disturbed but potentially productive habitats. A triangular model based upon the three strategies may be reconciled with the theory of r- and K-selection, provides an insight into the processes of vegetation succession and dominance, and appears to be capable of extension to fungi and to animals.

@article{doi101086283244,
    author = "Grime, J. P.",
    title = "Evidence for the Existence of Three Primary Strategies in Plants and Its Relevance to Ecological and Evolutionary Theory",
    year = "1977",
    journal = "The American Naturalist",
    abstract = "It is suggested that evolution in plants may be associated with the emergence of three primary strategies, each of which may be identified by reference to a number of characteristics including morphological features, resource allocation, phenology, and response to stress. The competitive strategy prevails in productive, relatively undisturbed vegetation, the stress-tolerant strategy is associated with continuously unproductive conditions, and the ruderal strategy is characteristic of severely disturbed but potentially productive habitats. A triangular model based upon the three strategies may be reconciled with the theory of r- and K-selection, provides an insight into the processes of vegetation succession and dominance, and appears to be capable of extension to fungi and to animals.",
    url = "https://doi.org/10.1086/283244",
    doi = "10.1086/283244",
    openalex = "W2055424972",
    references = "doi101038242344a0, doi101038250026a0, doi101086282454, doi101086282455, doi1015159781400881376, doi102307213332, doi1023072258728, doi10230725528056, doi1023073241344, doi105962bhltitle59991"
}

@book{houstan1979the31,
    author = "Houstan, D. C",
    title = "The Adaptations of Scavengers, in Sinclair, A. R. E., and Norton-Griffiths, M., eds., Serengeti",
    year = "1979",
    publisher = "Dynamics of an Ecosystem: Chicago, University of Chicago Press, p. 263-286",
    note = "talkorigins\_source = {true}; raw\_reference = {Houstan, D. C., 1979, The Adaptations of Scavengers, in Sinclair, A. R. E., and Norton-Griffiths, M., eds., Serengeti: Dynamics of an Ecosystem: Chicago, University of Chicago Press, p. 263-286.}"
}

@techreport{morman1979distribution35,
    author = "Morman, R. H",
    title = "Distribution and ecology of lampreys in the lower peninsula of Michigan, 1957-1975",
    year = "1979",
    howpublished = "Great Lakes Fishery Commission, Technical Report No. 33, 59 pp",
    note = "talkorigins\_source = {true}; raw\_reference = {Morman, R. H., 1979, Distribution and ecology of lampreys in the lower peninsula of Michigan, 1957-1975. Great Lakes Fishery Commission, Technical Report No. 33, 59 pp.}"
}

@book{auffenburg1981the2,
    author = "Auffenburg, W",
    title = "The Behavorial Ecology of the Komodo Monitor",
    year = "1981",
    publisher = "Gainesville, Florida, University of Florida Presses",
    note = "talkorigins\_source = {true}; raw\_reference = {Auffenburg, W., 1981, The Behavorial Ecology of the Komodo Monitor: Gainesville, Florida, University of Florida Presses.}"
}

Species distribution models (SDMs) are numerical tools that combine observations of species occurrence or abundance with environmental estimates. They are used to gain ecological and evolutionary insights and to predict distributions across landscapes,...Read More

@article{doi101146annureves13110182000245,
    author = "Greenwood, P. J. and Harvey, Paul",
    title = "The Natal and Breeding Dispersal of Birds",
    year = "1982",
    journal = "Annual Review of Ecology and Systematics",
    abstract = "Species distribution models (SDMs) are numerical tools that combine observations of species occurrence or abundance with environmental estimates. They are used to gain ecological and evolutionary insights and to predict distributions across landscapes,...Read More",
    url = "https://doi.org/10.1146/annurev.es.13.110182.000245",
    doi = "10.1146/annurev.es.13.110182.000245",
    openalex = "W2116166795",
    references = "doi1010160040580978900394, doi1023072828, openalexw2014317435"
}

There appears to be a general relationship between abundance and distribution that has two parts. First, within species, population density tends to be greatest in the center of the range and to decline gradually toward the boundaries. This pattern holds over a range of spatial scales from steep environmental gradients within local regions to the entire geographic range. Exceptions include: (1) abrupt changes in abundance that usually correspond to sharp, discontinuous changes in single environmental variables; and (2) multimodal patterns of abundance that are caused by environmental patchiness. The second general relationship is that among closely related, ecologically similar species spatial distribution is positively correlated with average abundance. Again this pattern holds over a variety of spatial scales from local regions to entire geographic ranges. These empirical patterns have already been reported in the literature, but their generality is demonstrated by analysis of additional data for diverse kinds of organisms. A single general theory accounts for these observations and follows logically from three assumptions. First, the abundance and distribution of each species are limited by the combination of physical and biotic environmental variables that determines the multidimensional niche. Second, spatial variation in these environmental variables is somewhat stochastic but autocorrelated, so that nearby sites tend to have more similar environmental conditions than more distant ones. Third, closely related, ecologically similar species differ in no more than a very few niche dimensions. A more formal model can be developed that predicts that under these assumptions the distribution of population density over space should approximate a normal probability density distribution. Most exceptions to this predicted pattern can be explained as cases in which assumptions of the model are clearly violated. This paper represents an example of a statistical approach that should be useful for investigating complex ecological systems comprised of many components, such as species of many individuals or communities of many species. The general relationships between abundance and distribution developed here eventually should contribute to our understanding of the biogeography, population genetics, and evolution of species as well as the ecological attributes of populations and communities.

@article{doi101086284267,
    author = "Brown, James H.",
    title = "On the Relationship between Abundance and Distribution of Species",
    year = "1984",
    journal = "The American Naturalist",
    abstract = "There appears to be a general relationship between abundance and distribution that has two parts. First, within species, population density tends to be greatest in the center of the range and to decline gradually toward the boundaries. This pattern holds over a range of spatial scales from steep environmental gradients within local regions to the entire geographic range. Exceptions include: (1) abrupt changes in abundance that usually correspond to sharp, discontinuous changes in single environmental variables; and (2) multimodal patterns of abundance that are caused by environmental patchiness. The second general relationship is that among closely related, ecologically similar species spatial distribution is positively correlated with average abundance. Again this pattern holds over a variety of spatial scales from local regions to entire geographic ranges. These empirical patterns have already been reported in the literature, but their generality is demonstrated by analysis of additional data for diverse kinds of organisms. A single general theory accounts for these observations and follows logically from three assumptions. First, the abundance and distribution of each species are limited by the combination of physical and biotic environmental variables that determines the multidimensional niche. Second, spatial variation in these environmental variables is somewhat stochastic but autocorrelated, so that nearby sites tend to have more similar environmental conditions than more distant ones. Third, closely related, ecologically similar species differ in no more than a very few niche dimensions. A more formal model can be developed that predicts that under these assumptions the distribution of population density over space should approximate a normal probability density distribution. Most exceptions to this predicted pattern can be explained as cases in which assumptions of the model are clearly violated. This paper represents an example of a statistical approach that should be useful for investigating complex ecological systems comprised of many components, such as species of many individuals or communities of many species. The general relationships between abundance and distribution developed here eventually should contribute to our understanding of the biogeography, population genetics, and evolution of species as well as the ecological attributes of populations and communities.",
    url = "https://doi.org/10.1086/284267",
    doi = "10.1086/284267",
    openalex = "W2031647551",
    references = "doi101111j1469185x1983tb00380x, doi101126science22246281123, doi1023071943577, doi1023072259626, doi1023073544021, doi1023073669094, doi104159harvard9780674865327, jablonski1983larval, openalexw1500291103, openalexw1532540194, openalexw3035987306"
}

@techreport{jablonski1986larval32,
    author = "Jablonski, D",
    title = "Larval ecology and macroevolution in marine invertebrates",
    year = "1986",
    howpublished = "Bulletin of Marine Science, v. 39, p. 565-587",
    note = "talkorigins\_source = {true}; raw\_reference = {Jablonski, D., 1986, Larval ecology and macroevolution in marine invertebrates: Bulletin of Marine Science, v. 39, p. 565-587.}"
}

@misc{leather1986the34,
    author = "Leather, D",
    title = "The tale of the Tasaday",
    year = "1986",
    howpublished = "The Geographical Magazine, v. 58, no. 10, p. 490-491",
    note = "talkorigins\_source = {true}; raw\_reference = {Leather, D., 1986, The tale of the Tasaday: The Geographical Magazine, v. 58, no. 10, p. 490-491.}"
}

Species distribution models (SDMs) are numerical tools that combine observations of species occurrence or abundance with environmental estimates. They are used to gain ecological and evolutionary insights and to predict distributions across landscapes,...Read More

@article{doi101146annureves18110187002421,
    author = "Avise, John C. and Arnold, Jonathan and Ball, Robert and Bermingham, Eldredge and Lamb, Trip and Neigel, Joseph E. and Reeb, Carol A. and Saunders, Nancy C.",
    title = "INTRASPECIFIC PHYLOGEOGRAPHY: The Mitochondrial DNA Bridge Between Population Genetics and Systematics",
    year = "1987",
    journal = "Annual Review of Ecology and Systematics",
    abstract = "Species distribution models (SDMs) are numerical tools that combine observations of species occurrence or abundance with environmental estimates. They are used to gain ecological and evolutionary insights and to predict distributions across landscapes,...Read More",
    url = "https://doi.org/10.1146/annurev.es.18.110187.002421",
    doi = "10.1146/annurev.es.18.110187.002421",
    openalex = "W2150477652",
    references = "doi10100703064746897, doi101007bf01734101, doi101038095550b0, doi101038325031a0, doi101073pnas7641967, doi101093aibsbulletin2214b, doi101093genetics1052437, doi101098rspb19790086, doi101111j155856461975tb00851x, doi101111j155856461983tb05533x, doi1023072407692, doi104159harvard9780674865327, doi107312nei92038, openalexw1495050269, openalexw2062594085, openalexw3135630760"
}

Species distribution models (SDMs) are numerical tools that combine observations of species occurrence or abundance with environmental estimates. They are used to gain ecological and evolutionary insights and to predict distributions across landscapes,...Read More

@article{doi101146annureves20110189001131,
    author = "Turner, Monica G.",
    title = "Landscape Ecology: The Effect of Pattern on Process",
    year = "1989",
    journal = "Annual Review of Ecology and Systematics",
    abstract = "Species distribution models (SDMs) are numerical tools that combine observations of species occurrence or abundance with environmental estimates. They are used to gain ecological and evolutionary insights and to predict distributions across landscapes,...Read More",
    url = "https://doi.org/10.1146/annurev.es.20.110189.001131",
    doi = "10.1146/annurev.es.20.110189.001131",
    openalex = "W2063548203",
    references = "doi1010079781461262329, doi101007bf02860857, doi10106312995555, doi10108010106048609354060, doi101119113295, doi1015159781400881376, doi102136sssaj198703615995005100050015x, doi1023071943577, doi1023072256497, doi1023072403105, doi1023072420377, doi105962bhltitle56234, openalexw1989371375"
}

Parasitoids and predators of herbivores have evolved and function within a multitrophic context.Consequently, their physiology and behavior are influenced by elements from other trophic levels such as their herbivore victim (second trophic level) and its plant food (first trophic level) (126).Natural enemies base their foraging decisions on information from these different trophic levels, and chemical information plays an important role.This review is restricted to the ecology of chemical information from the first and second trophic levels.The importance of so-called infochemicals, a subcategory of semiochemicals, in foraging by parasitoids and predators has been well documented (e.g.reviewed in 31,78, 111,183,185), and we do not intend repeat the details.But because of a lack of testable hypotheses, all this research is conducted rather haphazardly: the total puzzle of infochemical use has not been solved for any natural enemy species.Here we approach the use of infochemicals by natural enemies from an evolutionary and ecological standpoint.Our basic concept is that information from the first and second trophic levels differs in availability and in reliability, a difference that shapes the way infochemicals are used by a species.We generate hypotheses on (a)

