Historical geology

@book{schuchert1933a10,
    author = "Schuchert, C. and Dunbar, C. O",
    title = "A Textbook of Geology",
    year = "1933",
    publisher = "Part II Historical Geology: New York, John Wiley \& Sons, 551 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Schuchert, C., and Dunbar, C. O., 1933, A Textbook of Geology: Part II Historical Geology: New York, John Wiley \& Sons, 551 p.}"
}

@misc{komar1965additional4,
    author = "Komar, V. A. and Semikhatov, M. A",
    title = "Additional data about the geological history of the Siberian Platform during the late Precambrian",
    year = "1965",
    howpublished = "Academy of Sciences of the USSR Reports, v. 161, no. 2, p. 421-424; English translation by American Geological Institute, 1965, Academy of Science, USSR Doklady, v.161, p. 42-45",
    note = "talkorigins\_source = {true}; raw\_reference = {Komar, V. A., and Semikhatov, M. A., 1965, Additional data about the geological history of the Siberian Platform during the late Precambrian: Academy of Sciences of the USSR Reports, v. 161, no. 2, p. 421-424; English translation by American Geological Institute, 1965, Academy of Science, USSR Doklady, v.161, p. 42-45.}"
}

@article{doi102307213073,
    author = "Bennett, Charles F. and Carlquist, Sherwin",
    title = "Island Life: A Natural History of the Islands of the World",
    year = "1966",
    journal = "Geographical Review",
    url = "https://doi.org/10.2307/213073",
    doi = "10.2307/213073",
    openalex = "W2043849139"
}

@misc{newell1967revolutions7,
    author = "Newell, N. D",
    title = "Revolutions in the history of life",
    year = "1967",
    howpublished = "Geological Society of America, Special Paper, v. 89, p. 63-91",
    note = "talkorigins\_source = {true}; raw\_reference = {Newell, N. D., 1967, Revolutions in the history of life: Geological Society of America, Special Paper, v. 89, p. 63-91.}"
}

The Cambridge History of Iran is an eight-volume survey of Iranian history and culture, and its contribution to the civilisation of the world. All aspect of the religious, philosophical, political, economic, scientific and artistic elements in Iranian civilisation are studies, with some emphasis on geographical and ecological factors which have contributed to that civilisation's special character. The aim is to provide a collection of readable essays rather than a catalogue of information. The volumes offer scope for the publication of new ideas as well as providing summaries of established facts. They should act as a stimulus to specialists, but are primarily concerned to answer the sort of questions about the past and present of Iran that are asked by the non-specialist. Volume I sets the physical stage for the human events which follow. In a sense it is a companion volume to the rest of the series. The whole volume is devoted to geography, geology, anthropology, economic life, and flora and fauna. The physical environment of Iran is seen not as an unmoving backcloth against which the human drama is played; rather it is seen as a natural element which shapes in distinct and recognisable ways the whole course of human activity in the country. Iran offers a picture of sharp identity as a geographical unit. In spite of highly varies and often harsh natural conditions at local level, a consistent and recognisable pattern of physiographical and climatic features emerges at the national level. Because of these features the Iranians as a people suffered many vicissitudes. The complex character of the relationship between terrain and people is the major theme of this volume.

@book{doi101017chol9780521069359,
    author = "Fisher, William Bayne 1916-1984 and Fisher, W. B. and Gershevitch, Ilya 1914-2001 and Yāršātir, Iḥsān 1920-2018",
    title = "The Cambridge History of Iran",
    year = "1968",
    booktitle = "Cambridge University Press eBooks",
    abstract = "The Cambridge History of Iran is an eight-volume survey of Iranian history and culture, and its contribution to the civilisation of the world. All aspect of the religious, philosophical, political, economic, scientific and artistic elements in Iranian civilisation are studies, with some emphasis on geographical and ecological factors which have contributed to that civilisation's special character. The aim is to provide a collection of readable essays rather than a catalogue of information. The volumes offer scope for the publication of new ideas as well as providing summaries of established facts. They should act as a stimulus to specialists, but are primarily concerned to answer the sort of questions about the past and present of Iran that are asked by the non-specialist. Volume I sets the physical stage for the human events which follow. In a sense it is a companion volume to the rest of the series. The whole volume is devoted to geography, geology, anthropology, economic life, and flora and fauna. The physical environment of Iran is seen not as an unmoving backcloth against which the human drama is played; rather it is seen as a natural element which shapes in distinct and recognisable ways the whole course of human activity in the country. Iran offers a picture of sharp identity as a geographical unit. In spite of highly varies and often harsh natural conditions at local level, a consistent and recognisable pattern of physiographical and climatic features emerges at the national level. Because of these features the Iranians as a people suffered many vicissitudes. The complex character of the relationship between terrain and people is the major theme of this volume.",
    url = "https://doi.org/10.1017/chol9780521069359",
    doi = "10.1017/chol9780521069359",
    openalex = "W2077375257",
    references = "doi105281zenodo13650418"
}

@book{dunbar1969historical1,
    author = "Dunbar, C. and Waage, K. M",
    title = "Historical Geology [3rd ed.]",
    year = "1969",
    publisher = "New York, Wiley, 556 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Dunbar, C., and Waage, K. M., 1969, Historical Geology [3rd ed.]: New York, Wiley, 556 p.}"
}

@misc{kummel1970history5,
    author = "Kummel, B",
    title = "History of the Earth [2nd ed.]",
    year = "1970",
    howpublished = "San Francisco, Freeman, 707 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Kummel, B., 1970, History of the Earth [2nd ed.]: San Francisco, Freeman, 707 p.}"
}

@misc{mintz1977historical6,
    author = "Mintz, L. W",
    title = "Historical Geology",
    year = "1977",
    howpublished = "The Science of a Dynamic Earth [2nd ed.]: Columbus, Ohio, Charles E. Merrill Publishing Co., 588 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Mintz, L. W., 1977, Historical Geology: The Science of a Dynamic Earth [2nd ed.]: Columbus, Ohio, Charles E. Merrill Publishing Co., 588 p.}"
}

Platnick, N. I., and G. Nelson (Departments of Entomology and Ichthyology, The American Museum of Natural History, New York, New York 10024) 1978. A method of analysis for historical biogeography. Syst. Zool. 27:1–16.—Historical explanations of biotic distribution fall into two classes, dispersal explanations and vicariance explanations. Dispersal models explain disjunctions by dispersal across pre-existing barriers, vicariance models by the appearance of barriers fragmenting the ranges of ancestral species. Distributional data seem insufficient to resolve decisively either dispersal or vicariance as the cause of particular allopatric distribution patterns. When faced with such a pattern our first question should therefore be directed not to its cause, but to whether or not it conforms to a general pattern of relationships shown by taxa endemic to the areas occupied. Two-taxon statements are always compatible with a general pattern; three-taxon statements are therefore the most basic possible units of biogeographic (as well as phylogenetic) analysis. Analysis of three-taxon statements involves converting a hypothesis about the interrelationships of taxa (a cladogram indicating relative recency of common ancestry) to one concerning the interrelationships of areas (a cladogram indicating relative recency of common ancestral biotas). The generality of the area hypothesis may be tested by comparison with other groups endemic to the relevant areas. If the area hypothesis is corroborated as general, a statement of the relative recency of interconnections among areas is obtained, and evidence from historical geology may allow us to specify the nature of those interconnections and thereby the cause of those distributions that conform to the general pattern. Analysis of four-taxon statements indicates that the availability of structurally different patterns and of groups that can serve as adequate tests of the generality of those patterns increases with the addition of taxa to the hypothesis, and that neither extinction nor the failure of some groups to respond (by speciating) to given dispersal or vicariance events interferes with the analysis.

@article{doi1023072412808,
    author = "Platnick, Norman I. and Nelson, Gareth",
    title = "A Method of Analysis for Historical Biogeography",
    year = "1978",
    journal = "Systematic Zoology",
    abstract = "Platnick, N. I., and G. Nelson (Departments of Entomology and Ichthyology, The American Museum of Natural History, New York, New York 10024) 1978. A method of analysis for historical biogeography. Syst. Zool. 27:1–16.—Historical explanations of biotic distribution fall into two classes, dispersal explanations and vicariance explanations. Dispersal models explain disjunctions by dispersal across pre-existing barriers, vicariance models by the appearance of barriers fragmenting the ranges of ancestral species. Distributional data seem insufficient to resolve decisively either dispersal or vicariance as the cause of particular allopatric distribution patterns. When faced with such a pattern our first question should therefore be directed not to its cause, but to whether or not it conforms to a general pattern of relationships shown by taxa endemic to the areas occupied. Two-taxon statements are always compatible with a general pattern; three-taxon statements are therefore the most basic possible units of biogeographic (as well as phylogenetic) analysis. Analysis of three-taxon statements involves converting a hypothesis about the interrelationships of taxa (a cladogram indicating relative recency of common ancestry) to one concerning the interrelationships of areas (a cladogram indicating relative recency of common ancestral biotas). The generality of the area hypothesis may be tested by comparison with other groups endemic to the relevant areas. If the area hypothesis is corroborated as general, a statement of the relative recency of interconnections among areas is obtained, and evidence from historical geology may allow us to specify the nature of those interconnections and thereby the cause of those distributions that conform to the general pattern. Analysis of four-taxon statements indicates that the availability of structurally different patterns and of groups that can serve as adequate tests of the generality of those patterns increases with the addition of taxa to the hypothesis, and that neither extinction nor the failure of some groups to respond (by speciating) to given dispersal or vicariance events interferes with the analysis.",
    url = "https://doi.org/10.2307/2412808",
    doi = "10.2307/2412808",
    openalex = "W2114876283",
    references = "doi101093sysbio232265, doi101093sysbio242233, doi101093sysbio244431, doi1023071440574, doi1023072412735, openalexw1989371375"
}

Rosen, D. E. (Department of Ichthyology, American Museum of Natural History, New York, New York 10024) 1978. Vicariant patterns and historical explanation in biogeography. Syst. Zool. 27:159–188.—Geographic coincidence of animal and plant distributions to form recognizable patterns suggests that the separate components of the patterns are historically connected with each other and with geographic history. To seek evidence of these historical connections, cladograms of geographic areas, representing sequences of disruptive geologic, climatic, or geographic events, may be compared with biological cladograms, representing sequences of allopatric speciation events in relation to those geographic areas. Such comparisons, when they meet the minimum requirements of being among dichotomized threetaxon cladograms, can resolve similar or dissimilar historical factors; two-taxon statements do not distinguish between groups with different histories. Congruence of biological and geological area-cladograms at a high confidence level (such as congruence of a five-taxon cladogram or four three-taxon cladograms with a geological cladogram, where the confidence level can be shown in cladistic theory to be 99%) means that specified events of paleogeography can be adopted as an explanation of the biological patterns. In such a cause and effect relationship, where the earth and its life are assumed to have evolved together, paleogeography is taken by logical necessity to be the independent variable and biological history, the dependent variable. Drawing a mathematical simile, the biological cladogram y (dependent variable), is a function of the geological cladogram x (independent variable), as in a simple regression of effect y on cause x where we are given no free choice as to which is the independent variable. Such a view implies that any specified sequence in earth history must coincide with some discoverable biological patterns; it does not imply a necessary converse that each biological pattern must coincide with some discoverable paleogeographic pattern, because some biological distributions might have resulted from stochastic processes (chance dispersal). Determining that all discoverable biological patterns conflict with a given corroborated or observed sequence of geologic, climatic, or geographic change (i.e., that y is not a function of x), in theory, therefore should falsify vicariance biogeography. Because dispersal biogeography presupposes stochastic processes, and any failure to meet the expectation of a postulated dispersal is explained by an additional dispersal, dispersal biogeography is immune to falsification. Without resort to paleontology or earth history, whether a given historical relationship implied by congruence of biological area-cladograms is the result of dispersal or vicariance can also be thought of in terms which minimize the number of necessary assumptions: did the sedentary organisms disperse with the vagile ones or did the vagile organisms vicariate with the sedentary ones? Cladistic congruence of a group of sedentary organisms with a group of vagile ones rejects dispersal for both. Hence, distributions of sedentary organisms have the potential to falsify dispersal theories as applied to vagile organisms, but distributions of vagile organisms cannot falsify vicariance theories as applied to sedentary ones. The problems that arise in various kinds of historical explanation are exemplified by several specific distributions of fishes and other organisms in North and Middle America and in the larger context of Pangaean history, and are discussed in relation to current species concepts.

