@book{doi105962bhltitle166574, author = "of the 100th Meridian (U.S.), Geographical Surveys West and Cope, E. D.", title = "Report upon vertebrate fossils discovered in New Mexico: with descriptions of new species /", year = "1874", booktitle = "Government Printing Office eBooks", abstract = "Cope, paleontologist, from his camp, on Galinas Creek, in the Rio Grande basin, including a description of new species of vertebrate fossils, and of an extensive series of deposits of the Eocene age, indicating the existence", url = "https://doi.org/10.5962/bhl.title.166574", doi = "10.5962/bhl.title.166574", openalex = "W3006670842" } @article{doi101111j155856461949tb00004x, author = "Haldane, J. B. S.", title = "SUGGESTIONS AS TO QUANTITATIVE MEASUREMENT OF RATES OF EVOLUTION", year = "1949", journal = "Evolution", abstract = "Journal Article SUGGESTIONS AS TO QUANTITATIVE MEASUREMENT OF RATES OF EVOLUTION Get access J. B. S. Haldane J. B. S. Haldane Dept. of Biometry University College London Search for other works by this author on: Oxford Academic Google Scholar Evolution, Volume 3, Issue 1, 1 March 1949, Pages 51–56, https://doi.org/10.1111/j.1558-5646.1949.tb00004.x Published: 01 March 1949 Article history Received: 05 November 1948 Published: 01 March 1949", url = "https://doi.org/10.1111/j.1558-5646.1949.tb00004.x", doi = "10.1111/j.1558-5646.1949.tb00004.x", openalex = "W2325035367", references = "doi10100703064746897, doi101007bf02982278, doi101007bf02982279, doi101007bf02982536, doi101093aesa383396, doi101093biomet1634328, doi101093genetics262177, doi101093oxfordjournalsaoba083238, doi101098rspb19480002, openalexw2428846785" } @misc{haldane1949suggestions5, author = "Haldane, J. B. S", title = "Suggestions as to quantitative measurement of rates of evolution", year = "1949", howpublished = "Evolution, v. 3, p. 51-56", note = "talkorigins\_source = {true}; raw\_reference = {Haldane, J. B. S., 1949, Suggestions as to quantitative measurement of rates of evolution: Evolution, v. 3, p. 51-56.}" } @misc{dobzhansky1950evolution2, author = "Dobzhansky, T", title = "Evolution in the Tropics", year = "1950", howpublished = "American Scientist, v. 38, p. 208-221", note = "talkorigins\_source = {true}; raw\_reference = {Dobzhansky, T., 1950, Evolution in the Tropics: American Scientist, v. 38, p. 208-221.}" } @misc{ehrilch1963the3, author = "Ehrilch, P. R. and Holm, R. W", title = "The process of evolution", year = "1963", howpublished = "New York, McGraw-Hill, 347 p", note = "talkorigins\_source = {true}; raw\_reference = {Ehrilch, P. R., and Holm, R. W., 1963, The process of evolution: New York, McGraw-Hill, 347 p.}" } @article{doi101086405916, author = "Patterson, Bryan and Pascual, Rosendo", title = "The Fossil Mammal Fauna of South America", year = "1968", journal = "The Quarterly Review of Biology", abstract = "Of the three southern continents, South America was more isolated during the Tertiary than Africa, less isolated than Australia. Its record of Cenozoic mammalian life is better than that of either. This record suggests that around the beginning of the Cenozoic, South America received a few wait immigrants-marsupials, edentates, ungulates-that reached the continent across a water barrier. The source area was probably Central America, which formed a tropical North American peninsula until near the end of Tertiary time. A few later wait immigrants reached the continent across the water barrier-rodents in the later part of the Eocene, primates then or in the early Oligocene, and procyonids perhaps late in the Miocene. From the descendants of these few immigrants a balanced fauna evolved that was strikingly different in composition from those of other continents. The evolution of the various groups composing it is briefly presented and discussed. At the end of the Tertiary the isolation of the continent ended with the establishment of the Isthmus of Panama. Faunal interchange between North and South America then began and is still going on. Most of the northern participants in the interchange penetrated deeply into South America. The southern participants, advancing into a continent subjected to periodic continental glaciations, were less successful, the majority of them not penetrating beyond the tropical area. Competition and extinction during the faunal interchange went on mainly among the carnivores, the southern marsupials being replaced by the northern placentals. The spectacular extinctions, involving mainly large mammals of both northern and southern ancestry, came at the end of the Pleistocene; the arrival of man was probably a major factor.", url = "https://doi.org/10.1086/405916", doi = "10.1086/405916", openalex = "W2059320655" } @article{doi101111j150239311969tb01258x, author = "Glaessner, Martin F.", title = "TRACE FOSSILS FROM THE PRECAMBRIAN AND BASAL CAMBRIAN", year = "1969", journal = "Lethaia", abstract = "Certain worm-like configurations on rocks are recognized as shrinkage-crack infillings. Some genuine Precambrian trace fossils are briefly described. The early Cambrian contains a richer assemblage, including some distinctive and widespread form genera. The study of early trace fossils leads to conclusions not only on facies, but also on the evolution of behaviour and functional morphology in soft-bodied organisms.", url = "https://doi.org/10.1111/j.1502-3931.1969.tb01258.x", doi = "10.1111/j.1502-3931.1969.tb01258.x", openalex = "W1975727583", references = "doi1010160031018266900113, doi101038scientificamerican036172, doi10108011035896509448903, doi101086626811, doi101111j1469185x1962tb01331x, doi101111j150239311968tb01740x, doi101126science1543750766, doi101130gsab481873, doi101144gsljgs1890046010439, openalexw2170541304, openalexw2586923183" } @article{doi1023071378990, author = "Schlitter, Duane A. and Misonne, Xavier", title = "African and Indo-Australian Muridae: Evolutionary Trends", year = "1973", journal = "Journal of Mammalogy", abstract = "Misonne, X. African and Indo-Australian Muridae: Evolutionary Trends. Musee Royal de L'Afrique Centrale, Tervuren, Belgique. Annales, Serie In-8°, Sciences Zoologiques, 172:1–219 Get access Misonne X.African and Indo-Australian Muridae: Evolutionary Trends. Musee Royal de L'Afrique Centrale, Tervuren, Belgique. Annales, Serie In-8°, Sciences Zoologiques, 172: 1–219, 27 pls., 10 figs, in text, 1969. No price listed. Duane A. Schlitter Duane A. Schlitter Department of Zoology, University of Maryland, College Park, 20742 Search for other works by this author on: Oxford Academic Google Scholar Journal of Mammalogy, Volume 54, Issue 3, 31 August 1973, Pages 795–796, https://doi.org/10.2307/1378990 Published: 31 August 1973", url = "https://doi.org/10.2307/1378990", doi = "10.2307/1378990", openalex = "W2235767591" } @article{openalexw2145250129, author = "Valen, Leigh Van", title = "A NEW EVOLUTIONARY LAW.", year = "1973", journal = "Medical Entomology and Zoology", openalex = "W2145250129" } @article{openalexw2322266803, author = "Gingerich, Philip D.", title = "SIZE VARIABILITY OF THE TEETH IN LIVING MAMMALS AND THE DIAGNOSIS OF CLOSELY RELATED SYMPATRIC FOSSIL SPECIES", year = "1974", journal = "Journal of Paleontology", abstract = "The dentitions of sympatric fossil (or living) mammalian species which share a relatively recent common ancestor often cannot be distinguished by form alone. In such cases, size differences are important in diagnosing the species. Measurements of the length and width of the lower molars and premolars of large samples of 19 species of living mammals demonstrate that M1 is usually the least variable in size, and that P3, P4, and M3 are the most variable. The low variability of M1 is presumably related to the fact that it is the first permanent tooth to form and erupt, and to its central position in the tooth row. Because of its low variability, M1 is the best tooth on which to base size diagnoses of very closely related sympatric fossil species. Examples are given of the diagnosis of two species of the fossil primates Plesiadapis (at Cernay), Pelycodus (at Avenay), and Protoadapis (at Grauves). The ability to distinguish closely related sympatric species is fundamental to reconstructing the phylogenetic history of any group from the fossil record.", openalex = "W2322266803" } @book{crossref1977patterns, title = "Patterns of Evolution as Illustrated by the Fossil Record", year = "1977", booktitle = "Developments in Palaeontology and Stratigraphy", url = "https://doi.org/10.1016/s0920-5446(08)x7012-8", doi = "10.1016/s0920-5446(08)x7012-8", openalex = "W563635432" } @book{gingerich1977patterns4, author = "Gingerich, P. D", title = "Patterns of Evolution in the Mammalian Fossil Record, in Hallam, A., ed., Patterns of Evolution as Illustrated by the Fossil Record", year = "1977", publisher = "Amsterdam, Elsevier, p. 469-500", note = "talkorigins\_source = {true}; raw\_reference = {Gingerich, P. D., 1977, Patterns of Evolution in the Mammalian Fossil Record, in Hallam, A., ed., Patterns of Evolution as Illustrated by the Fossil Record: Amsterdam, Elsevier, p. 469-500.}" } @book{hallam1977patterns6, author = "Hallam, A", title = "Patterns of Evolution as Illustrated by the Fossil Record, 5 of Developments in Palaeontology and Stratigraphy", year = "1977", publisher = "Amsterdam, Elsevier", note = "talkorigins\_source = {true}; raw\_reference = {Hallam, A., 1977, Patterns of Evolution as Illustrated by the Fossil Record, 5 of Developments in Palaeontology and Stratigraphy: Amsterdam, Elsevier.}" } @article{bretsky1978patterns, author = "Bretsky, Sara S.", title = "Patterns of Evolution as Illustrated by the Fossil Record. A. Hallam", year = "1978", journal = "The Quarterly Review of Biology", url = "https://doi.org/10.1086/410816", doi = "10.1086/410816", number = "4", openalex = "W2514820112", pages = "431-432", volume = "53" } @article{simpson1978patterns, author = "SIMPSON, G", title = "Patterns of evolution, as illustrated by the fossil record", year = "1978", journal = "Earth-Science Reviews", url = "https://doi.org/10.1016/0012-8252(78)90014-4", doi = "10.1016/0012-8252(78)90014-4", number = "2", openalex = "W3036197351", pages = "177-178", volume = "14" } @article{cowen1979patterns, author = "Cowen, R.", title = "Patterns of evolution as illustrated by the fossil record", year = "1979", journal = "Palaeogeography, Palaeoclimatology, Palaeoecology", url = "https://doi.org/10.1016/0031-0182(79)90127-5", doi = "10.1016/0031-0182(79)90127-5", openalex = "W2323803959", pages = "323-324", volume = "28" } @article{haugh1979patterns, author = "Haugh, Bruce N.", title = "Patterns of evolution as illustrated by the fossil record", year = "1979", journal = "Precambrian Research", url = "https://doi.org/10.1016/0301-9268(79)90046-9", doi = "10.1016/0301-9268(79)90046-9", number = "1-2", openalex = "W2612078796", pages = "147-148", volume = "8" } @article{doi101017s0094837300003778, author = "Sepkoski, J. John", title = "A factor analytic description of the Phanerozoic marine fossil record", year = "1981", journal = "Paleobiology", abstract = "Data on numbers of marine families within 91 metazoan classes known from the Phanerozoic fossil record are analyzed. The distribution of the 2800 fossil families among the classes is very uneven, with most belonging to a small minority of classes. Similarly, the stratigraphic distribution of the classes is very uneven, with most first appearing early in the Paleozoic and with many of the smaller classes becoming extinct before the end of that era. However, despite this unevenness, a Q -mode factor analysis indicates that the structure of these data is rather simple. Only three factors are needed to account for more than 90\% of the data. These factors are interpreted as reflecting the three great “evolutionary faunas” of the Phanerozoic marine record: a trilobite-dominated Cambrian fauna, a brachiopod-dominated later Paleozoic fauna, and a mollusc-dominated Mesozoic-Cenozoic, or “modern,” fauna. Lesser factors relate to slow taxonomic turnover within the major faunas through time and to unique aspects of particular taxa and times. Each of the three major faunas seems to have its own characteristic diversity so that its expansion or contraction appears as being intimately associated with a particular phase in the history of total marine diversity. The Cambrian fauna expands rapidly during the Early Cambrian radiations and maintains dominance during the Middle to Late Cambrian “equilibrium.” The Paleozoic fauna then ascends to dominance during the Ordovician radiations, which increase diversity dramatically; this new fauna then maintains dominance throughout the long interval of apparent equilibrium that lasts until the end of the Paleozoic Era. The modern fauna, which slowly increases in importance during the Paleozoic Era, quickly rises to dominance with the Late Permian extinctions and maintains that status during the general rise in diversity to the apparent maximum in the Neogene. The increase in diversity associated with the expansion of each new fauna appears to coincide with an approximately exponential decline of the previously dominant fauna, suggesting possible displacement of each evolutionary fauna by its successor.", url = "https://doi.org/10.1017/s0094837300003778", doi = "10.1017/s0094837300003778", openalex = "W2505144080", references = "doi10100797814613088367, doi1010160012825272900724, doi101017s0094837300004917, doi101017s009483730000508x, doi101017s0094837300005236, doi101017s0094837300005352, doi101017s0094837300005649, doi101017s0094837300005972, doi101017s0094837300012549, doi101126science17740541065, doi101126science2064415217, doi101130spe89p63, doi1023071483846, doi1023071796560, doi1023072405671, doi1023072412725, doi1023072412728, doi1023072806339, doi107312simp93764, openalexw1504049102, openalexw645218623" } @article{doi1023072402394, author = "Cloudsley‐Thompson, J. L. and Soulé, Michael E. and Wilcox, Bruce A.", title = "Conservation Biology. An Evolutionary-Ecological Perspective.", year = "1981", journal = "Journal of Applied Ecology", url = "https://doi.org/10.2307/2402394", doi = "10.2307/2402394", openalex = "W1587420391" } @article{doi1023072806339, author = "Funk, Vicki A. and Eldredge, Niles and Cracraft, Joël", title = "Phylogenetic Patterns and the Evolutionary Process.", year = "1981", journal = "Brittonia", url = "https://doi.org/10.2307/2806339", doi = "10.2307/2806339", openalex = "W2330719889" } @misc{jaanusson1981functional7, author = "Jaanusson, V", title = "Functional thresholds in evolutionary progress", year = "1981", howpublished = "Lethaia, v. 14, p. 251-260", note = "talkorigins\_source = {true}; raw\_reference = {Jaanusson, V., 1981, Functional thresholds in evolutionary progress: Lethaia, v. 14, p. 251-260.