@article{brown1943some1, author = "Brown, R. W", title = "Some prehistoric trees of the United States", year = "1943", journal = "Journal of Forestry, v. 41, p. 861-868", note = "talkorigins\_source = {true}; raw\_reference = {Brown, R. W., 1943, Some prehistoric trees of the United States: Journal of Forestry, v. 41, p. 861-868.}" } @misc{cheney1948metasequoia3, author = "Cheney, R. W", title = "Metasequoia discovery", year = "1948", howpublished = "American Scientist, v. 36, p. 490- 494", note = "talkorigins\_source = {true}; raw\_reference = {Cheney, R. W., 1948, Metasequoia discovery: American Scientist, v. 36, p. 490- 494.}" } @book{chaney1949evolutionary2, author = "Chaney, R. W", title = "Evolutionary trends in the angiosperms, in Jepsen, G. L., Simpson, G. G., and Mayr, E., eds., Genetics, Paleontology and Evolution", year = "1949", publisher = "Princeton, New Jersey, Princeton University Press, p. 190-201; 474 p", note = "talkorigins\_source = {true}; raw\_reference = {Chaney, R. W., 1949, Evolutionary trends in the angiosperms, in Jepsen, G. L., Simpson, G. G., and Mayr, E., eds., Genetics, Paleontology and Evolution: Princeton, New Jersey, Princeton University Press, p. 190-201; 474 p.}" } @article{doi101111j155856461949tb00007x, author = "Grant, Verne", title = "POLLINATION SYSTEMS AS ISOLATING MECHANISMS IN ANGIOSPERMS", year = "1949", journal = "Evolution", abstract = "Journal Article POLLINATION SYSTEMS AS ISOLATING MECHANISMS IN ANGIOSPERMS Get access Verne Grant Verne Grant Department of Botany University of California Berkeley Search for other works by this author on: Oxford Academic Google Scholar Evolution, Volume 3, Issue 1, 1 March 1949, Pages 82–97, https://doi.org/10.1111/j.1558-5646.1949.tb00007.x Published: 01 March 1949 Article history Received: 08 December 1948 Published: 01 March 1949", url = "https://doi.org/10.1111/j.1558-5646.1949.tb00007.x", doi = "10.1111/j.1558-5646.1949.tb00007.x", openalex = "W2318566535", references = "doi101093aesa304641" } @article{beal1950genetics, author = "Beal, J. M.", title = "Genetics, Paleontology, and Evolution. G. L. Jepsen, G. G. Simpson, Ernst Mayr", year = "1950", journal = "Botanical Gazette", url = "https://doi.org/10.1086/335639", doi = "10.1086/335639", number = "1", pages = "141-141", volume = "112" } @article{crossref1950genetics, title = "Genetics, Paleontology, and Evolution. Glenn L. Jepsen, Ernst Mayr, George Gaylord Simpson", year = "1950", journal = "The Journal of Geology", url = "https://doi.org/10.1086/625741", doi = "10.1086/625741", number = "3", pages = "283-283", volume = "58" } @article{glass1951genetics, author = "Glass, Bentley", title = "Genetics, Paleontology, and Evolution. Glenn L. Jepsen, Ernst Mayr, George Gaylord Simpson", year = "1951", journal = "The Quarterly Review of Biology", url = "https://doi.org/10.1086/398105", doi = "10.1086/398105", number = "2", pages = "202-203", volume = "26" } @incollection{doi101016s0065266008600486, author = "Bradshaw, A. D.", title = "Evolutionary Significance of Phenotypic Plasticity in Plants", year = "1965", booktitle = "Advances in genetics", url = "https://doi.org/10.1016/s0065-2660(08)60048-6", doi = "10.1016/s0065-2660(08)60048-6", openalex = "W206110177", references = "doi101016s0065211308603971, doi101111j146918091949tb02451x, doi104159harvard9780674865327, doi107312steb94536" } @article{bryant1971genetics, author = "Bryant, Peter J.", title = "Genetics of Evolution Genetics of the Evolutionary Process T. Dobzhansky", year = "1971", journal = "BioScience", url = "https://doi.org/10.2307/1295826", doi = "10.2307/1295826", number = "16", openalex = "W2325350562", pages = "879-879", volume = "21" } @article{doi101093genetics782737, author = "Felsenstein, Joseph", title = "THE EVOLUTIONARY ADVANTAGE OF RECOMBINATION", year = "1974", journal = "Genetics", abstract = {The controversy over the evolutionary advantage of recombination initially discovered by Fisher and by Muller is reviewed. Those authors whose models had finite-population effects found an advantage of recombination, and those whose models had infinite populations found none. The advantage of recombination is that it breaks down random linkage disequilibrium generated by genetic drift. Hill and Robertson found that the average effect of this randomly-generated linkage disequilibrium was to cause linked loci to interfere with each other's response to selection, even where there was no gene interaction between the loci. This effect is shown to be identical to the original argument of Fisher and Muller. It also predicts the "ratchet mechanism" discovered by Muller, who pointed out that deleterious mutants would more readily increase in a population without recombination. Computer simulations of substitution of favorable mutants and of the long-term increase of deleterious mutants verified the essential correctness of the original Fisher-Muller argument and the reality of the Muller ratchet mechanism. It is argued that these constitute an intrinsic advantage of recombination capable of accounting for its persistence in the face of selection for tighter linkage between interacting polymorphisms, and possibly capable of accounting for its origin.}, url = "https://doi.org/10.1093/genetics/78.2.737", doi = "10.1093/genetics/78.2.737", openalex = "W2130315111", references = "doi1023072341823" } @article{doi101111j155856461975tb00851x, author = "Felsenstein, Joseph", title = "THE GENETIC BASIS OF EVOLUTIONARY CHANGE", year = "1975", journal = "Evolution", url = "https://doi.org/10.1111/j.1558-5646.1975.tb00851.x", doi = "10.1111/j.1558-5646.1975.tb00851.x", openalex = "W1547248981" } @book{openalexw1523843460, author = "Bell, Graham", title = "The Masterpiece of Nature: The Evolution and Genetics of Sexuality", year = "1981", abstract = "Originally published in 1982, The Masterpiece of Nature examines sex as representative of the most important challenge to the modern theory of evolution. The book suggests that sex evolved, not as the result of normal Darwinian processes of natural selection, but through competition between populations or species - a hypothesis elsewhere almost universally discredited. The book also discusses the nature of sex and its consequences for the individual and for the population, as well as various other theories of sex. Since the value of these theories is held to reside wholly in their ability to predict the patterns of sexuality observed in nature, the book seeks to provide an extensive review of the circumstances in which sexuality is attenuated or lost throughout the animal kingdom, and these facts are then used to weigh up the merits of the rival theories. This book will be of interest to researchers in the area of genetics, ecology and evolutionary biology.", openalex = "W1523843460" } @book{openalexw1525494019, author = "Hartl, Daniel L.", title = "A primer of population genetics", year = "1981", abstract = "Part 1 Genetic variation: genetic and molecular essentials types of polymorphisms organization of genetic variation inbreeding. Part 2 The causes of evolution: mutation migration natural selection random genetic drift. Part 3 Molecular population genetics: molecular polymorphisms patterns of change in nucleotide and amino acid sequences polymorphism and divergence molecular phylogenetics transposable elements. Part 4 The genetic architecture of complex traits: types of complex traits phenotypic variation genetics and environment artificial selection correlation between relatives quantitative genetics of natural populations complex traits with discrete expression quantitative trait loci (QTLs).", openalex = "W1525494019" } @article{doi1023072232409, author = "Loasby, Brian J. and Nelson, Richard R. and Winter, Sidney G.", title = "An Evolutionary Theory of Economic Change.", year = "1983", journal = "The Economic Journal", abstract = "Journal Article An Evolutionary Theory of Economic Change Get access An Evolutionary Theory of Economic Change. By Richard R. Nelson and Sidney G. Winter. (Cambridge, Massachusetts \& London: Harvard University Press, 1982. Pp. xi +437. £17.50.) Brian J. Loasby Brian J. Loasby University of Stirling Search for other works by this author on: Oxford Academic Google Scholar The Economic Journal, Volume 93, Issue 371, 1 September 1983, Pages 652–654, https://doi.org/10.2307/2232409 Published: 01 September 1983", url = "https://doi.org/10.2307/2232409", doi = "10.2307/2232409", openalex = "W2137358449" } @book{openalexw1495050269, author = "Hedrick, Philip W.", title = "Genetics of populations", year = "1983", abstract = "The Fourth Edition of Genetics of Populations is the most current, comprehensive, and accessible introduction to the field for advanced undergraduate and graduate students, and researchers in genetics, evolution, conservation, and related fields. In the past several years, interest in the application of population genetics principles to new molecular data has increased greatly, and Dr. Hedrick's new edition exemplifies his commitment to keeping pace with this dynamic area of study. Reorganized to allow students to focus more sharply on key material, the Fourth Edition integrates coverage of theoretical issues with a clear presentation of experimental population genetics and empirical data. Drawing examples from both recent and classic studies, and using a variety of organisms to illustrate the vast developments of population genetics, this text provides students and researchers with the most comprehensive resource in the field.", openalex = "W1495050269" } @incollection{doi10100797836425158802, author = "Nevo, Eviatar and Beiles, Avigdor and Ben‐Shlomo, Rachel", title = "The Evolutionary Significance of Genetic Diversity: Ecological, Demographic and Life History Correlates", year = "1984", booktitle = "Lecture notes in biomathematics", url = "https://doi.org/10.1007/978-3-642-51588-0\_2", doi = "10.1007/978-3-642-51588-0\_2", openalex = "W175060409", references = "doi101111j155856461960tb03113x, doi101126science16238611453, doi101146annureves10110179001133, openalexw1523843460" } @article{doi101146annureves18110187001321, author = "Charlesworth, Deborah and Charlesworth, Brian", title = "INBREEDING DEPRESSION AND ITS EVOLUTIONARY CONSEQUENCES", year = "1987", journal = "Annual Review of Ecology and Systematics", abstract = "(Uploaded by Plazi for the Bat Literature Project) No abstract provided.", url = "https://doi.org/10.1146/annurev.es.18.110187.001321", doi = "10.1146/annurev.es.18.110187.001321", openalex = "W2167243456", references = "doi101017s0305004100015644, doi101073pnas4211855, doi101111j155856461975tb00851x, doi105962bhltitle122451, doi107312steb94536, openalexw2062594085" } @article{doi101126science3420403, author = "Lande, Russell", title = "Genetics and Demography in Biological Conservation", year = "1988", journal = "Science", abstract = "Predicting the extinction of single populations or species requires ecological and evolutionary information. Primary demographic factors affecting population dynamics include social structure, life history variation caused by environmental fluctuation, dispersal in spatially heterogeneous environments, and local extinction and colonization. In small populations, inbreeding can greatly reduce the average individual fitness, and loss of genetic variability from random genetic drift can diminish future adaptability to a changing environment. Theory and empirical examples suggest that demography is usually of more immediate importance than population genetics in determining the minimum viable sizes of wild populations. The practical need in biological conservation for understanding the interaction of demographic and genetic factors in extinction may provide a focus for fundamental advances at the interface of ecology and evolution.", url = "https://doi.org/10.1126/science.3420403", doi = "10.1126/science.3420403", openalex = "W2094387116", references = "doi101016000632078690025x, doi101016c20090029523, doi101017s0016672300016037, doi101093besa153237, doi101111j146918091949tb02451x, doi101111j155856461975tb00851x, doi101126science2214609459, doi101126science2314734129, doi101146annureves18110187001321, doi1015159781400881376, doi1023071308256, doi1023072529912, openalexw1500291103, openalexw2318111898" } @book{doi101093oso97801985464120010001, author = "Harvey, Paul and Pagel, Mark", title = "The Comparative Method in Evolutionary Biology", year = "1991", abstract = "Abstract From Darwin onward, it has been second nature for evolutionary biologists to think comparatively because comparisons establish the generality of evolutionary phenomena. Do large genomes slow down