@article{doi101146annureven37010192001041,
    author = "Vet, L.E.M. and Dicke, Marcel",
    title = "Ecology of Infochemical Use by Natural Enemies in a Tritrophic Context",
    year = "1992",
    journal = "Annual Review of Entomology",
    abstract = "Parasitoids and predators of herbivores have evolved and function within a multitrophic context.Consequently, their physiology and behavior are influenced by elements from other trophic levels such as their herbivore victim (second trophic level) and its plant food (first trophic level) (126).Natural enemies base their foraging decisions on information from these different trophic levels, and chemical information plays an important role.This review is restricted to the ecology of chemical information from the first and second trophic levels.The importance of so-called infochemicals, a subcategory of semiochemicals, in foraging by parasitoids and predators has been well documented (e.g.reviewed in 31,78, 111,183,185), and we do not intend repeat the details.But because of a lack of testable hypotheses, all this research is conducted rather haphazardly: the total puzzle of infochemical use has not been solved for any natural enemy species.Here we approach the use of infochemicals by natural enemies from an evolutionary and ecological standpoint.Our basic concept is that information from the first and second trophic levels differs in availability and in reliability, a difference that shapes the way infochemicals are used by a species.We generate hypotheses on (a)",
    url = "https://doi.org/10.1146/annurev.en.37.010192.001041",
    doi = "10.1146/annurev.en.37.010192.001041",
    openalex = "W2163028358",
    references = "doi101086282454, doi101126science185414527, doi101126science2114485887"
}

It is argued that the problem of pattern and scale is the central problem in ecology, unifying population biology and ecosystems science, and marrying basic and applied ecology. Applied challenges, such as the prediction of the ecological causes and consequences of global climate change, require the interfacing of phenomena that occur on very different scales of space, time, and ecological organization. Furthermore, there is no single natural scale at which ecological phenomena should be studied; systems generally show characteristic variability on a range of spatial, temporal, and organizational scales. The observer imposes a perceptual bias, a filter through which the system is viewed. This has fundamental evolutionary significance, since every organism is an "observer" of the environment, and life history adaptations such as dispersal and dormancy alter the perceptual scales of the species, and the observed variability. It likewise has fundamental significance for our own study of ecological systems, since the patterns that are unique to any range of scales will have unique causes and biological consequences. The key to prediction and understanding lies in the elucidation of mechanisms underlying observed patterns. Typically, these mechanisms operate at different scales than those on which the patterns are observed; in some cases, the patterns must be understood as emerging form the collective behaviors of large ensembles of smaller scale units. In other cases, the pattern is imposed by larger scale constraints. Examination of such phenomena requires the study of how pattern and variability change with the scale of description, and the development of laws for simplification, aggregation, and scaling. Examples are given from the marine and terrestrial literatures.

@article{doi1023071941447,
    author = "Levin, Simon A.",
    title = "The Problem of Pattern and Scale in Ecology: The Robert H. MacArthur Award Lecture",
    year = "1992",
    journal = "Ecology",
    abstract = {It is argued that the problem of pattern and scale is the central problem in ecology, unifying population biology and ecosystems science, and marrying basic and applied ecology. Applied challenges, such as the prediction of the ecological causes and consequences of global climate change, require the interfacing of phenomena that occur on very different scales of space, time, and ecological organization. Furthermore, there is no single natural scale at which ecological phenomena should be studied; systems generally show characteristic variability on a range of spatial, temporal, and organizational scales. The observer imposes a perceptual bias, a filter through which the system is viewed. This has fundamental evolutionary significance, since every organism is an "observer" of the environment, and life history adaptations such as dispersal and dormancy alter the perceptual scales of the species, and the observed variability. It likewise has fundamental significance for our own study of ecological systems, since the patterns that are unique to any range of scales will have unique causes and biological consequences. The key to prediction and understanding lies in the elucidation of mechanisms underlying observed patterns. Typically, these mechanisms operate at different scales than those on which the patterns are observed; in some cases, the patterns must be understood as emerging form the collective behaviors of large ensembles of smaller scale units. In other cases, the pattern is imposed by larger scale constraints. Examination of such phenomena requires the study of how pattern and variability change with the scale of description, and the development of laws for simplification, aggregation, and scaling. Examples are given from the marine and terrestrial literatures.},
    url = "https://doi.org/10.2307/1941447",
    doi = "10.2307/1941447",
    openalex = "W2322480672",
    references = "doi101007bfb0091924, doi101086282400, doi101098rstb19520012, doi101111j146918091937tb02153x, doi101111j155856461964tb01674x, doi1015159781400881376, doi1023071941447, doi1023072529912, doi105860choice295104, doi107551mitpress30140010001, openalexw1558456135, openalexw1576847343"
}

@article{doi101007bf02338839,
    author = "Rannala, Bruce and Yang, Ziheng",
    title = "Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference",
    year = "1996",
    journal = "Journal of Molecular Evolution",
    url = "https://doi.org/10.1007/bf02338839",
    doi = "10.1007/bf02338839",
    openalex = "W2150783480",
    references = "doi101093oxfordjournalsmolbeva040259, doi101093sysbio422182, doi1023072992540"
}

@article{doi101016s0169534702025806,
    author = "Schlaepfer, Martin A. and Runge, Michael C. and Sherman, Paul W.",
    title = "Ecological and evolutionary traps",
    year = "2002",
    journal = "Trends in Ecology \& Evolution",
    url = "https://doi.org/10.1016/s0169-5347(02)02580-6",
    doi = "10.1016/s0169-5347(02)02580-6",
    openalex = "W1973455972",
    references = "doi1023073808148, doi1023075530"
}

▪ Abstract As better phylogenetic hypotheses become available for many groups of organisms, studies in community ecology can be informed by knowledge of the evolutionary relationships among coexisting species. We note three primary approaches to integrating phylogenetic information into studies of community organization: 1. examining the phylogenetic structure of community assemblages, 2. exploring the phylogenetic basis of community niche structure, and 3. adding a community context to studies of trait evolution and biogeography. We recognize a common pattern of phylogenetic conservatism in ecological character and highlight the challenges of using phylogenies of partial lineages. We also review phylogenetic approaches to three emergent properties of communities: species diversity, relative abundance distributions, and range sizes. Methodological advances in phylogenetic supertree construction, character reconstruction, null models for community assembly and character evolution, and metrics of community phylogenetic structure underlie the recent progress in these areas. We highlight the potential for community ecologists to benefit from phylogenetic knowledge and suggest several avenues for future research.

@article{doi101146annurevecolsys33010802150448,
    author = "Webb, Campbell O. and Ackerly, David D. and McPeek, Mark A. and Donoghue, Michael J.",
    title = "Phylogenies and Community Ecology",
    year = "2002",
    journal = "Annual Review of Ecology and Systematics",
    abstract = "▪ Abstract As better phylogenetic hypotheses become available for many groups of organisms, studies in community ecology can be informed by knowledge of the evolutionary relationships among coexisting species. We note three primary approaches to integrating phylogenetic information into studies of community organization: 1. examining the phylogenetic structure of community assemblages, 2. exploring the phylogenetic basis of community niche structure, and 3. adding a community context to studies of trait evolution and biogeography. We recognize a common pattern of phylogenetic conservatism in ecological character and highlight the challenges of using phylogenies of partial lineages. We also review phylogenetic approaches to three emergent properties of communities: species diversity, relative abundance distributions, and range sizes. Methodological advances in phylogenetic supertree construction, character reconstruction, null models for community assembly and character evolution, and metrics of community phylogenetic structure underlie the recent progress in these areas. We highlight the potential for community ecologists to benefit from phylogenetic knowledge and suggest several avenues for future research.",
    url = "https://doi.org/10.1146/annurev.ecolsys.33.010802.150448",
    doi = "10.1146/annurev.ecolsys.33.010802.150448",
    openalex = "W2109628725",
    references = "doi10100797814615696881, doi101007978303487527124, doi101007bf02806171, doi101016s0169534701021619, doi101038363342a0, doi10108010292389509380518, doi101086282106, doi101086282505, doi101086284325, doi101086285258, doi101086285357, doi101086627905, doi101093oso97801985052350010001, doi101093oso97801985464120010001, doi101093oxfordjournalsmolbeva003974, doi101093oxfordjournalsmolbeva025892, doi101098rstb19950125, doi101111j001438202001tb00826x, doi101111j109583122001tb01368x, doi101126science20343871299, doi101126science2354785167, doi101126science2785338692, doi101126science27953592115, doi101126science28554311265, doi101146annurevecolsys311343, doi1015159781400881376, doi1023071446122, doi1023071939377, doi1023072412182, doi1023072413039, doi1023072485224, doi1023073071998, doi1023073544421, doi1023075503, doi102307jctv1nzfgj7, doi105860choice295104, doi105860choice375647, doi105860choice392183, openalexw2273605253, openalexw3035987306"
}

Knowledge of the ecological and evolutionary causes of dispersal can be crucial in understanding the behaviour of spatially structured populations, and predicting how species respond to environmental change. Despite the focus of much theoretical research, simplistic assumptions regarding the dispersal process are still made. Dispersal is usually regarded as an unconditional process although in many cases fitness gains of dispersal are dependent on environmental factors and individual state. Condition-dependent dispersal strategies will often be superior to unconditional, fixed strategies. In addition, dispersal is often collapsed into a single parameter, despite it being a process composed of three interdependent stages: emigration, inter-patch movement and immigration, each of which may display different condition dependencies. Empirical studies have investigated correlates of these stages, emigration in particular, providing evidence for the prevalence of conditional dispersal strategies. Ill-defined use of the term 'dispersal', for movement across many different spatial scales, further hinders making general conclusions and relating movement correlates to consequences at the population level. Logistical difficulties preclude a detailed study of dispersal for many species, however incorporating unrealistic dispersal assumptions in spatial population models may yield inaccurate and costly predictions. Further studies are necessary to explore the importance of incorporating specific condition-dependent dispersal strategies for evolutionary and population dynamic predictions.

@article{doi101017s1464793104006645,
    author = "Bowler, Diana E. and Benton, Tim G.",
    title = "Causes and consequences of animal dispersal strategies: relating individual behaviour to spatial dynamics",
    year = "2005",
    journal = "Biological reviews/Biological reviews of the Cambridge Philosophical Society",
    abstract = "Knowledge of the ecological and evolutionary causes of dispersal can be crucial in understanding the behaviour of spatially structured populations, and predicting how species respond to environmental change. Despite the focus of much theoretical research, simplistic assumptions regarding the dispersal process are still made. Dispersal is usually regarded as an unconditional process although in many cases fitness gains of dispersal are dependent on environmental factors and individual state. Condition-dependent dispersal strategies will often be superior to unconditional, fixed strategies. In addition, dispersal is often collapsed into a single parameter, despite it being a process composed of three interdependent stages: emigration, inter-patch movement and immigration, each of which may display different condition dependencies. Empirical studies have investigated correlates of these stages, emigration in particular, providing evidence for the prevalence of conditional dispersal strategies. Ill-defined use of the term 'dispersal', for movement across many different spatial scales, further hinders making general conclusions and relating movement correlates to consequences at the population level. Logistical difficulties preclude a detailed study of dispersal for many species, however incorporating unrealistic dispersal assumptions in spatial population models may yield inaccurate and costly predictions. Further studies are necessary to explore the importance of incorporating specific condition-dependent dispersal strategies for evolutionary and population dynamic predictions.",
    url = "https://doi.org/10.1017/s1464793104006645",
    doi = "10.1017/s1464793104006645",
    openalex = "W2125207868",
    references = "doi1010160169534796100288, doi101093oso97801985406630010001, doi1018900012965820020831131scmise20co2, doi1023071935620, doi1023072389612"
}

Prediction of species’ distributions is central to diverse applications in ecology, evolution and conservation science. There is increasing electronic access to vast sets of occurrence records in museums and herbaria, yet little effective guidance on how best to use this information in the context of numerous approaches for modelling distributions. To meet this need, we compared 16 modelling methods over 226 species from 6 regions of the world, creating the most comprehensive set of model comparisons to date. We used presence‐only data to fit models, and independent presence‐absence data to evaluate the predictions. Along with well‐established modelling methods such as generalised additive models and GARP and BIOCLIM, we explored methods that either have been developed recently or have rarely been applied to modelling species’ distributions. These include machine‐learning methods and community models, both of which have features that may make them particularly well suited to noisy or sparse information, as is typical of species’ occurrence data. Presence‐only data were effective for modelling species’ distributions for many species and regions. The novel methods consistently outperformed more established methods. The results of our analysis are promising for the use of data from museums and herbaria, especially as methods suited to the noise inherent in such data improve.