@article{doi1023072412970,
    author = "Rosen, Donn Eric",
    title = "Vicariant Patterns and Historical Explanation in Biogeography",
    year = "1978",
    journal = "Systematic Zoology",
    abstract = "Rosen, D. E. (Department of Ichthyology, American Museum of Natural History, New York, New York 10024) 1978. Vicariant patterns and historical explanation in biogeography. Syst. Zool. 27:159–188.—Geographic coincidence of animal and plant distributions to form recognizable patterns suggests that the separate components of the patterns are historically connected with each other and with geographic history. To seek evidence of these historical connections, cladograms of geographic areas, representing sequences of disruptive geologic, climatic, or geographic events, may be compared with biological cladograms, representing sequences of allopatric speciation events in relation to those geographic areas. Such comparisons, when they meet the minimum requirements of being among dichotomized threetaxon cladograms, can resolve similar or dissimilar historical factors; two-taxon statements do not distinguish between groups with different histories. Congruence of biological and geological area-cladograms at a high confidence level (such as congruence of a five-taxon cladogram or four three-taxon cladograms with a geological cladogram, where the confidence level can be shown in cladistic theory to be 99\%) means that specified events of paleogeography can be adopted as an explanation of the biological patterns. In such a cause and effect relationship, where the earth and its life are assumed to have evolved together, paleogeography is taken by logical necessity to be the independent variable and biological history, the dependent variable. Drawing a mathematical simile, the biological cladogram y (dependent variable), is a function of the geological cladogram x (independent variable), as in a simple regression of effect y on cause x where we are given no free choice as to which is the independent variable. Such a view implies that any specified sequence in earth history must coincide with some discoverable biological patterns; it does not imply a necessary converse that each biological pattern must coincide with some discoverable paleogeographic pattern, because some biological distributions might have resulted from stochastic processes (chance dispersal). Determining that all discoverable biological patterns conflict with a given corroborated or observed sequence of geologic, climatic, or geographic change (i.e., that y is not a function of x), in theory, therefore should falsify vicariance biogeography. Because dispersal biogeography presupposes stochastic processes, and any failure to meet the expectation of a postulated dispersal is explained by an additional dispersal, dispersal biogeography is immune to falsification. Without resort to paleontology or earth history, whether a given historical relationship implied by congruence of biological area-cladograms is the result of dispersal or vicariance can also be thought of in terms which minimize the number of necessary assumptions: did the sedentary organisms disperse with the vagile ones or did the vagile organisms vicariate with the sedentary ones? Cladistic congruence of a group of sedentary organisms with a group of vagile ones rejects dispersal for both. Hence, distributions of sedentary organisms have the potential to falsify dispersal theories as applied to vagile organisms, but distributions of vagile organisms cannot falsify vicariance theories as applied to sedentary ones. The problems that arise in various kinds of historical explanation are exemplified by several specific distributions of fishes and other organisms in North and Middle America and in the larger context of Pangaean history, and are discussed in relation to current species concepts.",
    url = "https://doi.org/10.2307/2412970",
    doi = "10.2307/2412970",
    openalex = "W2097059816",
    references = "doi1010079781468488517, doi101093sysbio232265, doi1015159781400881376, doi1023071796560, doi1023072395199, doi1023072412140, doi1023072412744, doi1023072412808, doi1023073669094, doi105281zenodo13650418"
}

@incollection{patterson1980origin9,
    author = "Patterson, C",
    editor = "Panchen, A. L.",
    title = "Origin of Tetrapods: Historical Introduction of the Problem",
    year = "1980",
    booktitle = "The Terrestrial Environment and the Origin of Land Vertebrates",
    publisher = "London, Academic Press",
    note = "talkorigins\_source = {true}; raw\_reference = {Patterson, C., 1980, Origin of Tetrapods: Historical Introduction of the Problem, in Panchen, A. L., ed., The Terrestrial Environment and the Origin of Land Vertebrates: London, Academic Press.}"
}

@book{faul1983it2,
    author = "Faul, H. and Faul, C",
    title = "It Began with a Stone",
    year = "1983",
    publisher = "A History of Geology from the Stone Age to the Age of Plate Tectonics: New York, John Wiley \& Sons, 270 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Faul, H., and Faul, C., 1983, It Began with a Stone: A History of Geology from the Stone Age to the Age of Plate Tectonics: New York, John Wiley \& Sons, 270 p.}"
}

If it is agreed that an understanding of biohistory in some ways is tied to an understanding of geohistory, then one might also agree that what is needed is a precise means of specifying how a given biohistory is explicitly tied to a particular geohistory. The constraint in this type of analysis is the branching diagram, or cladogram, that permits a precise comparison of geographic area cladograms to demonstrate congruence between the cladistic message from biology with the cladistic message from geology. A proposal for identifying these cladistic constraints is given using a comparison of several different historical geologies of the Caribbean region as an example that contrasts with the constraints used by previous biogeographies in which an a priori notion of process, e.g., dispersal or extinction, was used to direct the outcome of biogeographic analysis. Whether espousing dispersalism (Darlington, 1957) or vicariism (Croizat, 1958, 1962), biologists have always assumed that the distributions of organisms in some way reflect the nature of the world's geologic history. It was, thus, implied that an understanding of biohistory is tied to an understanding of geohistory. In the DarwinianDarlingtonian tradition the relevant geohistory was assumed to be one of stabilism necessitating an interpretation of biohistory as one of active or passive dispersal. In other words, so long as the continents stood still something had to move to account for the occurrence of closely related organisms spanning large water gaps. Thus were invoked temporary land bridges suitable for crossing ocean barriers, birds with feet and feathers to which seeds and small animals would adhere during their transoceanic flights, and menageries supported on floating debris that was spewed into the ocean's currents from river mouths and deltas. The difficulties inherent in these scenarios of a haphazard biohistory are apparent in Darlington's (1957) hypothesis that ostariophysans arose in central Asia and made their risky way along ephemeral freshwater routes to the southern continents without leaving a trace of these great migrations. But the hypothesis of a steadfast geography and a dancing biota was deemphasized after the theory of plate tectonics was elaborated. Since most biologists had a penchant for believing that geologists had a special hold on the truth, the acceptance of continental drift caused some of these biologists to shift into reverse strategy of proposing that it was the geography that moved while the organisms got carried about to their new longitudes and latitudes. Other biologists (Darlington, 1965; McDowall, 1971; Briggs, 1984) tried and still try to rescue the past by agreeing that the geography did in fact move but that the timing of these great events was wrong in relation to the ages of the biotas. Such attitudes might invoke the ages of fossils to show that all the taxa are too young to have been influenced by the geographic cataclysms. This view involves two assumptions, both wrong at some level: 1) that fossils can tell us how old a taxon is and 2) that the ages of the geologic events have been correctly assigned. The first assumption is wrong because fossils give a minimum rather than maximum age of a taxon, and the second assumption is put into question by recent age reassignments. For example, parts of the Caribbean which were originally supposed to have been moving along a transform fault at the moderate rate of 2 cm per year (Kellogg & Bonini, 1982) are now believed to be moving at the brisker pace of 4 cm per year (Sykes et al., 1982; Wadge & Burke, 1983), thus doubling the rate of motion and halving the ages of the events associated with translocation. But these relations leave us still at the mercy of general supposition when what is needed is some precise means of specifying that this biohistory is tied explicitly to that geohistory. This still unrealized need for precision is supplied by another conceptual revolution that, in terms of time spans involved in human intellectual history, might be said to have occurred more I For comments during the work and review of the typescript I thank Drs. Kevin Burke, Arnold Kluge, Lynne Parenti, Norman Platnick, Edward Robinson, Peter Tolson, Lynn Sykes, and, especially, Gareth Nelson. 2 Department of Ichthyology, American Museum of Natural History, New York, New York 10024. ANN. MISSOURI BOT. GARD. 7 2: 6 3 6-6 5 9. 19 8 5. This content downloaded from 207.46.13.64 on Sat, 03 Sep 2016 04:52:04 UTC All use subject to http://about.jstor.org/terms 1985] ROSEN-GEOLOGICAL HIERARCHIES 637 or less simultaneously in systematics and biogeography. This revolution has been called cladistics, the science of character analysis and the use of branching diagrams. Its premises permit precise comparisons between biological and geological systems (e.g., Rosen, 1978). The general objective of cladistics is to discover congruence between the two that constrains historical explanation. In the Darwinian tradition in biogeography it is dispersalthat was the constraining concept, requiring an interpretation of the history of life in space contrary to what the data of life suggested. Leon Croizat (1958, 1962) was one of the pioneers who recognized that the biological data tell their own story, which can be at odds with a stabilist geology. Now that stabilist geology has been rejected in favor of a concept of mobilism, some biogeographers (Nelson & Platnick, 1981; Wiley, 1981) accept that biology has an independent story to tell about the history of the world. It is this independence of biological from geological data that makes the comparison of the two so interesting because it is hard to imagine how congruence between the two could be the result of anything but a causal history in which geology acts as the independent variable providing opportunities for change in the dependent biological world. The comparison becomes especially interesting if there is a congruence among geohistories based on different approaches to the geographic problem, and if there is a congruence among cladistic relations of different taxa with respect to the same geographic areas. The specific questions are: 1) do the members of different monophyletic groups of organisms have the same relations to each other with respect to geographic regions in which they are endemic and is their congruence with respect to these areas non-random; and 2) does this non-random congruence of different groups of organisms correspond to a branching diagram that represents part of the history of some geographic region? The constraint in these comparisons is the branching diagram rather than a process assumed to be of causal importance. In 1976 and 1978 I suggested a history for the Caribbean land and water that, at a rather general level, is consistent with the present distributions of plants and animals in the region including the Antilles, Central America, northern South America, and the southeastern and southwestern United States. The 1976 proposal, which was based largely on a descriptive history by Malfait and Dinkleman (1972) and Tedford (1974), was questioned by Pregill (1981) whose claim was that there is no geologic evidence warranting such a proposal. This claim was critically evaluated recently by Hedges (1982) who disagreed with Pregill on the grounds that ample geologic data had been available for some time in support of the Malfait and Dinkleman-Tedford theory (he cited 13 literature sources). Since the time of Hedges' reply to Pregill, I became aware of several other accounts of Caribbean history based on a variety of geologic data sources (Birnie, 1977: movement along major fault zones; Pindell & Dewey, 1982: plate contour matching and paleomagmatic data; Kellogg & Bonini, 1982: gravity data, seismic profiles, radiometric data, and earthquake data; Sykes et al., 1982: slip vectors of shallow earthquakes and other seismic data; Wadge & Burke, 1983: reconstructing plate motions by closing the Cayman Trough along its bounding transform faults). It is apparent, therefore, that Pregill was operating with a different set of constraints, namely, that the biota is recently distributed by means of dispersal. Hence, no number of geologic accounts or amount of data would be expected fundamentally to alter his position. My constraint is the cladogram and how it describes relationships of taxa and areas. What I propose is to divide the historical geology of the Caribbean into the minimum number of time periods in which different geologic theories agree on the geographic contacts between different areas and the severing of those contacts. In this way I have covered four main periods spanning 165 million years.