development? What lifestyles select for large brains? Are extinction rates related to body size? These are all questions for the comparative method, and this book is about how such questions can be answered. The first chapter elaborates on suitable questions for the comparative approach and shows how it complements other approaches to problem-solving in evolution. The second chapter identifies the biological causes of similarity among closely related species for almost any observed character. The third chapter discusses methods for reconstructing phylogenetic trees and ancestral character states. The fourth chapter sets out to develop statistical tests that will determine whether different characters that exist in discrete states show evidence for correlated evolution. Chapter 5 turns to comparative analyses of continuously varying characters. Chapter 6 looks at allometry to exemplify the themes and methods discussed earlier, while the last chapter looks to future development of the comparative approach in both molecular and organismic biology.", url = "https://doi.org/10.1093/oso/9780198546412.001.0001", doi = "10.1093/oso/9780198546412.001.0001", openalex = "W4388245928" } @article{doi105860choice295104, title = "The comparative method in evolutionary biology", year = "1992", journal = "Choice Reviews Online", abstract = "The comparative method for studying adaptation why worry about phylogeny? reconstructing phylogenetic trees and ancestral character states comparative analysis of discrete data comparative analysis of continuous variables determining the form of comparative relationships.", url = "https://doi.org/10.5860/choice.29-5104", doi = "10.5860/choice.29-5104", openalex = "W1488393970" } @article{doi1010160304377093900688, author = "Barrett, Spencer C. H. and Eckert, Christopher G. and Husband, Brian C.", title = "Evolutionary processes in aquatic plant populations", year = "1993", journal = "Aquatic Botany", url = "https://doi.org/10.1016/0304-3770(93)90068-8", doi = "10.1016/0304-3770(93)90068-8", openalex = "W1985368951", references = "doi101016037811199090073z, doi101086282771, doi101093genetics16297, doi101111j146918091949tb02451x, doi101146annureves16110185002141, doi1023072402622, doi1023072444338, doi1023072529912, laushman1993population, openalexw2021831883, openalexw2077454220, openalexw2146778590" } @article{laushman1993population, author = "Laushman, Roger H.", title = "Population genetics of hydrophilous angiosperms", year = "1993", journal = "Aquatic Botany", url = "https://doi.org/10.1016/0304-3770(93)90069-9", doi = "10.1016/0304-3770(93)90069-9", number = "2-3", openalex = "W2060939568", pages = "147-158", volume = "44", references = "doi101002j153721971987tb08586x, doi1010160304377093900688, doi101093oxfordjournalsjhereda109497, doi101111j155856461975tb00851x, doi101146annureves10110179001133, doi101146annureves15110184000433, doi1023072444338, openalexw1495050269, openalexw1525494019, openalexw2146778590" } @article{doi101046j15231739199610061500x, author = "Frankham, Richard", title = "Relationship of Genetic Variation to Population Size in Wildlife", year = "1996", journal = "Conservation Biology", abstract = "Genetic diversity is one of three levels of biological diversity requiring conservation. Genetic theory predicts that levels of genetic variation should increase with effective population size. Soulé (1976) compiled the first convincing evidence that levels of genetic variation in wildlife were related to population size, but this issue remains controversial. The hypothesis that genetic variation is related to population size leads to the following predictions: (1) genetic variation within species should be related to population size; (2) genetic variation within species should be related to island size; (3) genetic variation should be related to population size within taxonomic groups; (4) widespread species should have more genetic variation than restricted species; (5) genetic variation in animals should be negatively correlated with body size; (6) genetic variation should be negatively correlated with rate of chromosome evolution; (7) genetic variation across species should be related to population size; (8) vertebrates should have less genetic variation than invertebrates or plants; (9) island populations should have less genetic variation than mainland populations; and (10) endangered species should have less genetic variation than nonendangered species. Empirical observations support all these hypotheses. There can be no doubt that genetic variation is related to population size, as Soulé proposed. Small population size reduces the evolutionary potential of wildlife species.", url = "https://doi.org/10.1046/j.1523-1739.1996.10061500.x", doi = "10.1046/j.1523-1739.1996.10061500.x", openalex = "W2164595396", references = "openalexw2146778590" } @article{doi101146annurevecolsys271237, author = "Linhart, Yan B. and Grant, Michael C.", title = "EVOLUTIONARY SIGNIFICANCE OF LOCAL GENETIC DIFFERENTIATION IN PLANTS", year = "1996", journal = "Annual Review of Ecology and Systematics", abstract = "▪ Abstract The study of natural plant populations has provided some of the strongest and most convincing cases of the operation of natural selection currently known, partly because of amenability to reciprocal transplant experiments, common garden work, and long-term in situ manipulation. Genetic differentiation among plant populations over small scales (a few cm to a few hundred cm) has been documented and is reviewed here, in herbaceous annuals and perennials, woody perennials, aquatics, terrestrials, narrow endemics, and widely distributed species. Character differentiation has been documented for most important features of plant structure and function. Examples are known for seed characters, leaf traits, phenology, physiological and biochemical activities, heavy metal tolerance, herbicide resistance, parasite resistance, competitive ability, organellar characters, breeding systems, and life history. Among the forces that have shaped these patterns of differentiation are toxic soils, fertilizers, mowing and grazing, soil moisture, temperature, light intensity, pollinating vectors, parasitism, gene flow, and natural dynamics. The breadth and depth of the evidence reviewed here strongly support the idea that natural selection is the principal force shaping genetic architecture in natural plant populations; that view needs to be more widely appreciated than it is at present.", url = "https://doi.org/10.1146/annurev.ecolsys.27.1.237", doi = "10.1146/annurev.ecolsys.27.1.237", openalex = "W2130703487", references = "doi101002j153721971987tb08586x, doi10100797814615694425, doi1010079781489930439, doi101016037811199090073z, doi101038scientificamerican117998, doi101111j155856461993tb01215x, doi101126science15739260, doi101146annureves06110175002011, doi101146annureves10110179001133, doi101146annureves15110184000433, doi101146annureves18110187000323, doi101146annureves19110188000551, doi101146annurevge25120191000245, doi1015159781400820108, doi1023072444338, doi104159harvard9780674865327, openalexw2080618944, openalexw2146778590" } @article{doi1023071312967, author = "Philbrick, C. Thomas and Les, Donald H.", title = "Evolution of Aquatic Angiosperm Reproductive Systems", year = "1996", journal = "BioScience", abstract = "vironments and became aquatic. Aquatic plants are species that perpetuate their life cycle in still or flowing water, or on inundated or noninundated hydric soils. Aquatic angiosperms inhabit oceans, lakes, rivers, and wetlands. The transition to an aquatic life has been achieved by only 2\% of the approximately 350,000 angiosperm species (Cook 1990). Nonetheless, the evolutionary invasion of aquatic environments by terrestrial angiosperms is estimated to represent 50-100 independent events (Cook 1990). Although aquatic plants are typically discussed as a unified biological group, the ways that species have evolved to life in the aquatic milieu are as diverse as the different", url = "https://doi.org/10.2307/1312967", doi = "10.2307/1312967", openalex = "W1847045724", references = "laushman1993population" } @article{doi10230741165852, author = "Tushman, Michael L. and O’Reilly, Charles A.", title = "Ambidextrous Organizations: Managing Evolutionary and Revolutionary Change", year = "1996", journal = "California Management Review", abstract = "Organizations evolve through periods of incremental or evolutionary change punctuated by discontinuous or revolutionary change. The challenge for managers is to adapt the culture and strategy of their organizations to its current environment, but to do so in a way that does not undermine its ability to adjust to radical changes in that environment. They must, in other words, create an ambidextrous organization—one capable of simultaneously pursuing both incremental and discontinuous innovation.", url = "https://doi.org/10.2307/41165852", doi = "10.2307/41165852", openalex = "W2023596193" } @article{doi1023072419820, author = "Les, Donald H. and Cleland, Maryke A. and Waycott, Michelle", title = "Phylogenetic Studies in Alismatidae, II: Evolution of Marine Angiosperms (Seagrasses) and Hydrophily", year = "1997", journal = "Systematic Botany", abstract = "Donald H. Les, Maryke A. Cleland, Michelle Waycott, Phylogenetic Studies in Alismatidae, II: Evolution of Marine Angiosperms (Seagrasses) and Hydrophily, Systematic Botany, Vol. 22, No. 3 (Jul. - Sep., 1997), pp. 443-463", url = "https://doi.org/10.2307/2419820", doi = "10.2307/2419820", openalex = "W2149777618", references = "doi1010160304377093900688" } @article{doi101046j1365294x199800364x, author = "Fleischer, Robert C. and McIntosh, Carl and Tarr, Cheryl L.", title = "Evolution on a volcanic conveyor belt: using phylogeographic reconstructions and K–Ar‐based ages of the Hawaiian Islands to estimate molecular evolutionary rates", year = "1998", journal = "Molecular Ecology", abstract = "The Hawaiian Islands form as the Pacific Plate moves over a 'hot spot' in the earth's mantle where magma extrudes through the crust to build huge shield volcanos. The islands subside and erode as the plate carries them to the north-west, eventually to become coral atolls and seamounts. Thus islands are ordered linearly by age, with the oldest islands in the north-west (e.g. Kauai at 5.1 Ma) and the youngest in the south-east (e.g. Hawaii at 0.43 Ma). K-Ar estimates of the date of an island's formation provide a maximum age for the taxa inhabiting the island. These ages can be used to calibrate rates of molecular change under the following assumptions: (i) K-Ar dates are accurate; (ii) tree topologies show that derivation of taxa parallels the timing of island formation; (iii) populations do not colonize long after island emergence; (iv) the coalescent point for sister taxa does not greatly predate the formation of the colonized younger island; (v) saturation effects and (vi) among-lineage rate variation are minimal or correctable; and (vii) unbiased standard errors of distances and regressions can be estimated from multiple pairwise comparisons. We use the approach to obtain overall corrected rate calibrations for: (i) part of the mitochondrial cytochrome b gene in Hawaiian drepanidines (0.016 sequence divergence/Myr); (ii) the Yp1 gene in Hawaiian Drosophila (0.019/Myr Kambysellis et al. 1995); and (iii) parts of the mitochondrial 12S and 16S rRNA and tRNAval in Laupala crickets (0.024-0.102/Myr, Shaw 1996). We discuss the reliability of the estimates given the assumptions (i-vii) above and contrast the results with previous calibrations of Adh in Hawaiian Drosophila and chloroplast DNA in lobeliods.", url = "https://doi.org/10.1046/j.1365-294x.1998.00364.x", doi = "10.1046/j.1365-294x.1998.00364.x", openalex = "W2093111338", references = "doi101093oxfordjournalsjhereda109497" } @article{doi101111j155856461998tb01823x, author = "Orr, H. Allen", title = "THE POPULATION GENETICS OF ADAPTATION: THE DISTRIBUTION OF FACTORS FIXED DURING ADAPTIVE EVOLUTION", year = "1998", journal = "Evolution", abstract = {We know very little about the genetic basis of adaptation. Indeed, we can make no theoretical predictions, however heuristic, about the distribution of phenotypic effects among factors fixed during adaptation nor about the expected "size" of the largest factor fixed. Study of this problem requires taking into account that populations gradually approach a phenotypic optimum during adaptation via the stepwise substitution of favorable mutations. Using Fisher's geometric model of adaptation, I analyze this approach to the optimum, and derive an approximate solution to the size distribution of factors fixed during adaptation. I further generalize these results to allow the input of any distribution of mutational effects. The distribution of factors fixed during adaptation assumes a pleasingly simple, exponential form. This result is remarkably insensitive to changes in the fitness function and in the distribution of mutational effects. An exponential trend among factors fixed appears to be a general property of adaptation toward a fixed optimum.