@article{doi101111j20060906759004596x,
    author = "Elith, Jane and Graham, Catherine H. and Anderson, Robert P. and Dudı́k, Miroslav and Ferrier, Simon and Guisan, Antoine and Hijmans, Robert J. and Huettmann, Falk and Leathwick, John R. and Lehmann, Anthony and Li, Jin and Lohmann, Lúcia G. and Loiselle, Bette A. and Manion, Glenn and Moritz, Craig and Nakamura, Miguel and Nakazawa, Yoshinori and Overton, Jacob McC. and Peterson, A. Townsend and Phillips, Steven J. and Richardson, Karen and Scachetti‐Pereira, Ricardo and Schapire, Robert E. and Soberón, Jorge and Williams, Stephen E. and Wisz, Mary S. and Zimmermann, Niklaus E.",
    title = "Novel methods improve prediction of species’ distributions from occurrence data",
    year = "2006",
    journal = "Ecography",
    abstract = "Prediction of species’ distributions is central to diverse applications in ecology, evolution and conservation science. There is increasing electronic access to vast sets of occurrence records in museums and herbaria, yet little effective guidance on how best to use this information in the context of numerous approaches for modelling distributions. To meet this need, we compared 16 modelling methods over 226 species from 6 regions of the world, creating the most comprehensive set of model comparisons to date. We used presence‐only data to fit models, and independent presence‐absence data to evaluate the predictions. Along with well‐established modelling methods such as generalised additive models and GARP and BIOCLIM, we explored methods that either have been developed recently or have rarely been applied to modelling species’ distributions. These include machine‐learning methods and community models, both of which have features that may make them particularly well suited to noisy or sparse information, as is typical of species’ occurrence data. Presence‐only data were effective for modelling species’ distributions for many species and regions. The novel methods consistently outperformed more established methods. The results of our analysis are promising for the use of data from museums and herbaria, especially as methods suited to the noise inherent in such data improve.",
    url = "https://doi.org/10.1111/j.2006.0906-7590.04596.x",
    doi = "10.1111/j.2006.0906-7590.04596.x",
    openalex = "W2112315008",
    references = "doi101002joc1276, doi101016s0006320700000744, doi101038nature02121, doi101111j001438202004tb00461x, doi101111j09067590200503957x, doi101111j20060906759004272x, doi101148radiology14317063747, doi1023072669574, doi1023073802723, doi1023073803117, doi1023073808148, doi105860choice332720, openalexw2032279931"
}

The increasing availability of phylogenetic data, computing power and informatics tools has facilitated a rapid expansion of studies that apply phylogenetic data and methods to community ecology. Several key areas are reviewed in which phylogenetic information helps to resolve long-standing controversies in community ecology, challenges previous assumptions, and opens new areas of investigation. In particular, studies in phylogenetic community ecology have helped to reveal the multitude of processes driving community assembly and have demonstrated the importance of evolution in the assembly process. Phylogenetic approaches have also increased understanding of the consequences of community interactions for speciation, adaptation and extinction. Finally, phylogenetic community structure and composition holds promise for predicting ecosystem processes and impacts of global change. Major challenges to advancing these areas remain. In particular, determining the extent to which ecologically relevant traits are phylogenetically conserved or convergent, and over what temporal scale, is critical to understanding the causes of community phylogenetic structure and its evolutionary and ecosystem consequences. Harnessing phylogenetic information to understand and forecast changes in diversity and dynamics of communities is a critical step in managing and restoring the Earth's biota in a time of rapid global change.

@article{doi101111j14610248200901314x,
    author = "Cavender‐Bares, Jeannine and Kozak, Kenneth H. and Fine, Paul V. A. and Kembel, Steven W.",
    title = "The merging of community ecology and phylogenetic biology",
    year = "2009",
    journal = "Ecology Letters",
    abstract = "The increasing availability of phylogenetic data, computing power and informatics tools has facilitated a rapid expansion of studies that apply phylogenetic data and methods to community ecology. Several key areas are reviewed in which phylogenetic information helps to resolve long-standing controversies in community ecology, challenges previous assumptions, and opens new areas of investigation. In particular, studies in phylogenetic community ecology have helped to reveal the multitude of processes driving community assembly and have demonstrated the importance of evolution in the assembly process. Phylogenetic approaches have also increased understanding of the consequences of community interactions for speciation, adaptation and extinction. Finally, phylogenetic community structure and composition holds promise for predicting ecosystem processes and impacts of global change. Major challenges to advancing these areas remain. In particular, determining the extent to which ecologically relevant traits are phylogenetically conserved or convergent, and over what temporal scale, is critical to understanding the causes of community phylogenetic structure and its evolutionary and ecosystem consequences. Harnessing phylogenetic information to understand and forecast changes in diversity and dynamics of communities is a critical step in managing and restoring the Earth's biota in a time of rapid global change.",
    url = "https://doi.org/10.1111/j.1461-0248.2009.01314.x",
    doi = "10.1111/j.1461-0248.2009.01314.x",
    openalex = "W2102384105",
    references = "doi1010160006320792912013, doi101016jppees200710001, doi101016jtree200409011, doi101038nature02403, doi10108010635150802302427, doi101086282505, doi101086282687, doi101093aibsbulletin2214b, doi101098rspb20080630, doi101111j14610248200701020x, doi101111j155856461964tb01674x, doi101111j15585646200800317x, doi101126science2304728895, doi101126science2354785167, doi101126science27953592115, doi101146annurevecolsys311343, doi101146annurevecolsys33010802150448, doi1015159781400881376, doi101722611310, doi1023071435536, doi1023071446122, doi1023072259756, doi1023073071998, doi1023073544421, doi1023074549, doi105860choice432194, doi105962bhltitle56234, doi107208chicago97802261186970010001, openalexw2273605253"
}

ABSTRACT Aim Elevational gradients distributed across the globe are a powerful test system for understanding biodiversity. Here I use a comprehensive set of bird elevational gradients to test the main drivers of diversity, including sampling, area, mid‐domain effect, temperature, temperature and water availability, and hypotheses of evolutionary history. Location Seventy‐eight elevational gradients of bird diversity from mountains in both hemispheres spanning 24.5° S to 48.2° N, including gradients from various climates, biogeographical regions and habitat types. Methods Data on bird elevational diversity were taken from the literature. Of the 150 datasets found or compiled, only those with a high, unbiased sampling effort were used in analyses. Datasets sampled all birds, all breeding birds or all forest birds; a few studies detailed seasonal, elevational shifts. Eighteen predictions of diversity theory were tested, including three sets of interactions. Results Birds display four distinct diversity patterns in nearly equal frequency on mountains: decreasing diversity, low‐elevation plateaus, low‐elevation plateaus with mid‐peaks, and unimodal mid‐elevational peaks. Bird elevational diversity strongly supports current climate as the main driver of diversity, particularly combined trends in temperature and water availability. Bird diversity on humid mountains is either decreasing or shows a low‐elevation plateau in diversity, while on dry mountains it is unimodal or a broad, low‐elevation plateau usually with a mid‐elevation maximum. The predictions of sampling, area and mid‐domain effect were not consistently supported globally. The only evolutionary hypothesis with preliminary support was niche conservatism. Main conclusions Both water and temperature variables are needed to comprehensively predict elevational diversity patterns for birds. This result is consistent for breeding and forest birds, for both hemispheres, and for local‐ or regional‐scale montane gradients. More analyses are needed to discern whether the mechanism underlying these relationships is ecological, based on direct physiological limitations or indirect food resource limitations, or historical, based on phylogenetic niche conservation or other evolutionary trends related to climate. The species–area and mid‐domain effects are not supported as primary drivers of elevational diversity in birds.

@article{doi101111j14668238200800443x,
    author = "McCain, Christy M.",
    title = "Global analysis of bird elevational diversity",
    year = "2009",
    journal = "Global Ecology and Biogeography",
    abstract = "ABSTRACT Aim Elevational gradients distributed across the globe are a powerful test system for understanding biodiversity. Here I use a comprehensive set of bird elevational gradients to test the main drivers of diversity, including sampling, area, mid‐domain effect, temperature, temperature and water availability, and hypotheses of evolutionary history. Location Seventy‐eight elevational gradients of bird diversity from mountains in both hemispheres spanning 24.5° S to 48.2° N, including gradients from various climates, biogeographical regions and habitat types. Methods Data on bird elevational diversity were taken from the literature. Of the 150 datasets found or compiled, only those with a high, unbiased sampling effort were used in analyses. Datasets sampled all birds, all breeding birds or all forest birds; a few studies detailed seasonal, elevational shifts. Eighteen predictions of diversity theory were tested, including three sets of interactions. Results Birds display four distinct diversity patterns in nearly equal frequency on mountains: decreasing diversity, low‐elevation plateaus, low‐elevation plateaus with mid‐peaks, and unimodal mid‐elevational peaks. Bird elevational diversity strongly supports current climate as the main driver of diversity, particularly combined trends in temperature and water availability. Bird diversity on humid mountains is either decreasing or shows a low‐elevation plateau in diversity, while on dry mountains it is unimodal or a broad, low‐elevation plateau usually with a mid‐elevation maximum. The predictions of sampling, area and mid‐domain effect were not consistently supported globally. The only evolutionary hypothesis with preliminary support was niche conservatism. Main conclusions Both water and temperature variables are needed to comprehensively predict elevational diversity patterns for birds. This result is consistent for breeding and forest birds, for both hemispheres, and for local‐ or regional‐scale montane gradients. More analyses are needed to discern whether the mechanism underlying these relationships is ecological, based on direct physiological limitations or indirect food resource limitations, or historical, based on phylogenetic niche conservation or other evolutionary trends related to climate. The species–area and mid‐domain effects are not supported as primary drivers of elevational diversity in birds.",
    url = "https://doi.org/10.1111/j.1466-8238.2008.00443.x",
    doi = "10.1111/j.1466-8238.2008.00443.x",
    openalex = "W2138665541",
    references = "doi101046j1466822x200100229x"
}

Ecological opportunity--through entry into a new environment, the origin of a key innovation or extinction of antagonists--is widely thought to link ecological population dynamics to evolutionary diversification. The population-level processes arising from ecological opportunity are well documented under the concept of ecological release. However, there is little consensus as to how these processes promote phenotypic diversification, rapid speciation and adaptive radiation. We propose that ecological opportunity could promote adaptive radiation by generating specific changes to the selective regimes acting on natural populations, both by relaxing effective stabilizing selection and by creating conditions that ultimately generate diversifying selection. We assess theoretical and empirical evidence for these effects of ecological opportunity and review emerging phylogenetic approaches that attempt to detect the signature of ecological opportunity across geological time. Finally, we evaluate the evidence for the evolutionary effects of ecological opportunity in the diversification of Caribbean Anolis lizards. Some of the processes that could link ecological opportunity to adaptive radiation are well documented, but others remain unsupported. We suggest that more study is required to characterize the form of natural selection acting on natural populations and to better describe the relationship between ecological opportunity and speciation rates.