@article{doi1023072399218,
    author = "Rosen, Donn Eric",
    title = "Geological Hierarchies and Biogeographic Congruence in the Caribbean",
    year = "1985",
    journal = "Annals of the Missouri Botanical Garden",
    abstract = "If it is agreed that an understanding of biohistory in some ways is tied to an understanding of geohistory, then one might also agree that what is needed is a precise means of specifying how a given biohistory is explicitly tied to a particular geohistory. The constraint in this type of analysis is the branching diagram, or cladogram, that permits a precise comparison of geographic area cladograms to demonstrate congruence between the cladistic message from biology with the cladistic message from geology. A proposal for identifying these cladistic constraints is given using a comparison of several different historical geologies of the Caribbean region as an example that contrasts with the constraints used by previous biogeographies in which an a priori notion of process, e.g., dispersal or extinction, was used to direct the outcome of biogeographic analysis. Whether espousing dispersalism (Darlington, 1957) or vicariism (Croizat, 1958, 1962), biologists have always assumed that the distributions of organisms in some way reflect the nature of the world's geologic history. It was, thus, implied that an understanding of biohistory is tied to an understanding of geohistory. In the DarwinianDarlingtonian tradition the relevant geohistory was assumed to be one of stabilism necessitating an interpretation of biohistory as one of active or passive dispersal. In other words, so long as the continents stood still something had to move to account for the occurrence of closely related organisms spanning large water gaps. Thus were invoked temporary land bridges suitable for crossing ocean barriers, birds with feet and feathers to which seeds and small animals would adhere during their transoceanic flights, and menageries supported on floating debris that was spewed into the ocean's currents from river mouths and deltas. The difficulties inherent in these scenarios of a haphazard biohistory are apparent in Darlington's (1957) hypothesis that ostariophysans arose in central Asia and made their risky way along ephemeral freshwater routes to the southern continents without leaving a trace of these great migrations. But the hypothesis of a steadfast geography and a dancing biota was deemphasized after the theory of plate tectonics was elaborated. Since most biologists had a penchant for believing that geologists had a special hold on the truth, the acceptance of continental drift caused some of these biologists to shift into reverse strategy of proposing that it was the geography that moved while the organisms got carried about to their new longitudes and latitudes. Other biologists (Darlington, 1965; McDowall, 1971; Briggs, 1984) tried and still try to rescue the past by agreeing that the geography did in fact move but that the timing of these great events was wrong in relation to the ages of the biotas. Such attitudes might invoke the ages of fossils to show that all the taxa are too young to have been influenced by the geographic cataclysms. This view involves two assumptions, both wrong at some level: 1) that fossils can tell us how old a taxon is and 2) that the ages of the geologic events have been correctly assigned. The first assumption is wrong because fossils give a minimum rather than maximum age of a taxon, and the second assumption is put into question by recent age reassignments. For example, parts of the Caribbean which were originally supposed to have been moving along a transform fault at the moderate rate of 2 cm per year (Kellogg \& Bonini, 1982) are now believed to be moving at the brisker pace of 4 cm per year (Sykes et al., 1982; Wadge \& Burke, 1983), thus doubling the rate of motion and halving the ages of the events associated with translocation. But these relations leave us still at the mercy of general supposition when what is needed is some precise means of specifying that this biohistory is tied explicitly to that geohistory. This still unrealized need for precision is supplied by another conceptual revolution that, in terms of time spans involved in human intellectual history, might be said to have occurred more I For comments during the work and review of the typescript I thank Drs. Kevin Burke, Arnold Kluge, Lynne Parenti, Norman Platnick, Edward Robinson, Peter Tolson, Lynn Sykes, and, especially, Gareth Nelson. 2 Department of Ichthyology, American Museum of Natural History, New York, New York 10024. ANN. MISSOURI BOT. GARD. 7 2: 6 3 6-6 5 9. 19 8 5. This content downloaded from 207.46.13.64 on Sat, 03 Sep 2016 04:52:04 UTC All use subject to http://about.jstor.org/terms 1985] ROSEN-GEOLOGICAL HIERARCHIES 637 or less simultaneously in systematics and biogeography. This revolution has been called cladistics, the science of character analysis and the use of branching diagrams. Its premises permit precise comparisons between biological and geological systems (e.g., Rosen, 1978). The general objective of cladistics is to discover congruence between the two that constrains historical explanation. In the Darwinian tradition in biogeography it is dispersalthat was the constraining concept, requiring an interpretation of the history of life in space contrary to what the data of life suggested. Leon Croizat (1958, 1962) was one of the pioneers who recognized that the biological data tell their own story, which can be at odds with a stabilist geology. Now that stabilist geology has been rejected in favor of a concept of mobilism, some biogeographers (Nelson \& Platnick, 1981; Wiley, 1981) accept that biology has an independent story to tell about the history of the world. It is this independence of biological from geological data that makes the comparison of the two so interesting because it is hard to imagine how congruence between the two could be the result of anything but a causal history in which geology acts as the independent variable providing opportunities for change in the dependent biological world. The comparison becomes especially interesting if there is a congruence among geohistories based on different approaches to the geographic problem, and if there is a congruence among cladistic relations of different taxa with respect to the same geographic areas. The specific questions are: 1) do the members of different monophyletic groups of organisms have the same relations to each other with respect to geographic regions in which they are endemic and is their congruence with respect to these areas non-random; and 2) does this non-random congruence of different groups of organisms correspond to a branching diagram that represents part of the history of some geographic region? The constraint in these comparisons is the branching diagram rather than a process assumed to be of causal importance. In 1976 and 1978 I suggested a history for the Caribbean land and water that, at a rather general level, is consistent with the present distributions of plants and animals in the region including the Antilles, Central America, northern South America, and the southeastern and southwestern United States. The 1976 proposal, which was based largely on a descriptive history by Malfait and Dinkleman (1972) and Tedford (1974), was questioned by Pregill (1981) whose claim was that there is no geologic evidence warranting such a proposal. This claim was critically evaluated recently by Hedges (1982) who disagreed with Pregill on the grounds that ample geologic data had been available for some time in support of the Malfait and Dinkleman-Tedford theory (he cited 13 literature sources). Since the time of Hedges' reply to Pregill, I became aware of several other accounts of Caribbean history based on a variety of geologic data sources (Birnie, 1977: movement along major fault zones; Pindell \& Dewey, 1982: plate contour matching and paleomagmatic data; Kellogg \& Bonini, 1982: gravity data, seismic profiles, radiometric data, and earthquake data; Sykes et al., 1982: slip vectors of shallow earthquakes and other seismic data; Wadge \& Burke, 1983: reconstructing plate motions by closing the Cayman Trough along its bounding transform faults). It is apparent, therefore, that Pregill was operating with a different set of constraints, namely, that the biota is recently distributed by means of dispersal. Hence, no number of geologic accounts or amount of data would be expected fundamentally to alter his position. My constraint is the cladogram and how it describes relationships of taxa and areas. What I propose is to divide the historical geology of the Caribbean into the minimum number of time periods in which different geologic theories agree on the geographic contacts between different areas and the severing of those contacts. In this way I have covered four main periods spanning 165 million years.",
    url = "https://doi.org/10.2307/2399218",
    doi = "10.2307/2399218",
    openalex = "W2075640217",
    references = "doi101029jb087ib13p10656, doi101029tc001i002p00179, doi101029tc001i003p00251, doi101093sysbio244431, doi101130001676061973841105ctaiaa20co2, doi10113000167606198394941teomaa20co2, doi1023071376223, doi1023071440574, doi1023072412970, doi1023072413039"
}

@book{olsen1986is8,
    author = "Olsen, P. E",
    title = "Is the Past the Key to the Future?, in Lamont-Doherty Geological Observatory Yearbook 1984-1986",
    year = "1986",
    publisher = "Columbia University Press, p. 5- 10",
    note = "talkorigins\_source = {true}; raw\_reference = {Olsen, P. E., 1986, Is the Past the Key to the Future?, in Lamont-Doherty Geological Observatory Yearbook 1984-1986: Columbia University Press, p. 5- 10.}"
}

A revision of the best selling historical geology text, completely updated to provide a thorough but lucid introduction to the principles of historical geology. Stanley's assertion that 'the physical history and the biological history of the earth are inextricably interwined shapes his text throughout. The material is organized clearly and logically. The two-part progression resents basic principles first, then proceeds with a chronological study of the history of life. For everv interval, global events (such as general patterns of geographic change and major occurrences in the evolution and extinction of life) are reviewed within the context of plate tectonics. This review is followed bv a description of important regional events and their place within this global framework. Stanlev offers insightful observations on how environmental conditions have affected life through the ages. Numerous attractive illustrations enhance textual material. Chapter-ending reviews and exercises reinforce students' understanding and there are additional reading lists, a thorough glossary and useful appendices. Stanley has updated and improved his text to make i-t even more accessible to students. Notable changes include: Streamlined and reorganized chapter on mountain building, with new discussions of ancient plate movements Condensed and updated coverage of the Precambrian Updated and expanded discussions of mass extinctions throughout the text Additional material on isotopes and dating techniques Updated discussion of human evolution.

@book{openalexw1529355574,
    author = "Stanley, Steven M.",
    title = "Earth and life through time",
    year = "1986",
    journal = "Bulletin of Miscellaneous Information (Royal Gardens Kew)",
    abstract = "A revision of the best selling historical geology text, completely updated to provide a thorough but lucid introduction to the principles of historical geology. Stanley's assertion that 'the physical history and the biological history of the earth are inextricably interwined shapes his text throughout. The material is organized clearly and logically. The two-part progression resents basic principles first, then proceeds with a chronological study of the history of life. For everv interval, global events (such as general patterns of geographic change and major occurrences in the evolution and extinction of life) are reviewed within the context of plate tectonics. This review is followed bv a description of important regional events and their place within this global framework. Stanlev offers insightful observations on how environmental conditions have affected life through the ages. Numerous attractive illustrations enhance textual material. Chapter-ending reviews and exercises reinforce students' understanding and there are additional reading lists, a thorough glossary and useful appendices. Stanley has updated and improved his text to make i-t even more accessible to students. Notable changes include: Streamlined and reorganized chapter on mountain building, with new discussions of ancient plate movements Condensed and updated coverage of the Precambrian Updated and expanded discussions of mass extinctions throughout the text Additional material on isotopes and dating techniques Updated discussion of human evolution.",
    url = "https://openalex.org/W1529355574",
    openalex = "W1529355574"
}

@misc{gould1989wonderful3,
    author = "Gould, S. J",
    title = "Wonderful Life",
    year = "1989",
    howpublished = "The Burgess Shale and the Nature of History: New York, W. W. Norton",
    note = "talkorigins\_source = {true}; raw\_reference = {Gould, S. J., 1989, Wonderful Life: The Burgess Shale and the Nature of History: New York, W. W. Norton.}"
}

The concept of a reconciled tree arose independently in molecular systematics, parasitology, and biogeography as a means of describing historical associations. Examples of historical associations include genes and organisms, host and parasitic organisms, and organisms and areas. A reconciled tree combines the tree for a host and its associate into a single summary of the historical association between the two entities under the assumption that no horizontal transmission of associates has occurred. In this paper, I define reconciled trees, describe an algorithm for their computation, and develop measures to quantify the degree of fit between host and associate trees. Examples are given of applying the method to gene trees and species trees, host-parasite cospeciation, and biogeography. The problem of incorporating horizontal transmission of associates (e.g., dispersal or host switching) is also addressed by introducing the concept of maximizing the amount of codivergence (shared history) between the associates.

@article{doi101093sysbio43158,
    author = "Page, Roderic",
    title = "Maps Between Trees and Cladistic Analysis of Historical Associations among Genes,Organisms, and Areas",
    year = "1994",
    journal = "Systematic Biology",
    abstract = "The concept of a reconciled tree arose independently in molecular systematics, parasitology, and biogeography as a means of describing historical associations. Examples of historical associations include genes and organisms, host and parasitic organisms, and organisms and areas. A reconciled tree combines the tree for a host and its associate into a single summary of the historical association between the two entities under the assumption that no horizontal transmission of associates has occurred. In this paper, I define reconciled trees, describe an algorithm for their computation, and develop measures to quantify the degree of fit between host and associate trees. Examples are given of applying the method to gene trees and species trees, host-parasite cospeciation, and biogeography. The problem of incorporating horizontal transmission of associates (e.g., dispersal or host switching) is also addressed by introducing the concept of maximizing the amount of codivergence (shared history) between the associates.",
    url = "https://doi.org/10.1093/sysbio/43.1.58",
    doi = "10.1093/sysbio/43.1.58",
    openalex = "W2046039468",
    references = "doi1023072412808, doi1023072412970"
}

We studied correlations among traits related to body size and reproductive behavior in marine turtles, using data from 96 different populations representing seven species. Our analyses focused on patterns of phenotypic covariation among species and among populations within species. At the species level, body size correlated positively with several reproductive traits, including egg size and overall reproductive effort. A trade-off between clutch size and egg size was confirmed for marine turtles, after factoring out the effects of body size. Patterns of variation within species were different from those among species. For example, in five out of six species there was a positive relationship between adult body size and clutch size, although this correlation was not found at the interspecific level. We also found important differences among species in the way life-history traits correlated with one another. Four species having a sufficient number of samples exhibited congruent worldwide patterns of body size variation. A comparative approach may prove useful for extending demographic models developed for loggerhead turtles to less well-known species, even though many of the model parameters have not been estimated for other species.

@article{doi1023071446672,
    author = "Buskirk, Josh Van and Crowder, Larry B.",
    title = "Life-History Variation in Marine Turtles",
    year = "1994",
    journal = "Copeia",
    abstract = "We studied correlations among traits related to body size and reproductive behavior in marine turtles, using data from 96 different populations representing seven species. Our analyses focused on patterns of phenotypic covariation among species and among populations within species. At the species level, body size correlated positively with several reproductive traits, including egg size and overall reproductive effort. A trade-off between clutch size and egg size was confirmed for marine turtles, after factoring out the effects of body size. Patterns of variation within species were different from those among species. For example, in five out of six species there was a positive relationship between adult body size and clutch size, although this correlation was not found at the interspecific level. We also found important differences among species in the way life-history traits correlated with one another. Four species having a sufficient number of samples exhibited congruent worldwide patterns of body size variation. A comparative approach may prove useful for extending demographic models developed for loggerhead turtles to less well-known species, even though many of the model parameters have not been estimated for other species.",
    url = "https://doi.org/10.2307/1446672",
    doi = "10.2307/1446672",
    openalex = "W2334153368",
    references = "doi105281zenodo13650418"
}

Tropical reef fishes, along with many benthic invertebrates, have a life cycle that includes a sedentary, bottom-dwelling reproductive phase and a planktonic stage that occurs early in development. The adult benthic populations occupy disjunct, patchy habitats; the extent of gene flow due to dispersal of the planktonic life stage is generally unknown.