}, url = "https://doi.org/10.1111/j.1558-5646.1998.tb01823.x", doi = "10.1111/j.1558-5646.1998.tb01823.x", openalex = "W2004671976", references = "doi101038376479a0, doi101038scientificamerican117998, doi101073pnas91156808, doi101093aibsbulletin2214b, doi101098rspb19790086, doi101146annurevge27120193001225, doi1023071435536, doi104159harvard9780674865327, doi105962bhltitle27468, doi107312gumb92958, doi107312rens91062" } @article{doi1023072411226, author = "Orr, H. Allen", title = "The Population Genetics of Adaptation: The Distribution of Factors Fixed during Adaptive Evolution", year = "1998", journal = "Evolution", url = "https://doi.org/10.2307/2411226", doi = "10.2307/2411226", openalex = "W4252998353" } @article{doi101046j13652745199900389x, author = "Ouborg, N. Joop and Piquot, Yves and van Groenendael, J.M.", title = "Population genetics, molecular markers and the study of dispersal in plants", year = "1999", journal = "Journal of Ecology", abstract = "Summary 1 Long‐distance dispersal events are biologically very important for plants because they affect colonization probabilities, the probabilities of population persistence in a fragmented habitat, and metapopulation structure. They are, however, very difficult to investigate because of their low frequency. We reviewed the use of molecular markers in the population genetics approach to studying dispersal. With these methods the consequences of long‐distance dispersal are studied, rather than the frequency of the dispersal events themselves. 2 Molecular markers vary, displaying different amounts of variation and different modes of inheritance: they may be either dominant or codominant, and may or may not be subjected to genetic recombination. Use of markers has inspired the development of maximum likelihood techniques that take the evolutionary history of alleles into account while estimating gene flow. 3 Inferring seed dispersal rates from indirect measurements of gene flow involves three steps: (i) quantifying genetic differentiation among populations and using this to estimate the rate of gene flow; (ii) producing a genetic dispersal curve by regressing geographical distance among populations against the amount of gene flow; and (iii) separating seed‐mediated from pollen‐mediated gene flow, by comparing differentiation in nuclear vs. cytoplasmic molecular markers. In this way, potentially very low levels of gene flow can be detected. 4 The indirect approach is based on a number of assumptions. The validity of each assumption should be assessed by independent methods or the estimates of gene flow and dispersal should be mainly used in a comparative context. In metapopulations, with frequent extinction and colonization, the relationship between genetic differentiation and gene flow is not straightforward, and other methods should be used. 5 Highly variable molecular markers, especially microsatellites, have facilitated a direct genetic approach to measuring gene flow, based on parental analyses. 6 The population genetic approach provides different information about dispersal than ecological methods. Thus population genetic and ecological methods may supplement each other, and together lead to a better insight into the dispersal process than either of the methods on its own.", url = "https://doi.org/10.1046/j.1365-2745.1999.00389.x", doi = "10.1046/j.1365-2745.1999.00389.x", openalex = "W2032487465", references = "doi1010160304377093900688" } @article{doi10103835046017, author = "Kopp, Artyom and Duncan, Ian and Carroll, Sean B.", title = "Genetic control and evolution of sexually dimorphic characters in Drosophila", year = "2000", journal = "Nature", url = "https://doi.org/10.1038/35046017", doi = "10.1038/35046017", openalex = "W1588649406", references = "doi101038384236a0, doi101073pnas7863721, doi101093oxfordjournalsmolbeva040214, doi101111j155856461982tb05003x, doi101111j155856461998tb05132x, doi101146annurevgenet301637, doi101242dev1212333, doi1015159780691207278, doi1023072341823, doi105962bhltitle27468" } @article{doi101055s20005958, author = "Booy, G. and Hendriks, Rob J. J. and Smulders, M.J.M. and van Groenendael, J.M. and Vosman, B.", title = "Genetic Diversity and the Survival of Populations", year = "2000", journal = "Plant Biology", abstract = "Abstract: In this comprehensive review, a range of factors is considered that may influence the significance of genetic diversity for the survival of a population. Genetic variation is essential for the adaptability of a population in which quantitatively inherited, fitness‐related traits are crucial. Therefore, the relationship between genetic diversity and fitness should be studied in order to make predictions on the importance of genetic diversity for a specific population. The level of genetic diversity found in a population highly depends on the mating system, the evolutionary history of a species and the population history (the latter is usually unknown), and on the level of environmental heterogeneity. An accurate estimation of fitness remains complex, despite the availability of a range of direct and indirect fitness parameters. There is no general relationship between genetic diversity and various fitness components. However, if a lower level of heterozygosity represents an increased level of inbreeding, a reduction in fitness can be expected. Molecular markers can be used to study adaptability or fitness, provided that they represent a quantitative trait locus (QTL) or are themselves functional genes involved in these processes. Next to a genetic response of a population to environmental change, phenotypic plasticity in a genotype can affect fitness. The relative importance of plasticity to genetic diversity depends on the species and population under study and on the environmental conditions. The possibilities for application of current knowledge on genetic diversity and population survival for the management of natural populations are discussed.", url = "https://doi.org/10.1055/s-2000-5958", doi = "10.1055/s-2000-5958", openalex = "W1970411761", references = "doi101002j153721971987tb08586x, doi101086285558" } @article{doi1023072656886, author = "Gitzendanner, Matthew A. and Soltis, Pamela S.", title = "Patterns of genetic variation in rare and widespread plant congeners", year = "2000", journal = "American Journal of Botany", abstract = "Rare species are typically considered to maintain low levels of genetic variation, and this view has been supported by several reviews of large numbers of isozyme studies. Although these reviews have provided valuable data on levels of variability in plant species in general, and rare species in particular, these broad overviews involve comparisons that may confound the effects of rarity with a multitude of other factors that affect genetic variability. Additionally, the statistical analyses employed assume the data to be independent, which is not the case for organisms that share a common phylogenetic history. As the role of evolutionary history and historical constraints has become better understood, more researchers have studied widespread congeners when investigating the genetic diversity of rare species in an effort to control for these effects. We summarize the available data from such studies, comparing for rare and widespread congeners (1) the levels of genetic variability at the population and species levels and (2) measures of population substructuring. At the population level, we summarized data for percentage polymorphic loci (\%P(pop)), mean number of alleles per locus (A(pop)), and observed heterozygosity (H(o)). Species-level measures used were percentage polymorphic loci (\%P(spp)), mean number of alleles per locus (A(spp)), and total genetic diversity (H(T)). Indices of population subdivision (either F(ST) or G(ST)) were also examined. Using Wilcoxon signed rank tests, we found significant, but small, differences between rare and widespread species for all diversity measures except H(T). However, there does not appear to be a difference between rare and widespread congeners in terms of how genetic variation is partitioned within and among populations. Levels of diversity, for all measures examined, between rare and widespread congeners are highly correlated.", url = "https://doi.org/10.2307/2656886", doi = "10.2307/2656886", openalex = "W2141860334", references = "doi101146annureves10110179001133" } @book{doi101016b9780127300559x50058, title = "The Character Concept in Evolutionary Biology", year = "2001", booktitle = "Elsevier eBooks", url = "https://doi.org/10.1016/b978-0-12-730055-9.x5005-8", doi = "10.1016/b978-0-12-730055-9.x5005-8", openalex = "W565848724", references = "doi101038384236a0" } @book{doi101093oso97801951315430010001, title = "Evolutionary Ecology", year = "2001", booktitle = "Oxford University Press eBooks", abstract = "Evolutionary Ecology simultaneously unifies conceptual and empirical advances in evolutionary ecology and provides a volume that can be used as either a primary textbook or a supplemental reading in an advanced undergraduate or graduate course. The focus of the book is on current concepts in evolutionary ecology, and the empirical study of these concepts. The editors have assembled a group of prominent biologists who have made significant contributions to this field. They both synthesize the current state of knowledge and identity areas for future investigation. Evolutionary Ecology will be of general interest to researchers and students in both ecology and evolutionary biology. Researchers in evolutionary ecology that want an overview of the current state of the field, and graduate students that want an introduction the field, will find this book very valuable. This volume can also be used as a primary textbook or supplemental reading in both upper division and graduate courses/seminars in Evolutionary Ecology.", url = "https://doi.org/10.1093/oso/9780195131543.001.0001", doi = "10.1093/oso/9780195131543.001.0001", openalex = "W4235189111" } @article{gibson2001evolution, author = "Gibson, Greg and Palsson, Arnar", title = "Evolution: A complement for evolutionary genetics", year = "2001", journal = "Current Biology", url = "https://doi.org/10.1016/s0960-9822(01)00014-8", doi = "10.1016/s0960-9822(01)00014-8", number = "2", pages = "R74-R76", volume = "11" } @article{doi101038sjhdy6800154, author = "Gostling, Neil J.", title = "From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design", year = "2002", journal = "Heredity", url = "https://doi.org/10.1038/sj.hdy.6800154", doi = "10.1038/sj.hdy.6800154", openalex = "W1968814137", references = "doi101016s0168952598016710" } @article{doi105860choice395182, title = "From DNA to diversity: molecular genetics and the evolution of animal design", year = "2002", journal = "Choice Reviews Online", abstract = "Preface.1. A Brief History of Animals.2. The Genetic Toolkit for Development.3. Building Animals.4. Evolution of the Toolkit.5. Diversification of Body Plans and Body Parts.6. Evolution of Morphological Novelties.7. Morphological Variation and Species Divergence.8. From DNA to Diversity: The Primacy of Regulatory Evolution.Glossary.Index", url = "https://doi.org/10.5860/choice.39-5182", doi = "10.5860/choice.39-5182", openalex = "W2034536549", references = "doi1010079783642455322, doi101016b9780122053511x50009, doi101016b9780127300559x50058, doi101016s0070215321x00026, doi101037003329091274504, doi105860choice341536, openalexw1865748464, openalexw2506868775, openalexw587813093" } @article{doi101038nature01568, author = "Lenski, Richard E. and Ofria, Charles and Pennock, Robert T. and Adami, Christoph", title = "The evolutionary origin of complex features", year = "2003", journal = "Nature", url = "https://doi.org/10.1038/nature01568", doi = "10.1038/nature01568", openalex = "W2005946215", references = "doi101002j232619511995tb03633x, doi101002sici10990526199609102132aidcplx830co2h, doi10103835023115, doi10103835085569, doi101038nature01151, doi101093genetics14841667, doi101126science860134, doi1023072485224, doi107551mitpress10900010001, openalexw2074397232" } @article{doi101038nrg1088, author = "Elena, Santiago F. and Lenski, Richard E.", title = "Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation", year = "2003", journal = "Nature Reviews Genetics", url = "https://doi.org/10.1038/nrg1088", doi = "10.1038/nrg1088", openalex = "W2112945902", references = "doi101007978940115210512, doi101023a1017067816551, doi101038336435a0, doi10103842701, doi101038nature01568, doi101073pnas74115088, doi101073pnas91156808, doi101086285289, doi101093oso97801985052350010001, doi101093oso97801985464120010001, doi101111j155856461998tb01823x, doi101126science147365368, doi101126science28854691251, doi1011289781555816704, doi1015159780691209418, doi1023072485224, doi1023074785, doi102307jctvx5wbbh, doi105860choice273873, doi105860choice295104, doi105962bhltitle27468" } @article{doi101038nature02415, author = "Shapiro, Michael D. and Marks, Melissa E. and Peichel, Catherine L. and Blackman, Benjamin K. and Nereng, Kirsten S. and Jónsson, Bjarni and Schluter, Dolph and Kingsley, David M.", title = "Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks", year = "2004", journal = "Nature", url = "https://doi.org/10.1038/nature02415", doi = "10.1038/nature02415", openalex = "W2066908868", references = "doi1010020471142905, doi101016s0092867400808685, doi101016s0092867401004937, doi10103820944, doi10103835046017, doi101038414901a, doi101038nature02064, doi101073pnas9794530, doi101111j001438202000tb00544x, openalexw2062594085" } @article{doi101038nature02698, author = "Wittkopp, Patricia J. and Haerum, Belinda K. and Clark, Andrew G.", title = "Evolutionary changes in cis and trans gene regulation", year = "2004", journal = "Nature", url = "https://doi.org/10.1038/nature02698", doi = "10.1038/nature02698", openalex = "W2085454778", references = "doi101093molbevmsg140, doi105860choice395182" } @article{doi101038nrmicro863, author = "Moyá, Andrés and Holmes, Edward C. and Gónzález‐Candelas, Fernando", title = "The population genetics and evolutionary epidemiology of RNA viruses", year = "2004", journal = "Nature Reviews Microbiology", url = "https://doi.org/10.1038/nrmicro863", doi = "10.1038/nrmicro863", openalex = "W1990653767", references = "doi101038nature01151, doi101128mmbr6511511852001" } @article{doi101162106454604773563612, author = "Ofria, Charles and Wilke, Claus O.", title = "Avida: A Software Platform for Research in Computational Evolutionary Biology", year = "2004", journal = "Artificial Life", abstract = "Avida is a software platform for experiments with self-replicating and evolving computer programs. It provides detailed control over experimental settings and protocols, a large array of measurement tools, and sophisticated methods to analyze and post-process experimental data. We explain the general principles on which Avida is built, as well as its main components and their interactions. We also explain how experiments are set up, carried out, and analyzed.", url = "https://doi.org/10.1162/106454604773563612", doi = "10.1162/106454604773563612", openalex = "W2147276070", references = "doi101038nature01151, doi101038nature01568" } @article{bell2005evolutionary, author = "Bell, G", title = "Evolutionary genetics: The evolution of evolution", year = "2005", journal = "Heredity", url = "https://doi.org/10.1038/sj.hdy.6800608", doi = "10.1038/sj.hdy.6800608", number = "1", pages = "1-2", volume = "94" } @article{doi101038nature03842, author = "Dekel, E. and Alon, Uri", title = "Optimality and evolutionary tuning of the expression level of a protein", year = "2005", journal = "Nature", url = "https://doi.org/10.1038/nature03842", doi = "10.1038/nature03842", openalex = "W2068872007", references = "doi101038nrg1088, doi101146annurevge18120184000335" } @article{doi101146annurevecolsys36091704175539, author = "Goodwillie, Carol and Kalisz, Susan and Eckert, Christopher G.", title = "The Evolutionary Enigma of Mixed Mating Systems in Plants: Occurrence, Theoretical Explanations, and Empirical Evidence", year = "2005", journal = "Annual Review of Ecology Evolution and Systematics", abstract = "▪ Abstract Mixed mating, in which hermaphrodite plant species reproduce by both self- and cross-fertilization, presents a challenging problem for evolutionary biologists. Theory suggests that inbreeding depression, the main selective factor opposing the evolution of selfing, can be purged with self-fertilization, a process that is expected to yield pure strategies of either outcrossing or selfing. Here we present updated evidence suggesting that mixed mating systems are frequent in seed plants. We outline the floral and pollination mechanisms that can lead to intermediate outcrossing, review the theoretical models that address the stability of intermediate outcrossing, and examine relevant empirical evidence. A comparative analysis of estimated inbreeding coefficients and outcrossing rates suggests that mixed mating often evolves despite strong inbreeding depression. The adaptive significance of mixed mating has yet to be fully explained for any species. Recent theoretical and empirical work suggests that future progress will come from a better integration of studies of floral mechanisms, genetics, and ecology, and recognition of how selective pressures vary in space and time.", url = "https://doi.org/10.1146/annurev.ecolsys.36.091704.175539", doi = "10.1146/annurev.ecolsys.36.091704.175539", openalex = "W2127588110", references = "doi10100797814615694425, doi101111j109583122000tb01221x, doi101146annureves15110184000433, doi105860choice355054, doi105962bhltitle110800, openalexw2491318968" } @article{doi10155404272, author = "Weinreich, Daniel and Watson, Richard A. and Chao, Lin", title = "PERSPECTIVE:SIGN EPISTASIS AND GENETIC CONSTRAINT ON EVOLUTIONARY TRAJECTORIES", year = "2005", journal = "Evolution", abstract = "Epistasis for fitness means that the selective effect of a mutation is conditional on the genetic background in which it appears. Although epistasis is widely observed in nature, our understanding of its consequences for evolution by natural selection remains incomplete. In particular, much attention focuses only on its influence on the instantaneous rate of changes in frequency of selected alleles via epistatic contribution to the additive genetic variance for fitness. Thus, in this framework epistasis only has evolutionary importance if the interacting loci are simultaneously segregating in the population. However, the selective accessibility of mutational trajectories to high fitness genotypes may depend on the genetic background in which novel mutations appear, and this effect is independent of population polymorphism at other loci. Here we explore this second influence of epistasis on evolution by natural selection. We show that it is the consequence of a particular form of epistasis, which we designate sign epistasis. Sign epistasis means that the sign of the fitness effect of a mutation is under epistatic control; thus, such a mutation is beneficial on some genetic backgrounds and deleterious on others. Recent experimental innovations in microbial systems now permit assessment of the fitness effects of individual mutations on multiple genetic backgrounds. We review this literature and identify many examples of sign epistasis, and we suggest that the implications of these results may generalize to other organisms. These theoretical and empirical considerations imply that strong genetic constraint on the selective accessibility of trajectories to high fitness genotypes may exist and suggest specific areas of investigation for future research.", url = "https://doi.org/10.1554/04-272", doi = "10.1554/04-272", openalex = "W4246887724" } @article{doi101890041209, author = "Blows, Mark W. and Hoffmann, Ary A.", title = "A REASSESSMENT OF GENETIC LIMITS TO EVOLUTIONARY CHANGE", year = "2005", journal = "Ecology", abstract = "An absence of genetic variance in traits under selection is perhaps the oldest explanation for a limit to evolutionary change, but has also been the most easily dismissed. We review a range of theoretical and empirical results covering single traits to more complex multivariate systems, and show that an absence of genetic variance may be more common than is currently appreciated. From a single-trait perspective, we highlight that it is becoming clear that some trait types do not display significant levels of genetic variation, and we raise the possibility that species with restricted ranges may differ qualitatively from more widespread species in levels of genetic variance in ecologically important traits. A common misconception in many life-history studies is that a lack of genetic variance in single traits, and genetic constraints as a consequence of bivariate genetic correlations, are different causes of selection limits. We detail how interpretations of bivariate patterns are unlikely to demonstrate genetic limits to selection in many cases. We advocate a multivariate definition of genetic constraints that emphasizes the presence (or otherwise) of genetic variance in the multivariate direction of selection. For multitrait systems, recent results using longer term studies of organisms, in which more is understood concerning what traits may be under selection, have indicated that selection may exhaust genetic variance, resulting in a limit to the selection response.", url = "https://doi.org/10.1890/04-1209", doi = "10.1890/04-1209", openalex = "W1991431672", references = "doi1023072411226" } @article{doi101038nrc2013, author = "Merlo, Lauren M.F. and Pepper, John W. and Reid, Brian J. and Maley, Carlo C.", title = "Cancer as an evolutionary and ecological process", year = "2006", journal = "Nature reviews. Cancer", url = "https://doi.org/10.1038/nrc2013", doi = "10.1038/nrc2013", openalex = "W2123558100", references = "doi1010021521187820001222121057aidbies330co2w, doi101016s0169534701021012, doi101016s0169534702024953, doi10103842701, doi101038nrg1088, doi101146annurevgenet341401, doi1023072407274" } @article{doi101073pnas0511123103, author = "Charmantier, Anne and Perrins, Christopher M. and McCleery, R. H. and Sheldon, Ben C.", title = "Quantitative genetics of age at reproduction in wild swans: Support for antagonistic pleiotropy models of senescence", year = "2006", journal = "Proceedings of the National Academy of Sciences", abstract = "Why do individuals stop reproducing after a certain age, and how is this age determined? The antagonistic pleiotropy theory for the evolution of senescence predicts that increased early-life performance should be accompanied by earlier (or faster) senescence. Hence, an individual that has started to breed early should also lose its reproductive capacities early. We investigate here the relationship between age at first reproduction (AFR) and age at last reproduction (ALR) in a free-ranging mute swan (Cygnus olor) population monitored for 36 years. Using multivariate analyses on the longitudinal data, we show that both traits are strongly selected in opposite directions. Analysis of the phenotypic covariance between these characters shows that individuals vary in their inherent quality, such that some individuals have earlier AFR and later ALR than expected. Quantitative genetic pedigree analyses show that both traits possess additive genetic variance but also that AFR and ALR are positively genetically correlated. Hence, although both traits display heritable variation and are under opposing directional selection, their evolution is constrained by a strong evolutionary tradeoff. These results are consistent with the theory that increased early-life performance comes with faster senescence because of genetic tradeoffs.", url = "https://doi.org/10.1073/pnas.0511123103", doi = "10.1073/pnas.0511123103", openalex = "W2036516886", references = "doi101093oso97801951315430010001" } @article{doi101093jeglbi022, author = "Boschma, Ron and Frenken, Koen", title = "Why is economic geography not an evolutionary science? Towards an evolutionary economic geography", year = "2006", journal = "Journal of Economic Geography", abstract = "The paper explains the commonalities and differences between neoclassical, institutional and evolutionary approaches that have been influential in economic geography during the last couple of decades. By separating the three approaches in terms of theoretical content and research methodology, wecan appreciate both the commonalities and differences between the three approaches. It is also apparent that innovative theorizing currently occurs at the interface between neoclassical and evolutionary theory (especially in modelling) and at the interface between institutional and evolutionary theory (especially in ‘appreciative theorizing’). Taken together, we argue that Evolutionary Economic Geography