}" } @article{doi101002ajpa1330580110, author = "Gingerich, Philip D. and Smith, B. Holly and Rosenberg, Karen", title = "Allometric scaling in the dentition of primates and prediction of body weight from tooth size in fossils", year = "1982", journal = "American Journal of Physical Anthropology", abstract = "Tooth size varies exponentially with body weight in primates. Logarithmic transformation of tooth crown area and body weight yields a linear model of slope 0.67 as an isometric (geometric) baseline for study of dental allometry. This model is compared with that predicted by metabolic scaling (slope = 0.75). Tarsius and other insectivores have larger teeth for their body size than generalized primates do and they are not included in this analysis. Among generalized primates, tooth size is highly correlated with body size. Correlations of upper and lower cheek teeth with body size range from 0.90-0.97, depending on tooth position. Central cheek teeth (P44 and M11) have allometric coefficients ranging from 0.57-0.65, falling well below geometric scaling. Anterior and posterior cheek teeth scale at or above metabolic scaling. Considered individually or as a group, upper cheek teeth scale allometrically with lower coefficients than corresponding lower cheek teeth; the reverse is true for incisors. The sum of crown areas for all upper cheek teeth scales significantly below geometric scaling, while the sum of crown areas for all lower cheek teeth approximates geometric scaling. Tooth size can be used to predict the body weight of generalized fossil primates. This is illustrated for Aegyptopithecus and other Eocene, Oligocene, and miocene primates. Regressions based on tooth size in generalized primates yield reasonable estimates of body weight, but much remains to be learned about tooth size and body size scaling in more restricted systematic groups and dietary guilds.", url = "https://doi.org/10.1002/ajpa.1330580110", doi = "10.1002/ajpa.1330580110", openalex = "W2165987887", references = "doi101159000155026, doi1023072412851, openalexw201159638, wolpoff1975allometry" } @article{doi101126science21545391501, author = "Raup, David M. and Sepkoski, J. John", title = "Mass Extinctions in the Marine Fossil Record", year = "1982", journal = "Science", abstract = "A new compilation of fossil data on invertebrate and vertebrate families indicates that four mass extinctions in the marine realm are statistically distinct from background extinction levels. These four occurred late in the Ordovician, Permian, Triassic, and Cretaceous periods. A fifth extinction event in the Devonian stands out from the background but is not statistically significant in these data. Background extinction rates appear to have declined since Cambrian time, which is consistent with the prediction that optimization of fitness should increase through evolutionary time.", url = "https://doi.org/10.1126/science.215.4539.1501", doi = "10.1126/science.215.4539.1501", openalex = "W1976721572", references = "doi101017s009483730000511x, doi101017s0094837300006539, doi101130spe89p63, doi105281zenodo16226412, openalexw2335729143, openalexw2591197405, openalexw2596207362" } @article{doi101126science22246281123, author = "Jablonski, David and Sepkoski, J. John and Bottjer, David J. and Sheehan, Peter M.", title = "Onshore-Offshore Patterns in the Evolution of Phanerozoic Shelf Communities", year = "1983", journal = "Science", abstract = "Cluster analysis of Cambrian-Ordovician marine benthic communities and community-trophic analysis of Late Cretaceous shelf faunas indicate that major ecological innovations appeared in nearshore environments and then expanded outward across the shelf at the expense of older community types. This onshoreinnovation, offshore-archaic evolutionary pattern is surprising in light of the generally, higher species turnover rates of offshore clades. This pattern probably results from differential extinction rates of onshore as compared to offshore clades, or from differential origination rates of new ecological associations or evolutionary novelties in nearshore environments.", url = "https://doi.org/10.1126/science.222.4628.1123", doi = "10.1126/science.222.4628.1123", openalex = "W1973535425", references = "bretsky1968evolution, doi1010079781475707403, doi101017s0094837300003778, doi101017s0094837300005224, doi101017s0094837300005236, doi101017s0094837300005352, doi101017s009483730001246x, doi101038293435a0, doi101111j1469185x1983tb00380x, doi101126science21545391501, doi101126science2164542173, doi101130spe89p63" } @book{ali1984photoreception1, author = "Ali, M. A", title = "Photoreception and Vision in Invertebrates", year = "1984", publisher = "New York, Plenum Press", note = "talkorigins\_source = {true}; raw\_reference = {Ali, M. A., 1984, Photoreception and Vision in Invertebrates: New York, Plenum Press.}" } @article{doi101002ajpa1330270504, author = "Gingerich, Philip D.", title = "Primate evolution: Evidence from the fossil record, comparative morphology, and molecular biology", year = "1984", journal = "American Journal of Physical Anthropology", abstract = "Our understanding of primate evolution is ultimately based on patterns of phyletic relationship and morphological change documented in the fossil record. Stratophenetic interpretation of living and fossil primates yields an objective alternative to the arbitrary scala naturae assumed implicitly in traditional comparative biology. Fossils provide an outline of primate history constraining comparative analyses incorporating taxa and morphological characteristics not represented in the fossil record. Extant taxa without known prehistoric relatives may be interpolated into this outline using deductive cladistic analysis of morphological characteristics and overall molecular similarity. Cladistic analysis provides a method for evaluating the relative strength of stratophenetic links between taxa. The phyletic node connecting Anthropoidea-Adapoidea-Lemuroidea is analyzed here as an example: the link between Eocene Adapoidea and primitive Anthropoidea appears stronger than that between Adapoidea and Lemuroidea because it is based on shared-derived rather than shared-primitive characteristics. Full integration of molecular results with morphological information requires a better understanding of rates of molecular change over geological time. Rates of molecular evolution can be studied using paleontologically documented divergence times for Prosimii-Anthropoidea (ca. 55 m.y.B.P.), Platyrrhini-Catarrhini (ca. 40 m.y.B.P.), and Hominoidea-Cercopithecoidea (ca. 25 m.y.B.P.). Immunological distances combined with these divergence times indicate that primate albumin, widely used as a molecular clock in primatology, has evolved nonlinearly over geological time. A nonlinear albumin clock yields divergence times of about 9 million years before present for humans and chimpanzees, and about 13 million years before present for humans and orangutans (compared with 4 m.y.B.P. and 7 m.y.B.P., respectively, based on a linear albumin clock). Apparent slowing of albumin evolution over time remains to be fully explained. Other proteins and nucleic acids may provide better clocks. Cladistic analysis of morphological characteristics and comparative study of molecular structure, interpreted in the context of the fossil record, promise to contribute to a more complete understanding of primate evolution.", url = "https://doi.org/10.1002/ajpa.1330270504", doi = "10.1002/ajpa.1330270504", openalex = "W2048307773", references = "doi101093sysbio242209, doi101126science1683931578, doi1023072412851" } @article{doi101017s0094837300008289, author = "Charlesworth, Brian", title = "Some quantitative methods for studying evolutionary patterns in single characters", year = "1984", journal = "Paleobiology", abstract = "Some statistical methods are described for the detection and estimation of variability in the rate of evolution, from biometrical data on single characters in fossil lineages. The methods were applied to some published examples of protistan and mammalian lineages, extending between 0.8 and 6.4 Myr in duration. Of six cases examined, only one failed to show evidence for significant variation in the rate of evolution, and only four deviated significantly from a random walk pattern, despite significant net evolutionary change in all cases but one.", url = "https://doi.org/10.1017/s0094837300008289", doi = "10.1017/s0094837300008289", openalex = "W1906467586" } @incollection{doi101007978148990539010, author = "Vianey‐Liaud, Monique", title = "Possible Evolutionary Relationships among Eocene and Lower Oligocene Rodents of Asia, Europe and North America", year = "1985", url = "https://doi.org/10.1007/978-1-4899-0539-0\_10", doi = "10.1007/978-1-4899-0539-0\_10", openalex = "W170267095", references = "openalexw201159638" } @article{doi101111j109583121985tb02048x, author = "Wilson, Allan C. and Cann, Rebecca L. and Carr, Steven M. and George, Matthew and GYLLENSTEN, ULF B. and Helm‐Bychowski, Kathleen and Higuchi, Russell and Palumbi, Stephen R. and Prager, Ellen M. and Sage, Richard D. and Stoneking, Mark", title = "Mitochondrial DNA and two perspectives on evolutionary genetics", year = "1985", journal = "Biological Journal of the Linnean Society", abstract = "Journal Article Mitochondrial DNA and two perspectives on evolutionary genetics Get access ALLAN C. WILSON, ALLAN C. WILSON 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A Search for other works by this author on: Oxford Academic Google Scholar REBECCA L. CANN, REBECCA L. CANN 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A2Howard Hughes Medical Institute, U426, University of California, San Francisco, California 94143, U.S.A Search for other works by this author on: Oxford Academic Google Scholar STEVEN M. CARR, STEVEN M. CARR 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A3Wildlife Genetics Laboraiory, Department of Wildlge and Fisheries Sciences, Texas A \& M University, College Station, Texas 77843, U.S.A Search for other works by this author on: Oxford Academic Google Scholar MATTHEW GEORGE, MATTHEW GEORGE 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A4Department of Biochemistry, Howard University, Washington, DC 20059, U.S.A Search for other works by this author on: Oxford Academic Google Scholar ULF B. GYLLENSTEN, ULF B. GYLLENSTEN 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A5Department of Clinical Genetics, Karolinska Hospital, Box 60500, S-104 01 Stockholm, Sweden Search for other works by this author on: Oxford Academic Google Scholar KATHLEEN M. HELM-BYCHOWSKI, KATHLEEN M. HELM-BYCHOWSKI 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A Search for other works by this author on: Oxford Academic Google Scholar RUSSELL G. HIGUCHI, RUSSELL G. HIGUCHI 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A Search for other works by this author on: Oxford Academic Google Scholar STEPHEN R. PALUMBI, STEPHEN R. PALUMBI 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A6Department of Zoology, University of Hawaii, Honolulu, Hawaii 96822, U.S.A Search for other works by this author on: Oxford Academic Google Scholar ELLEN M. PRAGER, ELLEN M. PRAGER 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A Search for other works by this author on: Oxford Academic Google Scholar RICHARD D. SAGE, RICHARD D. SAGE 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A7Museum of Vertebrate Zoology, University of California, Berkeley, California 94720, U.S.A Search for other works by this author on: Oxford Academic Google Scholar... Show more MARK STONEKING MARK STONEKING 1Department of Biochemistry, University of California, Berkeley, California 94720, U.S.A Search for other works by this author on: Oxford Academic Google Scholar Biological Journal of the Linnean Society, Volume 26, Issue 4, December 1985, Pages 375–400, https://doi.org/10.1111/j.1095-8312.1985.tb02048.x Published: 28 June 2008 Article history Accepted: 01 July 1985 Published: 28 June 2008", url = "https://doi.org/10.1111/j.1095-8312.1985.tb02048.x", doi = "10.1111/j.1095-8312.1985.tb02048.x", openalex = "W2065697254", references = "doi101038202147a0, doi101073pnas504672, doi101073pnas581142, doi101111j155856461983tb05533x, doi101126science15838051200, doi1023071438156, doi1023072407274, doi107312simp93764, openalexw788933220, sarich1967immunological" } @article{doi101017s0094837300013658, author = "Cheetham, Alan H.", title = "Tempo of evolution in a Neogene bryozoan: rates of morphologic change within and across species boundaries", year = "1986", journal = "Paleobiology", abstract = "Inadequacies in stratigraphic resolution or completeness can make true rates of morphologic change through geologic time impossible to estimate precisely. However, relative rates may be sufficient to test whether the tempo of change within species can account for morphologic differences across species boundaries, and hence to distinguish between gradual and punctuated patterns of evolution. The conditions under which these patterns can be distinguished statistically are explored by simulating varying degrees of within-species rate variability relative to across-species morphologic difference. The statistical methods are then applied to multiple-character morphologic data from closely spaced sequential populations of the Neogene bryozoan Metrarabdotos, using discriminant analysis to compare overall morphologies. In nine comparisons of