@article{doi101111j14209101201002029x,
    author = "Yoder, Jeremy B. and Clancey, Erin and Roches, Simone Des and Eastman, Jonathan M. and Gentry, Lydia R. and Godsoe, William and Hagey, Travis J. and Jochimsen, Denim M. and Oswald, Benjamin P. and Robertson, Jeanne M. and Sarver, Brice A. J. and Schenk, John J. and Spear, Stephen F. and Harmon, Luke J.",
    title = "Ecological opportunity and the origin of adaptive radiations",
    year = "2010",
    journal = "Journal of Evolutionary Biology",
    abstract = "Ecological opportunity--through entry into a new environment, the origin of a key innovation or extinction of antagonists--is widely thought to link ecological population dynamics to evolutionary diversification. The population-level processes arising from ecological opportunity are well documented under the concept of ecological release. However, there is little consensus as to how these processes promote phenotypic diversification, rapid speciation and adaptive radiation. We propose that ecological opportunity could promote adaptive radiation by generating specific changes to the selective regimes acting on natural populations, both by relaxing effective stabilizing selection and by creating conditions that ultimately generate diversifying selection. We assess theoretical and empirical evidence for these effects of ecological opportunity and review emerging phylogenetic approaches that attempt to detect the signature of ecological opportunity across geological time. Finally, we evaluate the evidence for the evolutionary effects of ecological opportunity in the diversification of Caribbean Anolis lizards. Some of the processes that could link ecological opportunity to adaptive radiation are well documented, but others remain unsupported. We suggest that more study is required to characterize the form of natural selection acting on natural populations and to better describe the relationship between ecological opportunity and speciation rates.",
    url = "https://doi.org/10.1111/j.1420-9101.2010.02029.x",
    doi = "10.1111/j.1420-9101.2010.02029.x",
    openalex = "W1566874056",
    references = "crowell1962reduced, doi101007978940100585210, doi101016jtree200810011, doi101016s0169534702024990, doi101017s0094837300003778, doi101038303614a0, doi101086284196, doi101086285404, doi101086510633, doi101093molbevmsi103, doi101093oso97801985052350010001, doi101098rspb20080630, doi101111j001438202003tb00285x, doi101111j001438202004tb00462x, doi101111j109583121996tb01434x, doi101111j155856461964tb01674x, doi101111j155856461982tb05068x, doi101111j155856461983tb00236x, doi101126science1157966, doi101186147121487214, doi101722611310, doi1023071438156, doi1023071932042, doi1023071934090, doi1023073071998, doi1043249780203509104"
}

Reference phylogenies are crucial for providing a taxonomic framework for interpretation of marker gene and metagenomic surveys, which continue to reveal novel species at a remarkable rate. Greengenes is a dedicated full-length 16S rRNA gene database that provides users with a curated taxonomy based on de novo tree inference. We developed a 'taxonomy to tree' approach for transferring group names from an existing taxonomy to a tree topology, and used it to apply the Greengenes, National Center for Biotechnology Information (NCBI) and cyanoDB (Cyanobacteria only) taxonomies to a de novo tree comprising 408,315 sequences. We also incorporated explicit rank information provided by the NCBI taxonomy to group names (by prefixing rank designations) for better user orientation and classification consistency. The resulting merged taxonomy improved the classification of 75% of the sequences by one or more ranks relative to the original NCBI taxonomy with the most pronounced improvements occurring in under-classified environmental sequences. We also assessed candidate phyla (divisions) currently defined by NCBI and present recommendations for consolidation of 34 redundantly named groups. All intermediate results from the pipeline, which includes tree inference, jackknifing and transfer of a donor taxonomy to a recipient tree (tax2tree) are available for download. The improved Greengenes taxonomy should provide important infrastructure for a wide range of megasequencing projects studying ecosystems on scales ranging from our own bodies (the Human Microbiome Project) to the entire planet (the Earth Microbiome Project). The implementation of the software can be obtained from http://sourceforge.net/projects/tax2tree/.

@article{doi101038ismej2011139,
    author = "McDonald, Daniel and Price, Morgan N. and Goodrich, Julia K. and Nawrocki, Eric P. and DeSantis, Todd Z. and Probst, Alexander J. and Andersen, Gary L. and Knight, Rob and Hugenholtz, Philip",
    title = "An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea",
    year = "2011",
    journal = "The ISME Journal",
    abstract = "Reference phylogenies are crucial for providing a taxonomic framework for interpretation of marker gene and metagenomic surveys, which continue to reveal novel species at a remarkable rate. Greengenes is a dedicated full-length 16S rRNA gene database that provides users with a curated taxonomy based on de novo tree inference. We developed a 'taxonomy to tree' approach for transferring group names from an existing taxonomy to a tree topology, and used it to apply the Greengenes, National Center for Biotechnology Information (NCBI) and cyanoDB (Cyanobacteria only) taxonomies to a de novo tree comprising 408,315 sequences. We also incorporated explicit rank information provided by the NCBI taxonomy to group names (by prefixing rank designations) for better user orientation and classification consistency. The resulting merged taxonomy improved the classification of 75\% of the sequences by one or more ranks relative to the original NCBI taxonomy with the most pronounced improvements occurring in under-classified environmental sequences. We also assessed candidate phyla (divisions) currently defined by NCBI and present recommendations for consolidation of 34 redundantly named groups. All intermediate results from the pipeline, which includes tree inference, jackknifing and transfer of a donor taxonomy to a recipient tree (tax2tree) are available for download. The improved Greengenes taxonomy should provide important infrastructure for a wide range of megasequencing projects studying ecosystems on scales ranging from our own bodies (the Human Microbiome Project) to the entire planet (the Earth Microbiome Project). The implementation of the software can be obtained from http://sourceforge.net/projects/tax2tree/.",
    url = "https://doi.org/10.1038/ismej.2011.139",
    doi = "10.1038/ismej.2011.139",
    openalex = "W2154026962",
    references = "doi101371journalpone0009490, doi1073260003481911154487, doi1073260003481911253913"
}

ABSTRACT Aim Concerns over how global change will influence species distributions, in conjunction with increased emphasis on understanding niche dynamics in evolutionary and community contexts, highlight the growing need for robust methods to quantify niche differences between or within taxa. We propose a statistical framework to describe and compare environmental niches from occurrence and spatial environmental data. Location Europe, North America and South America. Methods The framework applies kernel smoothers to densities of species occurrence in gridded environmental space to calculate metrics of niche overlap and test hypotheses regarding niche conservatism. We use this framework and simulated species with pre‐defined distributions and amounts of niche overlap to evaluate several ordination and species distribution modelling techniques for quantifying niche overlap. We illustrate the approach with data on two well‐studied invasive species. Results We show that niche overlap can be accurately detected with the framework when variables driving the distributions are known. The method is robust to known and previously undocumented biases related to the dependence of species occurrences on the frequency of environmental conditions that occur across geographical space. The use of a kernel smoother makes the process of moving from geographical space to multivariate environmental space independent of both sampling effort and arbitrary choice of resolution in environmental space. However, the use of ordination and species distribution model techniques for selecting, combining and weighting variables on which niche overlap is calculated provide contrasting results. Main conclusions The framework meets the increasing need for robust methods to quantify niche differences. It is appropriate for studying niche differences between species, subspecies or intra‐specific lineages that differ in their geographical distributions. Alternatively, it can be used to measure the degree to which the environmental niche of a species or intra‐specific lineage has changed over time.

@article{doi101111j14668238201100698x,
    author = "Broennimann, Olivier and Fitzpatrick, Matthew C. and Pearman, Peter B. and Petitpierre, Blaise and Pellissier, Loïc and Yoccoz, Nigel G. and Thuiller, Wilfried and Fortin, Marie‐Josée and Randin, Christophe F. and Zimmermann, Niklaus E. and Graham, Catherine H. and Guisan, Antoine",
    title = "Measuring ecological niche overlap from occurrence and spatial environmental data",
    year = "2011",
    journal = "Global Ecology and Biogeography",
    abstract = "ABSTRACT Aim Concerns over how global change will influence species distributions, in conjunction with increased emphasis on understanding niche dynamics in evolutionary and community contexts, highlight the growing need for robust methods to quantify niche differences between or within taxa. We propose a statistical framework to describe and compare environmental niches from occurrence and spatial environmental data. Location Europe, North America and South America. Methods The framework applies kernel smoothers to densities of species occurrence in gridded environmental space to calculate metrics of niche overlap and test hypotheses regarding niche conservatism. We use this framework and simulated species with pre‐defined distributions and amounts of niche overlap to evaluate several ordination and species distribution modelling techniques for quantifying niche overlap. We illustrate the approach with data on two well‐studied invasive species. Results We show that niche overlap can be accurately detected with the framework when variables driving the distributions are known. The method is robust to known and previously undocumented biases related to the dependence of species occurrences on the frequency of environmental conditions that occur across geographical space. The use of a kernel smoother makes the process of moving from geographical space to multivariate environmental space independent of both sampling effort and arbitrary choice of resolution in environmental space. However, the use of ordination and species distribution model techniques for selecting, combining and weighting variables on which niche overlap is calculated provide contrasting results. Main conclusions The framework meets the increasing need for robust methods to quantify niche differences. It is appropriate for studying niche differences between species, subspecies or intra‐specific lineages that differ in their geographical distributions. Alternatively, it can be used to measure the degree to which the environmental niche of a species or intra‐specific lineage has changed over time.",
    url = "https://doi.org/10.1111/j.1466-8238.2011.00698.x",
    doi = "10.1111/j.1466-8238.2011.00698.x",
    openalex = "W2095766166",
    references = "doi101073pnas6951109, doi101093oso97801985264070010001, doi103354cr021001, openalexw3149745985"
}