is an emerging paradigm in economic geography, yet does so without isolating itself from developments in other theoretical approaches.", url = "https://doi.org/10.1093/jeg/lbi022", doi = "10.1093/jeg/lbi022", openalex = "W2130277684", references = "doi101002sici10970266199708187509aidsmj88230co2z, doi101007s001910050089, doi101017cbo9780511808678, doi101017cbo9780511815478, doi101086228311, doi101093iccdth026, doi101093oxfordjournalscjea013725, doi101103revmodphys7447, doi101111j146802971997tb00064x, doi101126science2865439509, doi1015159780691206820, doi1023071060065, doi1023071884852, doi1023072232409, doi105860choice416654, openalexw2061901927" } @article{doi101111j13652745200601150x, author = "Leimu, Roosa and Mutikäinen, Pia and Koricheva, Julia and Fischer, Markus", title = "How general are positive relationships between plant population size, fitness and genetic variation?", year = "2006", journal = "Journal of Ecology", abstract = "Summary Relationships between plant population size, fitness and within‐population genetic diversity are fundamental for plant ecology, evolution and conservation. We conducted meta‐analyses of studies published between 1987 and 2005 to test whether these relationships are generally positive, whether they are sensitive to methodological differences among studies, whether they differ between species of different life span, mating system or rarity and whether they depend on the size ranges of the studied populations. Mean correlations between population size, fitness and genetic variation were all significantly positive. The positive correlation between population size and female fitness tended to be stronger in field studies than in common garden studies, and the positive correlation between genetic variation and fitness was significantly stronger in DNA than in isoenzyme studies. The strength and direction of correlations between population size, fitness and genetic variation were independent of plant life span and the size range of the studied populations. The mean correlations tended to be stronger for the rare species than for common species. Expected heterozygosity, the number of alleles and the number or proportion of polymorphic loci significantly increased with population size, but the level of inbreeding F IS was independent of population size. The positive relationship between population size and the number of alleles and the number or proportion of polymorphic loci was stronger in self‐incompatible than in self‐compatible species. Furthermore, fitness and genetic variation were positively correlated in self‐incompatible species, but independent of each other in self‐compatible species. The close relationships between population size, genetic variation and fitness suggest that population size should always be taken into account in multipopulation studies of plant fitness or genetic variation. The observed generality of the positive relationships between population size, plant fitness and genetic diversity implies that the negative effects of habitat fragmentation on plant fitness and genetic variation are common. Moreover, the stronger positive associations observed in self‐incompatible species and to some degree in rare species, suggest that these species are most prone to the negative effects of habitat fragmentation.", url = "https://doi.org/10.1111/j.1365-2745.2006.01150.x", doi = "10.1111/j.1365-2745.2006.01150.x", openalex = "W2041902086", references = "doi101146annureves10110179001133" } @article{doi101111j1365294x200602890x, author = "Waples, Robin S. and Gaggiotti, Oscar E.", title = "INVITED REVIEW: What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity", year = "2006", journal = "Molecular Ecology", abstract = "We review commonly used population definitions under both the ecological paradigm (which emphasizes demographic cohesion) and the evolutionary paradigm (which emphasizes reproductive cohesion) and find that none are truly operational. We suggest several quantitative criteria that might be used to determine when groups of individuals are different enough to be considered 'populations'. Units for these criteria are migration rate (m) for the ecological paradigm and migrants per generation (Nm) for the evolutionary paradigm. These criteria are then evaluated by applying analytical methods to simulated genetic data for a finite island model. Under the standard parameter set that includes L = 20 High mutation (microsatellite-like) loci and samples of S = 50 individuals from each of n = 4 subpopulations, power to detect departures from panmixia was very high (approximately 100\%; P < 0.001) even with high gene flow (Nm = 25). A new method, comparing the number of correct population assignments with the random expectation, performed as well as a multilocus contingency test and warrants further consideration. Use of Low mutation (allozyme-like) markers reduced power more than did halving S or L. Under the standard parameter set, power to detect restricted gene flow below a certain level X (H(0): Nm < X) can also be high, provided that true Nm < or = 0.5X. Developing the appropriate test criterion, however, requires assumptions about several key parameters that are difficult to estimate in most natural populations. Methods that cluster individuals without using a priori sampling information detected the true number of populations only under conditions of moderate or low gene flow (Nm < or = 5), and power dropped sharply with smaller samples of loci and individuals. A simple algorithm based on a multilocus contingency test of allele frequencies in pairs of samples has high power to detect the true number of populations even with Nm = 25 but requires more rigorous statistical evaluation. The ecological paradigm remains challenging for evaluations using genetic markers, because the transition from demographic dependence to independence occurs in a region of high migration where genetic methods have relatively little power. Some recent theoretical developments and continued advances in computational power provide hope that this situation may change in the future.", url = "https://doi.org/10.1111/j.1365-294x.2006.02890.x", doi = "10.1111/j.1365-294x.2006.02890.x", openalex = "W2172086791", references = "doi101046j1365294x200402008x, doi101093jheredesh074, doi101111j146918091975tb00129x, doi105281zenodo10742832, openalexw1495050269" } @article{doi101111j13652958200605172x, author = "Wirth, Thierry and Falush, Daniel and Lan, Ruiting and Colles, Frances M. and Mensa, Patience and Wieler, Lothar H. and Karch, Helge and Reeves, Peter R. and Maiden, Martin and Ochman, Howard and Achtman, Mark", title = "Sex and virulence in Escherichia coli: an evolutionary perspective", year = "2006", journal = "Molecular Microbiology", abstract = "Pathogenic Escherichia coli cause over 160 million cases of dysentery and one million deaths per year, whereas non-pathogenic E. coli constitute part of the normal intestinal flora of healthy mammals and birds. The evolutionary pathways underlying this dichotomy in bacterial lifestyle were investigated by multilocus sequence typing of a global collection of isolates. Specific pathogen types [enterohaemorrhagic E. coli, enteropathogenic E. coli, enteroinvasive E. coli, K1 and Shigella] have arisen independently and repeatedly in several lineages, whereas other lineages contain only few pathogens. Rates of evolution have accelerated in pathogenic lineages, culminating in highly virulent organisms whose genomic contents are altered frequently by increased rates of homologous recombination; thus, the evolution of virulence is linked to bacterial sex. This long-term pattern of evolution was observed in genes distributed throughout the genome, and thereby is the likely result of episodic selection for strains that can escape the host immune response.", url = "https://doi.org/10.1111/j.1365-2958.2006.05172.x", doi = "10.1111/j.1365-2958.2006.05172.x", openalex = "W2161060487", references = "doi101007bf02111283, doi10103842701, doi101093bioinformatics183502, doi101111j1365294x200502553x" } @article{doi101146annurevecolsys37091305110215, author = "Petit, Rémy J. and Hampe, Arndt", title = "Some Evolutionary Consequences of Being a Tree", year = "2006", journal = "Annual Review of Ecology Evolution and Systematics", abstract = "Trees do not form a natural group but share attributes such as great size, longevity, and high reproductive output that affect their mode and tempo of evolution. In particular, trees are unique in that they maintain high levels of diversity while accumulating new mutations only slowly. They are also capable of rapid local adaptation and can evolve quickly from nontree ancestors, but most existing tree lineages typically experience low speciation and extinction rates. We discuss why the tree growth habit should lead to these seemingly paradoxical features.", url = "https://doi.org/10.1146/annurev.ecolsys.37.091305.110215", doi = "10.1146/annurev.ecolsys.37.091305.110215", openalex = "W2102352162", references = "doi101111j001438202001tb00826x, doi101111j14610248200500739x, doi101126science1061967, doi101146annurevecolsys271237, doi101146annureves10110179001133, doi101146annureves15110184000433, doi107208chicago97802261186970010001, openalexw2065039187, openalexw2145250129, openalexw2146778590" } @article{doi101038nrg2063, author = "Wray, Gregory A.", title = "The evolutionary significance of cis-regulatory mutations", year = "2007", journal = "Nature Reviews Genetics", url = "https://doi.org/10.1038/nrg2063", doi = "10.1038/nrg2063", openalex = "W2012354488", references = "doi101016s0022283661800727, doi10103835046017, doi101038nature02415, doi101038ng1946, doi101038sjmp4001851, doi101056nejm197608052950602, doi101073pnas0431157100, doi101073pnas9794530, doi101086406830, doi101086421051, doi101093genetics15141531, doi101093molbevmsg140, doi101111j001438202000tb00544x, doi101126science1071829, doi101126science1072290, doi101126science1090005" } @article{doi101093icbicm025, author = "Young, Rebecca L. and Badyaev, Alexander V.", title = "Evolution of ontogeny: linking epigenetic remodeling and genetic adaptation in skeletal structures", year = "2007", journal = "Integrative and Comparative Biology", abstract = "Evolutionary diversifications are commonly attributed to the continued modifications of a conserved genetic toolkit of developmental pathways, such that complexity and convergence in organismal forms are assumed to be due to similarity in genetic mechanisms or environmental conditions. This approach, however, confounds the causes of organismal development with the causes of organismal differences and, as such, has only limited utility for addressing the cause of evolutionary change. Molecular mechanisms that are closely involved in both developmental response to environmental signals and major evolutionary innovations and diversifications are uniquely suited to bridge this gap by connecting explicitly the causes of within-generation variation with the causes of divergence of taxa. Developmental pathways of bone formation and a common role for bone morphogenetic proteins (BMPs) in both epigenetic bone remodeling and the evolution of major adaptive diversifications provide such opportunity. We show that variation in timing of ossification can result in similar phenotypic patterns through epigenetically induced changes in gene expression and propose that both genetic accommodation of environmentally induced developmental pathways and flexibility in development across environments evolve through heterochronic shifts in bone maturation relative to exposure to unpredictable environments. We suggest that such heterochronic shifts in ossification can not only buffer development under fluctuating environments while maintaining epigenetic sensitivity critical for normal skeletal formation, but also enable epigenetically induced gene expression to generate specialized morphological adaptations. We review studies of environmental sensitivity of BMP pathways and their regulation of formation, remodeling, and repair of cartilage and bone to examine the hypothesis that BMP-mediated skeletal adaptations are facilitated by evolved reactivity of BMPs to external signals. Surprisingly, no empirical study to date has identified the molecular mechanism behind developmental plasticity in skeletal traits. We outline a conceptual framework for future studies that focus on mediation of phenotypic plasticity in skeletal development by the patterns of BMP expression.", url = "https://doi.org/10.1093/icb/icm025", doi = "10.1093/icb/icm025", openalex = "W2129912251", references = "doi101046j14209101200200455x" } @article{doi101111j15585646200700105x, author = "Hoekstra, Hopi E. and Coyne, Jerry A.", title = "THE LOCUS OF EVOLUTION: EVO DEVO AND THE GENETICS OF ADAPTATION", year = "2007", journal = "Evolution", abstract = {An important tenet of evolutionary developmental biology ("evo devo") is that adaptive mutations affecting morphology are more likely to occur in the cis-regulatory regions than in the protein-coding regions of genes. This argument rests on two claims: (1) the modular nature of cis-regulatory elements largely frees them from deleterious pleiotropic effects, and (2) a growing body of empirical evidence appears to support the predominant role of gene regulatory change in adaptation, especially morphological adaptation. Here we discuss and critique these assertions. We first show that there is no theoretical or empirical basis for the evo devo contention that adaptations involving morphology evolve by genetic mechanisms different from those involving physiology and other traits. In addition, some forms of protein evolution can avoid the negative consequences of pleiotropy, most notably via gene duplication. In light of evo devo claims, we then examine the substantial data on the genetic basis of adaptation from both genome-wide surveys and single-locus studies. Genomic studies lend little support to the cis-regulatory theory: many of these have detected adaptation in protein-coding regions, including transcription factors, whereas few have examined regulatory regions. Turning to single-locus studies, we note that the most widely cited examples of adaptive cis-regulatory mutations focus on trait loss rather than gain, and none have yet pinpointed an evolved regulatory site. In contrast, there are many studies that have both identified structural mutations and functionally verified their contribution to adaptation and speciation. Neither the theoretical arguments nor the data from nature, then, support the claim for a predominance of cis-regulatory mutations in evolution. Although this claim may be true, it is at best premature. Adaptation and speciation probably proceed through a combination of cis-regulatory and structural mutations, with a substantial contribution of the latter.}, url = "https://doi.org/10.1111/j.1558-5646.2007.00105.x", doi = "10.1111/j.1558-5646.2007.00105.x", openalex = "W2101103652", references = "doi1010079783642866593, doi101016s0022283661800727, doi101017s0094837300005224, doi101038366223a0, doi10103847412, doi101038nature04843, doi101038nrg2063, doi101038scientificamerican117998, doi101038sjhdy6800154, doi101073pnas0431157100, doi101073pnas7183028, doi101073pnas9794530, doi101093molbevmsg140, doi101111j001438202000tb00544x, doi101111j001438202004tb00462x, doi101126science1090005, doi101126science1098095, doi101126science1113832, doi101126science29054941151, doi101126science860134, doi101146annurevphysiol631359, doi101371journalpbio0030245, doi105860choice395182, doi105962bhltitle27468, openalexw3135630760" } @article{doi101111j15585646200700246x, author = "Pigliucci, Massimo", title = "DO WE NEED AN EXTENDED EVOLUTIONARY SYNTHESIS?", year = "2007", journal = "Evolution", abstract = "The Modern Synthesis (MS) is the current paradigm in evolutionary biology. It was actually built by expanding on the conceptual foundations laid out by its predecessors, Darwinism and neo-Darwinism. For sometime now there has been talk of a new Extended Evolutionary Synthesis (EES), and this article begins to outline why we may need such an extension, and how it may come about. As philosopher Karl Popper has noticed, the current evolutionary theory is a theory of genes, and we still lack a theory of forms. The field began, in fact, as a theory of forms in Darwin's days, and the major goal that an EES will aim for is a unification of our theories of genes and of forms. This may be achieved through an organic grafting of novel concepts onto the foundational structure of the MS, particularly evolvability, phenotypic plasticity, epigenetic inheritance, complexity theory, and the theory of evolution in highly dimensional adaptive landscapes.", url = "https://doi.org/10.1111/j.1558-5646.2007.00246.x", doi = "10.1111/j.1558-5646.2007.00246.x", openalex = "W2114930668", references = "doi1010021097010x200012152884304aidjez330co2g, doi101002jezb21081, doi101017cbo9780511701559, doi101046j14209101200200455x" } @article{turner2007the, author = "Turner, Thomas F.", title = "The Evolution of Evolutionary Genetics", year = "2007", journal = "BioScience", url = "https://doi.org/10.1641/b570413", doi = "10.1641/b570413", number = "4", pages = "375-376", volume = "57" } @article{doi101016jcell200806030, author = "Carroll, Sean B.", title = "Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution", year = "2008", journal = "Cell", url = "https://doi.org/10.1016/j.cell.2008.06.030", doi = "10.1016/j.cell.2008.06.030", openalex = "W2171193618", references = "doi1010079783642866593, doi101016b9781483227344500176, doi101038276565a0, doi101038376479a0, doi10103841710, doi101038nature02415, doi101038nature03158, doi101038nrg2063, doi101086406830, doi101111j001438202000tb00544x, doi101111j15585646200700105x, doi101126science1090005, doi101126science1107239, doi101126science147365368, doi101126science7892602, doi101242dev1212333, doi101371journalpbio0030245, doi105860choice395182, openalexw591049712, openalexw614012683" } @article{doi101038nrg2323, author = "Duffy, Siobain and Shackelton, Laura A. and Holmes, Edward C.", title = "Rates of evolutionary change in viruses: patterns and determinants", year = "2008", journal = "Nature Reviews Genetics", url = "https://doi.org/10.1038/nrg2323", doi = "10.1038/nrg2323", openalex = "W2020939898", references = "doi1010021521187820001222121057aidbies330co2w, doi101016s0169534703002167, doi101038nrg2146, doi101371journalpbio0040088" } @article{doi101038nrg2398, author = "López‐Maury, Luis and Marguerat, Samuel and Bähler, Jürg", title = "Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation", year = "2008", journal = "Nature Reviews Genetics", url = "https://doi.org/10.1038/nrg2398", doi = "10.1038/nrg2398", openalex = "W2028979517", references = "doi101038nrg1088, doi101038nrg2063" } @article{doi101038nrg2452, author = "Phillips, Patrick C.", title = "Epistasis — the essential role of gene interactions in the structure and evolution of genetic systems", year = "2008", journal = "Nature Reviews Genetics", url = "https://doi.org/10.1038/nrg2452", doi = "10.1038/nrg2452", openalex = "W2094189284", references = "doi1010160020711x94901198, doi101017s0080456800012163, doi101038091009b0, doi101038nature05874, doi101038nature05911, doi101038ng1537, doi101073pnas0702207104, doi101093hmg11202463, doi101111j001438202003tb00377x, doi101126science1065810, doi101126science1091317, doi101126science1123348, doi101126science1123539, doi101126science860134, doi101159000073735, doi105962bhltitle27468, doi105962bhltitle44575, openalexw1554403518" } @article{doi101086523357, author = "Silvertown, Jonathan", title = "The Evolutionary Maintenance of Sexual Reproduction: Evidence from the Ecological Distribution of Asexual Reproduction in Clonal Plants", year = "2008", journal = "International Journal of Plant Sciences", abstract = "In theory, females that reproduce asexually should enjoy a twofold advantage in fitness over sexual females, yet sex remains the predominant mode of reproduction in virtually all eukaryotes. The evolutionary maintenance of sex is especially puzzling in clonal plants because the transition from sexual to exclusively asexual reproduction is an ever‐present possibility in these species. In this article, I use published data on the genotypic diversity of populations of clonal plants to test five hypotheses about the ecological situations that limit or favor clonal reproduction in vascular plants. The data were drawn from 248 studies covering 69,000 individuals in >2000 populations of 218 species in 74 plant families. The tests showed the following: (1) the frequency of clonality increases with population age, indicating that clonal reproduction is limited by disturbance; (2) clonal reproduction is limited by dispersal; clones are more frequent in aquatic and apomictic species in which the dispersal of clonally produced propagules is less limiting; (3) clones are more frequent in populations of rare or endangered species; (4) populations of alien plants have higher frequencies of clonality; and (5) clones are more frequent at the edges of species’ geographical ranges. Thus, it appears that the ultimately successful clonal plant would be a rare, aquatic, alien apomict living in an undisturbed, geographically marginal habitat. Since this combination of circumstances is so restrictive, it is perhaps better regarded as a sign of sexual failure than as a recipe for clonal success.", url = "https://doi.org/10.1086/523357", doi = "10.1086/523357", openalex = "W2127863127", references = "doi1010160304377093900688" } @article{doi101111j1365294x200803971x, author = "Aguilar, Ramiro and Quesada, Maurício and Ashworth, Lorena and Herrerías‐Diego, Yvonne and Lobo, Jorge A.", title = "Genetic consequences of habitat fragmentation in plant populations: susceptible signals in plant traits and methodological approaches", year = "2008", journal = "Molecular Ecology", abstract = "Conservation of genetic diversity, one of the three main forms of biodiversity, is a fundamental concern in conservation biology as it provides the raw material for evolutionary change and thus the potential to adapt to changing environments. By means of meta-analyses, we tested the generality of the hypotheses that habitat fragmentation affects genetic diversity of plant populations and that certain life history and ecological traits of plants can determine differential susceptibility to genetic erosion in fragmented habitats. Additionally, we assessed whether certain methodological approaches used by authors influence the ability to detect fragmentation effects on plant genetic diversity. We found overall large and negative effects of fragmentation on genetic diversity and outcrossing rates but no effects on inbreeding coefficients. Significant increases in inbreeding coefficient in fragmented habitats were only observed in studies analyzing progenies. The mating system and the rarity status of plants explained the highest proportion of variation in the effect sizes among species. The age of the fragment was also decisive in explaining variability among effect sizes: the larger the number of generations elapsed in fragmentation conditions, the larger the negative magnitude of effect sizes on heterozygosity. Our results also suggest that fragmentation is shifting mating patterns towards increased selfing. We conclude that current conservation efforts in fragmented habitats should be focused on common or recently rare species and mainly outcrossing species and outline important issues that need to be addressed in future research on this area.", url = "https://doi.org/10.1111/j.1365-294x.2008.03971.x", doi = "10.1111/j.1365-294x.2008.03971.x", openalex = "W2143144439", references = "doi101126science8290956, doi101146annureves15110184000433" } @article{doi101111j15585646200800450x, author = "Stern, David L. and Courtier‐Orgogozo, Virginie", title = "THE LOCI OF EVOLUTION: HOW PREDICTABLE IS GENETIC EVOLUTION?", year = "2008", journal = "Evolution", abstract = {Is genetic evolution predictable? Evolutionary developmental biologists have argued that, at least for morphological traits, the answer is a resounding yes. Most mutations causing morphological variation are expected to reside in the cis-regulatory, rather than the coding, regions of developmental genes. This "cis-regulatory hypothesis" has recently come under attack. In this review, we first describe and critique the arguments that have been proposed in support of the cis-regulatory hypothesis. We then test the empirical support for the cis-regulatory hypothesis with a comprehensive survey of mutations responsible for phenotypic evolution in multicellular organisms. Cis-regulatory mutations currently represent approximately 22\% of 331 identified genetic changes although the number of cis-regulatory changes published annually is rapidly increasing. Above the species level, cis-regulatory mutations altering morphology are more common than coding changes. Also, above the species level cis-regulatory mutations predominate for genes not involved in terminal differentiation. These patterns imply that the simple question "Do coding or cis-regulatory mutations cause more phenotypic evolution?" hides more interesting phenomena. Evolution in different kinds of populations and over different durations may result in selection of different kinds of mutations. Predicting the genetic basis of evolution requires a comprehensive synthesis of molecular developmental biology and population genetics.