ancestor-descendant species pairs, all show within-species rates of morphologic change that do not vary significantly from zero, hence accounting for none of the across-species difference. In all cases the ratio of within-species fluctuation to across-species difference is low enough to allow the punctuated pattern to be distinguished with virtual certainty. In at least seven of the cases, ancestor species persisted after giving rise to descendants, in conformity with the punctuated equilibrium mode of evolution.", url = "https://doi.org/10.1017/s0094837300013658", doi = "10.1017/s0094837300013658", openalex = "W2500056974", references = "doi101017s0094837300004000" } @article{doi101073pnas8351383, author = "Sogin, M L and Elwood, Hille J. and Gunderson, John H.", title = "Evolutionary diversity of eukaryotic small-subunit rRNA genes.", year = "1986", journal = "Proceedings of the National Academy of Sciences", abstract = "The small-subunit rRNA gene sequences of the flagellated protists Euglena gracilis and Trypanosoma brucei were determined and compared to those of other eukaryotes. A phylogenetic tree was constructed in which the earliest branching among the eukaryotes is represented by E. gracilis. The E. gracilis divergence far antedates a period of massive evolutionary radiation that gave rise to the plants, animals, fungi, and certain groups of protists such as ciliates and the acanthamoebae. The genetic diversity in this collection of eukaryotes is seen to exceed that displayed within either the eubacterial or the archaebacterial lines of descent.", url = "https://doi.org/10.1073/pnas.83.5.1383", doi = "10.1073/pnas.83.5.1383", openalex = "W2062738309" } @article{doi101126science3082006, author = "Britten, Roy J.", title = "Rates of DNA Sequence Evolution Differ Between Taxonomic Groups", year = "1986", journal = "Science", abstract = "The mutation rates of DNA sequences during evolution can be estimated from interspecies DNA sequence differences by assaying changes that have little or no effect on the phenotype (neutral mutations). Examination of available measurements shows that rates of DNA change of different phylogenetic groups differ by a factor of 5. The slowest rates are observed for higher primates and some bird lineages, while faster rates are seen in rodents, sea urchins, and drosophila. The rate of DNA sequence change has decreased markedly during primate evolution. The contrast in rates of DNA sequence change is probably due to evolutionary variation and selection of biochemical mechanisms such as DNA replication or repair.", url = "https://doi.org/10.1126/science.3082006", doi = "10.1126/science.3082006", openalex = "W2027574957", references = "doi101038233604a0" } @article{doi1023071367778, author = "Griesemer, James R. and Boyd, Robert and Richerson, Peter J.", title = "Culture and the Evolutionary Process", year = "1986", journal = "Ornithological Applications", abstract = "Culture and the evolutionary process Culture and the evolutionary process. Robert Boyd, Peter J. Richerson(ed.), 1985. The University of Chicago Press, Chicago viii + 331 pages. $29.95 Marcy F. Lawton Marcy F. Lawton Search for other works by this author on: Oxford Academic Google Scholar The Condor, Volume 88, Issue 1, 1 February 1986, Pages 123–124, https://doi.org/10.2307/1367778 Published: 01 February 1986", url = "https://doi.org/10.2307/1367778", doi = "10.2307/1367778", openalex = "W1811781384" } @article{gingerich1987evolution, author = "Gingerich, Philip D.", title = "Evolution and the fossil record: patterns, rates, and processes", year = "1987", journal = "Canadian Journal of Zoology", abstract = "Mammals have an unusually good Cenozoic fossil record providing evidence of their evolutionary diversification. We view this record in hindsight, which biases our perception in many ways. Overall worldwide diversity appears to increase exponentially through time, while intensive sampling in local areas indicates that modern levels of diversity were achieved early in the Cenozoic. The evident significance of Pleistocene extinctions depends critically on how extinction rates are quantified. Our taxonomic hierarchy probably reflects the number of major faunal turnovers a group has survived rather than declining intensity of successive turnovers. Morphological innovation and taxonomic diversification appear following intervals of climatic cooling, suggesting that major features of evolution are extrinsically controlled. Favorable stratigraphic settings yield detailed records of gradual anagenesis and cladogenesis in mammals, with intermediates present as evidence of transition. The apparent dichotomy between high evolutionary rates measured by neontologists over short intervals of time and low evolutionary rates measured by paleontologists over long intervals of time disappears when rates are measured on intermediate scales of time. Microevolution and macroevolution are manifestations of common underlying processes expressed on different time scales.", url = "https://doi.org/10.1139/z87-169", doi = "10.1139/z87-169", number = "5", openalex = "W2089767140", pages = "1053-1060", volume = "65", references = "doi101017s0094837300005649, doi101093aibsbulletin2214b, doi101111j155856461949tb00004x, doi1023071218194, doi1023072412851, doi105281zenodo13648988, openalexw201159638, openalexw2065039187, openalexw2989964553, openalexw610180004" } @misc{runnegar1987rates9, author = "Runnegar, B", title = "Rates and Modes of Evolution in the Mollusca, in Campbell, K. S. W., and Day, M. F., eds., Rates of Evolution", year = "1987", howpublished = "London, Allen and Unwin, p. 39-60", note = "talkorigins\_source = {true}; raw\_reference = {Runnegar, B., 1987, Rates and Modes of Evolution in the Mollusca, in Campbell, K. S. W., and Day, M. F., eds., Rates of Evolution: London, Allen and Unwin, p. 39-60.}" } @article{doi101111j109600311988tb00514x, author = "Gauthier, Jacques and Kluge, Arnold G. and Rowe, Timothy", title = "AMNIOTE PHYLOGENY AND THE IMPORTANCE OF FOSSILS", year = "1988", journal = "Cladistics", abstract = "Abstract- Several prominent cladists have questioned the importance of fossils in phylogenctic inference, and it is becoming increasingly popular to simply fit extinct forms, if they are considered at all, to a cladogram of Recent taxa. Gardiner's (1982) and Løvtrup's (1985) study of amniote phylogeny exemplifies this differential treatment, and we focused on that group of organisms to test the proposition that fossils cannot overturn a theory of relationships based only on the Recent biota. Our parsimony analysis of amniote phylogeny, special knowledge contributed by fossils being scrupulously avoided, led to the following best fitting classification, which is similar to the novel hypothesis Gardiner published: (lepidosaurs (turtles (mammals (birds, crocodiles)))). However, adding fossils resulted in a markedly different most parsimonious cladogram of the extant taxa: (mammals (turtles (lepidosaurs (birds, crocodiles)))). That classification is like the traditional hypothesis, and it provides a better fit to the stratigraphic record. To isolate the extinct taxa responsible for the latter classification, the data were successively partitioned with each phylogenetic analysis, and we concluded that: (1) the ingroup, not the outgroup, fossils were important; (2) synapsid, not reptile, fossils were pivotal; (3) certain synapsid fossils, not the earliest or latest, were responsible. The critical nature of the synapsid fossils seemed to lie in the particular combination of primitive and derived character slates they exhibited. Classifying those fossils, along with mammals, as the sister group to the lineage consisting of birds and crocodiles resulted in a relatively poor fit to data; one involving a 2-4 fold increase in evolutionary reversals! Thus, the importance of the critical fossils, collectively or individually, seems to reside in their relative primitive-ness, and the simplest explanation for their more conservative nature is that they have had less time to evolve. While fossils may be important in phylogenetic inference only under certain conditions, there is no compelling reason to prejudge their contribution. We urge systematists to evaluate fairly all of the available evidence.", url = "https://doi.org/10.1111/j.1096-0031.1988.tb00514.x", doi = "10.1111/j.1096-0031.1988.tb00514.x", openalex = "W1978557909", references = "crossref1943the, currie1985cranial, doi101001jama194302840160064031, doi1010079781468488517, doi101007978146848851721, doi101016002555648290027x, doi1010160169534789901626, doi101016b9781483198279500198, doi101016b9781483231426500124, doi101017cbo9780511693281002, doi101038142004a0, doi10108002724634198810011708, doi101086628623, doi101093sysbio1811, doi101093sysbio33183, doi1010970000505319311100000026, doi101098rstb19830079, doi101111j109636421977tb01031x, doi101111j109636421985tb01796x, doi101146annureven10010165000525, doi1023071005355, doi1023071220820, doi1023071292217, doi1023071441916, doi1023072412407, doi1023072412685, doi1023072413134, doi1023072413259, doi1023072413454, doi1023072485224, doi105281zenodo16171435, doi10560219780801847806, doi105962bhltitle6408, doi105962bhltitle82144, openalexw1534787790, openalexw1534857865, openalexw2954279587, openalexw2983381470, openalexw3146596760, openalexw3184837389, openalexw575222456, roaf1943the" } @article{doi1023071311135, author = "Stearns, Stephen C.", title = "The Evolutionary Significance of Phenotypic Plasticity", year = "1989", journal = "BioScience", abstract = "Journal Article The Evolutionary Significance of Phenotypic Plasticity: Phenotypic sources of variation among organisms can be described by developmental switches and reaction norms Get access Stephen C. Stearns Stephen C. Stearns Search for other works by this author on: Oxford Academic Google Scholar BioScience, Volume 39, Issue 7, July/August 1989, Pages 436–445, https://doi.org/10.2307/1311135 Published: 01 August 1989", url = "https://doi.org/10.2307/1311135", doi = "10.2307/1311135", openalex = "W2058670567", references = "doi101001jama195002910300087029, doi1015159780691224244, doi1023071439305, doi1023072389364, openalexw1635425035" } @misc{milner1990the8, author = "Milner, R", title = "The Encyclopedia of Evolution", year = "1990", howpublished = "Humanity's Search for Its Origin: New York, Facts on File, Inc., 482 p", note = "talkorigins\_source = {true}; raw\_reference = {Milner, R., 1990, The Encyclopedia of Evolution: Humanity's Search for Its Origin: New York, Facts on File, Inc., 482 p.}" } @article{doi10108002724634199110011424, author = "Grande, Lance and Bemis, William E.", title = "Osteology and Phylogenetic Relationships of Fossil and Recent Paddlefishes (Polyodontidae) with Comments on the Interrelationships of Acipenseriformes", year = "1991", journal = "Journal of Vertebrate Paleontology", abstract = "ABSTRACT The comparative osteology and phylogenetic relationships of fossil and living paddlefishes (Polyodontidae) are investigated in detail for the first time. This peculiar, poorly known group is of great significance to phylogenetic studies of primitive actinopterygians, because it is one of only two chondrostean families that have survived to the present. Consequently the group is frequently used as an outgroup for studies of the many fossil chondrostean groups and for higher-level studies of actinopterygian (and even osteichthyan) interrelationships. The family has a long but spotty fossil record dating back to the Upper Cretaceous, including species represented by relatively complete skeletons or at least skulls. These relatively complete fossils are extremely rare and belong to the species †Paleopsephurus wilsoni MacAlpin, 1947 from the Upper Cretaceous Hell Creek Formation of Montana (redescribed here); †Polyodon sp. nov. from the lower Paleocene Tullock Formation of Montana (described here); and †Crossopholis magnicaudatus Cope, 1883 from lower Eocene deposits of the Green River Formation in Wyoming (described in detail here for the first time based on much new material). Among the fossils, †Crossopholis is of particular interest, because it is now known by several nearly complete skeletons (reported and described here for the first time). †Paleopsephurus and †Polyodon sp. nov. are known from a single partial skull each, and some fragmentary postcranial material, but are well enough represented to include in our phylogenetic analysis. Other, more fragmentary, Upper Cretaceous and Paleocene material (some newly reported here) is placed in Polyodontidae incertae sedis. There are two extant species in the family, frequently referred to in the literature as “living fossils.” These two species are Polyodon spathula from the Mississippi River drainage of North America, and Psephurus gladius primarily from the upper Yangtze River drainage in China. The osteology of Psephurus gladius is described here in detail for the first time. Previous studies of Polyodontidae have been almost exclusively based on Polyodon spathula, because specimens of the other species are extremely rare and very poorly known. After accumulating and preparing material for several years, we were able to describe more fully all polyodontid species and examine the family phylogenetically. Our study reveals that Polyodon spathula is a highly derived member of the family, and generally not a good representative of the family when the family is used as an outgroup for higher-level phylogenetic studies of actinopterygians. The use of Polyodon spathula as the primitive polyodontid has previously led to several serious errors in the literature. We therefore also summarize certain primitive characters of Polyodontidae in this paper. Contrary to previous studies, we show that †Paleopsephurus has the stellate rostral bones unique to polyodontids (in addition to the long median rostral bones and extremely elongate snout also unique to the group). Also contrary to previous studies, Polyodontidae (at least primitively) does have ossifications of the quadratojugal, interclavicle and postcleithrum. We also report several other