@article{doi101111j155856461995tb02325x,
    author = "Shulman, Myra J. and Bermingham, Eldredge",
    title = "EARLY LIFE HISTORIES, OCEAN CURRENTS, AND THE POPULATION GENETICS OF CARIBBEAN REEF FISHES",
    year = "1995",
    journal = "Evolution",
    abstract = "Tropical reef fishes, along with many benthic invertebrates, have a life cycle that includes a sedentary, bottom-dwelling reproductive phase and a planktonic stage that occurs early in development. The adult benthic populations occupy disjunct, patchy habitats; the extent of gene flow due to dispersal of the planktonic life stage is generally unknown.",
    url = "https://doi.org/10.1111/j.1558-5646.1995.tb02325.x",
    doi = "10.1111/j.1558-5646.1995.tb02325.x",
    openalex = "W2331375795",
    references = "doi101007978140206754912413, doi101073pnas70123321, doi101086284325, doi101093genetics1312479, doi101093nar8194321, doi101093oso97801985464120010001, doi101111j1365294x200602908x, doi101111j1469185x1950tb00585x, doi1023072399218, doi105860choice295104, doi107312nei92038"
}

The five basic historical biogeographic methods are: dispersalism, phylogenetic biogeography, panbiogeography, cladistic biogeography, and parsimony analysis of endemicity. Dispersalism derives from the traditional concepts of center of origin and dispersal. Bremer's recent cladistic implementation of dispersalism estimates the relative probability that different areas were part of the ancestral distribution of a group. Phylogenetic biogeography applies the rules of progression and deviation to elucidate the history of the geographical distribution of a group. Panbiogeography consists of plotting distributions of different taxa on maps, connecting their distribution areas together with lines called individual tracks, and looking for coincidence among individual tracks to determine generalized tracks. Generalized tracks indicate the preexistence of widespread ancestral biotas, subsequently fragmented by geological or climatic changes. Cladistic biogeography assumes a correspondence between taxonomic relationships and area relationships, where comparisons between area cladograms derived from different taxa allow one to obtain general area cladograms. The most important cladistic biogeographic procedures are: component analysis, Brooks parsimony analysis, three-area statements, and reconciled trees. Parsimony analysis of endemicity (PAE) classifies areas by their shared taxa, analogous to characters, according to the most parsimonious solution. We think the various methods are not mutually-exclusive alternatives, but some of them can be integrated in a single biogeographic approach, with the capability of resolving different problems, such as the recognition of spatial homology (panbiogeography), the identification of areas of endemism (PAE), and the formulation of hypotheses about area relationships (cladistic biogeography).

@article{doi101146annureves26110195002105,
    author = "Morrone, Juan J. and Crisci, Jorge V.",
    title = "HISTORICAL BIOGEOGRAPHY: Introduction to Methods",
    year = "1995",
    journal = "Annual Review of Ecology and Systematics",
    abstract = "The five basic historical biogeographic methods are: dispersalism, phylogenetic biogeography, panbiogeography, cladistic biogeography, and parsimony analysis of endemicity. Dispersalism derives from the traditional concepts of center of origin and dispersal. Bremer's recent cladistic implementation of dispersalism estimates the relative probability that different areas were part of the ancestral distribution of a group. Phylogenetic biogeography applies the rules of progression and deviation to elucidate the history of the geographical distribution of a group. Panbiogeography consists of plotting distributions of different taxa on maps, connecting their distribution areas together with lines called individual tracks, and looking for coincidence among individual tracks to determine generalized tracks. Generalized tracks indicate the preexistence of widespread ancestral biotas, subsequently fragmented by geological or climatic changes. Cladistic biogeography assumes a correspondence between taxonomic relationships and area relationships, where comparisons between area cladograms derived from different taxa allow one to obtain general area cladograms. The most important cladistic biogeographic procedures are: component analysis, Brooks parsimony analysis, three-area statements, and reconciled trees. Parsimony analysis of endemicity (PAE) classifies areas by their shared taxa, analogous to characters, according to the most parsimonious solution. We think the various methods are not mutually-exclusive alternatives, but some of them can be integrated in a single biogeographic approach, with the capability of resolving different problems, such as the recognition of spatial homology (panbiogeography), the identification of areas of endemism (PAE), and the formulation of hypotheses about area relationships (cladistic biogeography).",
    url = "https://doi.org/10.1146/annurev.es.26.110195.002105",
    doi = "10.1146/annurev.es.26.110195.002105",
    openalex = "W2110750222",
    references = "doi101073pnas8951909, doi101093sysbio232265, doi101093sysbio244431, doi101144gslsp19880370119, doi1023072412808, doi1023072412970"
}

Quantification in historical biogeography has usually been based on the search for a single branching relationship among areas of endemism. Unlike organisms, however, areas rarely have a unique hierarchical history. Dispersal barriers appear and disappear and may have different effects on different species. As a result, the biota of an area may consist of several components with separate histories, each of which may be reticulate rather than branching. In an attempt to address these problems, I present a new biogeographic method, dispersal–vicariance analysis, which reconstructs the ancestral distributions in a given phylogeny without any prior assumptions about the form of area relationships. A three-dimensional step matrix based on a simple biogeographic model is used in the reconstruction. Speciation is assumed to subdivide the ranges of widespread species into vicariant components; the optimal ancestral distributions are those that minimize the number of implied dispersal and extinction events. Exact algorithms that find the optimal reconstruction(s) are described. In addition to their use in taxon biogeography, the inferred distribution histories of individual groups serve as a basis for the study of general patterns in historical biogeography, particularly if the relative age of the nodes in the source cladograms is known.

@article{doi101093sysbio461195,
    author = "Ronquist, Fredrik",
    title = "Dispersal-Vicariance Analysis: A New Approach to the Quantification of Historical Biogeography",
    year = "1997",
    journal = "Systematic Biology",
    abstract = "Quantification in historical biogeography has usually been based on the search for a single branching relationship among areas of endemism. Unlike organisms, however, areas rarely have a unique hierarchical history. Dispersal barriers appear and disappear and may have different effects on different species. As a result, the biota of an area may consist of several components with separate histories, each of which may be reticulate rather than branching. In an attempt to address these problems, I present a new biogeographic method, dispersal–vicariance analysis, which reconstructs the ancestral distributions in a given phylogeny without any prior assumptions about the form of area relationships. A three-dimensional step matrix based on a simple biogeographic model is used in the reconstruction. Speciation is assumed to subdivide the ranges of widespread species into vicariant components; the optimal ancestral distributions are those that minimize the number of implied dispersal and extinction events. Exact algorithms that find the optimal reconstruction(s) are described. In addition to their use in taxon biogeography, the inferred distribution histories of individual groups serve as a basis for the study of general patterns in historical biogeography, particularly if the relative age of the nodes in the source cladograms is known.",
    url = "https://doi.org/10.1093/sysbio/46.1.195",
    doi = "10.1093/sysbio/46.1.195",
    openalex = "W2098673312",
    references = "doi101006clad19941010, doi101093sysbio293254, doi101093sysbio414436, doi101093sysbio43158, doi101111j109600311990tb00532x, doi101111j155856461994tb01326x, doi101111j155856461996tb04494x, doi1023072992205, doi104159harvard9780674865327, doi105860choice392183"
}

Historical biogeography seeks to explain contemporary distributions of taxa in the context of intrinsic biological and extrinsic geological and climatic factors. To decipher the relative importance of biological characteristics vs. environmental conditions, it is necessary to ask whether groups of taxa with similar distributions share the same history of diversification. Because all of the taxa will have shared the same climatic and geological history, evidence of shared history across multiple species provides an estimate of the role of extrinsic factors in shaping contemporary biogeographic patterns. Similarly, differences in the records of evolutionary history across species will probably be signatures of biological differences. In this study, we focus on inferring the evolutionary history for geographical populations and closely related species representing three genera of primary freshwater fishes that are widely distributed in lower Central America (LCA) and northwestern Colombia. Analysis of mitochondrial gene trees provides the opportunity for robust tests of shared history across taxa. Moreover, because mtDNA permits inference of the temporal scale of diversification we can test hypotheses regarding the chronological development of the Isthmian corridor linking North and South America. We have focused attention on two issues. First, we show that many of the distinct populations of LCA fishes diverged in a relatively brief period of time thus limiting the phylogenetic signal available for tests of shared history. Second, our results provide reduced evidence of shared history when all drainages are included in the analysis because of inferred dispersion events that obscure the evolutionary history among drainage basins. When we restrict the analysis to areas that harbour endemic mitochondrial lineages, there is evidence of shared history across taxa. We hypothesize that there were two to three distinct waves of invasion into LCA from putative source populations in northwestern Colombia. The first probably happened in the late Miocene, prior to the final emergence of the Isthmus in the mid-Pliocene; the second was probably coincident with the rise of the Isthmus in the mid-Pliocene, and the third event occurred more recently, perhaps in the Pleistocene. In each case the geographical scale of the dispersion of lineages was progressively more limited, a pattern we attribute to the continuing development of the landscape due to orogeny and the consequent increase in the insularization of drainage basins. Thus, the fisheye view of LCA suggests a complex biogeographic history of overlaid cycles of colonization, diversification, sorting and extinction of lineages.

@article{doi101046j1365294x199800358x,
    author = "Bermingham, Eldredge and Martin, A. P.",
    title = "Comparative mtDNA phylogeography of neotropical freshwater fishes: testing shared history to infer the evolutionary landscape of lower Central America",
    year = "1998",
    journal = "Molecular Ecology",
    abstract = "Historical biogeography seeks to explain contemporary distributions of taxa in the context of intrinsic biological and extrinsic geological and climatic factors. To decipher the relative importance of biological characteristics vs. environmental conditions, it is necessary to ask whether groups of taxa with similar distributions share the same history of diversification. Because all of the taxa will have shared the same climatic and geological history, evidence of shared history across multiple species provides an estimate of the role of extrinsic factors in shaping contemporary biogeographic patterns. Similarly, differences in the records of evolutionary history across species will probably be signatures of biological differences. In this study, we focus on inferring the evolutionary history for geographical populations and closely related species representing three genera of primary freshwater fishes that are widely distributed in lower Central America (LCA) and northwestern Colombia. Analysis of mitochondrial gene trees provides the opportunity for robust tests of shared history across taxa. Moreover, because mtDNA permits inference of the temporal scale of diversification we can test hypotheses regarding the chronological development of the Isthmian corridor linking North and South America. We have focused attention on two issues. First, we show that many of the distinct populations of LCA fishes diverged in a relatively brief period of time thus limiting the phylogenetic signal available for tests of shared history. Second, our results provide reduced evidence of shared history when all drainages are included in the analysis because of inferred dispersion events that obscure the evolutionary history among drainage basins. When we restrict the analysis to areas that harbour endemic mitochondrial lineages, there is evidence of shared history across taxa. We hypothesize that there were two to three distinct waves of invasion into LCA from putative source populations in northwestern Colombia. The first probably happened in the late Miocene, prior to the final emergence of the Isthmus in the mid-Pliocene; the second was probably coincident with the rise of the Isthmus in the mid-Pliocene, and the third event occurred more recently, perhaps in the Pleistocene. In each case the geographical scale of the dispersion of lineages was progressively more limited, a pattern we attribute to the continuing development of the landscape due to orogeny and the consequent increase in the insularization of drainage basins. Thus, the fisheye view of LCA suggests a complex biogeographic history of overlaid cycles of colonization, diversification, sorting and extinction of lineages.",
    url = "https://doi.org/10.1046/j.1365-294x.1998.00358.x",
    doi = "10.1046/j.1365-294x.1998.00358.x",
    openalex = "W2166585991",
    references = "doi1010079781461523819, doi101007bf02100115, doi101007bf02101694, doi101038342637a0, doi101093genetics1322583, doi101093oxfordjournalsmolbeva025664, doi101093sysbio232265, doi101093sysbio244431, doi101111jbi14281, doi101126science2354785167, doi101146annureves18110187001413, doi101146annureves18110187002421, doi1023072399218"
}

Abstract Aim To examine how the genetic diversity of selected taxa of forest‐dwelling small mammals is distributed between and within the major rain forest domains of Amazonia and Atlantic Forest and the intervening interior forests of Brazil, as inferred by the relationships between gene genealogies and geography. I also addressed the historical importance of the central Brazilian forests in connecting Amazon and Atlantic Forest populations of rodents and marsupials. Methods I evaluated variation in the mitochondrial cytochrome b gene to estimate the levels of sequence divergence between those taxa occurring throughout the Amazon, Atlantic Forest, and forests in the Cerrado and Caatinga regions. I inferred the hierarchical relationships between haplotypes, populations and formal taxa using the cladistic approach of maximum parsimony. I compared areas and the clades identified by superimposing cladograms on the geographical distribution of samples. The degree of concordance both in phylogeny and the depth of the nodes in these phylogenies, in addition to patterns of geographical distribution of clades, permitted me to make inferences on how, when and where the taxa differentiated. Results Sequence similarity is often greater between samples from the Atlantic Forest and either Amazon or central Brazilian forests than it is within each of the two rain forest domains. The Atlantic Forest clades are either not reciprocally monophyletic or are the sister group to all the other clades. There is some indication of northern and southern components in the Atlantic Forest. Given the geographical distribution of clades and the relatively deep levels of divergence, the central Brazilian area does not behave as a separate region but is complementary to either Amazon or Atlantic Forest. Patterns of area relationships differ across taxa, suggesting that different processes and/or historic events affected the diversification within each lineage. Main conclusions The Amazon and the Atlantic forests are not exclusive in terms of their small mammal faunas; both overlap broadly with taxa occurring in gallery forests and dry forests in central Brazil. Central Brazilian forests are an integral part of the evolutionary scenario of lowland small mammals, playing an important role as present and past habitats for rain forest species. Therefore, representatives from this area should always be included in analyses of the evolutionary history of lowland rain forest faunas. The incongruence of branching patterns among areas is in agreement with recent results presented for Neotropical passerine birds and indicates that a single hypothesis of Neotropical area relationships is unlikely. These findings reinforce the idea that speciation in the Neotropics will not be explained by any single model of vicariance or climatic changes.