Journal of Applied Ecology encourages contributions that can influence environmental management, policy or both, with evidence based on the most robust science possible. Natural resource management is often contentious, and any perceived weaknesses in the underpinning science are easily exploited by interest groups to undermine the wider endeavour (see, e.g. the experiences of the Intergovernmental Panel on Climate Change, Ravindranath 2010). Thus, the robustness of science designed to underpin management and policy is particularly important. Unfortunately, robust and unambiguous results are difficult to obtain in ecology. In particular, causal pathways in ecology are seldom linear, but are part of a ‘vast web of cause and effect’ of which, typically, we can study only a small part (Peters 1991; p. 134). Meaningful spatial and temporal scales for ecological processes often defy experiments, controlled manipulations and adequate replication; most modern ecological science is reliant on observational data and correlation is far easier to demonstrate than causation (cf. Sugihara et al. 2012). Formal experimentation is clearly impossible in the context of many of the most pressing questions of societal relevance, such as those regarding the impacts of climate change, large-scale agricultural intensification and habitat loss. The conceptual frameworks that inform our understanding of these processes often rely on entities that can be hard to measure directly and, thus, ecologists often depend on proxies or surrogates for those entities. In natural resource management, for example, common proxies include measures assumed to capture the conservation status of species, as well as measures assumed to provide information on ecosystems’ distribution, structure, functioning and service delivery (Mace et al. 2008; Ayanu et al. 2012; Pettorelli et al. 2014). Several studies have already pointed out issues and pitfalls related to the use of proxies in ecology and evolution (see, e.g. Nieberding & Olivieri 2007; Sekar 2012; Best & Stachowicz 2013) but less consideration has been given to the impacts of proxies on the robustness of management recommendations at a range of scales (but see Eigenbrod et al. 2010). This is despite the fact that proxies are a vital part of an applied ecologist's toolkit and are frequently used to link science with management and policy (Turnhout, Hisschemöller & Eijsackers 2007). Here, we discuss the role of proxies in applied ecology and management by examining three recent examples of problematic issues: proxies for the abundance of animal populations; proxies for habitat quality; and proxies for ecosystem functions and ecosystem services delivery. While this list is far from exhaustive, these are issues we frequently see as journal editors. They provide a useful starting point to discuss possible directions to improve our use of proxies in natural resource management. Population size is a key requirement for supporting local decision-making in species-based management and is also used to inform several national and international policies and regulations. For example, population size and the rate at which it changes are fundamental to species listing and delisting decisions under the Endangered Species Act (U.S. Senate Committee on Environment & Public Works 1973) and for the IUCN Red List (Mace et al. 2008); these decisions have knock-on implications for the international trade of organisms (CITES 1973). The use of indices as proxies for population abundance is perhaps one of the most widely recognized areas of contention in applied ecology. Across vast geographic areas, the relative abundances of many wildlife populations of cultural or economic importance are assessed using surveys that yield indices, rather than estimates, of abundance (Schwarz & Seber 1999). These include, for example, track counts used to monitor the abundance of many mammal species, camera trapping rates used to index the abundance of elusive or low-density species, pitfall traps to assess invertebrate populations, and hunting offtake used as an index of the abundance of many game birds and mammals. These proxy methods have all been the focus of considerable concern (McDonald & Harris 1999; Jennelle, Runge & MacKenzie 2002; Pollock et al. 2002; Webbon, Baker & Harris 2004; Keane, Jones & Milner-Gulland 2011; Saska et al. 2013). The central criticism relates to the generally unverified assumption that the relationship between the index and the true abundance is direct and constant (Pollock et al. 2002). One basic issue underpinning this criticism is that all of these methods depend on encounters (between observers, cameras, traps or hunters and tracks, animals or quarry) which, in turn, depend on the levels of activity of individuals of the focal populations, the detectability of their signs and the extent of efforts to locate them. These factors are not expected to be static in either space or time (Pollock et al. 2002) and could be affected by behavioural changes along ecological gradients of management interest (such as agricultural intensification). In spite of these criticisms, indices of abundance remain in widespread use for a combination of reasons. First, collecting indices tends to be a lower-cost approach than determining absolute estimates of abundance (Jones 2011). Second, as Caughley (1977) observed, ‘absolute estimates of density [are often] unnecessary luxuries’, and management practices such as threshold harvesting or studies of relative habitat utilization are not reliant on estimates of absolute abundance. Third, in some situations, evidence suggests that indices can provide a reasonable proxy for abundance. A recent applied example relates to a critical issue in Australian wildlife management. Specifically, the extent to which track counts reflect true abundance is a key concern about studies of the ecological impacts of the dingo Canis lupus dingo (Hayward & Marlow 2014). In defence of those studies, Nimmo et al. (2015) cite work showing that track counts were linearly related to the true abundances of various carnivores in a number of specific studies. Moreover, they point out that, for elusive species, indices based on abundant field signs might well be associated with lower uncertainty than population estimates based on sporadic but infrequent direct sightings (Nimmo et al. 2015). In summary, proxies for population abundance are widely used and often criticized. They might be adequate in some situations but that will usually depend on the specific management question being addressed. More often, indices of abundance are vulnerable to criticism and will require careful calibration. Identifying potential sites suitable for species translocations, or sites at which we should prioritize restoration efforts, are important management activities world-wide. Habitat monitoring is also strongly encouraged by international conventions: the Convention on the conservation of migratory species (CMS), for example, explicitly states that ‘parties that are range states of a migratory species shall endeavour to conserve and, where feasible and appropriate, restore those habitats of the species which are of importance in removing the species from danger of extinction’ (www.cms.int). Habitat is usually defined as the resources and conditions present in an area that produce occupancy – including survival and reproduction – by a given organism (Morrison, Marcot & Mannan 1992). The spatial extent and resolution at which habitat is defined tends to be a function of several variables, such as the number of individuals considered, the body size of the species considered, and the spatial resolution at which habitat selection patterns are explored (itself shaped by the availability of environmental and species occurrence data; Pettorelli 2013a,b). Within this context, habitat quality is sometimes perceived as some function of fitness or per-capita population growth (Van Horne 1983; Johnson 2007), where these are expected to be higher in high-quality habitats. The problem with this definition of habitat quality is that measuring per-capita contributions to population growth in a given habitat requires intensive monitoring, usually over a long period. As a result, attempts to capture variation in per-capita population growth often use information that is less costly and time consuming to obtain, such as abundance, survival, body condition or corticosterone levels of the focal species (see, e.g. Van Horne 1983; Marra & Holberton 1998; Johnson 2007). It has also been assumed that habitat suitability, usually determined from occurrence or presence/absence data using species distribution models (SDMs), will provide a useful indication of habitat quality (see, e.g. Larson et al. 2004; Martin et al. 2012). Working with the giant kangaroo rat Dipodomys ingens, Bean et al. (2014) compared these different proxies for habitat quality, using SDMs generated at a range of scales. They found that habitat suitability from SDMs correlated with abundance (especially when SDMs were parameterized at a fine scale) but not with survival or body condition. Life-history theory is reassuring in this regard, providing good reasons why neither survival (Pilastro, Tavecchia & Marin 2003) nor body condition (Houston & McNamara 1993) need be strongly related to habitat quality. More troubling, however, is that ecology also provides reasons to question the relationship between population abundance and habitat quality, especially where despotic behavioural processes can result in large numbers of individuals being excluded from high-quality (and into marginal) habitats (Van Horne 1983). These considerations call into question a number of widely used proxies for habitat quality. Habitat quality is unquestionably related to the availability of resources, but also to levels of predation. Which of these predominates in determining the quality of habitat for a given population is often described using the terminology of ‘bottom-up’ vs. ‘top-down’ control (e.g. Hunter & Price 1992). The proportion of mortality attributable to predation is sometimes used as a proxy for the extent of top-down control (Sinclair, Mduma & Brashares 2003; Hopcraft, Olff & Sinclair 2010). Paradoxically, however, behavioural modelling of risk-sensitive foraging shows that an increase in predation may well result from a decline in food availability (McNamara & Houston 1987). These results appear to be borne out in empirical systems (Sinclair & Arcese 1995), undermining the use of predation rate as an index of top-down control and emphasizing the difficulty of teasing apart these processes. Overall, theoretical considerations suggest that proxies for habitat quality and the processes that determine it will often be flawed. As with proxies for abundance, however, proxies for habitat quality might be suitable for addressing management questions at some spatial scales. The challenge remains to identify those situations under which proxies are useful and to determine alternative approaches where they cannot be used. With a policy agenda increasingly focused on ecosystem service provision (Perrings et al. 2010), understanding the ecology of ecosystem functioning and its implications for the delivery of ecosystem services has never been more important. It can be extremely difficult to measure ecosystem function or service directly, and spatial proxies, such as small-scale above-ground biomass in plants, are often employed (e.g. Tilman et al. 2001). Perhaps less widely appreciated, however, is the fact that certain easily measured ecosystem functions are sometimes used as proxies for more difficult to measure ecosystem functions and services. For example, most biodiversity–ecosystem function experiments measure productivity and assume that this parameter correlates with a broader suite of ecosystem functions and services. Yet recent work has shown that ecosystem productivity can be quite divergent from functions and services such as methane consumption, pest control and pollination (Werling et al. 2014). A vast array of approaches to measure ecosystem functions and/or ecosystem services is currently available to ecologists and managers. Large-scale attempts to assess ecosystem productivity might rely on proxies such as climatic and structural variables that correlate with productivity (Ruiz-Benito et al. 2014), or vegetation indices derived from remote sensing information (Pettorelli 2013b). Identifying which methodological approaches and proxies are likely to support robust decision-making in a given context is a particular challenge. The European Union's Water Framework Directive (WFD), for example, uses an ecological status score for aquatic habitats to represent the amount of ecosystem service provisioned. One recent assessment of the WFD's use of ecological status found that status correlates with some ecosystem services and taxonomic diversity (Tolonen et al. 2014), suggesting that this proxy is useful for quickly assessing overall service delivery (though caution is required when considering single or few services). By contrast, recent analyses have shown that land cover type (e.g. Ayanu et al. 2012) is a poor proxy for ecosystem service, with potential to mislead management strategies (Eigenbrod et al. 2010). Species-based proxies for assessing ecosystem function and service delivery have also been heavily discussed. Two decades of research have now been devoted to testing the hypotheses that higher species diversity leads to greater ecosystem function and service delivery, with the view to establishing species richness as a proxy for these ecosystem attributes (Balvanera et al. 2006; Cardinale et al. 2006). Results so far, however, seem to indicate that functional diversity (Petchey & Gaston 2006; Mouchet et al. 2010; Cadotte, Carscadden & Mirotchnick 2011), rather than species richness itself, directly affects ecosystem function and the delivery of ecosystem services (Tilman et al. 2001; Cadotte, Carscadden & Mirotchnick 2011; Woodcock et al. 2014). Species loss may be functionally random, with the result that certain extinction scenarios may have minimal effects on functional diversity (Sasaki et al. 2014), rendering species loss an unreliable indicator of ecosystem function loss. Interestingly, both functional and phylogenetic diversity have actually been shown to explain variation in ecosystem function (Flynn et al. 2011; Cadotte 2013). However, there are cases where phylogenetic and functional diversity may not be strongly correlated and actually show different responses to disturbance or management (Cadotte, Albert & Walker 2013; Bässler et al. 2014). Clearly, more work is required to understand how well these facets of diversity correspond to the important ecological differences that influence the ecosystem functions that may attract management interventions. Overall, the validity of different proxies for ecosystem function and service provision has been the focus of much research but few proxies have been shown to work well across a wide range of scenarios. Proxies should be used cautiously in situations in which they have been shown to work, or subjected to further validation beyond those circumstances. The examples above highlight the challenges of drawing robust management-relevant inferences from ecological science, providing insights into the appropriate use of proxies and ways to move forward. Here, we suggest three essential considerations when using and/or developing proxies. As with so much in ecology, the relevance of proxies often depends on the scale of enquiry. As illustrated by Bean et al. (2014), spatial resolution and spatial extent are correlated entities in most habitat quality assessments. Unsurprisingly, assessments focused on smaller areas or utilizing environmental data collected at greater spatial resolution are capable of detecting greater variability in apparent quality than coarser, large-scale studies. Extent and resolution are, thus, important parameters that directly shape the usefulness of habitat quality assessments: broad-scale models are more likely to be adequate for identifying potential protected areas, whilst finer-scale models will be required to inform local management strategies such as habitat restoration. Spatial scale is also likely to be fundamental to debates about the usefulness of prey availability as an indicator of habitat quality for predators. Recent work on the sublethal effects of predation and the ‘landscape of fear’, shows that prey will often be most abundant in areas in which they are relatively inaccessible to predators and, thus, that the correlation between prey abundance and prey availability may be low (Laundré 2010). This suggests that, at a fine scale, prey availability might be a poor proxy for habitat quality – but, at a landscape scale, predators will still prefer areas with abundant prey. Thus, the spatial scale at which a question is posed has a strong bearing on the relevance of a given proxy. Temporal scale might also shape the relevance of a proxy. Owing to variation in activity among years, proxies for population density based on either sighting rates or spoor abundance might be poor indicators of interannual changes in population size. However, unless activity or detectability show long-term, deterministic trends, such indices will be useful to identify the existence of trends in abundance over longer time frames. Even over short time frames, indices might be useful, as long as the variation in detectability and activity is independent of abundance and of substantially lower magnitude than the variation in population size that researchers wish to or not this is the should be a focus of work at these proxies. studies and which an between spatial and the resolution of temporal While the recent use of occupancy and detectability models encourages temporal this can at a of understanding important spatial of species which, in many may be more important from a conservation et al. 2014). in a given proxy is directly related to the amount of evidence its Proxies to be to local so is often a requirement of various proxies for population abundance has been the focus of As Nimmo et al. (2015) a range of evidence to support the use of track abundance as a useful proxy for abundance of to large this not that track abundance will be a useful proxy in all work has focused on indices of abundance and for factors that determine how the relationship between the index and abundance across time and For example, et al. data on of in the to identify factors that In this they were to for time of when index to absolute Saska et al. assessed the of on the activity of to control for activity when pitfall trapping to relative abundance. for activity or can also of abundance indices across species, those indices are based on track counts or trapping rates et al. 2008; et al. are also available for for of when using indices of population density based on abundance. Specifically, & approaches for for from both observational and both of which can undermine the use of counts as proxies for abundance. assessing the validity of various proxies of habitat quality are also (see, e.g. Johnson 2007; Pettorelli 2013b). for proxies of habitat quality derived from habitat suitability modelling can be found in work that to the quality of This used by et al. for assessing the of that habitat suitability modelling can areas that these models produce useful proxies for habitat quality that is to the One to this is that habitat suitability modelling based on or presence/absence data cannot between and habitats. et al. measures of into habitat suitability however, those measures will often be proxies for As proxies for ecosystem function and service provision have also been subjected to but with several proxies have ecosystem service in particular, a wide array of processes Thus, further validation is likely to be required to show that proxies well across One of the fundamental for proxies from the spatial and temporal scale of most ecological However, and research can to and proxies and might also our on them. The for example, is a large-scale which will information on distribution with The is to over decades at an of sites and has the potential to provide direct of the link between and ecosystem to our understanding of this also ecological with a of sites across the are on scales. The for will include animal monitoring on a research of the This will remote monitoring of the and of large numbers of individuals of species far smaller than can be at many this will direct of habitat use and the of habitat on a scale beyond currently our understanding of the validity of proxies for habitat quality. Applied ecologists should to the that natural resource management and environmental policy the possible underpinning the lower of monitoring work, robust approaches to policy and management often require monitoring, to key ecological on a scale that the need for proxies. As Martin of the has we it for that will to provide vast to for on – but we still about the one where we already that not be about for monitoring that yield insights into the key ecological processes supporting on insights could our understanding of ecological systems and, the of and to with