}, url = "https://doi.org/10.1111/j.1558-5646.2008.00450.x", doi = "10.1111/j.1558-5646.2008.00450.x", openalex = "W2094005099", references = "doi101006dbio19960034, doi1010079783642866593, doi101016jibmb200403018, doi101038376479a0, doi101038nature05874, doi101073pnas9794530, doi101093genetics15141531, doi101093genetics16297, doi101098rspb19790086, doi101111j001438202000tb00002x, doi101126science1098095, doi101126science1113832, doi101126science29054941151, doi1023072529912, doi104159harvard9780674865327, doi105962bhltitle27468, doi105962bhltitle46292, doi105962bhltitle59991" } @article{doi101371journalpgen1000304, author = "Kryazhimskiy, Sergey and Plotkin, Joshua B.", title = "The Population Genetics of dN/dS", year = "2008", journal = "PLoS Genetics", abstract = "Evolutionary pressures on proteins are often quantified by the ratio of substitution rates at non-synonymous and synonymous sites. The dN/dS ratio was originally developed for application to distantly diverged sequences, the differences among which represent substitutions that have fixed along independent lineages. Nevertheless, the dN/dS measure is often applied to sequences sampled from a single population, the differences among which represent segregating polymorphisms. Here, we study the expected dN/dS ratio for samples drawn from a single population under selection, and we find that in this context, dN/dS is relatively insensitive to the selection coefficient. Moreover, the hallmark signature of positive selection over divergent lineages, dN/dS>1, is violated within a population. For population samples, the relationship between selection and dN/dS does not follow a monotonic function, and so it may be impossible to infer selection pressures from dN/dS. These results have significant implications for the interpretation of dN/dS measurements among population-genetic samples.", url = "https://doi.org/10.1371/journal.pgen.1000304", doi = "10.1371/journal.pgen.1000304", openalex = "W2045641296", references = "doi101007978940115210512, doi101023a1017067816551, doi101146annureves23110192001403" } @article{doi101057jibs200995, author = "Cantwell, John and Dunning, John H. and Lundan, Sarianna M.", title = "An evolutionary approach to understanding international business activity: The co-evolution of MNEs and the institutional environment", year = "2009", journal = "Journal of International Business Studies", url = "https://doi.org/10.1057/jibs.2009.95", doi = "10.1057/jibs.2009.95", openalex = "W2093229054", references = "doi105860choice416654" } @article{doi101086599084, author = "Otto, Sarah P.", title = "The Evolutionary Enigma of Sex", year = "2009", journal = "The American Naturalist", abstract = "Sexual reproduction entails a number of costs, and yet the majority of eukaryotes engage in sex, at least occasionally. In this article, I review early models to explain the evolution of sex and why they failed to do so. More recent efforts have attempted to account for the complexities of evolution in the real world, with selection that varies over time and space, with differences among individuals in the tendency to reproduce sexually, and with populations that are limited in size. These recent efforts have clarified the conditions that are most likely to explain why sex is so common, as exemplified by the articles in this symposium issue of the American Naturalist.", url = "https://doi.org/10.1086/599084", doi = "10.1086/599084", openalex = "W1995865334", references = "doi101111j001438202002tb00188x" } @article{doi101146annurevbiochem030409143718, author = "Khersonsky, Olga and Tawfik, Dan S.", title = "Enzyme Promiscuity: A Mechanistic and Evolutionary Perspective", year = "2010", journal = "Annual Review of Biochemistry", abstract = "Many, if not most, enzymes can promiscuously catalyze reactions, or act on substrates, other than those for which they evolved. Here, we discuss the structural, mechanistic, and evolutionary implications of this manifestation of infidelity of molecular recognition. We define promiscuity and related phenomena and also address their generality and physiological implications. We discuss the mechanistic enzymology of promiscuity--how enzymes, which generally exert exquisite specificity, catalyze other, and sometimes barely related, reactions. Finally, we address the hypothesis that promiscuous enzymatic activities serve as evolutionary starting points and highlight the unique evolutionary features of promiscuous enzyme functions.", url = "https://doi.org/10.1146/annurev-biochem-030409-143718", doi = "10.1146/annurev-biochem-030409-143718", openalex = "W2128312954", references = "doi1010079783642866593, doi101038nature06879, doi101038nrg2482, doi101073pnas95158420, doi101126science1123348, doi101126science1123539, doi101126science1152692, doi101126science860134, doi101146annurevmi30100176002205, doi105860choice370939, openalexw3086983054, openalexw588942190" } @article{doi101146annurevecolsys110308120258, author = "Vallejo‐Marín, Mario and Dorken, Marcel E. and Barrett, Spencer C. H.", title = "The Ecological and Evolutionary Consequences of Clonality for Plant Mating", year = "2010", journal = "Annual Review of Ecology Evolution and Systematics", abstract = "Many flowering plants exhibit dual reproductive modes, producing both sexual and asexual offspring. The commonest form of asexual reproduction is clonal growth, in which vegetative modules (ramets) are produced by the parental genotype (genet). In plants, sexual and asexual reproduction usually occur simultaneously, and this can lead to allocation trade-offs and antagonism between reproductive modes. Our review considers the ecological and evolutionary consequences of functional interactions between clonal reproduction and pollination and mating. Clonal reproduction is commonly associated with mass flowering, restricted pollen dispersal, and geitonogamous self-pollination, processes that can result in inbreeding depression and pollen discounting. We review evidence for the correlated evolution of clonality and sexual systems, particularly self-incompatibility, and identify several floral mechanisms that function to reduce mating costs by limiting selfing and pollen discounting. We conclude by discussing the loss of sexuality in clonal plants and consider the genetic and environmental basis of sexual dysfunction.", url = "https://doi.org/10.1146/annurev.ecolsys.110308.120258", doi = "10.1146/annurev.ecolsys.110308.120258", openalex = "W1993026968", references = "doi1010160304377093900688" } @incollection{doi107551mitpress82780030003, author = "Pigliucci, Massimo and Müller, Gerd B.", title = "Elements of an Extended Evolutionary Synthesis", year = "2010", booktitle = "The MIT Press eBooks", abstract = "More than half a century has passed since the integration of several strands of evolutionary thought into what came to be called the Modern Synthesis (MS), the conceptual framework that has defi ned evolutionary theory since the 1940s. Despite signifi cant advances since then in all methodological and disciplinary domains of biology, including molecular genetics, developmental biology, and the “-omics” fi elds, the Modern Synthesis framework has remained surprisingly unchanged. Although it is still regarded as the standard theoretical paradigm of evolutionary biology, for several years now dissenters from diverse fi elds of biology have been questioning aspects of the Modern Synthesis, and pivotal novel concepts have been elaborated that extend beyond its original scope (e.g., Maynard Smith and Szathmary 1995; Jablonka and Lamb 1995; Schlichting and Pigliucci 1998; Gould 2002; Muller and Newman 2003; Odling-Smee et al. 2003; West-Eberhard 2003; Kirschner and Gerhart 2005). As a result, calls for an expansion of the Modern Synthesis framework have intensifi ed (R. L. Carroll 2000; Love 2003a; Kutschera and Niklas 2004; Muller 2007; Pigliucci 2007; Rose and Oakley 2007; S. B. Carroll 2008), prompting further scientifi c debate (Pennisi 2008; Whitfi eld 2008). Under the heading “Extended Synthesis” this volume represents a broad survey of key ideas in this multifaceted research program, and a fi rst look at an expanded theory of evolution as a work-in-progress. We have gathered some of the most prominent authors who have been writing about new directions in evolutionary biology and asked them to explain where they think the fi eld is headed, and how the new concepts square with the Modern Synthesis’s view of what evolution is. Some of these authors are skeptical that any fundamental changes are discernible in the current positions, while others lean toward major revisions of the MS. Most contributors fall somewhere in between, accepting many of", url = "https://doi.org/10.7551/mitpress/8278.003.0003", doi = "10.7551/mitpress/8278.003.0003", openalex = "W2461851698", references = "doi101046j14209101200200455x" } @article{doi101038ng1034, author = "Toprak, Erdal and Veres, Adrian and Michel, Jean-Baptiste and Chait, Remy and Hartl, Daniel L. and Kishony, Roy", title = "Evolutionary paths to antibiotic resistance under dynamically sustained drug selection", year = "2011", journal = "Nature Genetics", url = "https://doi.org/10.1038/ng.1034", doi = "10.1038/ng.1034", openalex = "W2012977051", references = "doi101126science1123539" } @article{doi101098rspb20110971, author = "Moczek, Armin P. and Sultan, Sonia E. and Foster, Susan A. and Ledón-Rettig, Cris C. and Dworkin, Ian and Nijhout, H. Fred and Abouheif, Ehab and Pfennig, David W.", title = "The role of developmental plasticity in evolutionary innovation", year = "2011", journal = "Proceedings of the Royal Society B Biological Sciences", abstract = "Explaining the origins of novel traits is central to evolutionary biology. Longstanding theory suggests that developmental plasticity, the ability of an individual to modify its development in response to environmental conditions, might facilitate the evolution of novel traits. Yet whether and how such developmental flexibility promotes innovations that persist over evolutionary time remains unclear. Here, we examine three distinct ways by which developmental plasticity can promote evolutionary innovation. First, we show how the process of genetic accommodation provides a feasible and possibly common avenue by which environmentally induced phenotypes can become subject to heritable modification. Second, we posit that the developmental underpinnings of plasticity increase the degrees of freedom by which environmental and genetic factors influence ontogeny, thereby diversifying targets for evolutionary processes to act on and increasing opportunities for the construction of novel, functional and potentially adaptive phenotypes. Finally, we examine the developmental genetic architectures of environment-dependent trait expression, and highlight their specific implications for the evolutionary origin of novel traits. We critically review the empirical evidence supporting each of these processes, and propose future experiments and tests that would further illuminate the interplay between environmental factors, condition-dependent development, and the initiation and elaboration of novel phenotypes.", url = "https://doi.org/10.1098/rspb.2011.0971", doi = "10.1098/rspb.2011.0971", openalex = "W2142774476", references = "doi101038sjhdy6800154, doi101098rstb20090263, doi101111j001438202003tb00377x, doi1023072411226" } @article{salverda2011evolutionary, author = "Salverda, Merijn L.M. and de Visser, J. Arjan G.M.", title = "Evolutionary Genetics: Evolution with Foresight", year = "2011", journal = "Current Biology", url = "https://doi.org/10.1016/j.cub.2011.04.023", doi = "10.1016/j.cub.2011.04.023", number = "10", pages = "R398-R400", volume = "21" } @article{doi103390insects3010339, author = "Six, Diana L.", title = "Ecological and Evolutionary Determinants of Bark Beetle —Fungus Symbioses", year = "2012", journal = "Insects", abstract = "Ectosymbioses among bark beetles (Curculionidae, Scolytinae) and fungi (primarily ophiostomatoid Ascomycetes) are widespread and diverse. Associations range from mutualistic to commensal, and from facultative to obligate. Some fungi are highly specific and associated only with a single beetle species, while others can be associated with many. In addition, most of these symbioses are multipartite, with the host beetle associated with two or more consistent partners. Mycangia, structures of the beetle integument that