@article{doi101046j13652699200300792x,
    author = "Costa, Leonora Pires",
    title = "The historical bridge between the Amazon and the Atlantic Forest of Brazil: a study of molecular phylogeography with small mammals",
    year = "2003",
    journal = "Journal of Biogeography",
    abstract = "Abstract Aim To examine how the genetic diversity of selected taxa of forest‐dwelling small mammals is distributed between and within the major rain forest domains of Amazonia and Atlantic Forest and the intervening interior forests of Brazil, as inferred by the relationships between gene genealogies and geography. I also addressed the historical importance of the central Brazilian forests in connecting Amazon and Atlantic Forest populations of rodents and marsupials. Methods I evaluated variation in the mitochondrial cytochrome b gene to estimate the levels of sequence divergence between those taxa occurring throughout the Amazon, Atlantic Forest, and forests in the Cerrado and Caatinga regions. I inferred the hierarchical relationships between haplotypes, populations and formal taxa using the cladistic approach of maximum parsimony. I compared areas and the clades identified by superimposing cladograms on the geographical distribution of samples. The degree of concordance both in phylogeny and the depth of the nodes in these phylogenies, in addition to patterns of geographical distribution of clades, permitted me to make inferences on how, when and where the taxa differentiated. Results Sequence similarity is often greater between samples from the Atlantic Forest and either Amazon or central Brazilian forests than it is within each of the two rain forest domains. The Atlantic Forest clades are either not reciprocally monophyletic or are the sister group to all the other clades. There is some indication of northern and southern components in the Atlantic Forest. Given the geographical distribution of clades and the relatively deep levels of divergence, the central Brazilian area does not behave as a separate region but is complementary to either Amazon or Atlantic Forest. Patterns of area relationships differ across taxa, suggesting that different processes and/or historic events affected the diversification within each lineage. Main conclusions The Amazon and the Atlantic forests are not exclusive in terms of their small mammal faunas; both overlap broadly with taxa occurring in gallery forests and dry forests in central Brazil. Central Brazilian forests are an integral part of the evolutionary scenario of lowland small mammals, playing an important role as present and past habitats for rain forest species. Therefore, representatives from this area should always be included in analyses of the evolutionary history of lowland rain forest faunas. The incongruence of branching patterns among areas is in agreement with recent results presented for Neotropical passerine birds and indicates that a single hypothesis of Neotropical area relationships is unlikely. These findings reinforce the idea that speciation in the Neotropics will not be explained by any single model of vicariance or climatic changes.",
    url = "https://doi.org/10.1046/j.1365-2699.2003.00792.x",
    doi = "10.1046/j.1365-2699.2003.00792.x",
    openalex = "W2116889779",
    references = "doi101093sysbio461195, doi101111j155856461988tb04164x, doi10230740168278"
}

Cladistic biogeographic methods remain susceptible to the confounding effects of "pseudo-congruence" and "pseudo-incongruence" because they were not designed to incorporate information on the absolute timing of the diversification of lineages. Consequently, results from cladistic biogeographic studies are difficult to interpret and cannot be confidently attributed to any particular cause. We illustrate these points with concrete examples, paying special attention to recent work on the biogeography of the Northern Hemisphere, and outline ways in which topological and temporal information might be better integrated. The development of historical biogeography over the last few decades provides general insights into the nature of integration through the life of a discipline.

@article{doi101093icb432261,
    author = "Donoghue, Michael J.",
    title = "Toward an Integrative Historical Biogeography",
    year = "2003",
    journal = "Integrative and Comparative Biology",
    abstract = {Cladistic biogeographic methods remain susceptible to the confounding effects of "pseudo-congruence" and "pseudo-incongruence" because they were not designed to incorporate information on the absolute timing of the diversification of lineages. Consequently, results from cladistic biogeographic studies are difficult to interpret and cannot be confidently attributed to any particular cause. We illustrate these points with concrete examples, paying special attention to recent work on the biogeography of the Northern Hemisphere, and outline ways in which topological and temporal information might be better integrated. The development of historical biogeography over the last few decades provides general insights into the nature of integration through the life of a discipline.},
    url = "https://doi.org/10.1093/icb/43.2.261",
    doi = "10.1093/icb/43.2.261",
    openalex = "W2180920901",
    references = "doi1023071793007, doi1023072412140"
}

Abstract We investigate the relative importance of stochastic and environmental/topographic effects on the occurrence of avian centres of endemism, evaluating their potential historical importance for broad‐scale patterns in species richness across Sub‐Saharan Africa. Because species‐rich areas are more likely to be centres of endemism by chance alone, we test two null models: Model 1 calculates expected patterns of endemism using a random draw from the occurrence records of the continental assemblage, whereas Model 2 additionally implements the potential role of geometric constraints. Since Model 1 yields better quantitative predictions we use it to identify centres of endemism controlled for richness. Altitudinal range and low seasonality emerge as core environmental predictors for these areas, which contain unusually high species richness compared to other parts of sub‐Saharan Africa, even when controlled for environmental differences. This result supports the idea that centres of endemism may represent areas of special evolutionary history, probably as centres of diversification.

@article{doi101111j14610248200400678x,
    author = "Jetz, Walter and Rahbek, Carsten and Colwell, Robert K.",
    title = "The coincidence of rarity and richness and the potential signature of history in centres of endemism",
    year = "2004",
    journal = "Ecology Letters",
    abstract = "Abstract We investigate the relative importance of stochastic and environmental/topographic effects on the occurrence of avian centres of endemism, evaluating their potential historical importance for broad‐scale patterns in species richness across Sub‐Saharan Africa. Because species‐rich areas are more likely to be centres of endemism by chance alone, we test two null models: Model 1 calculates expected patterns of endemism using a random draw from the occurrence records of the continental assemblage, whereas Model 2 additionally implements the potential role of geometric constraints. Since Model 1 yields better quantitative predictions we use it to identify centres of endemism controlled for richness. Altitudinal range and low seasonality emerge as core environmental predictors for these areas, which contain unusually high species richness compared to other parts of sub‐Saharan Africa, even when controlled for environmental differences. This result supports the idea that centres of endemism may represent areas of special evolutionary history, probably as centres of diversification.",
    url = "https://doi.org/10.1111/j.1461-0248.2004.00678.x",
    doi = "10.1111/j.1461-0248.2004.00678.x",
    openalex = "W2129060951",
    references = "doi101093sysbio232265, doi1023072412139"
}

Separated from the mainland of Africa for 160 million years, has evolved an incredible wealth of biodiversity, with thousands of species that can be found nowhere else on earth. For instance, of its estimated 12,000 plant species, nearly 10,000 are unique to Madagascar. Malagasy animals are just as spectacular, from its almost forty currently recognized species of lemursa primate group found only hereto the numerous species of tiny dwarf chameleons. With astounding frequency scientists discover a previously unknown species in Madagascarand at almost the same rate another natural area of habitat is degraded or destroyed, a combination that recently led conservation organizations to name one of the most important and threatened conservation priorities on the planet. The Natural History of Madagascar provides the most comprehensive, up-to-date synthesis available of this island nation's priceless biological treasures. Contributions by nearly three hundred world-renowned experts cover the history of scientific exploration in Madagascar, its geology and soils, climate, forest ecology, human ecology, marine and coastal ecosystems, plants, invertebrates, fishes, amphibians, reptiles, birds, and mammals. Detailed discussions of conservation efforts in highlight several successful park reserve programs that could serve as models for other areas. Beautifully illustrated throughout, the book includes over one hundred color illustrations, with fifty color photos by nature photographer Harald Schutz, as well as more than three hundred black-and-white photographs and line drawings. The Natural History of Madagascar will be the invaluable reference for anyone interested in the Malagasy environment, from biologists and conservationists to policymakers and ecotourists.

@article{doi105860choice416524,
    title = "The Natural history of Madagascar",
    year = "2004",
    journal = "Choice Reviews Online",
    abstract = "Separated from the mainland of Africa for 160 million years, has evolved an incredible wealth of biodiversity, with thousands of species that can be found nowhere else on earth. For instance, of its estimated 12,000 plant species, nearly 10,000 are unique to Madagascar. Malagasy animals are just as spectacular, from its almost forty currently recognized species of lemursa primate group found only hereto the numerous species of tiny dwarf chameleons. With astounding frequency scientists discover a previously unknown species in Madagascarand at almost the same rate another natural area of habitat is degraded or destroyed, a combination that recently led conservation organizations to name one of the most important and threatened conservation priorities on the planet. The Natural History of Madagascar provides the most comprehensive, up-to-date synthesis available of this island nation's priceless biological treasures. Contributions by nearly three hundred world-renowned experts cover the history of scientific exploration in Madagascar, its geology and soils, climate, forest ecology, human ecology, marine and coastal ecosystems, plants, invertebrates, fishes, amphibians, reptiles, birds, and mammals. Detailed discussions of conservation efforts in highlight several successful park reserve programs that could serve as models for other areas. Beautifully illustrated throughout, the book includes over one hundred color illustrations, with fifty color photos by nature photographer Harald Schutz, as well as more than three hundred black-and-white photographs and line drawings. The Natural History of Madagascar will be the invaluable reference for anyone interested in the Malagasy environment, from biologists and conservationists to policymakers and ecotourists.",
    url = "https://doi.org/10.5860/choice.41-6524",
    doi = "10.5860/choice.41-6524",
    openalex = "W583503205"
}

Abstract The evolutionary history of life includes two primary components: phylogeny and timescale. Phylogeny refers to the branching order (relationships) of species or other taxa within a group and is crucial for understanding the inheritance of traits and for erecting classifications. However, a timescale is equally important because it provides a way to compare phylogeny directly with the evolution of other organisms and with planetary history such as geology, climate, extraterrestrial impacts, and other features. The Timetree of Life is the first reference book to synthesize the wealth of information relating to the temporal component of phylogenetic trees. In the past, biologists have relied exclusively upon the fossil record to infer an evolutionary timescale. However, recent revolutionary advances in molecular biology have made it possible to not only estimate the relationships of many groups of organisms, but also to estimate their times of divergence with molecular clocks. The routine estimation and utilization of these so-called ‘time-trees’ could add exciting new dimensions to biology including enhanced opportunities to integrate large molecular data sets with fossil and biogeographic evidence (and thereby foster greater communication between molecular and traditional systematists). They could help estimate not only ancestral character states but also evolutionary rates in numerous categories of organismal phenotype; establish more reliable associations between causal historical processes and biological outcomes; develop a universally standardized scheme for biological classifications; and generally promote novel avenues of thought in many arenas of comparative evolutionary biology. This authoritative reference work brings together, for the first time, experts on all major groups of organisms to assemble a timetree of life. The result is a comprehensive resource on evolutionary history which will be an indispensable reference for scientists, educators, and students in the life sciences, earth sciences, and molecular biology. For each major group of organism, a representative is illustrated and a timetree of families and higher taxonomic groups is shown. Basic aspects of the evolutionary history of the group, the fossil record, and competing hypotheses of relationships are discussed. Details of the divergence times are presented for each node in the timetree, and primary literature references are included.