@article{doi1011111365266412383,
    author = "Stephens, Philip A. and Pettorelli, Nathalie and Barlow, Jos and Whittingham, Mark J. and Cadotte, Marc W.",
    title = "Management by proxy? The use of indices in applied ecology",
    year = "2014",
    journal = "Journal of Applied Ecology",
    abstract = "Journal of Applied Ecology encourages contributions that can influence environmental management, policy or both, with evidence based on the most robust science possible. Natural resource management is often contentious, and any perceived weaknesses in the underpinning science are easily exploited by interest groups to undermine the wider endeavour (see, e.g. the experiences of the Intergovernmental Panel on Climate Change, Ravindranath 2010). Thus, the robustness of science designed to underpin management and policy is particularly important. Unfortunately, robust and unambiguous results are difficult to obtain in ecology. In particular, causal pathways in ecology are seldom linear, but are part of a ‘vast web of cause and effect’ of which, typically, we can study only a small part (Peters 1991; p. 134). Meaningful spatial and temporal scales for ecological processes often defy experiments, controlled manipulations and adequate replication; most modern ecological science is reliant on observational data and correlation is far easier to demonstrate than causation (cf. Sugihara et al. 2012). Formal experimentation is clearly impossible in the context of many of the most pressing questions of societal relevance, such as those regarding the impacts of climate change, large-scale agricultural intensification and habitat loss. The conceptual frameworks that inform our understanding of these processes often rely on entities that can be hard to measure directly and, thus, ecologists often depend on proxies or surrogates for those entities. In natural resource management, for example, common proxies include measures assumed to capture the conservation status of species, as well as measures assumed to provide information on ecosystems’ distribution, structure, functioning and service delivery (Mace et al. 2008; Ayanu et al. 2012; Pettorelli et al. 2014). Several studies have already pointed out issues and pitfalls related to the use of proxies in ecology and evolution (see, e.g. Nieberding \& Olivieri 2007; Sekar 2012; Best \& Stachowicz 2013) but less consideration has been given to the impacts of proxies on the robustness of management recommendations at a range of scales (but see Eigenbrod et al. 2010). This is despite the fact that proxies are a vital part of an applied ecologist's toolkit and are frequently used to link science with management and policy (Turnhout, Hisschemöller \& Eijsackers 2007). Here, we discuss the role of proxies in applied ecology and management by examining three recent examples of problematic issues: proxies for the abundance of animal populations; proxies for habitat quality; and proxies for ecosystem functions and ecosystem services delivery. While this list is far from exhaustive, these are issues we frequently see as journal editors. They provide a useful starting point to discuss possible directions to improve our use of proxies in natural resource management. Population size is a key requirement for supporting local decision-making in species-based management and is also used to inform several national and international policies and regulations. For example, population size and the rate at which it changes are fundamental to species listing and delisting decisions under the Endangered Species Act (U.S. Senate Committee on Environment \& Public Works 1973) and for the IUCN Red List (Mace et al. 2008); these decisions have knock-on implications for the international trade of organisms (CITES 1973). The use of indices as proxies for population abundance is perhaps one of the most widely recognized areas of contention in applied ecology. Across vast geographic areas, the relative abundances of many wildlife populations of cultural or economic importance are assessed using surveys that yield indices, rather than estimates, of abundance (Schwarz \& Seber 1999). These include, for example, track counts used to monitor the abundance of many mammal species, camera trapping rates used to index the abundance of elusive or low-density species, pitfall traps to assess invertebrate populations, and hunting offtake used as an index of the abundance of many game birds and mammals. These proxy methods have all been the focus of considerable concern (McDonald \& Harris 1999; Jennelle, Runge \& MacKenzie 2002; Pollock et al. 2002; Webbon, Baker \& Harris 2004; Keane, Jones \& Milner-Gulland 2011; Saska et al. 2013). The central criticism relates to the generally unverified assumption that the relationship between the index and the true abundance is direct and constant (Pollock et al. 2002). One basic issue underpinning this criticism is that all of these methods depend on encounters (between observers, cameras, traps or hunters and tracks, animals or quarry) which, in turn, depend on the levels of activity of individuals of the focal populations, the detectability of their signs and the extent of efforts to locate them. These factors are not expected to be static in either space or time (Pollock et al. 2002) and could be affected by behavioural changes along ecological gradients of management interest (such as agricultural intensification). In spite of these criticisms, indices of abundance remain in widespread use for a combination of reasons. First, collecting indices tends to be a lower-cost approach than determining absolute estimates of abundance (Jones 2011). Second, as Caughley (1977) observed, ‘absolute estimates of density [are often] unnecessary luxuries’, and management practices such as threshold harvesting or studies of relative habitat utilization are not reliant on estimates of absolute abundance. Third, in some situations, evidence suggests that indices can provide a reasonable proxy for abundance. A recent applied example relates to a critical issue in Australian wildlife management. Specifically, the extent to which track counts reflect true abundance is a key concern about studies of the ecological impacts of the dingo Canis lupus dingo (Hayward \& Marlow 2014). In defence of those studies, Nimmo et al. (2015) cite work showing that track counts were linearly related to the true abundances of various carnivores in a number of specific studies. Moreover, they point out that, for elusive species, indices based on abundant field signs might well be associated with lower uncertainty than population estimates based on sporadic but infrequent direct sightings (Nimmo et al. 2015). In summary, proxies for population abundance are widely used and often criticized. They might be adequate in some situations but that will usually depend on the specific management question being addressed. More often, indices of abundance are vulnerable to criticism and will require careful calibration. Identifying potential sites suitable for species translocations, or sites at which we should prioritize restoration efforts, are important management activities world-wide. Habitat monitoring is also strongly encouraged by international conventions: the Convention on the conservation of migratory species (CMS), for example, explicitly states that ‘parties that are range states of a migratory species shall endeavour to conserve and, where feasible and appropriate, restore those habitats of the species which are of importance in removing the species from danger of extinction’ (www.cms.int). Habitat is usually defined as the resources and conditions present in an area that produce occupancy – including survival and reproduction – by a given organism (Morrison, Marcot \& Mannan 1992). The spatial extent and resolution at which habitat is defined tends to be a function of several variables, such as the number of individuals considered, the body size of the species considered, and the spatial resolution at which habitat selection patterns are explored (itself shaped by the availability of environmental and species occurrence data; Pettorelli 2013a,b). Within this context, habitat quality is sometimes perceived as some function of fitness or per-capita population growth (Van Horne 1983; Johnson 2007), where these are expected to be higher in high-quality habitats. The problem with this definition of habitat quality is that measuring per-capita contributions to population growth in a given habitat requires intensive monitoring, usually over a long period. As a result, attempts to capture variation in per-capita population growth often use information that is less costly and time consuming to obtain, such as abundance, survival, body condition or corticosterone levels of the focal species (see, e.g. Van Horne 1983; Marra \& Holberton 1998; Johnson 2007). It has also been assumed that habitat suitability, usually determined from occurrence or presence/absence data using species distribution models (SDMs), will provide a useful indication of habitat quality (see, e.g. Larson et al. 2004; Martin et al. 2012). Working with the giant kangaroo rat Dipodomys ingens, Bean et al. (2014) compared these different proxies for habitat quality, using SDMs generated at a range of scales. They found that habitat suitability from SDMs correlated with abundance (especially when SDMs were parameterized at a fine scale) but not with survival or body condition. Life-history theory is reassuring in this regard, providing good reasons why neither survival (Pilastro, Tavecchia \& Marin 2003) nor body condition (Houston \& McNamara 1993) need be strongly related to habitat quality. More troubling, however, is that ecology also provides reasons to question the relationship between population abundance and habitat quality, especially where despotic behavioural processes can result in large numbers of individuals being excluded from high-quality (and into marginal) habitats (Van Horne 1983). These considerations call into question a number of widely used proxies for habitat quality. Habitat quality is unquestionably related to the availability of resources, but also to levels of predation. Which of these predominates in determining the quality of habitat for a given population is often described using the terminology of ‘bottom-up’ vs. ‘top-down’ control (e.g. Hunter \& Price 1992). The proportion of mortality attributable to predation is sometimes used as a proxy for the extent of top-down control (Sinclair, Mduma \& Brashares 2003; Hopcraft, Olff \& Sinclair 2010). Paradoxically, however, behavioural modelling of risk-sensitive foraging shows that an increase in predation may well result from a decline in food availability (McNamara \& Houston 1987). These results appear to be borne out in empirical systems (Sinclair \& Arcese 1995), undermining the use of predation rate as an index of top-down control and emphasizing the difficulty of teasing apart these processes. Overall, theoretical considerations suggest that proxies for habitat quality and the processes that determine it will often be flawed. As with proxies for abundance, however, proxies for habitat quality might be suitable for addressing management questions at some spatial scales. The challenge remains to identify those situations under which proxies are useful and to determine alternative approaches where they cannot be used. With a policy agenda increasingly focused on ecosystem service provision (Perrings et al. 2010), understanding the ecology of ecosystem functioning and its implications for the delivery of ecosystem services has never been more important. It can be extremely difficult to measure ecosystem function or service directly, and spatial proxies, such as small-scale above-ground biomass in plants, are often employed (e.g. Tilman et al. 2001). Perhaps less widely appreciated, however, is the fact that certain easily measured ecosystem functions are sometimes used as proxies for more difficult to measure ecosystem functions and services. For example, most biodiversity–ecosystem function experiments measure productivity and assume that this parameter correlates with a broader suite of ecosystem functions and services. Yet recent work has shown that ecosystem productivity can be quite divergent from functions and services such as methane consumption, pest control and pollination (Werling et al. 2014). A vast array of approaches to measure ecosystem functions and/or ecosystem services is currently available to ecologists and managers. Large-scale attempts to assess ecosystem productivity might rely on proxies such as climatic and structural variables that correlate with productivity (Ruiz-Benito et al. 2014), or vegetation indices derived from remote sensing information (Pettorelli 2013b). Identifying which methodological approaches and proxies are likely to support robust decision-making in a given context is a particular challenge. The European Union's Water Framework Directive (WFD), for example, uses an ecological status score for aquatic habitats to represent the amount of ecosystem service provisioned. One recent assessment of the WFD's use of ecological status found that status correlates with some ecosystem services and taxonomic diversity (Tolonen et al. 2014), suggesting that this proxy is useful for quickly assessing overall service delivery (though caution is required when considering single or few services). By contrast, recent analyses have shown that land cover type (e.g. Ayanu et al. 2012) is a poor proxy for ecosystem service, with potential to mislead management strategies (Eigenbrod et al. 2010). Species-based proxies for assessing ecosystem function and service delivery have also been heavily discussed. Two decades of research have now been devoted to testing the hypotheses that higher species diversity leads to greater ecosystem function and service delivery, with the view to establishing species richness as a proxy for these ecosystem attributes (Balvanera et al. 2006; Cardinale et al. 2006). Results so far, however, seem to indicate that functional diversity (Petchey \& Gaston 2006; Mouchet et al. 2010; Cadotte, Carscadden \& Mirotchnick 2011), rather than species richness itself, directly affects ecosystem function and the delivery of ecosystem services (Tilman et al. 2001; Cadotte, Carscadden \& Mirotchnick 2011; Woodcock et al. 2014). Species loss may be functionally random, with the result that certain extinction scenarios may have minimal effects on functional diversity (Sasaki et al. 2014), rendering species loss an unreliable indicator of ecosystem function loss. Interestingly, both functional and phylogenetic diversity have actually been shown to explain variation in ecosystem function (Flynn et al. 2011; Cadotte 2013). However, there are cases where phylogenetic and functional diversity may not be strongly correlated and actually show different responses to disturbance or management (Cadotte, Albert \& Walker 2013; Bässler et al. 2014). Clearly, more work is required to understand how well these facets of diversity correspond to the important ecological differences that influence the ecosystem functions that may attract management interventions. Overall, the validity of different proxies for ecosystem function and service provision has been the focus of much research but few proxies have been shown to work well across a wide range of scenarios. Proxies should be used cautiously in situations in which they have been shown to work, or subjected to further validation beyond those circumstances. The examples above highlight the challenges of drawing robust management-relevant inferences from ecological science, providing insights into the appropriate use of proxies and ways to move forward. Here, we suggest three essential considerations when using and/or developing proxies. As with so much in ecology, the relevance of proxies often depends on the scale of enquiry. As illustrated by Bean et al. (2014), spatial resolution and spatial extent are correlated entities in most habitat quality assessments. Unsurprisingly, assessments focused on smaller areas or utilizing environmental data collected at greater spatial resolution are capable of detecting greater variability in apparent quality than coarser, large-scale studies. Extent and resolution are, thus, important parameters that directly shape the usefulness of habitat quality assessments: broad-scale models are more likely to be adequate for identifying potential protected areas, whilst finer-scale models will be required to inform local management strategies such as habitat restoration. Spatial scale is also likely to be fundamental to debates about the usefulness of prey availability as an indicator of habitat quality for predators. Recent work on the sublethal effects of predation and the ‘landscape of fear’, shows that prey will often be most abundant in areas in which they are relatively inaccessible to predators and, thus, that the correlation between prey abundance and prey availability may be low (Laundré 2010). This suggests that, at a fine scale, prey availability might be a poor proxy for habitat quality – but, at a landscape scale, predators will still prefer areas with abundant prey. Thus, the spatial scale at which a question is posed has a strong bearing on the relevance of a given proxy. Temporal scale might also shape the relevance of a proxy. Owing to variation in activity among years, proxies for population density based on either sighting rates or spoor abundance might be poor indicators of interannual changes in population size. However, unless activity or detectability show long-term, deterministic trends, such indices will be useful to identify the existence of trends in abundance over longer time frames. Even over short time frames, indices might be useful, as long as the variation in detectability and activity is independent of abundance and of substantially lower magnitude than the variation in population size that researchers wish to or not this is the should be a focus of work at these proxies. studies and which an between spatial and the resolution of temporal While the recent use of occupancy and detectability models encourages temporal this can at a of understanding important spatial of species which, in many may be more important from a conservation et al. 2014). in a given proxy is directly related to the amount of evidence its Proxies to be to local so is often a requirement of various proxies for population abundance has been the focus of As Nimmo et al. (2015) a range of evidence to support the use of track abundance as a useful proxy for abundance of to large this not that track abundance will be a useful proxy in all work has focused on indices of abundance and for factors that determine how the relationship between the index and abundance across time and For example, et al. data on of in the to identify factors that In this they were to for time of when index to absolute Saska et al. assessed the of on the activity of to control for activity when pitfall trapping to relative abundance. for activity or can also of abundance indices across species, those indices are based on track counts or trapping rates et al. 2008; et al. are also available for for of when using indices of population density based on abundance. Specifically, \& approaches for for from both observational and both of which can undermine the use of counts as proxies for abundance. assessing the validity of various proxies of habitat quality are also (see, e.g. Johnson 2007; Pettorelli 2013b). for proxies of habitat quality derived from habitat suitability modelling can be found in work that to the quality of This used by et al. for assessing the of that habitat suitability modelling can areas that these models produce useful proxies for habitat quality that is to the One to this is that habitat suitability modelling based on or presence/absence data cannot between and habitats. et al. measures of into habitat suitability however, those measures will often be proxies for As proxies for ecosystem function and service provision have also been subjected to but with several proxies have ecosystem service in particular, a wide array of processes Thus, further validation is likely to be required to show that proxies well across One of the fundamental for proxies from the spatial and temporal scale of most ecological However, and research can to and proxies and might also our on them. The for example, is a large-scale which will information on distribution with The is to over decades at an of sites and has the potential to provide direct of the link between and ecosystem to our understanding of this also ecological with a of sites across the are on scales. The for will include animal monitoring on a research of the This will remote monitoring of the and of large numbers of individuals of species far smaller than can be at many this will direct of habitat use and the of habitat on a scale beyond currently our understanding of the validity of proxies for habitat quality. Applied ecologists should to the that natural resource management and environmental policy the possible underpinning the lower of monitoring work, robust approaches to policy and management often require monitoring, to key ecological on a scale that the need for proxies. As Martin of the has we it for that will to provide vast to for on – but we still about the one where we already that not be about for monitoring that yield insights into the key ecological processes supporting on insights could our understanding of ecological systems and, the of and to with",
    url = "https://doi.org/10.1111/1365-2664.12383",
    doi = "10.1111/1365-2664.12383",
    openalex = "W2021416891",
    references = "doi101038nature05202, doi101111j13652664201102048x, doi101111j14610248200600924x, doi101111j14610248200600963x, doi101126science1060391, doi101126science1227079, doi1023073808148, doi104324978184977263119, doi105281zenodo18167309, openalexw2014317435"
}