function in fungal transport, have evolved numerous times in the Scolytinae. The evolution of such complex, specialized structures indicates a high degree of mutual dependence among the beetles and their fungal partners. Unfortunately, the processes that shaped current day beetle-fungus symbioses remain poorly understood. Phylogeny, the degree and type of dependence on partners, mode of transmission of symbionts (vertical vs. horizontal), effects of the abiotic environment, and interactions among symbionts themselves or with other members of the biotic community, all play important roles in determining the composition, fidelity, and longevity of associations between beetles and their fungal associates. In this review, I provide an overview of these associations and discuss how evolution and ecological processes acted in concert to shape these fascinating, complex symbioses.", url = "https://doi.org/10.3390/insects3010339", doi = "10.3390/insects3010339", openalex = "W1982731458", references = "doi101093oso97801951315430010001" } @article{doi101038nrg3483, author = "Stern, David L.", title = "The genetic causes of convergent evolution", year = "2013", journal = "Nature Reviews Genetics", url = "https://doi.org/10.1038/nrg3483", doi = "10.1038/nrg3483", openalex = "W2046793790", references = "doi101016jcell200806030, doi101016jtree200709008, doi101038287795a0, doi101038nature10944, doi101038nature11041, doi101038ng1946, doi101038nrg2452, doi101073pnas9794530, doi101093acref97801995711230010001, doi101105tpc115949, doi101111j001438202000tb00544x, doi101111j15585646200800450x, doi101111j15585646201101289x, doi101126science1113832, doi101126science1123539, doi101126science1188021, doi101126science1208227, doi101146annurevento451371, openalexw2080618944" } @article{doi101098rspb20122863, author = "Clune, Jeff and Mouret, Jean-Baptiste and Lipson, Hod", title = "The evolutionary origins of modularity", year = "2013", journal = "Proceedings of the Royal Society B Biological Sciences", abstract = "A central biological question is how natural organisms are so evolvable (capable of quickly adapting to new environments). A key driver of evolvability is the widespread modularity of biological networks--their organization as functional, sparsely connected subunits--but there is no consensus regarding why modularity itself evolved. Although most hypotheses assume indirect selection for evolvability, here we demonstrate that the ubiquitous, direct selection pressure to reduce the cost of connections between network nodes causes the emergence of modular networks. Computational evolution experiments with selection pressures to maximize network performance and minimize connection costs yield networks that are significantly more modular and more evolvable than control experiments that only select for performance. These results will catalyse research in numerous disciplines, such as neuroscience and genetics, and enhance our ability to harness evolution for engineering purposes.", url = "https://doi.org/10.1098/rspb.2012.2863", doi = "10.1098/rspb.2012.2863", openalex = "W2097351860", references = "doi101038nature01568, doi101038nrg2278" } @article{doi101111evo12134, author = "Wang, Ian", title = "EXAMINING THE FULL EFFECTS OF LANDSCAPE HETEROGENEITY ON SPATIAL GENETIC VARIATION: A MULTIPLE MATRIX REGRESSION APPROACH FOR QUANTIFYING GEOGRAPHIC AND ECOLOGICAL ISOLATION", year = "2013", journal = "Evolution", abstract = "Understanding the effects of landscape heterogeneity on spatial genetic variation is a primary goal of landscape genetics. Ecological and geographic variables can contribute to genetic structure through geographic isolation, in which geographic barriers and distances restrict gene flow, and ecological isolation, in which gene flow among populations inhabiting different environments is limited by selection against dispersers moving between them. Although methods have been developed to study geographic isolation in detail, ecological isolation has received much less attention, partly because disentangling the effects of these mechanisms is inherently difficult. Here, I describe a novel approach for quantifying the effects of geographic and ecological isolation using multiple matrix regression with randomization. I explored the parameter space over which this method is effective using a series of individual-based simulations and found that it accurately describes the effects of geographic and ecological isolation over a wide range of conditions. I also applied this method to a set of real-world datasets to show that ecological isolation is an often overlooked but important contributor to patterns of spatial genetic variation and to demonstrate how this analysis can provide new insights into how landscapes contribute to the evolution of genetic variation in nature.", url = "https://doi.org/10.1111/evo.12134", doi = "10.1111/evo.12134", openalex = "W1976017021", references = "doi101093aesa304641, doi101146annurevecolsys102209144644" } @article{doi101111nyas12974, author = "Kinnison, Michael T. and Hairston, Nelson G. and Hendry, Andrew P.", title = "Cryptic eco‐evolutionary dynamics", year = "2015", journal = "Annals of the New York Academy of Sciences", abstract = "Natural systems harbor complex interactions that are fundamental parts of ecology and evolution. These interactions challenge our inclinations and training to seek the simplest explanations of patterns in nature. Not least is the likelihood that some complex processes might be missed when their patterns look similar to predictions for simpler mechanisms. Along these lines, theory and empirical evidence increasingly suggest that environmental, ecological, phenotypic, and genetic processes can be tightly intertwined, resulting in complex and sometimes surprising eco‐evolutionary dynamics. The goal of this review is to temper inclinations to unquestioningly seek the simplest explanations in ecology and evolution, by recognizing that some eco‐evolutionary outcomes may appear very similar to purely ecological, purely evolutionary, or even null expectations, and thus be cryptic. We provide theoretical and empirical evidence for observational biases and mechanisms that might operate among the various links in eco‐evolutionary feedbacks to produce cryptic patterns. Recognition that cryptic dynamics can be associated with outcomes like stability, resilience, recovery, or coexistence in a dynamically changing world provides added impetus for finding ways to study them.", url = "https://doi.org/10.1111/nyas.12974", doi = "10.1111/nyas.12974", openalex = "W2173108007", references = "doi101093oso97801951315430010001" } @article{doi101038nrg2016104, author = "Lynch, Michael and Ackerman, Matthew S. and Goût, Jean-François and Long, Hongan and Sung, Way and Thomas, W. Kelley and Foster, Patricia L.", title = "Genetic drift, selection and the evolution of the mutation rate", year = "2016", journal = "Nature Reviews Genetics", url = "https://doi.org/10.1038/nrg.2016.104", doi = "10.1038/nrg.2016.104", openalex = "W2529873061", references = "doi1010021521187820001222121057aidbies330co2w, doi101016jtig201005003, doi101038nrg2146, doi101073pnas0404656101" } @book{doi1015159780691185507, author = "Williams, George C.", title = "Adaptation and Natural Selection: A Critique of Some Current Evolutionary Thought", year = "2018", abstract = "Biological evolution is a fact-but the many conflicting theories of evolution remain controversial even today. When Adaptation and Natural Selection was first published in 1966, it struck a powerful blow against those who argued for the concept of group selection-the idea that evolution acts to select entire species rather than individuals. Williams's famous work in favor of simple Darwinism over group selection has become a classic of science literature, valued for its thorough and convincing argument and its relevance to many fields outside of biology. Now with a new foreword by Richard Dawkins, Adaptation and Natural Selection is an essential text for understanding the nature of scientific debate", url = "https://doi.org/10.1515/9780691185507", doi = "10.1515/9780691185507", openalex = "W1480083809" } @article{doi101162artla00319, author = "Lehman, Joel and Clune, Jeff and Misevic, Dusan and Adami, Christoph and Altenberg, Lee and Beaulieu, Julie and Bentley, Peter J. and BERNARD, S and Beslon, Guillaume and Bryson, David M. and Cheney, Nick and Chrabąszcz, Patryk and Cully, Antoine and Doncieux, Stéphane and Dyer, Fred C. and Ellefsen, Kai Olav and Feldt, Robert and Fischer, Stephan and Forrest, Stephanie and Frénoy, Antoine and Gagné, Christian and Goff, Léni Le and Grabowski, Laura M. and Hodjat, Babak and Hutter, Frank and Keller, Laurent and Knibbe, Carole and Krčah, Peter and Lenski, Richard E. and Lipson, Hod and MacCurdy, Robert and Maestre, Carlos and Miikkulainen, Risto and Mitri, Sara and Moriarty, David E. and Mouret, Jean-Baptiste and Nguyen, Anh and Ofria, Charles and Parizeau, Marc and Parsons, David and Pennock, Robert T. and Punch, William F. and Ray, Thomas S. and Schoenauer, Marc and Schulte, Eric and Sims, Karl and Stanley, Kenneth O. and Taddei, François and Tarapore, Danesh and Thibault, Simon and Watson, Richard A. and Weimer, Westley and Yosinski, Jason", title = "The Surprising Creativity of Digital Evolution: A Collection of Anecdotes from the Evolutionary Computation and Artificial Life Research Communities", year = "2020", journal = "Artificial Life", abstract = "process that transcends the substrate in which it occurs. Indeed, many researchers in the field of digital evolution can provide examples of how their evolving algorithms and organisms have creatively subverted their expectations or intentions, exposed unrecognized bugs in their code, produced unexpectedly adaptations, or engaged in behaviors and outcomes, uncannily convergent with ones found in nature. Such stories routinely reveal surprise and creativity by evolution in these digital worlds, but they rarely fit into the standard scientific narrative. Instead they are often treated as mere obstacles to be overcome, rather than results that warrant study in their own right. Bugs are fixed, experiments are refocused, and one-off surprises are collapsed into a single data point. The stories themselves are traded among researchers through oral tradition, but that mode of information transmission is inefficient and prone to error and outright loss. Moreover, the fact that these stories tend to be shared only among practitioners means that many natural scientists do not realize how interesting and lifelike digital organisms are and how natural their evolution can be. To our knowledge, no collection of such anecdotes has been published before. This article is the crowd-sourced product of researchers in the fields of artificial life and evolutionary computation who have provided first-hand accounts of such cases. It thus serves as a written, fact-checked collection of scientifically important and even entertaining stories. In doing so we also present here substantial evidence that the existence and importance of evolutionary surprises extends beyond the natural world, and may indeed be a universal property of all complex evolving systems.", url = "https://doi.org/10.1162/artl\_a\_00319", doi = "10.1162/artl\_a\_00319", openalex = "W3015475346", references = "doi101017cbo9780511730191, doi101038nature01151" } @book{doi101016s0070215321x00026, title = "Evolutionary Developmental Biology", year = "2021", booktitle = "Current topics in developmental biology/Current Topics in Developmental Biology", url = "https://doi.org/10.1016/s0070-2153(21)x0002-6", doi = "10.1016/s0070-2153(21)x0002-6", openalex = "W1556619877" } @article{vagyn2021evolution, author = "Vagyn, Yu. V.", title = "Evolution of darwinism. A new evolutionary synthesis: combining evolutionary genetics and development genetics", year = "2021", journal = "Visnik ukrains'kogo tovaristva genetikiv i selekcioneriv", abstract = "The results of the synthesis of evolutionary genetics and developmental genetics are presented, the causes of the crisis of evolutionary genetics and ways to overcome it are explained, and the mechanism of speciation of higher organisms is explained.Keywords: new evolutionary synthesis, evolutionary genetics, genetics of ontogenesis, morphogenetic program, developmental genes.", url = "https://doi.org/10.7124/visnyk.utgis.18.1-2.1356", doi = "10.7124/visnyk.utgis.18.1-2.1356", number = "1-2", openalex = "W3134902110", pages = "70-75", volume = "18", references = "doi105860choice474406, doi105962bhltitle61216, doi107124visnykutgis161904, doi107124visnykutgis1711201" }