osteological features previously unknown from the family. Our study results in a phylogenetic hypothesis for paddlefishes that is radically different from the only other published cladogram (Gardiner, 1984b). We demonstrate that †Paleopsephurus clearly belongs in Polyodontidae, rather than Acipenseridae as proposed by Gardiner (1984b). †Paleopsephurus is the sistergroup to Polyodontinae, new subfamily (a group containing Psephurus, †Crossopholis, and two species of Polyodon). Psephurus is the sistergroup to Polyodontini, new tribe (a group containing †Crossopholis and Polyodon). Polyodon contains the extant Polyodon spathula as well as a new fossil species from early Paleocene freshwater deposits of Montana. A better understanding of polyodontid osteology also enables us to provide a phylogenetic hypothesis for Acipenseriformes (assuming monophyly of Acipenseridae) that differs from that of previous authors. In particular we find that †Chondrosteidae is the sistergroup to a group containing Acipenseridae plus Polyodontidae. Polyodontidae also provide evidence that the supraneurals in actinopterygians are the serial homologues of epurals, and not of fin radials. As has previously been apparent, Polyodontidae is one of several groups that indicate a transpacific biogeographic relationship for western North America (west of the continental divide) during the Early Tertiary. We also describe ontogenetic and intraspecific variation in paddlefish osteology. Based on the large amount of variation, we conclude that, in at least some fishes, it is important to examine large numbers of specimens, including extremely old individuals (i.e., “upper end ontogeny”) in the developmental series to more completely document the morphology. Normal-sized, reproductively active adult paddlefishes lack particular ossifications of the scapulocoracoid, vertebral column and neurocranium present in other osteichthyans; but as we show here, these elements eventually ossify in very large, older individuals. In this sense, paddlefishes appear to be the axolotls of the fish world, offering one of the best documented cases of paedomorphosis (or neoteny) known to date.", url = "https://doi.org/10.1080/02724634.1991.10011424", doi = "10.1080/02724634.1991.10011424", openalex = "W1980955783", references = "doi101038170405e0, doi101111j109636421932tb01553x, doi105281zenodo16298542, doi105962bhltitle159141, doi105962bhltitle6408, gardiner1989interrelationships, openalexw2246336267, openalexw610180004" } @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{doi101038361219a0, author = "Morris, Simon Conway", title = "The fossil record and the early evolution of the Metazoa", year = "1993", journal = "Nature", url = "https://doi.org/10.1038/361219a0", doi = "10.1038/361219a0", openalex = "W2143380472", references = "doi101016001670379290064p, doi1010160301926885900518, doi101016030192688590066x, doi101016s0959437x05801923, doi101017cbo9780511601064002, doi101038345802a0, doi101093oso97801985771880010001, doi101111j146364091991tb00303x, doi101111j150239311989tb01332x, doi101126science1585174, doi101126science1598573, doi101126science2464928339, doi101126science3277277, doi101144gsjgs14920171, doi101144gsjgs14940607, doi1023072992562, doi105860choice273873" } @article{doi101126science11536548, author = "Labandeira, Conrad C. and Sepkoski, J. John", title = "Insect Diversity in the Fossil Record", year = "1993", journal = "Science", abstract = "Insects possess a surprisingly extensive fossil record. Compilation of the geochronologic ranges of insect families demonstrates that their diversity exceeds that of preserved vertebrate tetrapods through 91 percent of their evolutionary history. The great diversity of insects was achieved not by high origination rates but rather by low extinction rates comparable to the low rates of slowly evolving marine invertebrate groups. The great radiation of modern insects began 245 million years ago and was not accelerated by the expansion of angiosperms during the Cretaceous period. The basic trophic machinery of insects was in place nearly 100 million years before angiosperms appeared in the fossil record.", url = "https://doi.org/10.1126/science.11536548", doi = "10.1126/science.11536548", openalex = "W1984084181", references = "doi1010079781468491814, doi101017s0094837300003778, doi101038293435a0, doi101038303614a0, doi101086284840, doi101111j155856461964tb01674x, doi101111j155856461966tb03364x, doi101126science13334591105, doi101126science21545391501, doi101126science2314734129, doi101146annureves10110179001335, doi107312simp93764, openalexw2038423019" } @article{doi101126science11539488, author = "Bowring, Samuel A. and Grotzinger, J. P. and Isachsen, C. E. and Knoll, Andrew H. and Pelechaty, Shane M. and Kolosov, Peter", title = "Calibrating Rates of Early Cambrian Evolution", year = "1993", journal = "Science", abstract = "An explosive episode of biological diversification occurred near the beginning of the Cambrian period. Evolutionary rates in the Cambrian have been difficult to quantify accurately because of a lack of high-precision ages. Currently, uranium-lead zircon geochronology is the most powerful method for dating rocks of Cambrian age. Uranium-lead zircon data from lower Cambrian rocks located in northeast Siberia indicate that the Cambrian period began at approximately 544 million years ago and that its oldest (Manykaian) stage lasted no less than 10 million years. Other data indicate that the Tommotian and Atdabanian stages together lasted only 5 to 10 million years. The resulting compression of Early Cambrian time accentuates the rapidity of both the faunal diversification and subsequent Cambrian turnover.", url = "https://doi.org/10.1126/science.11539488", doi = "10.1126/science.11539488", openalex = "W2080974066", references = "doi101017s0094837300005649, doi101017s0094837300005972, doi101017s0094837300006539" } @article{doi101126science8469985, author = "Wainright, Patricia O. and Hinkle, Gregory and Sogin, Mitchell L. and Stickel, Shawn K.", title = "Monophyletic Origins of the Metazoa: an Evolutionary Link with Fungi", year = "1993", journal = "Science", abstract = "A phylogenetic framework inferred from comparisons of small subunit ribosomal RNA sequences describes the evolutionary origin and early branching patterns of the kingdom Animalia. Maximum likelihood analyses show the animal lineage is monophyletic and includes choanoflagellates. Within the metazoan assemblage, the divergence of sponges is followed by the Ctenophora, the Cnidaria plus the placozoan Trichoplax adhaerens, and finally by an unresolved polychotomy of bilateral animal phyla. From these data, it was inferred that animals and fungi share a unique evolutionary history and that their last common ancestor was a flagellated protist similar to extant choanoflagellates.", url = "https://doi.org/10.1126/science.8469985", doi = "10.1126/science.8469985", openalex = "W2034733986", references = "doi101126science3277277, openalexw2076004673" } @book{openalexw1599677799, author = "Benton, Michael J.", title = "The fossil record 2", year = "1993", abstract = "Introduction. Basal Groups. Monera (bacteria blue-green algae). Fungi.Algae. Animals: Invertebrates. Protozoa. Porifera. Coelenterata. Mollusca: Amphineura and Monoplacophora. Mollusca: Gastropoda. Mollusca: Cephalopoda (Nautiloidea). Mollusca: Cephalopoda (Pre-Jurassic Ammonoidea). Mollusca: Cephalopoda (Ammonoidea: Phylloceratina, Lytoceratina, Ammonitina, Ancyloceratina). Mollusca: Cephalopoda (Coleoidea). Mollusca: Rostroconchia, Scaphopoda, and Bivalvia. Mollusca: incertae sedis. Annelida. Arthropoda (Trilobita). Arthropoda (Aglaspidida, Chelicerata, Pycnogonida). Arthropoda (Crustacea, excluding Ostracoda). Arthropoda (Crustacea: Ostracoda). Arthropoda (Euthycarcinoidea and Myriapoda). Arthropoda (Hexapoda: Insecta). Brachiopoda. Phoronida. Bryozoa. Echinodermata. Basal deuterostomes (chaetognaths, hemichordates, calcichordates, cephalochordates, and tunicates). Graptolithina. Problematica. Miscellania. Animals: Vertebrates. Conodonta. Agnatha. Placodermi. Acanthodii. Chondrichthyes. Osteichthyes: basal actinopterygians. Osteichthyes: Teleostei. Osteichthyes: Sarcopterygii. Amphibian-grade Tetrapoda. Reptilia. Aves. Mammalia. Plants. Bryophyta. Pteridophyta. Gymnospermophyta. Magnoliophyta (Angiospermae). Index.", openalex = "W1599677799" } @article{doi101017s0094837300012963, author = "Clyde, William C. and Gingerich, Philip D.", title = "Rates of evolution in the dentition of early Eocene Cantius: comparison of size and shape", year = "1994", journal = "Paleobiology", abstract = "Cantius is an early Eocene adapid primate with an exceptionally well known fossil record. Measurements were recorded to describe the size and shape of upper and lower first molars collected from a measured stratigraphic section in the Clarks Fork Basin of Wyoming. Rates of change of size and shape are quantified by calculating evolutionary rates in standard deviation units per generation (haldanes). Temporal scaling of rates shows that change in size was generated by a significantly nonrandom directional process, while change in shape was generated by a significantly nonrandom stabilizing process. Size change in Cantius is interpreted to be the result of weak directional selection, and shape change is interpreted to be the result of strong stabilizing selection.", url = "https://doi.org/10.1017/s0094837300012963", doi = "10.1017/s0094837300012963", openalex = "W1408983869", references = "openalexw201159638" } @article{doi101093oxfordjournalsmolbeva040136, author = "Lockhart, Peter J. and Steel, Mike and Hendy, Michael D. and Penny, David", title = "Recovering evolutionary trees under a more realistic model of sequence evolution.", year = "1994", journal = "Molecular Biology and Evolution", abstract = "We report a new transformation, the LogDet, that is consistent for sequences with differing nucleotide composition and that have arisen under simple but asymmetric stochastic models of evolution. This transformation is required because existing methods tend to group sequences on the basis of their nucleotide composition, irrespective of their evolutionary history. This effect of differing nucleotide frequencies is illustrated by using a tree-selection criterion on a simple distance measure defined solely on the basis of base composition, independent of the actual sequences. The new LogDet transformation uses determinants of the observed divergence matrices and works because multiplication of determinants (real numbers) is commutative, whereas multiplication of matrices is not,except in special symmetric cases. The use of determinants thus allows more general models of evolution with a symmetric rates of nucleotide change. The transformation is illustrated on a theoretical data set (where existing methods select the wrong tree) and with three biological data sets: chloroplasts, birds/mammals (nuclear), and honeybees (mitochondrial). The LogDet transformation reinforces the logical distinction between transformations on the data and tree-selection criteria. The overall conclusions from this study are that irregular A,C,G,T compositions are an important and possible general cause of patterns that can mislead tree-reconstruction methods, even when high bootstrap values are obtained. Consequently, many published studies may need to be reexamined.", url = "https://doi.org/10.1093/oxfordjournals.molbev.a040136", doi = "10.1093/oxfordjournals.molbev.a040136", openalex = "W2162443218", references = "doi101093oxfordjournalsmolbeva040752, doi101093oxfordjournalsmolbeva040771, doi101126science3277277" } @article{doi101126science2645157421, author = "Masterson, Jane", title = "Stomatal Size in Fossil Plants: Evidence for Polyploidy in Majority of Angiosperms", year = "1994", journal = "Science", abstract = "Three published estimates of the frequency of polyploidy in angiosperms (30 to 35 percent, 47 percent, and 70 to 80 percent) were tested by estimating the genome size of extinct woody angiosperms with the use of fossil guard cell size as a proxy for cellular DNA content. The inferred chromosome numbers of these extinct species suggest that seven to nine is the primitive haploid chromosome number of angiosperms and that most angiosperms (approximately 70 percent) have polyploidy in their history.", url = "https://doi.org/10.1126/science.264.5157.421", doi = "10.1126/science.264.5157.421", openalex = "W2049670427", references = "doi1023072412932, openalexw2065039187" } @article{doi101017s0094837300016201, author = "Renaud, Sabrina and Michaux, Jacques and Jaeger, Jean‐Jacques and Auffray, Jean‐Christophe", title = "Fourier analysis applied to Stephanomys (Rodentia, Muridae) molars: nonprogressive evolutionary pattern in a gradual lineage", year = "1996", journal = "Paleobiology", abstract = "Size and shape are analyzed for Pliocene lineages of the rodent genus Stephanomys Schaub 1938. Previous phylogenetic studies were based mainly on size variation and descriptive comparisons, without any attempt to quantify shape changes. Hence, on the basis of regular size increase, Stephanomys has been considered a prime example of phyletic gradualism. In order to quantify morphological variation within the lineage, a method for analyzing complex outlines, the elliptic Fourier transform, was applied to tooth contour (upper and lower first molars). It was then possible to compare evolution in size, estimated by tooth area, as well as evolution of shape, represented by Fourier coefficients. While size seems to change gradually through time, morphology gives a rather discontinuous evolutionary pattern for both the upper and lower molar. Such a discrepancy between the evolution of size and shape of a single structure suggests that different genetic determinisms and mechanical constraints may act on size and shape. Hence it may be misleading to infer generalized evolutionary processes from either size or shape alone.", url = "https://doi.org/10.1017/s0094837300016201", doi = "10.1017/s0094837300016201", openalex = "W2504052297", references = "doi1010160146664x8290034x, doi101016016953479390024j, doi101017s0094837300008289, doi101017s0094837300012963, doi101017s0094837300013658, doi101038366223a0, doi101038368696a0, doi1023071378990, doi1023072413076, doi1023072413345, gingerich1987evolution" } @article{foote1996perspective, author = "Foote, Mike", title = "PERSPECTIVE: EVOLUTIONARY PATTERNS IN THE FOSSIL RECORD", year = "1996", journal = "Evolution", url = "https://doi.org/10.1111/j.1558-5646.1996.tb04467.x", doi = "10.1111/j.1558-5646.1996.tb04467.x", number = "1", openalex = "W2327034943", pages = "1-11", volume = "50", references = "doi10100703064746897, doi101017s0094837300003778, doi101093aesa383396, doi101111j155856461985tb00420x, doi101146annureven10010165000525, doi1015159780691224244, doi1023073224530, doi107312simp93764, openalexw1528487914, openalexw2145250129" } @article{doi101126science27553081934, author = "Reznick, David N. and Shaw, Frank H. and Rodd, F. Helen and Shaw, Ruth G.", title = "Evaluation of the Rate of Evolution in Natural Populations of Guppies (Poecilia reticulata)", year = "1997", journal = "Science", abstract = "Natural populations of guppies were subjected to an episode of directional selection that mimicked natural processes. The resulting rate of evolution of age and size at maturity was similar to rates typically obtained for traits subjected to artificial selection in laboratory settings and up to seven orders of magnitude greater than rates inferred from the paleontological record. Male traits evolved more rapidly than female traits largely because males had more genetic variation upon which natural selection could act. These results are considered in light of the ongoing debate about the importance of natural selection versus other processes in the paleontological record of evolution.", url = "https://doi.org/10.1126/science.275.5308.1934", doi = "10.1126/science.275.5308.1934", openalex = "W1981048891", references = "doi10100797894015768267, doi101111j155856461949tb00004x, doi101126science2224620159" } @article{doi101093oxfordjournalsmolbeva025892, author = "Thorne, Jeffrey L. and Kishino, Hirohisa and Painter, Ian", title = "Estimating the rate of evolution of the rate of molecular evolution", year = "1998", journal = "Molecular Biology and Evolution", abstract = "A simple model for the evolution of the rate of molecular evolution is presented. With a Bayesian approach, this model can serve as the basis for estimating dates of important evolutionary events even in the absence of the assumption of constant rates among evolutionary lineages. The method can be used in conjunction with any of the widely used models for nucleotide substitution or amino acid replacement. It is illustrated by analyzing a data set of rbcL protein sequences.", url = "https://doi.org/10.1093/oxfordjournals.molbev.a025892", doi = "10.1093/oxfordjournals.molbev.a025892", openalex = "W2051296828", references = "doi101007bf01734359, doi101007bf01797451, doi101007bf02111276, doi101007bf02338839, doi101016b9781483227344500176, doi101016b9781483232119500097, doi101038scientificamerican117998, doi101093bioinformatics83275, doi101093biomet57197, doi101198tech2001s608, doi1012019780429258411, doi1023072291187" } @article{doi10103844766, author = "Pagel, Mark", title = "Inferring the historical patterns of biological evolution", year = "1999", journal = "Nature", url = "https://doi.org/10.1038/44766", doi = "10.1038/44766", openalex = "W2114525641", references = "doi101016s0092867400803104, doi10103818872, doi101038366223a0, doi101038384055a0, doi101086284325, doi101086286013, doi101093oso97801985464120010001, doi101093sysbio41118, doi101098rspb19940006, doi101111j146364091997tb00423x, doi101126science2740904, doi101126science2765313734, doi101128mr5122212711987, doi1015159781503621534, doi1023072407154, doi1023072485224, doi105860choice295104, rambaut1998estimating" } @article{doi101080106351599260472, author = "Alroy, John", title = "The Fossil Record of North American Mammals: Evidence for a Paleocene Evolutionary Radiation", year = "1999", journal = "Systematic Biology", abstract = "Paleontologists long have argued that the most important evolutionary radiation of mammals occurred during the early Cenozoic, if not that all eutherians originated from a single common post-Cretaceous ancestor. Nonetheless, several recent molecular analyses claim to show that because several interordinal splits occurred during the Cretaceous, a major therian radiation was then underway. This claim conflicts with statistical evidence from the well-sampled latest Cretaceous and Cenozoic North American fossil record. Paleofaunal data confirm that there were fewer mammalian species during the latest Cretaceous than during any interval of the Cenozoic, and that a massive diversification took place during the early Paleocene, immediately after a mass extinction. Measurement data show that Cretaceous mammals were on average small and occupied a narrow range of body sizes; after the Cretaceous-Tertiary mass extinction, there was a rapid and permanent shift in the mean. The fact that there was an early Cenozoic mammalian radiation is entirely compatible with the existence of a few Cretaceous splits among modern mammal lineages.", url = "https://doi.org/10.1080/106351599260472", doi = "10.1080/106351599260472", openalex = "W2099893880", references = "doi1023071218194, openalexw610180004" } @article{doi101126science28554321386, author = "McElwain, Jennifer C. and Beerling, David J. and Woodward, F. I.", title = "Fossil Plants and Global Warming at the Triassic-Jurassic Boundary", year = "1999", journal = "Science", abstract = {The Triassic-Jurassic boundary marks a major faunal mass extinction, but records of accompanying environmental changes are limited. Paleobotanical evidence indicates a fourfold increase in atmospheric carbon dioxide concentration and suggests an associated 3 degrees to 4 degrees C "greenhouse" warming across the boundary. These environmental conditions are calculated to have raised leaf temperatures above a highly conserved lethal limit, perhaps contributing to the >95 percent species-level turnover of Triassic-Jurassic megaflora.}, url = "https://doi.org/10.1126/science.285.5432.1386", doi = "10.1126/science.285.5432.1386", openalex = "W2007663434", references = "doi1010160034666777900070, doi1010160034666780900226, doi1010160034666781900695, doi101093oso97801985491780010001, doi101126science21545391501, doi101126science2845414616, doi101126science3616622, doi101126science7701342, doi101144gsjgs15450773" } @article{doi101146annurevearth271313, author = "Grotzinger, J. P. and Knoll, Andrew H.", title = "STROMATOLITES IN PRECAMBRIAN CARBONATES: Evolutionary Mileposts or Environmental Dipsticks?", year = "1999", journal = "Annual Review of Earth and Planetary Sciences", abstract = "Stromatolites are attached, lithified sedimentary growth structures, accretionary away from a point or limited surface of initiation. Though the accretion process is commonly regarded to result from the sediment trapping or precipitation-inducing activities of microbial mats, little evidence of this process is preserved in most Precambrian stromatolites. The successful study and interpretation of stromatolites requires a process-based approach, oriented toward deconvolving the replacement textures of ancient stromatolites. The effects of diagenetic recrystallization first must be accounted for, followed by analysis of lamination textures and deduction of possible accretion mechanisms. Accretion hypotheses can be tested using numerical simulations based on modem stromatolite growth processes. Application of this approach has shown that stromatolites were originally formed largely through in situ precipitation of laminae during Archean and older Proterozoic times, but that younger Proterozoic stromatolites grew largely through the accretion of carbonate sediments, most likely through the physical process of microbial trapping and binding. This trend most likely reflects long-term evolution of the earth's environment rather than microbial communities.", url = "https://doi.org/10.1146/annurev.earth.27.1.313", doi = "10.1146/annurev.earth.27.1.313", openalex = "W2142539052", references = "doi101007978364276884234, doi101016001670379390347y, doi101016030192688590066x, doi101016s0070457108711373, doi101016s0070457108711567, doi101016s0070457108x70451, doi101017cbo9780511599798, doi101017cbo9780511601064, doi101038324055a0, doi101038368046a0, doi101038383423a0, doi101086628623, doi101103physrevb275686, doi101103physrevlett56889, doi101126science11539686, doi101126science1585174, doi101126science1744011825, doi101139e79088, doi101146annurevecolsys281129, doi1023073514631, doi1023073514973" } @article{doi1016410006356820000500217esaaef23co2, author = "Hoffmann, Ary A. and Hercus, Miriam J.", title = "Environmental Stress as an Evolutionary Force", year = "2000", journal = "BioScience", abstract = "Stressful environmental conditions can be defined as those that lead to a sharp reduction in fitness in populations. That is, when changed environmental con­ ditions cause a drastic reduction in reproductive output, and when persistence of the conditions leads to permanent damage, these conditions constitute an environmental stress. Physical stresses that are encountered rarely in populations-such as periods of drought or extreme cold­ or that are encountered by a minority of a species-such as in populations that are located at distribution borders or are exposed to local chemical stresses arising from human activities-can, through their direct or indirect effects, lead to marked reductions in the size of populations (Glynn 1988, Hoffmann and Parsons 1991) and to repeated cycles of colonization and extinction (Andrewartha and Birch 1954).", url = "https://doi.org/10.1641/0006-3568(2000)050[0217:esaaef]2.3.co;2", doi = "10.1641/0006-3568(2000)050[0217:esaaef]2.3.co;2", openalex = "W2157843549", references = "doi101016s0031018296000995, doi101146annureves10110179001335" } @article{doi101016s0031018201002085, author = "Steiner, Michael and Wallis, Eckart and Erdtmann, Bernd-Dietrich and Zhao, Yuanlong and Yang, Ruidong", title = "Submarine-hydrothermal exhalative ore layers in black shales from South China and associated fossils — insights into a Lower Cambrian facies and bio-evolution", year = "2001", journal = "Palaeogeography Palaeoclimatology Palaeoecology", url = "https://doi.org/10.1016/s0031-0182(01)00208-5", doi = "10.1016/s0031-0182(01)00208-5", openalex = "W2115053158", references = "doi1010160009254180900479, doi1010160009254186900781, doi1010160012821x84900396, doi101016003101829390065q, doi1010160031920186900932, doi101016003192018990263x, doi101017cbo9780511601064, doi101038267403a0, doi101126science2464928339, doi101126science2705236598, doi1011300091761319940220179pcbgsr23co2, doi101144gsjgs14920171, doi101306m20377, doi10182618200374742199101, doi1023072992562, openalexw1624806571" } @article{doi101046j1365294x2001t01101411x, author = "Fraser, Dylan J. and Bernatchez, Louis", title = "Adaptive evolutionary conservation: towards a unified concept for defining conservation units", year = "2001", journal = "Molecular Ecology", abstract = "Recent years have seen a debate over various methods that could objectively prioritize conservation value below the species level. Most prominent among these has been the evolutionarily significant unit (ESU). We reviewed ESU concepts with the aim of proposing a more unified concept that would reconcile opposing views. Like species concepts, conflicting ESU concepts are all essentially aiming to define the same thing: segments of species whose divergence can be measured or evaluated by putting differential emphasis on the role of evolutionary forces at varied temporal scales. Thus, differences between ESU concepts lie more in the criteria used to define the ESUs themselves rather than in their fundamental essence. We provide a context-based framework for delineating ESUs which circumvents much of this situation. Rather than embroil in a befuddled debate over an optimal criterion, the key to a solution is accepting that differing criteria will work more dynamically than others and can be used alone or in combination depending on the situation. These assertions constitute the impetus behind adaptive evolutionary conservation.", url = "https://doi.org/10.1046/j.1365-294x.2001.t01-1-01411.x", doi = "10.1046/j.1365-294x.2001.t01-1-01411.x", openalex = "W2141234232", references = "doi10100797814615678136, doi101126science27953592115, doi1023073224530, doi107202032681ar, doi107312simp92414" } @article{doi101093oxfordjournalsmolbeva003811, author = "Kishino, Hirohisa and Thorne, Jeffrey L. and Bruno, William", title = "Performance of a Divergence Time Estimation Method under a Probabilistic Model of Rate Evolution", year = "2001", journal = "Molecular Biology and Evolution", abstract = "Rates of molecular evolution vary over time and, hence, among lineages. In contrast, widely used methods for estimating divergence times from molecular sequence data assume constancy of rates. Therefore, methods for estimation of divergence times that incorporate rate variation are attractive. Improvements on a previously proposed Bayesian technique for divergence time estimation are described. New parameterization more effectively captures the phylogenetic structure of rate evolution on a tree. Fossil information and other evidence can now be included in Bayesian analyses in the form of constraints on divergence times. Simulation results demonstrate that the accuracy of divergence time estimation is substantially enhanced when constraints are included.", url = "https://doi.org/10.1093/oxfordjournals.molbev.a003811", doi = "10.1093/oxfordjournals.molbev.a003811", openalex = "W2045517599" } @article{doi101111j109583122001tb01368x, author = "Sanmartín, Isabel and Enghoff, Henrik and Ronquist, Fredrik", title = "Patterns of animal dispersal, vicariance and diversification in the Holarctic", year = "2001", journal = "Biological Journal of the Linnean Society", abstract = "We analysed patterns of animal dispersal, vicariance