@book{doi101093oso97801995350330010001,
    title = "The Timetree of Life",
    year = "2009",
    abstract = "Abstract The evolutionary history of life includes two primary components: phylogeny and timescale. Phylogeny refers to the branching order (relationships) of species or other taxa within a group and is crucial for understanding the inheritance of traits and for erecting classifications. However, a timescale is equally important because it provides a way to compare phylogeny directly with the evolution of other organisms and with planetary history such as geology, climate, extraterrestrial impacts, and other features. The Timetree of Life is the first reference book to synthesize the wealth of information relating to the temporal component of phylogenetic trees. In the past, biologists have relied exclusively upon the fossil record to infer an evolutionary timescale. However, recent revolutionary advances in molecular biology have made it possible to not only estimate the relationships of many groups of organisms, but also to estimate their times of divergence with molecular clocks. The routine estimation and utilization of these so-called ‘time-trees’ could add exciting new dimensions to biology including enhanced opportunities to integrate large molecular data sets with fossil and biogeographic evidence (and thereby foster greater communication between molecular and traditional systematists). They could help estimate not only ancestral character states but also evolutionary rates in numerous categories of organismal phenotype; establish more reliable associations between causal historical processes and biological outcomes; develop a universally standardized scheme for biological classifications; and generally promote novel avenues of thought in many arenas of comparative evolutionary biology. This authoritative reference work brings together, for the first time, experts on all major groups of organisms to assemble a timetree of life. The result is a comprehensive resource on evolutionary history which will be an indispensable reference for scientists, educators, and students in the life sciences, earth sciences, and molecular biology. For each major group of organism, a representative is illustrated and a timetree of families and higher taxonomic groups is shown. Basic aspects of the evolutionary history of the group, the fossil record, and competing hypotheses of relationships are discussed. Details of the divergence times are presented for each node in the timetree, and primary literature references are included.",
    url = "https://doi.org/10.1093/oso/9780199535033.001.0001",
    doi = "10.1093/oso/9780199535033.001.0001",
    openalex = "W4388253550"
}

We present a new, broadly applicable measure of the spatial restriction of phylogenetic diversity, termed phylogenetic endemism (PE). PE combines the widely used phylogenetic diversity and weighted endemism measures to identify areas where substantial components of phylogenetic diversity are restricted. Such areas are likely to be of considerable importance for conservation. PE has a number of desirable properties not combined in previous approaches. It assesses endemism consistently, independent of taxonomic status or level, and independent of previously defined political or biological regions. The results can be directly compared between areas because they are based on equivalent spatial units. PE builds on previous phylogenetic analyses of endemism, but provides a more general solution for mapping endemism of lineages. We illustrate the broad applicability of PE using examples of Australian organisms having contrasting life histories: pea-flowered shrubs of the genus Daviesia (Fabaceae) and the Australian species of the Australo-Papuan tree frog radiation within the family Hylidae.

@article{doi101111j1365294x200904311x,
    author = "Rosauer, Dan F. and Laffan, Shawn W. and Crisp, Michael D. and Donnellan, Stephen C. and Cook, Lyn G.",
    title = "Phylogenetic endemism: a new approach for identifying geographical concentrations of evolutionary history",
    year = "2009",
    journal = "Molecular Ecology",
    abstract = "We present a new, broadly applicable measure of the spatial restriction of phylogenetic diversity, termed phylogenetic endemism (PE). PE combines the widely used phylogenetic diversity and weighted endemism measures to identify areas where substantial components of phylogenetic diversity are restricted. Such areas are likely to be of considerable importance for conservation. PE has a number of desirable properties not combined in previous approaches. It assesses endemism consistently, independent of taxonomic status or level, and independent of previously defined political or biological regions. The results can be directly compared between areas because they are based on equivalent spatial units. PE builds on previous phylogenetic analyses of endemism, but provides a more general solution for mapping endemism of lineages. We illustrate the broad applicability of PE using examples of Australian organisms having contrasting life histories: pea-flowered shrubs of the genus Daviesia (Fabaceae) and the Australian species of the Australo-Papuan tree frog radiation within the family Hylidae.",
    url = "https://doi.org/10.1111/j.1365-294x.2009.04311.x",
    doi = "10.1111/j.1365-294x.2009.04311.x",
    openalex = "W1995816647",
    references = "doi101146annurevecolsys35112202130201, doi1012060003009020062970001tatol20co2"
}

Abstract Accretionary orogens form at intraoceanic and continental margin convergent plate boundaries. They include the supra-subduction zone forearc, magmatic arc and back-arc components. Accretionary orogens can be grouped into retreating and advancing types, based on their kinematic framework and resulting geological character. Retreating orogens (e.g. modern western Pacific) are undergoing long-term extension in response to the site of subduction of the lower plate retreating with respect to the overriding plate and are characterized by back-arc basins. Advancing orogens (e.g. Andes) develop in an environment in which the overriding plate is advancing towards the downgoing plate, resulting in the development of foreland fold and thrust belts and crustal thickening. Cratonization of accretionary orogens occurs during continuing plate convergence and requires transient coupling across the plate boundary with strain concentrated in zones of mechanical and thermal weakening such as the magmatic arc and back-arc region. Potential driving mechanisms for coupling include accretion of buoyant lithosphere (terrane accretion), flat-slab subduction, and rapid absolute upper plate motion overriding the downgoing plate. Accretionary orogens have been active throughout Earth history, extending back until at least 3.2 Ga, and potentially earlier, and provide an important constraint on the initiation of horizontal motion of lithospheric plates on Earth. They have been responsible for major growth of the continental lithosphere through the addition of juvenile magmatic products but are also major sites of consumption and reworking of continental crust through time, through sediment subduction and subduction erosion. It is probable that the rates of crustal growth and destruction are roughly equal, implying that net growth since the Archaean is effectively zero.

@article{doi101144sp3181,
    author = "Cawood, Peter A. and Kröner, Alfred and Collins, William J. and Kusky, Timothy and Mooney, Walter D. and Windley, Brian F.",
    title = "Accretionary orogens through Earth history",
    year = "2009",
    journal = "Geological Society London Special Publications",
    abstract = "Abstract Accretionary orogens form at intraoceanic and continental margin convergent plate boundaries. They include the supra-subduction zone forearc, magmatic arc and back-arc components. Accretionary orogens can be grouped into retreating and advancing types, based on their kinematic framework and resulting geological character. Retreating orogens (e.g. modern western Pacific) are undergoing long-term extension in response to the site of subduction of the lower plate retreating with respect to the overriding plate and are characterized by back-arc basins. Advancing orogens (e.g. Andes) develop in an environment in which the overriding plate is advancing towards the downgoing plate, resulting in the development of foreland fold and thrust belts and crustal thickening. Cratonization of accretionary orogens occurs during continuing plate convergence and requires transient coupling across the plate boundary with strain concentrated in zones of mechanical and thermal weakening such as the magmatic arc and back-arc region. Potential driving mechanisms for coupling include accretion of buoyant lithosphere (terrane accretion), flat-slab subduction, and rapid absolute upper plate motion overriding the downgoing plate. Accretionary orogens have been active throughout Earth history, extending back until at least 3.2 Ga, and potentially earlier, and provide an important constraint on the initiation of horizontal motion of lithospheric plates on Earth. They have been responsible for major growth of the continental lithosphere through the addition of juvenile magmatic products but are also major sites of consumption and reworking of continental crust through time, through sediment subduction and subduction erosion. It is probable that the rates of crustal growth and destruction are roughly equal, implying that net growth since the Archaean is effectively zero.",
    url = "https://doi.org/10.1144/sp318.1",
    doi = "10.1144/sp318.1",
    openalex = "W2106713244",
    references = "crossref1974the, doi101007978940172809615, doi1010160031920186900932, doi1010160040195190900162, doi1010160301926894000775, doi101016s1367912001000694, doi101016s1367912002000172, doi1010292002tc001484, doi101038211676a0, doi101038288329a0, doi10108008120099608728282, doi101093petrology23277, doi101126science105978, doi101126science25250111409, doi101130g23193a1, doi1011440016764903165, doi101144001676492006022, doi101144gslsp19981430117, doi1013062f9188fb16ce11d78645000102c1865d, doi1018814epiiugs2000v23i2001, doi1023071796560, openalexw1624806571"
}

Asian frogs of the tribe Paini (Anura: Dicroglossidae) range across several first-order tectono-morphological domains of the Cenozoic Indo-Asian collision that include the Tibetan Plateau, the Himalayas, and Indochina. We show how the tectonic events induced by the Indo-Asian collision affected the regional biota and, in turn, how the geological history of the earth can be viewed from a biological perspective. Our analysis of a concatenated dataset comprising four nuclear gene sequences of Paini revealed two main radiations, corresponding to the genera Nanorana (I) and Quasipaa (II). Five distinct clades are recognized: Tibetan plateau clade (I-1), Himalaya clade (I-2), environs of Himalaya-Tibetan plateau clade (I-3), South China clade (II-1), and Indochina clade (II-2). This pattern of relationships highlights the significance of geography in shaping evolutionary history. Building on our molecular dating, ancestral region reconstruction, and distributional patterns, we hypothesize a distinct geographic and climatic transition in Asia beginning in the Oligocene and intensifying in the Miocene; this stimulated rapid diversification of Paini. Vicariance explains species formation among major lineages within Nanorana. Dispersal, in contrast, plays an important role among Quasipaa, with the southern Chinese taxa originating from Indochina. Our results support the tectonic hypothesis that an uplift in the Himalaya-Tibetan plateau region resulting from crustal thickening and lateral extrusion of Indochina occurred synchronously during the transition between Oligocene and Miocene in reaction to the Indo-Asian collision. The phylogenetic history of Paini illuminates critical aspects of the timing of geological events responsible for the current geography of Southeast Asia.

@article{doi101073pnas1008415107,
    author = "Che, Jing and Zhou, Weiwei and Hu, Jiansheng and Fang, Yan and Papenfuss, Theodore J. and Wake, David B. and Zhang, Ya‐Ping",
    title = "Spiny frogs (Paini) illuminate the history of the Himalayan region and Southeast Asia",
    year = "2010",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "Asian frogs of the tribe Paini (Anura: Dicroglossidae) range across several first-order tectono-morphological domains of the Cenozoic Indo-Asian collision that include the Tibetan Plateau, the Himalayas, and Indochina. We show how the tectonic events induced by the Indo-Asian collision affected the regional biota and, in turn, how the geological history of the earth can be viewed from a biological perspective. Our analysis of a concatenated dataset comprising four nuclear gene sequences of Paini revealed two main radiations, corresponding to the genera Nanorana (I) and Quasipaa (II). Five distinct clades are recognized: Tibetan plateau clade (I-1), Himalaya clade (I-2), environs of Himalaya-Tibetan plateau clade (I-3), South China clade (II-1), and Indochina clade (II-2). This pattern of relationships highlights the significance of geography in shaping evolutionary history. Building on our molecular dating, ancestral region reconstruction, and distributional patterns, we hypothesize a distinct geographic and climatic transition in Asia beginning in the Oligocene and intensifying in the Miocene; this stimulated rapid diversification of Paini. Vicariance explains species formation among major lineages within Nanorana. Dispersal, in contrast, plays an important role among Quasipaa, with the southern Chinese taxa originating from Indochina. Our results support the tectonic hypothesis that an uplift in the Himalaya-Tibetan plateau region resulting from crustal thickening and lateral extrusion of Indochina occurred synchronously during the transition between Oligocene and Miocene in reaction to the Indo-Asian collision. The phylogenetic history of Paini illuminates critical aspects of the timing of geological events responsible for the current geography of Southeast Asia.",
    url = "https://doi.org/10.1073/pnas.1008415107",
    doi = "10.1073/pnas.1008415107",
    openalex = "W2069063902",
    references = "doi101073pnas0611051104"
}

Understanding how historical processes have either similarly, or differentially, shaped the evolution of lineages or biotic assemblages is important for a broad spectrum of fields. Gaining such understanding can be particularly challenging, however, especially for regions that have a complex geologic and biological history. In this study we apply a broad comparative approach to distill such regional biogeographic perspectives, by characterizing sets of divergence times for major biogeographic boundaries estimated from multiple codistributed lineages of snakes. We use a large combined (mitochondrial gene sequence) phylogeographic/phylogenetic dataset containing several clades of snakes that range across Middle America – the tropical region between Mexico and northwestern South America. This region is known for its complex tectonic history, and poorly understood historical biogeography. Based on our results, we highlight how phylogeographic transition zones between Middle and South America and the Nicaragua Depression appear to have undergone multiple episodes of diversification in different lineages. This is in contrast to other examples we find where apparently a single vicariant period is shared across multiple lineages. We specifically evaluate the distributions of divergence time estimates across multiple lineages and estimate the number of temporal periods of lineage diversification per biogeographic break. Overall, our results highlight a great deal of shared temporal divergence, and provide important hypotheses for yet unstudied lineages. These multi‐lineage comparisons across multiple spatial and temporal scales provide excellent predictive power for identifying the roles of geology, climate, ecology and natural history in shaping regional biodiversity.