Habitat selection is a fundamental animal behavior that shapes a wide range of ecological processes, including animal movement, nutrient transfer, trophic dynamics and population distribution. Although habitat selection has been a focus of ecological studies for decades, technological, conceptual and methodological advances over the last 20 yr have led to a surge in studies addressing this process. Despite the substantial literature focused on quantifying the habitat-selection patterns of animals, there is a marked lack of guidance on best analytical practices. The conceptual foundations of the most commonly applied modeling frameworks can be confusing even to those well versed in their application. Furthermore, there has yet to be a synthesis of the advances made over the last 20 yr. Therefore, there is a need for both synthesis of the current state of knowledge on habitat selection, and guidance for those seeking to study this process. Here, we provide an approachable overview and synthesis of the literature on habitat-selection analyses (HSAs) conducted using selection functions, which are by far the most applied modeling framework for understanding the habitat-selection process. This review is purposefully non-technical and focused on understanding without heavy mathematical and statistical notation, which can confuse many practitioners. We offer an overview and history of HSAs, describing the tortuous conceptual path to our current understanding. Through this overview, we also aim to address the areas of greatest confusion in the literature. We synthesize the literature outlining the most exciting conceptual advances in the field of habitat-selection modeling, discussing the substantial ecological and evolutionary inference that can be made using contemporary techniques. We aim for this paper to provide clarity for those navigating the complex literature on HSAs while acting as a reference and best practices guide for practitioners.

@article{doi101002eap2470,
    author = "Northrup, Joseph M. and Wal, Eric Vander and Bonar, Maegwin and Fieberg, John and Laforge, Michel P. and Leclerc, Martin and Prokopenko, Christina M. and Gerber, Brian D.",
    title = "Conceptual and methodological advances in habitat‐selection modeling: guidelines for ecology and evolution",
    year = "2021",
    journal = "Ecological Applications",
    abstract = "Habitat selection is a fundamental animal behavior that shapes a wide range of ecological processes, including animal movement, nutrient transfer, trophic dynamics and population distribution. Although habitat selection has been a focus of ecological studies for decades, technological, conceptual and methodological advances over the last 20 yr have led to a surge in studies addressing this process. Despite the substantial literature focused on quantifying the habitat-selection patterns of animals, there is a marked lack of guidance on best analytical practices. The conceptual foundations of the most commonly applied modeling frameworks can be confusing even to those well versed in their application. Furthermore, there has yet to be a synthesis of the advances made over the last 20 yr. Therefore, there is a need for both synthesis of the current state of knowledge on habitat selection, and guidance for those seeking to study this process. Here, we provide an approachable overview and synthesis of the literature on habitat-selection analyses (HSAs) conducted using selection functions, which are by far the most applied modeling framework for understanding the habitat-selection process. This review is purposefully non-technical and focused on understanding without heavy mathematical and statistical notation, which can confuse many practitioners. We offer an overview and history of HSAs, describing the tortuous conceptual path to our current understanding. Through this overview, we also aim to address the areas of greatest confusion in the literature. We synthesize the literature outlining the most exciting conceptual advances in the field of habitat-selection modeling, discussing the substantial ecological and evolutionary inference that can be made using contemporary techniques. We aim for this paper to provide clarity for those navigating the complex literature on HSAs while acting as a reference and best practices guide for practitioners.",
    url = "https://doi.org/10.1002/eap.2470",
    doi = "10.1002/eap.2470",
    openalex = "W3207191671",
    references = "doi1011111365265612359, doi10249262020081320"
}

Since the early 1990s, ecologists and evolutionary biologists have aggregated primary research using meta-analytic methods to understand ecological and evolutionary phenomena. Meta-analyses can resolve long-standing disputes, dispel spurious claims, and generate new research questions. At their worst, however, meta-analysis publications are wolves in sheep's clothing: subjective with biased conclusions, hidden under coats of objective authority. Conclusions can be rendered unreliable by inappropriate statistical methods, problems with the methods used to select primary research, or problems within the primary research itself. Because of these risks, meta-analyses are increasingly conducted as part of systematic reviews, which use structured, transparent, and reproducible methods to collate and summarise evidence. For readers to determine whether the conclusions from a systematic review or meta-analysis should be trusted - and to be able to build upon the review - authors need to report what they did, why they did it, and what they found. Complete, transparent, and reproducible reporting is measured by 'reporting quality'. To assess perceptions and standards of reporting quality of systematic reviews and meta-analyses published in ecology and evolutionary biology, we surveyed 208 researchers with relevant experience (as authors, reviewers, or editors), and conducted detailed evaluations of 102 systematic review and meta-analysis papers published between 2010 and 2019. Reporting quality was far below optimal and approximately normally distributed. Measured reporting quality was lower than what the community perceived, particularly for the systematic review methods required to measure trustworthiness. The minority of assessed papers that referenced a guideline (~16%) showed substantially higher reporting quality than average, and surveyed researchers showed interest in using a reporting guideline to improve reporting quality. The leading guideline for improving reporting quality of systematic reviews is the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) statement. Here we unveil an extension of PRISMA to serve the meta-analysis community in ecology and evolutionary biology: PRISMA-EcoEvo (version 1.0). PRISMA-EcoEvo is a checklist of 27 main items that, when applicable, should be reported in systematic review and meta-analysis publications summarising primary research in ecology and evolutionary biology. In this explanation and elaboration document, we provide guidance for authors, reviewers, and editors, with explanations for each item on the checklist, including supplementary examples from published papers. Authors can consult this PRISMA-EcoEvo guideline both in the planning and writing stages of a systematic review and meta-analysis, to increase reporting quality of submitted manuscripts. Reviewers and editors can use the checklist to assess reporting quality in the manuscripts they review. Overall, PRISMA-EcoEvo is a resource for the ecology and evolutionary biology community to facilitate transparent and comprehensively reported systematic reviews and meta-analyses.