and diversification in the Holarctic based on complete phylogenies of 57 extant non-marine taxa, together comprising 770 species, documenting biogeographic events from the Late Mesozoic to the present. Four major areas, each corresponding to a historically persistent landmass, were used in the analyses: eastern Nearctic (EN), western Nearctic (WN), eastern Palaeoarctic (EP) and western Palaeoarctic (WP). Parsimony-based tree fitting showed that there is no significantly supported general area cladogram for the dataset. Yet, distributions are strongly phylogenetically conserved, as revealed by dispersal-vicariance analysis (DIVA). DIVA-based permutation tests were used to pinpoint phylogenetically determined biogeographic patterns. Consistent with expectations, continental dispersals (WP↓EP and WN↓EN) are significantly more common than palaeocontinental dispersals (WN↓EP and EN↓WP), which in turn are more common than disjunct dispersals (EN↓EP and WN↓WP). There is significant dispersal asymmetry both within the Nearctic (WN⇒EN more common than EN⇒WN) and the Palaeoarctic (EP⇒WP more common than WP⇒EP). Cross-Beringian faunal connections have traditionally been emphasized but are not more important than cross-Atlantic connections in our data set. To analyse changes over time, we sorted biogeographic events into four major time periods using fossil, biogeographic and molecular evidence combined with a «branching clock». These analyses show that trans-Atlantic distributions (EN–WP) were common in the Early–Mid Tertiary (70–20 Myr), whereas trans-Beringian distributions (WN–EP) were rare in that period. Most EN–EP disjunctions date back to the Early Tertiary (70–45 Myr), suggesting that they resulted from division of cross-Atlantic rather than cross-Beringian distributions. Diversification in WN and WP increased in the Quaternary (< 3 Myr), whereas in EP and EN it decreased from a maximum in the Early–Mid Tertiary.", url = "https://doi.org/10.1111/j.1095-8312.2001.tb01368.x", doi = "10.1111/j.1095-8312.2001.tb01368.x", openalex = "W2142884638", references = "doi101007978146133485919, doi101007978303487527124, doi1010160169534794901635, doi10103835025052, doi101093oxfordjournalsmolbeva026092, doi101093sysbio461195, doi101146annurevecolsys301421, doi101146annureven15010170000525, doi1023071440574, doi1023072395021, doi1023072412970, doi105962bhlpart13183, openalexw1486025919, openalexw2989964553" } @book{doi102307jctvjsf433, author = "Gould, Stephen Jay", title = "The Structure of Evolutionary Theory", year = "2002", booktitle = "Harvard University Press eBooks", url = "https://doi.org/10.2307/j.ctvjsf433", doi = "10.2307/j.ctvjsf433", openalex = "W4300925890" } @article{doi105860choice396411, author = "Gould, Stephen Jay", title = "The structure of evolutionary theory", year = "2002", journal = "Choice Reviews Online", abstract = "* *1. Defining and Revising the Structure of Evolutionary Theory * Part I: The History of Darwinian Logic and Debate *2. The Essence of Darwinism and the Basis of Modern Orthodoxy: An Exegesis of the Origin of Species *3. Seeds of Hierarchy *4. Internalism and Laws of Form: Pre-Darwinian Alternatives to Functionalism *5. The Fruitful Facets of Galton's Polyhedron: Channels and Saltations in Post-Darwinian Formalism *6. Pattern and Progress on the Geological Stage *7. The Modern Synthesis as a Limited Consensus * Part II: Towards a Revised and Expanded Evolutionary Theory *8. Species as Individuals in the Hierarchical Theory of Selection *9. Punctuated Equilibrium and the Validation of Macroevolutionary Theory *10. The Integration of Constraint and Adaptation (Structure and Function) in Ontogeny and Phylogeny: Historical Constraints and the Evolution of Development *11. The Integration of Constraint and Adaptation (Structure and Function) in Ontogeny and Phylogeny: Structural Constraints, Spandrels, and the Centrality of Exaptation in Macroevolution *12. Tiers of Time and Trials of Extrapolationism, With an Epilog on the Interaction of General Theory and Contingent History * Bibliography * Index", url = "https://doi.org/10.5860/choice.39-6411", doi = "10.5860/choice.39-6411", openalex = "W1539968307" } @article{doi101671027246342003231apfast20co2, author = "Smith, Joshua B. and Dodson, Peter", title = "A proposal for a standard terminology of anatomical notation and orientation in fossil vertebrate dentitions", year = "2003", journal = "Journal of Vertebrate Paleontology", abstract = "ABSTRACT There is little consistency in the notation and orientation terminology used in discussions of non-mammalian fossil venebrate dentitions. The standardization of this terminology, as done in the medical and dental sciences, would facilitate all future research on fossil teeth. For mammals, we recommend following convention, where incisors, canines, premolare, and molars are abbreviated as In, Cn, Pn, and Mn (n = tooth number) in upper jaws and as in, cn, pn, and mn in lower jaws. Right, left, and deciduous teeth are indicated by R, L, and D (e.g., DP4, Rp2). For non-mammals, which can have dentigerous premaxillae, maxillae, and dentaries, as well as additional tooth-bearing bones (e.g., vomers, palatines, pterygoids, ectopterygoids, sphenoids, splenials, and even parasphenoids), we encourage identifying teeth using the bone abbreviation (e.g., pmn, mxn, dn, vn, pain). A number and slash (/) combination can be used to distinguish between multiple tooth rows (e.g., Pal1/n, Pal2/n), and specimen-specific maps can be created for very complicated dentitions. We suggest the use of the terms mesial and distal to designate tooth surfaces and directions facing toward and away from the mandibular symphysis. Labial is offered for those surfaces and directions facing the lips or cheeks and lingual for those facing the tongue. We offer the terms basal for the direction toward crown bases, apical for the direction toward crown tips, occlusal for views of the occlusal surfaces, and basal and root apical for views of crown bases and roots, respectively.", url = "https://doi.org/10.1671/0272-4634(2003)23[1:apfast]2.0.co;2", doi = "10.1671/0272-4634(2003)23[1:apfast]2.0.co;2", openalex = "W2177918895", references = "doi101001jama191104260090143037, doi101007bf02987808, doi101017cbo9780511608377011, doi101017s0094837300016201, doi10108002724634198710011638, doi10108002724634199510011250, doi10108002724634199810011101, doi10108002724634199810011114, doi101086273307, doi101098rstb19740001, doi101111j109636421978tb01049x, doi101126science10246376, doi101126science2665183267, doi101126science2725264986, doi101144gsjgs15310005, doi1016660022336020010750208lcsdaf20co2, doi1023073514548, doi1023073514751, doi105281zenodo1048848, doi105281zenodo16492064, doi105860choice383310, openalexw197683541, openalexw2609000594, rowe1989a, sues1978a" } @article{doi101093bib52150, author = "Kumar, Sudhir", title = "MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment", year = "2004", journal = "Briefings in Bioinformatics", abstract = "With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of species and multigene families, estimating rates of molecular evolution, and inferring the nature and extent of selective forces shaping the evolution of genes and genomes. The scope of these investigations has now expanded greatly owing to the development of high-throughput sequencing techniques and novel statistical and computational methods. These methods require easy-to-use computer programs. One such effort has been to produce Molecular Evolutionary Genetics Analysis (MEGA) software, with its focus on facilitating the exploration and analysis of the DNA and protein sequence variation from an evolutionary perspective. Currently in its third major release, MEGA3 contains facilities for automatic and manual sequence alignment, web-based mining of databases, inference of the phylogenetic trees, estimation of evolutionary distances and testing evolutionary hypotheses. This paper provides an overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA.", url = "https://doi.org/10.1093/bib/5.2.150", doi = "10.1093/bib/5.2.150", openalex = "W2146396346", references = "doi101007bf01731581, doi101007bf02407308, doi101016b9781483232119500097, doi101093bioinformatics17121244, doi101093genetics1233585, doi101093nar22224673, doi101093nar25173389, doi101093oso97801951358480010001, doi101093oxfordjournalsmolbeva040023, doi101093oxfordjournalsmolbeva040259, doi101093oxfordjournalsmolbeva040343, doi101093oxfordjournalsmolbeva040410, doi101093oxfordjournalsmolbeva040454, doi101093oxfordjournalsmolbeva040771, doi101111j155856461985tb00420x, doi1023072408678, doi1023072412074, doi105860choice392183, openalexw2032279931, openalexw3217097258" } @article{doi101093molbevmsj030, author = "Huson, Daniel H. and Bryant, David", title = "Application of Phylogenetic Networks in Evolutionary Studies", year = "2005", journal = "Molecular Biology and Evolution", abstract = "The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolutionary scenarios are poorly described by such models. Further, even when evolution proceeds in a tree-like manner, analysis of the data may not be best served by using methods that enforce a tree structure but rather by a richer visualization of the data to evaluate its properties, at least as an essential first step. Thus, phylogenetic networks should be employed when reticulate events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved, and, even in the absence of such events, phylogenetic networks have a useful role to play. This article reviews the terminology used for phylogenetic networks and covers both split networks and reticulate networks, how they are defined, and how they can be interpreted. Additionally, the article outlines the beginnings of a comprehensive statistical framework for applying split network methods. We show how split networks can represent confidence sets of trees and introduce a conservative statistical test for whether the conflicting signal in a network is treelike. Finally, this article describes a new program, SplitsTree4, an interactive and comprehensive tool for inferring different types of phylogenetic networks from sequences, distances, and trees.", url = "https://doi.org/10.1093/molbev/msj030", doi = "10.1093/molbev/msj030", openalex = "W2055298722", references = "doi101016s0169534700020267, doi101038nrg929, doi10108010635150390235520, doi101093bioinformaticsbtg180, doi101093molbevmsi111, doi101093sysbio463523, doi101111j155856461985tb00420x" } @article{doi101126science1105113, author = "Teeling, Emma C. and Springer, Mark S. and Madsen, Ole and Bates, Paul J. J. and O’Brien, Stephen J. and Murphy, William J.", title = "A Molecular Phylogeny for Bats Illuminates Biogeography and the Fossil Record", year = "2005", journal = "Science", abstract = "Bats make up more than 20\% of extant mammals, yet their evolutionary history is largely unknown because of a limited fossil record and conflicting or incomplete phylogenies. Here, we present a highly resolved molecular phylogeny for all extant bat families. Our results support the hypothesis that megabats are nested among four major microbat lineages, which originated in the early Eocene [52 to 50 million years ago (Mya)], coincident with a significant global rise in temperature, increase in plant diversity and abundance, and the zenith of Tertiary insect diversity. Our data suggest that bats originated in Laurasia, possibly in North America, and that three of the major microbat lineages are Laurasian in origin, whereas the fourth is Gondwanan. Combining principles of ghost lineage analysis with molecular divergence dates, we estimate that the bat fossil record underestimates (unrepresented basal branch length, UBBL) first occurrences by, on average, 73\% and that the sum of missing fossil history is 61\%.", url = "https://doi.org/10.1126/science.1105113", doi = "10.1126/science.1105113", openalex = "W1997655974", references = "doi101007bf01454359, doi101017cbo9780511529924, doi10103835003188, doi10103835055536, doi101073pnas0334222100, doi101073pnas111551998, doi101126science1067179, doi101126science11536548, doi101126science15437541333, doi101126science28454232153, doi1023071223169" } @article{doi101073pnas0601928103, author = "Hughes, Colin E. and Eastwood, Ruth J.", title = "Island radiation on a continental scale: Exceptional rates of plant diversification after uplift of the Andes", year = "2006", journal = "Proceedings of the National Academy of Sciences", abstract = "Species radiations provide unique insights into evolutionary processes underlying species diversification and patterns of biodiversity. To compare plant diversification over a similar time period to the recent cichlid fish radiations, which are an order of magnitude faster than documented bird, arthropod, and plant radiations, we focus on the high-altitude flora of the Andes, which is the most species-rich of any tropical mountains. Because of the recent uplift of the northern Andes, the upland environments where much of this rich endemic flora is found have been available for colonization only since the late Pliocene or Pleistocene, 2-4 million years (Myr) ago. Using DNA sequence data we identify a monophyletic group within the genus Lupinus representing 81 species endemic to the Andes. The age of this clade is estimated to be 1.18-1.76 Myr, implying a diversification rate of 2.49-3.72 species per Myr. This exceeds previous estimates for plants, providing the most spectacular example of explosive plant species diversification documented to date. Furthermore, it suggests that the high cichlid diversification rates are not unique. Lack of key innovations associated with the Andean Lupinus clade suggests that diversification was driven by ecological opportunities afforded by the emergence of island-like habitats after Andean uplift. Data from other genera indicate that lupines are one of a set of similarly rapid Andean plant radiations, continental in scale and island-like in stimulus, suggesting that the high-elevation Andean flora provides a system that rivals other groups, including cichlids, for understanding