@article{doi101111j16000587201006281x,
    author = "Daza, Juan M. and Castoe, Todd A. and Parkinson, Christopher L.",
    title = "Using regional comparative phylogeographic data from snake lineages to infer historical processes in Middle America",
    year = "2010",
    journal = "Ecography",
    abstract = "Understanding how historical processes have either similarly, or differentially, shaped the evolution of lineages or biotic assemblages is important for a broad spectrum of fields. Gaining such understanding can be particularly challenging, however, especially for regions that have a complex geologic and biological history. In this study we apply a broad comparative approach to distill such regional biogeographic perspectives, by characterizing sets of divergence times for major biogeographic boundaries estimated from multiple codistributed lineages of snakes. We use a large combined (mitochondrial gene sequence) phylogeographic/phylogenetic dataset containing several clades of snakes that range across Middle America – the tropical region between Mexico and northwestern South America. This region is known for its complex tectonic history, and poorly understood historical biogeography. Based on our results, we highlight how phylogeographic transition zones between Middle and South America and the Nicaragua Depression appear to have undergone multiple episodes of diversification in different lineages. This is in contrast to other examples we find where apparently a single vicariant period is shared across multiple lineages. We specifically evaluate the distributions of divergence time estimates across multiple lineages and estimate the number of temporal periods of lineage diversification per biogeographic break. Overall, our results highlight a great deal of shared temporal divergence, and provide important hypotheses for yet unstudied lineages. These multi‐lineage comparisons across multiple spatial and temporal scales provide excellent predictive power for identifying the roles of geology, climate, ecology and natural history in shaping regional biodiversity.",
    url = "https://doi.org/10.1111/j.1600-0587.2010.06281.x",
    doi = "10.1111/j.1600-0587.2010.06281.x",
    openalex = "W2118088239",
    references = "doi10274700206814489791"
}

Abstract Aim (1) To synthesize data on the physical and phylogeographical history of the Mexican highlands, with a focus on the Trans‐Mexican Volcanic Belt (TMVB), and (2) to propose approaches and analyses needed for examining the interaction of climate and volcanism. Location Mexico. Methods We performed a literature and data survey of the climatic, geological and phylogeographical history of the Mexican highlands. We then assessed how the expected effects of topographic isolation, co‐occurring palaeoclimatic fluctuations and volcanism can be tested against the distribution of genetic diversity of high‐elevation taxa. Results The Mexican highlands present a complex biogeographical, climatic and geological history. Montane taxa have been exposed to a sky‐island dynamic through climate fluctuations, allowing for long‐term in situ population persistence, while also promoting recent divergence and speciation events. Volcanic activity transformed part of the Mexican highlands during the Pleistocene, mainly in the TMVB, leading to co‐occurring climate and topographical changes. The TMVB highlands provide a suitable template to examine how low‐latitude mountains can facilitate both the long‐term persistence of biodiversity as well as allopatric and parapatric speciation driven by climatic and geological events. Main conclusions Climate fluctuations, together with recent volcanism, have driven the diversification and local persistence of biodiversity within the Mexican highlands. The climate–volcanism interaction is challenging to study; however, this can be overcome by coupling genomic data with landscape analyses that integrate the geological and climatic history of the region.

@article{doi101111jbi12546,
    author = "Mastretta‐Yanes, Alicia and Moreno‐Letelier, Alejandra and Piñero, Daniel and Jorgensen, Tove H. and Emerson, Brent C.",
    title = "Biodiversity in the Mexican highlands and the interaction of geology, geography and climate within the Trans‐Mexican Volcanic Belt",
    year = "2015",
    journal = "Journal of Biogeography",
    abstract = "Abstract Aim (1) To synthesize data on the physical and phylogeographical history of the Mexican highlands, with a focus on the Trans‐Mexican Volcanic Belt (TMVB), and (2) to propose approaches and analyses needed for examining the interaction of climate and volcanism. Location Mexico. Methods We performed a literature and data survey of the climatic, geological and phylogeographical history of the Mexican highlands. We then assessed how the expected effects of topographic isolation, co‐occurring palaeoclimatic fluctuations and volcanism can be tested against the distribution of genetic diversity of high‐elevation taxa. Results The Mexican highlands present a complex biogeographical, climatic and geological history. Montane taxa have been exposed to a sky‐island dynamic through climate fluctuations, allowing for long‐term in situ population persistence, while also promoting recent divergence and speciation events. Volcanic activity transformed part of the Mexican highlands during the Pleistocene, mainly in the TMVB, leading to co‐occurring climate and topographical changes. The TMVB highlands provide a suitable template to examine how low‐latitude mountains can facilitate both the long‐term persistence of biodiversity as well as allopatric and parapatric speciation driven by climatic and geological events. Main conclusions Climate fluctuations, together with recent volcanism, have driven the diversification and local persistence of biodiversity within the Mexican highlands. The climate–volcanism interaction is challenging to study; however, this can be overcome by coupling genomic data with landscape analyses that integrate the geological and climatic history of the region.",
    url = "https://doi.org/10.1111/jbi.12546",
    doi = "10.1111/jbi.12546",
    openalex = "W1602162740",
    references = "doi101146annurevento50071803130447"
}

The result of a major international effort involving authors and organizations from 13 countries, this volume summarizes the complex geology and tectonic evolution of the Caribbean plate and its relation to the adjacent North American, South American, Nazca, and Cocos plates. Focuses on regional geology and geophysics, magmatic processes, neotectonic features, geologic hazards, and energy and metallic resources. Contrasting views for the Mesozoic and Cenozoic geological evolution are presented in chapters on plate tectonics and mantle surge tectonics. Chapters on marine geology and geophysics are new syntheses for the entire Caribbean region. Highlights of the volume include extensive bibliographies and new syntheses of stratigraphic-lithologic columnar sections, seismicity, gravity and magnetic anomalies, neotectonic features, resource data, and crustal properties.

@incollection{doi101130dnaggnah405,
    author = "Pindell, James and Barrett, S. F.",
    title = "Geological evolution of the Caribbean region; A plate-tectonic perspective",
    year = "2015",
    booktitle = "Geological Society of America eBooks",
    abstract = "The result of a major international effort involving authors and organizations from 13 countries, this volume summarizes the complex geology and tectonic evolution of the Caribbean plate and its relation to the adjacent North American, South American, Nazca, and Cocos plates. Focuses on regional geology and geophysics, magmatic processes, neotectonic features, geologic hazards, and energy and metallic resources. Contrasting views for the Mesozoic and Cenozoic geological evolution are presented in chapters on plate tectonics and mantle surge tectonics. Chapters on marine geology and geophysics are new syntheses for the entire Caribbean region. Highlights of the volume include extensive bibliographies and new syntheses of stratigraphic-lithologic columnar sections, seismicity, gravity and magnetic anomalies, neotectonic features, resource data, and crustal properties.",
    url = "https://doi.org/10.1130/dnag-gna-h.405",
    doi = "10.1130/dnag-gna-h.405",
    openalex = "W2501206676",
    references = "doi101029jb087ib13p10656, doi101086628336, doi101130001676061973841105ctaiaa20co2, doi10113000167606198394941teomaa20co2"
}

Abstract Aim Orchidaceae is the most species‐rich angiosperm family and has one of the broadest distributions. Until now, the lack of a well‐resolved phylogeny has prevented analyses of orchid historical biogeography. In this study, we use such a phylogeny to estimate the geographical spread of orchids, evaluate the importance of different regions in their diversification and assess the role of long‐distance dispersal (LDD) in generating orchid diversity. Location Global. Methods Analyses use a phylogeny including species representing all five orchid subfamilies and almost all tribes and subtribes, calibrated against 17 angiosperm fossils. We estimated historical biogeography and assessed the importance of different regions for rates of speciation, extinction and net species diversification. We evaluated the impact of particular LDD events on orchid diversity by asking how many species evolved in the new range subsequent to those events. Results Orchids appear to have arisen in Australia 112 Ma (95% higher probability distribution: 102.0–120.0 Ma), then spread to the Neotropics via Antarctica by 90 Ma (HPD: 79.7–99.5 Ma), when all three continents were in close contact and apostasioids split from the ancestor of all other orchids. Ancestors of vanilloids, cypripedioids and orchidoids+epidendroids appear to have originated in the Neotropics 84–64 Ma. Repeated long‐ and short‐distance dispersal occurred through orchid history: stochastic mapping identified a mean total of 74 LDD events or 0.8 Ma −1. Across orchid history, Southeast Asia was the most important source and maximally accelerated net diversification; across epidendroids, the Neotropics maximally accelerated diversification. Main conclusions Our analysis provides the first biogeographical history of the orchids, implicating Australia, the Neotropics and Antarctica in their origin. LDD and life in the Neotropics – especially the Andes – had profound effects on their spread and diversification; > 97% of all orchid species are restricted to individual continents.

@article{doi101111jbi12854,
    author = "Givnish, Thomas J. and Spalink, Daniel and Ames, Mercedes and Lyon, Stephanie P. and Hunter, Steven and Zuluaga, Alejandro and Doucette, Alfonso and Giraldo, Giovanny and McDaniel, James and Clements, Mark A. and Arroyo, Mary T. K. and Endara, Lorena and Kriebel, Ricardo and Williams, Norris H. and Cameron, Kenneth M.",
    title = "Orchid historical biogeography, diversification, Antarctica and the paradox of orchid dispersal",
    year = "2016",
    journal = "Journal of Biogeography",
    abstract = "Abstract Aim Orchidaceae is the most species‐rich angiosperm family and has one of the broadest distributions. Until now, the lack of a well‐resolved phylogeny has prevented analyses of orchid historical biogeography. In this study, we use such a phylogeny to estimate the geographical spread of orchids, evaluate the importance of different regions in their diversification and assess the role of long‐distance dispersal (LDD) in generating orchid diversity. Location Global. Methods Analyses use a phylogeny including species representing all five orchid subfamilies and almost all tribes and subtribes, calibrated against 17 angiosperm fossils. We estimated historical biogeography and assessed the importance of different regions for rates of speciation, extinction and net species diversification. We evaluated the impact of particular LDD events on orchid diversity by asking how many species evolved in the new range subsequent to those events. Results Orchids appear to have arisen in Australia 112 Ma (95\% higher probability distribution: 102.0–120.0 Ma), then spread to the Neotropics via Antarctica by 90 Ma (HPD: 79.7–99.5 Ma), when all three continents were in close contact and apostasioids split from the ancestor of all other orchids. Ancestors of vanilloids, cypripedioids and orchidoids+epidendroids appear to have originated in the Neotropics 84–64 Ma. Repeated long‐ and short‐distance dispersal occurred through orchid history: stochastic mapping identified a mean total of 74 LDD events or 0.8 Ma −1. Across orchid history, Southeast Asia was the most important source and maximally accelerated net diversification; across epidendroids, the Neotropics maximally accelerated diversification. Main conclusions Our analysis provides the first biogeographical history of the orchids, implicating Australia, the Neotropics and Antarctica in their origin. LDD and life in the Neotropics – especially the Andes – had profound effects on their spread and diversification; > 97\% of all orchid species are restricted to individual continents.",
    url = "https://doi.org/10.1111/jbi.12854",
    doi = "10.1111/jbi.12854",
    openalex = "W2516743570",
    references = "doi101093sysbiosyu056"
}

Across the entire mantle we interpret 94 positive seismic wave-speed anomalies as subducted lithosphere and associate these slabs with their geological record. We document this as the Atlas of the Underworld, also accessible online at www.atlas-of-the-underworld.org, a compilation comprising subduction systems active in the past ~ 300 Myr. Deeper slabs are correlated to older geological records, assuming no relative horizontal motions between adjacent slabs following break-off, using knowledge of global plate circuits, but without assuming a mantle reference frame. The longest actively subducting slabs identified reach the depth of ~ 2500 km and some slabs have impinged on Large Low Shear Velocity Provinces in the deepest mantle. Anomously fast sinking of some slabs occurs in regions affected by long-term plume rising. We conclude that slab remnants eventually sink from the upper mantle to the core-mantle boundary. The range in subduction-age versus – depth in the lower mantle is largely inherited from the upper mantle history of subduction. We find a significant depth variation in average sinking speed of slabs. At the top of the lower mantle average slab sinking speeds are between 10 and 40 mm/yr, followed by a deceleration to 10–15 mm/yr down to depths around 1600–1700 km. In this interval, in situ time-stationary sinking rates suggest deceleration from 20 to 30 mm/yr to 4–8 mm/yr, increasing to 12–15 mm/yr below 2000 km. This corroborates the existence of a slab deceleration zone but we do not observe long-term (> 60 My) slab stagnation, excluding long-term stagnation due to compositional effects. Conversion of slab sinking profiles to viscosity profiles shows the general trend that mantle viscosity increases in the slab deceleration zone below which viscosity slowly decreases in the deep mantle. This is at variance with most published viscosity profiles that are derived from different observations, but agrees qualitatively with recent viscosity profiles suggested from material experiments.