@article{doi101111brv12721,
    author = "O’Dea, Rose E. and Lagisz, Malgorzata and Jennions, Michael D. and Koricheva, Julia and Noble, Daniel W. A. and Parker, Timothy and Gurevitch, Jessica and Page, Matthew J. and Stewart, Gavin and Moher, David and Nakagawa, Shinichi",
    title = "Preferred reporting items for systematic reviews and meta‐analyses in ecology and evolutionary biology: a PRISMA extension",
    year = "2021",
    journal = "Biological reviews/Biological reviews of the Cambridge Philosophical Society",
    abstract = "Since the early 1990s, ecologists and evolutionary biologists have aggregated primary research using meta-analytic methods to understand ecological and evolutionary phenomena. Meta-analyses can resolve long-standing disputes, dispel spurious claims, and generate new research questions. At their worst, however, meta-analysis publications are wolves in sheep's clothing: subjective with biased conclusions, hidden under coats of objective authority. Conclusions can be rendered unreliable by inappropriate statistical methods, problems with the methods used to select primary research, or problems within the primary research itself. Because of these risks, meta-analyses are increasingly conducted as part of systematic reviews, which use structured, transparent, and reproducible methods to collate and summarise evidence. For readers to determine whether the conclusions from a systematic review or meta-analysis should be trusted - and to be able to build upon the review - authors need to report what they did, why they did it, and what they found. Complete, transparent, and reproducible reporting is measured by 'reporting quality'. To assess perceptions and standards of reporting quality of systematic reviews and meta-analyses published in ecology and evolutionary biology, we surveyed 208 researchers with relevant experience (as authors, reviewers, or editors), and conducted detailed evaluations of 102 systematic review and meta-analysis papers published between 2010 and 2019. Reporting quality was far below optimal and approximately normally distributed. Measured reporting quality was lower than what the community perceived, particularly for the systematic review methods required to measure trustworthiness. The minority of assessed papers that referenced a guideline (\textasciitilde 16\%) showed substantially higher reporting quality than average, and surveyed researchers showed interest in using a reporting guideline to improve reporting quality. The leading guideline for improving reporting quality of systematic reviews is the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) statement. Here we unveil an extension of PRISMA to serve the meta-analysis community in ecology and evolutionary biology: PRISMA-EcoEvo (version 1.0). PRISMA-EcoEvo is a checklist of 27 main items that, when applicable, should be reported in systematic review and meta-analysis publications summarising primary research in ecology and evolutionary biology. In this explanation and elaboration document, we provide guidance for authors, reviewers, and editors, with explanations for each item on the checklist, including supplementary examples from published papers. Authors can consult this PRISMA-EcoEvo guideline both in the planning and writing stages of a systematic review and meta-analysis, to increase reporting quality of submitted manuscripts. Reviewers and editors can use the checklist to assess reporting quality in the manuscripts they review. Overall, PRISMA-EcoEvo is a resource for the ecology and evolutionary biology community to facilitate transparent and comprehensively reported systematic reviews and meta-analyses.",
    url = "https://doi.org/10.1111/brv.12721",
    doi = "10.1111/brv.12721",
    openalex = "W3158015415",
    references = "doi101016jbiocon201506006, doi101038s4155901704025"
}

Functional traits offer a rich quantitative framework for developing and testing theories in evolutionary biology, ecology and ecosystem science. However, the potential of functional traits to drive theoretical advances and refine models of global change can only be fully realised when species-level information is complete. Here we present the AVONET dataset containing comprehensive functional trait data for all birds, including six ecological variables, 11 continuous morphological traits, and information on range size and location. Raw morphological measurements are presented from 90,020 individuals of 11,009 extant bird species sampled from 181 countries. These data are also summarised as species averages in three taxonomic formats, allowing integration with a global phylogeny, geographical range maps, IUCN Red List data and the eBird citizen science database. The AVONET dataset provides the most detailed picture of continuous trait variation for any major radiation of organisms, offering a global template for testing hypotheses and exploring the evolutionary origins, structure and functioning of biodiversity.

@article{doi101111ele13898,
    author = "Tobias, Joseph A. and Sheard, Catherine and Pigot, Alex L. and Devenish, Adam J. M. and Yang, Jingyi and Sayol, Ferran and Neate‐Clegg, Montague H. C. and Alioravainen, Nico and Weeks, Thomas and Barber, Robert A. and Walkden, Patrick A. and MacGregor, Hannah E. A. and Jones, Samuel E. I. and Vincent, Claire and Phillips, Anna G. and Marples, Nicola M. and Montaño‐Centellas, Flavia and Leandro‐Silva, Victor and Claramunt, Santiago and Darski, Bianca and Freeman, Benjamin G. and Bregman, Tom P. and Cooney, Christopher R. and Hughes, Emma C. and Capp, Elliot J. R. and Varley, Zoë K. and Friedman, Nicholas R. and Korntheuer, Heiko and Corrales‐Vargas, Andrea and Trisos, Christopher H. and Weeks, Brian C. and Hanz, Dagmar M. and Töpfer, Till and Bravo, Gustavo A. and Remeš, Vladimír and Nowak, Larissa and Carneiro, Lincoln Silva and R., Amilkar J. Moncada and Matysioková, Beata and Baldassarre, Daniel T. and Martínez‐Salinas, Alejandra and Wolfe, Jared D. and Chapman, Philip M. and Daly, Benjamin G. and Sorensen, Marjorie C. and Neu, Alexander and Ford, Michael A. and Mayhew, Rebekah J. and Silveira, Luís Fábio and Kelly, David and Annorbah, Nathaniel N. D. and Pollock, Henry S. and Grabowska-Zhang, Ada and McEntee, Jay P. and Gonzalez, Juan Carlos T. and Meneses, Camila G. and Muñoz, Marcia C. and Powell, Luke L. and Jamie, Gabriel A. and Matthews, Thomas J. and Johnson, Oscar W. and Brito, Guilherme Renzo Rocha and Zyskowski, Kristof and Crates, Ross and Harvey, Michael and Zevallos, Maura Jurado and Hosner, Peter A. and Bradfer‐Lawrence, Tom and Maley, James M. and Stiles, F. Gary and Lima, Hevana S. and Provost, Kaiya L. and Chibesa, Moses and Mashao, Mmatjie and Howard, Jeffrey T. and Mlamba, Edson and Chua, Marcus A.H. and Li, Bicheng and Gómez, María Isabel and García, Natalia C. and Päckert, Martin and Fuchs, Jérôme and Ali, Jarome R. and Derryberry, Elizabeth P. and Carlson, Monica L. and Urriza, Rolly C. and Brzeski, Kristin E. and Prawiradilaga, Dewi M. and Rayner, Matt J. and Miller, Eliot T. and Bowie, Rauri C. K. and Lafontaine, René‐Marie and Scofield, R. Paul and Lou, Yingqiang and Somarathna, Lankani and Lepage, Denis and Illif, Marshall and Neuschulz, Eike Lena and Templin, Mathias and Dehling, D. Matthias",
    title = "AVONET: morphological, ecological and geographical data for all birds",
    year = "2022",
    journal = "Ecology Letters",
    abstract = "Functional traits offer a rich quantitative framework for developing and testing theories in evolutionary biology, ecology and ecosystem science. However, the potential of functional traits to drive theoretical advances and refine models of global change can only be fully realised when species-level information is complete. Here we present the AVONET dataset containing comprehensive functional trait data for all birds, including six ecological variables, 11 continuous morphological traits, and information on range size and location. Raw morphological measurements are presented from 90,020 individuals of 11,009 extant bird species sampled from 181 countries. These data are also summarised as species averages in three taxonomic formats, allowing integration with a global phylogeny, geographical range maps, IUCN Red List data and the eBird citizen science database. The AVONET dataset provides the most detailed picture of continuous trait variation for any major radiation of organisms, offering a global template for testing hypotheses and exploring the evolutionary origins, structure and functioning of biodiversity.",
    url = "https://doi.org/10.1111/ele.13898",
    doi = "10.1111/ele.13898",
    openalex = "W4213419599",
    references = "doi101038nature11631, doi101038nature21074, doi101038s4155901704025, doi101111j13652664201102048x, doi101111j14610248201001509x, doi1018900814941, openalexw1904943263"
}

High-elevation systems support species adapted to extreme conditions, and their rugged terrain and variable microclimates strongly shape evolution and persistence. Yet few studies have evaluated how geography and climate jointly shape genetic diversity, local adaptation and vulnerability to environmental change. Here, we investigate these processes in the Tibetan Partridge (Perdix hodgsoniae), a high-altitude endemic distributed across arid western and humid northeastern regions of the Sino-Himalayan landscape. This region's complex topography and contrasting climatic conditions provide a natural setting for examining population divergence, climate-associated adaptation and future resilience. We integrated whole-genome sequencing, ecological, climatic, landscape and morphological data to examine current patterns of local adaptation and forecast climate-induced risks. Our findings show that both biogeographic barriers and climatic gradients drive rapid population divergence in P. hodgsoniae, reflected in distinct morphological traits and population genetic structure. Populations in dry, fragmented western landscapes show adaptation to temperature, whereas those in humid northeastern regions exhibit adaptation primarily to precipitation. These contrasting adaptive trajectories lead to varying levels of vulnerability, with arid, isolated landscapes limiting gene flow and genetic diversity, thereby heightening sensitivity to future climate change. In contrast, humid regions maintain stronger connectivity and larger effective population sizes, supporting higher genetic diversity and facilitating precipitation-linked adaptation. Together, we demonstrate that mountain landscapes function as a 'double-edged sword' by simultaneously generating and limiting biodiversity through isolation, and by constraining persistence within microclimatic refugia. This study underscores the value of integrating genomic, ecological, climate and landscape data to uncover mechanisms of divergence and inform conservation planning under rapid environmental change.

@article{doi101111mec70274,
    author = "Wang, Nan and Ghimire, Prashant and Chhetri, Pritam and Dahal, Nishma and Yi, Cheng and Zhang, Tong and Zhuoga, Suonan and Jiangyong, Zhaxi and Lamichhaney, Sangeet",
    title = "Biogeography and Climate Drive Population Divergence and Genomic Vulnerability in High Altitude Endemic Bird.",
    year = "2026",
    journal = "Molecular ecology",
    abstract = "High-elevation systems support species adapted to extreme conditions, and their rugged terrain and variable microclimates strongly shape evolution and persistence. Yet few studies have evaluated how geography and climate jointly shape genetic diversity, local adaptation and vulnerability to environmental change. Here, we investigate these processes in the Tibetan Partridge (Perdix hodgsoniae), a high-altitude endemic distributed across arid western and humid northeastern regions of the Sino-Himalayan landscape. This region's complex topography and contrasting climatic conditions provide a natural setting for examining population divergence, climate-associated adaptation and future resilience. We integrated whole-genome sequencing, ecological, climatic, landscape and morphological data to examine current patterns of local adaptation and forecast climate-induced risks. Our findings show that both biogeographic barriers and climatic gradients drive rapid population divergence in P. hodgsoniae, reflected in distinct morphological traits and population genetic structure. Populations in dry, fragmented western landscapes show adaptation to temperature, whereas those in humid northeastern regions exhibit adaptation primarily to precipitation. These contrasting adaptive trajectories lead to varying levels of vulnerability, with arid, isolated landscapes limiting gene flow and genetic diversity, thereby heightening sensitivity to future climate change. In contrast, humid regions maintain stronger connectivity and larger effective population sizes, supporting higher genetic diversity and facilitating precipitation-linked adaptation. Together, we demonstrate that mountain landscapes function as a 'double-edged sword' by simultaneously generating and limiting biodiversity through isolation, and by constraining persistence within microclimatic refugia. This study underscores the value of integrating genomic, ecological, climate and landscape data to uncover mechanisms of divergence and inform conservation planning under rapid environmental change.",
    url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC12924089/",
    doi = "10.1111/mec.70274",
    openalex = "W7130831913",
    pmcid = "PMC12924089",
    pmid = "41721581",
    references = "doi1010020471250953bi1110s43, doi101002joc5086, doi101093bioinformaticsbtp324, doi101093bioinformaticsbtr330, doi101093sysbiosyy032, doi101111j13652664200601214x, doi101148radiology14317063747, doi101186147121487214, doi101371journalpone0009490, doi1018637jssv022i04"
}