@article{doi101016jtecto201710004,
    author = "van der Meer, Douwe G. and van Hinsbergen, Douwe J.J. and Spakman, Wim",
    title = "Atlas of the underworld: Slab remnants in the mantle, their sinking history, and a new outlook on lower mantle viscosity",
    year = "2017",
    journal = "Tectonophysics",
    abstract = "Across the entire mantle we interpret 94 positive seismic wave-speed anomalies as subducted lithosphere and associate these slabs with their geological record. We document this as the Atlas of the Underworld, also accessible online at www.atlas-of-the-underworld.org, a compilation comprising subduction systems active in the past \textasciitilde\ 300 Myr. Deeper slabs are correlated to older geological records, assuming no relative horizontal motions between adjacent slabs following break-off, using knowledge of global plate circuits, but without assuming a mantle reference frame. The longest actively subducting slabs identified reach the depth of \textasciitilde\ 2500 km and some slabs have impinged on Large Low Shear Velocity Provinces in the deepest mantle. Anomously fast sinking of some slabs occurs in regions affected by long-term plume rising. We conclude that slab remnants eventually sink from the upper mantle to the core-mantle boundary. The range in subduction-age versus – depth in the lower mantle is largely inherited from the upper mantle history of subduction. We find a significant depth variation in average sinking speed of slabs. At the top of the lower mantle average slab sinking speeds are between 10 and 40 mm/yr, followed by a deceleration to 10–15 mm/yr down to depths around 1600–1700 km. In this interval, in situ time-stationary sinking rates suggest deceleration from 20 to 30 mm/yr to 4–8 mm/yr, increasing to 12–15 mm/yr below 2000 km. This corroborates the existence of a slab deceleration zone but we do not observe long-term (> 60 My) slab stagnation, excluding long-term stagnation due to compositional effects. Conversion of slab sinking profiles to viscosity profiles shows the general trend that mantle viscosity increases in the slab deceleration zone below which viscosity slowly decreases in the deep mantle. This is at variance with most published viscosity profiles that are derived from different observations, but agrees qualitatively with recent viscosity profiles suggested from material experiments.",
    url = "https://doi.org/10.1016/j.tecto.2017.10.004",
    doi = "10.1016/j.tecto.2017.10.004",
    openalex = "W2766661285",
    references = "doi1010022013rg000444, doi1010022013tc003349, doi101007s0053101410603, doi1010160025322771900533, doi1010160040195181902754, doi101016jearscirev201006002, doi101016jearscirev201101007, doi101016jearscirev201203002, doi101016jearscirev201403008, doi101016jjsames200806002, doi101016jpalaeo200402033, doi101016s0012821x0100588x, doi101016s1367912001000694, doi1010292005jb004035, doi1010292007gc001743, doi101029tc001i003p00251, doi101073pnas1411762111, doi101093gjiggt095, doi101126science29054981910, doi1011300091761320020301031euaads20co2, doi101130b257081, doi101130g23193a1, doi101130ges000541, doi101146annurevearth281211"
}

Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships among all passerine families. Then, we calibrated this phylogeny using 13 fossils to examine the effects of different events in Earth history on the timing and rate of passerine diversification. Our analyses reconcile passerine diversification with the fossil and geological records; suggest that passerines originated on the Australian landmass ∼47 Ma; and show that subsequent dispersal and diversification of passerines was affected by a number of climatological and geological events, such as Oligocene glaciation and inundation of the New Zealand landmass. Although passerine diversification rates fluctuated throughout the Cenozoic, we find no link between the rate of passerine diversification and Cenozoic global temperature, and our analyses show that the increases in passerine diversification rate we observe are disconnected from the colonization of new continents. Taken together, these results suggest more complex mechanisms than temperature change or ecological opportunity have controlled macroscale patterns of passerine speciation.

@article{doi101073pnas1813206116,
    author = "Oliveros, Carl H. and Field, Daniel J. and Ksepka, Daniel T. and Barker, F. Keith and Aleixo, Alexandre Luis Padovan and Andersen, Michael J. and Alström, Per and Benz, Brett W. and Braun, Edward L. and Braun, Michael J. and Bravo, Gustavo A. and Brumfield, Robb T. and Chesser, R. Terry and Claramunt, Santiago and Cracraft, Joël and Cuervo, Andrés M. and Derryberry, Elizabeth P. and Glenn, Travis C. and Harvey, Michael and Hosner, Peter A. and Joseph, Leo and Kimball, Rebecca T. and Mack, Andrew L. and Miskelly, Colin M. and Peterson, A. Townsend and Robbins, Mark B. and Sheldon, Frederick H. and Silveira, Luís Fábio and Smith, Brian Tilston and White, Noor D. and Moyle, Robert G. and Faircloth, Brant C.",
    title = "Earth history and the passerine superradiation",
    year = "2019",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships among all passerine families. Then, we calibrated this phylogeny using 13 fossils to examine the effects of different events in Earth history on the timing and rate of passerine diversification. Our analyses reconcile passerine diversification with the fossil and geological records; suggest that passerines originated on the Australian landmass ∼47 Ma; and show that subsequent dispersal and diversification of passerines was affected by a number of climatological and geological events, such as Oligocene glaciation and inundation of the New Zealand landmass. Although passerine diversification rates fluctuated throughout the Cenozoic, we find no link between the rate of passerine diversification and Cenozoic global temperature, and our analyses show that the increases in passerine diversification rate we observe are disconnected from the colonization of new continents. Taken together, these results suggest more complex mechanisms than temperature change or ecological opportunity have controlled macroscale patterns of passerine speciation.",
    url = "https://doi.org/10.1073/pnas.1813206116",
    doi = "10.1073/pnas.1813206116",
    openalex = "W2931899952",
    references = "doi101016jcub201804062, doi101017s0016756807004268, doi101038nature03150, doi101038nature11631, doi101038nature15697, doi101038nbt1883, doi10108001621459199510476572, doi10108010635150701883881, doi101093bioinformaticsbtu033, doi101093molbevmss075, doi101093sysbiosyu056, doi101126science1059412, doi101126science1157704, doi101126science1194585, doi101126science1253451"
}

Studies of the Papuan region have provided fundamental insights into the evolutionary processes generating its exceptional biodiversity, but the influence of geological processes merits further study. Lying at the junction of five tectonic plates, this region has experienced a turbulent geological history that has not only produced towering mountains allowing elevational specialization and island archipelagos with varying degrees of isolation promoting vicariance, but also active margins where land masses have collided and been subsequently rifted apart creating a mosaic of intermixed terranes with vastly different geological histories. Asterophryine frogs are a hyperdiverse clade representing half the world's microhylid diversity (over 360 species) centered on New Guinea and its satellite islands. We show that vicariance facilitated by geological history explains this far and wide distribution of a clade that should have poor dispersal abilities. We recovered a mainland tectonic unit, the East Papua Composite Terrane (EPCT), as the center of origin for Asterophryinae and no fewer than 71 instances of what appear to be long-distance dispersal events, 29 of which are between mainland regions, with 42 from the mainland to the islands, some presently as far as 200 km away from source populations over open ocean. Furthermore, we find strong support for a "Slow and Steady" hypothesis for the formation of the northern margin of New Guinea by many separate accretion events during the Miocene, over other major geological alternatives, consistent with the 20 M year age of the clade and arrival via the EPCT. In addition, the historical biogeography of our frogs strongly supports an affiliation of the Louisiade Archipelago and Woodlark Island with the Owen Stanley Range on the EPCT, and the recent proximity of the large New Britain Island. Our results show that Asterophryinae did not have to repeatedly and independently disperse across large ocean barriers to the offshore islands, against the predictions of island biogeography theory, but that the current distribution can be explained through vicariance and short-distance oceanic dispersal as historical land connections disappeared and islands slowly became separated from each other. We show that islands have a life history, changing in distance from other land masses, with consequent opportunities for dispersal, isolation, and cladogenesis of their biotas. More broadly, we can begin to see how the geological history of the Papuan region can result in the rapid accumulation and staggering number of extant species.

@article{doi101093iobobad028,
    author = "Hill, Ethan C and Gao, Diana F and Polhemus, Dan A and Fraser, Claire J and Iova, Bulisa and Allison, Allen and Butler, Marguerite A",
    title = "Testing Geology with Biology: Plate Tectonics and the Diversification of Microhylid Frogs in the Papuan Region.",
    year = "2023",
    journal = "Integrative organismal biology (Oxford, England)",
    abstract = {Studies of the Papuan region have provided fundamental insights into the evolutionary processes generating its exceptional biodiversity, but the influence of geological processes merits further study. Lying at the junction of five tectonic plates, this region has experienced a turbulent geological history that has not only produced towering mountains allowing elevational specialization and island archipelagos with varying degrees of isolation promoting vicariance, but also active margins where land masses have collided and been subsequently rifted apart creating a mosaic of intermixed terranes with vastly different geological histories. Asterophryine frogs are a hyperdiverse clade representing half the world's microhylid diversity (over 360 species) centered on New Guinea and its satellite islands. We show that vicariance facilitated by geological history explains this far and wide distribution of a clade that should have poor dispersal abilities. We recovered a mainland tectonic unit, the East Papua Composite Terrane (EPCT), as the center of origin for Asterophryinae and no fewer than 71 instances of what appear to be long-distance dispersal events, 29 of which are between mainland regions, with 42 from the mainland to the islands, some presently as far as 200 km away from source populations over open ocean. Furthermore, we find strong support for a "Slow and Steady" hypothesis for the formation of the northern margin of New Guinea by many separate accretion events during the Miocene, over other major geological alternatives, consistent with the 20 M year age of the clade and arrival via the EPCT. In addition, the historical biogeography of our frogs strongly supports an affiliation of the Louisiade Archipelago and Woodlark Island with the Owen Stanley Range on the EPCT, and the recent proximity of the large New Britain Island. Our results show that Asterophryinae did not have to repeatedly and independently disperse across large ocean barriers to the offshore islands, against the predictions of island biogeography theory, but that the current distribution can be explained through vicariance and short-distance oceanic dispersal as historical land connections disappeared and islands slowly became separated from each other. We show that islands have a life history, changing in distance from other land masses, with consequent opportunities for dispersal, isolation, and cladogenesis of their biotas. More broadly, we can begin to see how the geological history of the Papuan region can result in the rapid accumulation and staggering number of extant species.},
    url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC10476510/",
    doi = "10.1093/iob/obad028",
    openalex = "W4385394856",
    pmcid = "PMC10476510",
    pmid = "37670952",
    references = "doi101016s1367912001000694, doi101038nature07893, doi10108010635150701883881, doi101093sysbiosyu056, doi1011112041210x12628, doi101126science1127609, doi1012060003009020062970001tatol20co2, doi1023073802723, openalexw641398428"
}

The Indo-Australian Archipelago (IAA) is a biodiversity hotspot characterized by high levels of biotic endemism and turnover. Explanations for these biodiversity patterns tend to focus on the role of the complex and dynamic geological history of the region. However, it is only in the last decade that large-scale phylogenetically informed analyses of macroevolutionary dynamics across the region have become feasible. A recent study of bird distributions and diversity across the archipelago highlighted marked turnover of species across geographically proximate areas in the IAA and the overarching role of sea barriers in shaping turnover. To build on this work and better understand the relative histories of bird diversification in the different areas of the IAA, we compile an updated and as-complete-as-possible supermatrix phylogenetic tree for passerine birds from the region and use this to estimate and compare levels of endemism in different areas of the IAA. This genetic framework further emphasizes contrasting histories of diversification in different areas of the archipelago. As expected for this clade, we found that Australia is consistently inferred as a hotspot of paleoendemism, the islands of East Melanesia and possibly Maluku are characterized by neoendemism, while the world's largest and highest tropical island, New Guinea, is inferred to be a center of superendemism, that is, both paleo- and neoendemism. Our updated tree also highlights a significant increase in the number of recognized bird species across the IAA in the last 10 years, as well as improved completeness of genetic sampling.

@article{doi101002ece371471,
    author = "Prasetya, Audrey and Jaya, Frederick R. and Moritz, Craig and Joseph, Leo and Oliver, Paul M.",
    title = "Supermatrix Phylogenetic Tree of Passerine Birds From the Indo‐Australian Archipelago Highlights Contrasting Histories of Regional Endemism",
    year = "2025",
    journal = "Ecology and Evolution",
    abstract = "The Indo-Australian Archipelago (IAA) is a biodiversity hotspot characterized by high levels of biotic endemism and turnover. Explanations for these biodiversity patterns tend to focus on the role of the complex and dynamic geological history of the region. However, it is only in the last decade that large-scale phylogenetically informed analyses of macroevolutionary dynamics across the region have become feasible. A recent study of bird distributions and diversity across the archipelago highlighted marked turnover of species across geographically proximate areas in the IAA and the overarching role of sea barriers in shaping turnover. To build on this work and better understand the relative histories of bird diversification in the different areas of the IAA, we compile an updated and as-complete-as-possible supermatrix phylogenetic tree for passerine birds from the region and use this to estimate and compare levels of endemism in different areas of the IAA. This genetic framework further emphasizes contrasting histories of diversification in different areas of the archipelago. As expected for this clade, we found that Australia is consistently inferred as a hotspot of paleoendemism, the islands of East Melanesia and possibly Maluku are characterized by neoendemism, while the world's largest and highest tropical island, New Guinea, is inferred to be a center of superendemism, that is, both paleo- and neoendemism. Our updated tree also highlights a significant increase in the number of recognized bird species across the IAA in the last 10 years, as well as improved completeness of genetic sampling.",
    url = "https://doi.org/10.1002/ece3.71471",
    doi = "10.1002/ece3.71471",
    openalex = "W4410798488",
    references = "doi1010160006320792912013, doi101038nature11631, doi101038nmeth4285, doi101093bioinformaticsbtp348, doi101093bioinformaticsbtq166, doi101093bioinformaticsbts199, doi101093iobobad028, doi101093molbevmsaa015, doi101093molbevmsm088, doi101093molbevmsx281, doi101093nargkh340"
}