rapid species diversification.", url = "https://doi.org/10.1073/pnas.0601928103", doi = "10.1073/pnas.0601928103", openalex = "W2045366837", references = "doi101038nrg1316, doi101073pnas0506330102, doi101073pnas89178322, doi1011300016760620001121091uhotca23co2, doi1023072419593" } @article{doi101146annurevecolsys37091305110100, author = "Parmesan, Camille", title = "Ecological and Evolutionary Responses to Recent Climate Change", year = "2006", journal = "Annual Review of Ecology Evolution and Systematics", abstract = "Ecological changes in the phenology and distribution of plants and animals are occurring in all well-studied marine, freshwater, and terrestrial groups. These observed changes are heavily biased in the directions predicted from global warming and have been linked to local or regional climate change through correlations between climate and biological variation, field and laboratory experiments, and physiological research. Range-restricted species, particularly polar and mountaintop species, show severe range contractions and have been the first groups in which entire species have gone extinct due to recent climate change. Tropical coral reefs and amphibians have been most negatively affected. Predator-prey and plant-insect interactions have been disrupted when interacting species have responded differently to warming. Evolutionary adaptations to warmer conditions have occurred in the interiors of species' ranges, and resource use and dispersal have evolved rapidly at expanding range margins. Observed genetic shifts modulate local effects of climate change, but there is little evidence that they will mitigate negative effects at the species level.", url = "https://doi.org/10.1146/annurev.ecolsys.37.091305.110100", doi = "10.1146/annurev.ecolsys.37.091305.110100", openalex = "W2135858501", references = "doi1010160169534794902488, doi10103835079180, doi101038369448a0, doi101038382146a0, doi101038386698a0, doi101038nature01286, doi101038nature04095, doi101038nature04246, doi101071mf99078, doi101093aesa492190, doi101126science28954872068, doi101126science2925517673, doi1023071939337, doi1023071940431, doi105860choice301495, openalexw1500291103, openalexw2151235472" } @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{doi101016jcell200710022, author = "Otto, Sarah P.", title = "The Evolutionary Consequences of Polyploidy", year = "2007", journal = "Cell", url = "https://doi.org/10.1016/j.cell.2007.10.022", doi = "10.1016/j.cell.2007.10.022", openalex = "W2010032067", references = "doi101371journalpbio0030314, openalexw1493831303, openalexw2065039187" } @article{doi101073pnas0704088104, author = "Hunt, Gene", title = "The relative importance of directional change, random walks, and stasis in the evolution of fossil lineages", year = "2007", journal = "Proceedings of the National Academy of Sciences", abstract = "The nature of evolutionary changes recorded by the fossil record has long been controversial, with particular disagreement concerning the relative frequency of gradual change versus stasis within lineages. Here, I present a large-scale, statistical survey of evolutionary mode in fossil lineages. Over 250 sequences of evolving traits were fit by using maximum likelihood to three evolutionary models: directional change, random walk, and stasis. Evolution in these traits was rarely directional; in only 5\% of fossil sequences was directional evolution the most strongly supported of the three modes of change. The remaining 95\% of sequences were divided nearly equally between random walks and stasis. Variables related to body size were significantly less likely than shape traits to experience stasis. This finding is in accord with previous suggestions that size may be more evolutionarily labile than shape and is consistent with some but not all of the mechanisms proposed to explain evolutionary stasis. In general, similar evolutionary patterns are observed across other variables, such as clade membership and temporal resolution, but there is some evidence that directional change in planktonic organisms is more frequent than in benthic organisms. The rarity with which directional evolution was observed in this study corroborates a key claim of punctuated equilibria and suggests that truly directional evolution is infrequent or, perhaps more importantly, of short enough duration so as to rarely register in paleontological sampling.", url = "https://doi.org/10.1073/pnas.0704088104", doi = "10.1073/pnas.0704088104", openalex = "W2123848440", references = "doi10100703064746897, doi10100797814613088367, doi101016s003101829600096x, doi101016s0031018296000995, doi101017s0094837300004000, doi101017s0094837300005224, doi101017s0094837300012549, doi101093aesa383396, doi101111j155856461979tb04694x, doi101111j155856461982tb05068x, doi1023073803199, doi102307jctvjsf433, doi105860choice333929, doi105860choice396411" } @article{doi101093bioinformaticsbtm538, author = "Harmon, Luke J. and Weir, Jason T. and Brock, Chad D. and Glor, Richard E. and Challenger, Wendell", title = "GEIGER: investigating evolutionary radiations", year = "2007", journal = "Bioinformatics", abstract = "This open source software is written entirely in the R language and is freely available through the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/.", url = "https://doi.org/10.1093/bioinformatics/btm538", doi = "10.1093/bioinformatics/btm538", openalex = "W2117368100", references = "doi10103844766, doi101093oso97801985052350010001, doi101111j001438202001tb00826x" } @article{doi101111j13652435200701275x, author = "Fussmann, Gregor F. and Loreau, Michel and Abrams, Peter A.", title = "Eco‐evolutionary dynamics of communities and ecosystems", year = "2007", journal = "Functional Ecology", abstract = "Summary We review theoretical and empirical studies to identify instances where evolutionary processes significantly affect the dynamics of populations, communities and ecosystems. Early theoretical work on eco‐evolutionary dynamics was concerned with the effect of (co)evolution on the stability of two‐species predator–prey systems and the occurrence of character displacement in simple competitive systems. Today's theoretical ecologists are extending this work to study the eco‐evolutionary dynamics of multispecies communities and the functioning and evolutionary emergence of ecosystems. In terms of methodology, eco‐evolutionary modelling has diversified from simple, locus‐based population genetic models to encompass models of clonal selection, quantitative trait dynamics and adaptive dynamics. The few empirical studies on community dynamics that explicitly considered evolutionary processes support the view that evolutionary and ecological dynamics often occur on similar time‐scales, and that they co‐determine the dynamical behaviour of ecological communities.", url = "https://doi.org/10.1111/j.1365-2435.2007.01275.x", doi = "10.1111/j.1365-2435.2007.01275.x", openalex = "W2143913979", references = "doi101023a1006554906681, doi101038116461b0, doi10103822521, doi101086282160, doi101111j155856461976tb00911x, doi101126science1070315, doi1015159780691209418, doi1015159780691224244, doi1015159781400847266, doi101890039000, doi1023072408012, doi1023072411924, doi102307jctvx5wbbh, openalexw1528487914" } @article{doi101111j14754983200600614x, author = "Erwin, Douglas H.", title = "DISPARITY: MORPHOLOGICAL PATTERN AND DEVELOPMENTAL CONTEXT", year = "2007", journal = "Palaeontology", abstract = "Abstract: The distribution of organic forms is clumpy at any scale from populations to the highest taxonomic categories, and whether considered within clades or within ecosystems. The fossil record provides little support for expectations that the morphological gaps between species or groups of species have increased through time as it might if the gaps were created by extinction of a more homogeneous distribution of morphologies. As the quantitative assessments of morphology have replaced counts of higher taxa as a metric of morphological disparity, numerous studies have demonstrated the rapid construction of morphospace early in evolutionary radiations, and have emphasized the difference between taxonomic measures of morphological diversity and quantitative assessments of disparity. Other studies have evaluated changing patterns of disparity across mass extinctions, ecomorphological patterns and the patterns of convergence within ecological communities, while the development of theoretical morphology has greatly aided efforts to understand why some forms do not occur. A parallel, and until recently, largely separate research effort in evolutionary developmental biology has established that the developmental toolkit underlying the remarkable breadth of metazoan form is largely identical among Bilateria, and many components are shared among all metazoa. Underlying this concern with disparity is a question about temporal variation in the production of morphological innovations, a debate over the relative significance of the generation of new morphologies vs. differential probabilities of their successful introduction, and the relative importance of constraint, convergence and contingency in the evolution of form.", url = "https://doi.org/10.1111/j.1475-4983.2006.00614.x", doi = "10.1111/j.1475-4983.2006.00614.x", openalex = "W2091948436", references = "doi101016jprecamres200511003, doi101017cbo9781139164856, doi101017s009483730001263x, doi101017s0094837300015864, doi101073pnas050586297, doi101111j1525142x200600101x, doi101666009483731999251mditer20co2, doi1016660094837320000260056cefisg20co2, doi1016660094837320040300652atrode20co2, doi105860choice333929, foote1996perspective, openalexw2055967869, openalexw635257420" } @article{doi101139e07003, author = "Gehlîng, James G. and Narbonne, Guy M.", title = "Spindle-shaped Ediacara fossils from the Mistaken Point assemblage, Avalon Zone, Newfoundland", year = "2007", journal = "Canadian Journal of Earth Sciences", abstract = "The Mistaken Point assemblage of the Ediacara fossils is dominated by rangeomorphs with homologous fractal branching elements. The most distinctive are the fusiform fossils, herein named Fractofusus misrai n.gen., and n.sp., and Fractofusus andersoni n.gen., and n.sp. Although endemic to the Newfoundland portion of the Avalonia terrane, they dominated deep sea-floor communities below the photic zone, in the mid-Ediacaran Period (ca. 575–560 Ma). Their biological affinities remain uncertain, but their architecture suggests a phylogenetic position near the base of the Metazoa.", url = "https://doi.org/10.1139/e07-003", doi = "10.1139/e07-003", openalex = "W2142748826", references = "doi101016jearscirev200508004" } @article{doi101186147121487214, author = "Drummond, Alexei J. and Rambaut, Andrew", title = "BEAST: Bayesian evolutionary analysis by sampling trees", year = "2007", journal = "BMC Evolutionary Biology", abstract = "BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provides a resource for the further development of new models and statistical methods of evolutionary analysis.", url = "https://doi.org/10.1186/1471-2148-7-214", doi = "10.1186/1471-2148-7-214", openalex = "W2110835349", references = "doi101007bf00160154, doi101007bf02101694, doi101007bf02101990, doi101016b9781483227344500176, doi101016s0169534703002167, doi10106311699114, doi101073pnas6341088, doi10108010635150290102456, doi101093bioinformatics178754, doi101093biomet57197, doi101093molbevmsi103, doi101093oxfordjournalsmolbeva003974, doi101093oxfordjournalsmolbeva025892, doi101093oxfordjournalsmolbeva040153, doi101126science1101074, doi101371journalpbio0040088, rambaut1998estimating" } @article{doi101016jjhevol200811001, author = "Lyman, R. Lee", title = "Graphing evolutionary pattern and process: a history of techniques in archaeology and paleobiology", year = "2008", journal = "Journal of Human Evolution", url = "https://doi.org/10.1016/j.jhevol.2008.11.001", doi = "10.1016/j.jhevol.2008.11.001", openalex = "W2111567600", references = "doi101017s001675680008660x, doi101111j1469185x1930tb00901x, doi101111j155856461947tb01335x, openalexw201159638" } @article{doi101073pnas0802597105, author = "Alroy, John", title = "Dynamics of origination and extinction in the marine fossil record", year = "2008", journal = "Proceedings of the National Academy of Sciences", abstract = "The discipline-wide effort to database the fossil record at the occurrence level has made it possible to estimate marine invertebrate extinction and origination rates with much greater accuracy. The new data show that two biotic mechanisms have hastened recoveries from mass extinctions and confined diversity to a relatively narrow range over the past 500 million years (Myr). First, a drop in diversity of any size correlates with low extinction rates immediately afterward, so much so that extinction would almost come to a halt if diversity dropped by 90\%. Second, very high extinction rates are followed by equally high origination rates. The two relationships predict that the rebound from the current mass extinction will take at least 10 Myr, and perhaps 40 Myr if it rivals the Permo-Triassic catastrophe. Regardless, any large event will result in a dramatic ecological and taxonomic restructuring of the biosphere. The data also confirm that extinction and origination rates both declined through the Phanerozoic and that several extinctions in addition to the Permo-Triassic event were particularly severe. However, the trend may be driven by taxonomic biases and the rates vary in accord with a simple log normal distribution, so there is no sharp distinction between background and mass extinctions. Furthermore, the lack of any significant autocorrelation in the data is inconsistent with macroevolutionary theories of periodicity or self-organized criticality.", url = "https://doi.org/10.1073/pnas.0802597105", doi = "10.1073/pnas.0802597105", openalex = "W2075331526", references = "doi101017s0094837300003778, doi101017s0094837300004917, doi101017s0094837300006539, doi101073pnas111144698, doi101073pnas813801, doi101126science1156963, doi101666009483731999251mditer20co2, doi1016660094837320040300522oeamdo20co2, doi1016660094837320050310006poaeit20co2" } @article{doi101093molbevmsr121, author = "Tamura, Koichiro and Peterson, Daniel G. and Peterson, Nora and Stecher, Glen and Nei, M and Kumar, Sudhir", title = "MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods", year = "2011", journal = "Molecular Biology and Evolution", abstract = "Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net.", url = "https://doi.org/10.1093/molbev/msr121", doi = "10.1093/molbev/msr121", openalex = "W2132632499", references = "doi101007bf01734359, doi101007bf02101694, doi10108010635150390235520, doi10108010635150490522304, doi101093bioinformatics149817, doi101093bioinformaticsbtl446, doi101093biomet762297, doi101093oso97801951358480010001, doi101093oxfordjournalsmolbeva040023, doi101093oxfordjournalsmolbeva040454, doi101093sysbiosyq010, doi101111j155856461985tb00420x, doi101186147121055113, openalexw3217097258" } @article{doi101073pnas1120774109, author = "Evans, Alistair R. and Jones, David and Boyer, Alison G. and Brown, James H. and Costa, Daniel P. and Ernest, S. K. Morgan and Fitzgerald, Erich M. G. and Fortelius, Mikael and Gittleman, John L. and Hamilton, Marcus J. and Harding, Larisa E. and Lintulaakso, Kari and Lyons, S. Kathleen and Okie, Jordan G. and Saarinen, Juha and Sibly, Richard M. and Smith, Felisa A. and Stephens, Patrick R. and Theodor, Jessica M. and Uhen, Mark D.", title = "The maximum rate of mammal evolution", year = "2012", journal = "Proceedings of the National Academy of Sciences", abstract = "How fast can a mammal evolve from the size of a mouse to the size of an elephant? Achieving such a large transformation calls for major biological reorganization. Thus, the speed at which this occurs has important implications for extensive faunal changes, including adaptive radiations and recovery from mass extinctions. To quantify the pace of large-scale evolution we developed a metric, clade maximum rate, which represents the maximum evolutionary rate of a trait within a clade. We applied this metric to body mass evolution in mammals over the last 70 million years, during which multiple large evolutionary transitions occurred in oceans and on continents and islands. Our computations suggest that it took a minimum of 1.6, 5.1, and 10 million generations for terrestrial mammal mass to increase 100-, and 1,000-, and 5,000-fold, respectively. Values for whales were down to half the length (i.e., 1.1, 3, and 5 million generations), perhaps due to the reduced mechanical constraints of living in an aquatic environment. When differences in generation time are considered, we find an exponential increase in maximum mammal body mass during the 35 million years following the Cretaceous-Paleogene (K-Pg) extinction event. Our results also indicate a basic asymmetry in macroevolution: very large decreases (such as extreme insular dwarfism) can happen at more than 10 times the rate of increases. Our findings allow more rigorous comparisons of microevolutionary and macroevolutionary patterns and processes.", url = "https://doi.org/10.1073/pnas.1120774109", doi = "10.1073/pnas.1120774109", openalex = "W2035228868", references = "colbert1948evolution, doi101017cbo9780511608551, doi101017cbo9781139167826, doi101017s0094837300016201, doi101038387173a0, doi1018900814941, doi1023072405671, doi1023072529762, doi107312simp93764, openalexw1504049102, openalexw1558456135" } @article{doi101111j15585646201101567x, author = "Baets, Kenneth De and Klug, Christian and Korn, Dieter and Landman, Neil H.", title = "EARLY EVOLUTIONARY TRENDS IN AMMONOID EMBRYONIC DEVELOPMENT", year = "2012", journal = "Evolution", abstract = "During the Devonian Nekton Revolution, ammonoids show a progressive coiling of their shell just like many other pelagic mollusk groups. These now extinct, externally shelled cephalopods derived from bactritoid cephalopods with a straight shell in the Early Devonian. During the Devonian, evolutionary trends toward tighter coiling and a size reduction occurred in ammonoid embryonic shells. In at least three lineages, descendants with a closed umbilicus evolved convergently from forms with an opening in the first whorl (umbilical window). Other lineages having representatives with open umbilici became extinct around important Devonian events whereas only those with more tightly coiled embryonic shells survived. This change was accompanied by an evolutionary trend in shape of the initial chamber, but no clear trend in its size. The fact that several ammonoid lineages independently reduced and closed the umbilical window more or less synchronously indicates that common driving factors were involved. A trend in size decrease of the embryos as well as the concurrent increase in adult size in some lineages likely reflects a fundamental change in reproductive strategies toward a higher fecundity early in the evolutionary history of ammonoids. This might have played an important role in their subsequent success as well as in their demise.", url = "https://doi.org/10.1111/j.1558-5646.2011.01567.x", doi = "10.1111/j.1558-5646.2011.01567.x", openalex = "W1919528436", references = "doi101007978147579153213, doi101007978147579153216, doi1011861471214811115, openalexw2531009674" } @article{doi101111j15585646201201723x, author = "Slater, Graham J. and Harmon, Luke J. and Alfaro, Michael E.", title = "INTEGRATING FOSSILS WITH MOLECULAR PHYLOGENIES IMPROVES INFERENCE OF TRAIT EVOLUTION", year = "2012", journal = "Evolution", abstract = "Comparative biologists often attempt to draw inferences about tempo and mode in evolution by comparing the fit of evolutionary models to phylogenetic comparative data consisting of a molecular phylogeny with branch lengths and trait measurements from extant taxa. These kinds of approaches ignore historical evidence for evolutionary pattern and process contained in the fossil record. In this article, we show through simulation that incorporation of fossil information dramatically improves our ability to distinguish among models of quantitative trait evolution using comparative data. We further suggest a novel Bayesian approach that allows fossil information to be integrated even when explicit phylogenetic hypotheses are lacking for extinct representatives of extant clades. By applying this approach to a comparative dataset comprising body sizes for caniform carnivorans, we show that incorporation of fossil information not only improves ancestral state estimates relative to those derived from extant taxa alone, but also results in preference of a model of evolution with trend toward large body size over alternative models such as Brownian motion or Ornstein-Uhlenbeck processes. Our approach highlights the importance of considering fossil information when making macroevolutionary inference, and provides a way to integrate the kind of sparse fossil information that is available to most evolutionary biologists.", url = "https://doi.org/10.1111/j.1558-5646.2012.01723.x", doi = "10.1111/j.1558-5646.2012.01723.x", openalex = "W1735656240", references = "doi101007s116920129171x, doi101017s0022336000059126, doi10106311699114, doi101073pnas0704088104, doi10108001621459199510476572, doi101086284325, doi101093bioinformaticsbtm538, doi101093biomet57197, doi101093oso97801985052350010001, doi101093sysbio274401, doi101111j001438202003tb00285x, doi101111j1469185x201100178x, doi101146annurevearth271463, doi101186147121487214, doi1023073802723, foote1996perspective, gingerich1987evolution" } @article{doi105860choice500902, title = "Rereading the fossil record: the growth of paleobiology as an evolutionary discipline", year = "2012", journal = "Choice Reviews Online", abstract = "Although fossils have provided some of the most important evidence for evolution, the discipline of paleontology has not always had a central place in evolutionary biology. Beginning in Darwin's day, and for much of the twentieth century, paleontologists were often regarded as mere fossil collectors by many evolutionary biologists, their attempts to contribute to evolutionary theory ignored or regarded with scorn. In the 1950s, however, paleontologists began mounting a counter-movement that insisted on the valid, important, and original contribution of paleontology to evolutionary theory. This movement, called by its proponents, advocated for an approach to the fossil record that was theoretical, quantitative, and oriented towards explaining the broad patterns of evolution and extinction in the history of life. Rereading the Fossil Record provides, as never before, a historical account of the origin, rise, and importance of paleobiology, from the mid-nineteenth century to the late 1980s. Drawing on a wealth of archival material, David Sepkoski shows how the movement was conceived and promoted by a small but influential group of paleontologists - including Stephen Jay Gould and Niles Eldredge, among others - and examines the intellectual, disciplinary, and political dynamics involved in the ascendancy of paleobiology. By emphasizing the close relationship between paleobiology and other evolutionary disciplines, this book writes a new chapter in the history of evolutionary biology, while also offering insights into the dynamics of disciplinary change in modern science.", url = "https://doi.org/10.5860/choice.50-0902", doi = "10.5860/choice.50-0902", openalex = "W653308317" } @article{doi101038ncomms2958, author = "Rabosky, Daniel L. and Santini, Francesco and Eastman, Jonathan M. and Smith, Stephen A. and Sidlauskas, Brian L. and Chang, Jonathan and Alfaro, Michael E.", title = "Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation", year = "2013", journal = "Nature Communications", url = "https://doi.org/10.1038/ncomms2958", doi = "10.1038/ncomms2958", openalex = "W2054715003", references = "doi10100797894010058529, doi101016jtree201204012, doi101017s009483730001280x, doi101023a1013311015886, doi10103714088000, doi101038248107a0, doi101038nature07893, doi101038nature10516, doi101038nrg2278, doi101073pnas0704088104, doi101086303327, doi101093bibbbn013, doi101093bioinformaticsbtl446, doi101093biomet824711, doi101093oxfordjournalsmolbeva003974, doi101093oxfordjournalsmolbeva025811, doi101111j155856461971tb01868x, doi101111j15585646201001026x, doi101146annurevecolsys281129, doi101146annurevecolsys291293, doi101186147121055113, doi1011861471214811275, doi1023072405671, doi105962bhltitle82303, doi107312simp93764" } @article{doi101371journalpone0073535, author = "Miya, Masaki and Friedman, Matt and Satoh, Takashi and Takeshima, Hirohiko and Sado, Tetsuya and Iwasaki, Wataru and Yamanoue, Yusuke and Nakatani, Masanori and Mabuchi, Kohji and Inoue, Jun and Poulsen, Jan Yde and Fukunaga, Tsukasa and Sato, Yukuto and Nishida, Mutsumi", title = "Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families", year = "2013", journal = "PLoS ONE", abstract = {Uncertainties surrounding the evolutionary origin of the epipelagic fish family Scombridae (tunas and mackerels) are symptomatic of the difficulties in resolving suprafamilial relationships within Percomorpha, a hyperdiverse teleost radiation that contains approximately 17,000 species placed in 13 ill-defined orders and 269 families. Here we find that scombrids share a common ancestry with 14 families based on (i) bioinformatic analyses using partial mitochondrial and nuclear gene sequences from all percomorphs deposited in GenBank (10,733 sequences) and (ii) subsequent mitogenomic analysis based on 57 species from those targeted 15 families and 67 outgroup taxa. Morphological heterogeneity among these 15 families is so extraordinary that they have been placed in six different perciform suborders. However, members of the 15 families are either coastal or oceanic pelagic in their ecology with diverse modes of life, suggesting that they represent a previously undetected adaptive radiation in the pelagic realm. Time-calibrated phylogenies imply that scombrids originated from a deep-ocean ancestor and began to radiate after the end-Cretaceous when large predatory epipelagic fishes were selective victims of the Cretaceous-Paleogene mass extinction. We name this clade of open-ocean fishes containing Scombridae "Pelagia" in reference to the common habitat preference that links the 15 families.}, url = "https://doi.org/10.1371/journal.pone.0073535", doi = "10.1371/journal.pone.0073535", openalex = "W2087061078", references = "doi101111j14754983201201165x" } @article{doi104404hystrix2416298, author = "Collyer, Michael L. and Adams, Dean C.", title = "Phenotypic trajectory analysis: comparison of shape change patterns in evolution and ecology", year = "2013", journal = "Bollettino del CILEA (CILEA)", abstract = {Research using shape data from geometric morphometric (GM) methods in ecology and evolutionary biology is typically comparative, analyzing shapes and shape change over different points along ecological or evolutionary gradients. Whereas standard multivariate statistics procedures are fine for "static" variation - testing for location differences of groups in multivariate data spaces - they are limited for "dynamic" variation - testing specific differences in the ways groups change locations associated with changes in state along ecological, developmental or evolutionary gradients. In this paper, we show that continuous phenotypic change can be described by trajectories in multivariate data spaces. We describe the geometric attributes of phenotypic change trajectories (size, direction, and shape), specifically for GM data. We illustrate, with examples, how differences in such attributes can function as test statistics for comparative analyses in order to understand the mechanisms that produce dynamic differences in shape change. We demonstrate that analysis of such attributes - called phenotypic trajectory analysis (PTA) - is a general analysis that can be applied to various types of research questions concerned with measuring dynamic variation. Finally, we posit some challenges for the future for this novel analytical method.}, url = "https://doi.org/10.4404/hystrix-24.1-6298", doi = "10.4404/hystrix-24.1-6298", openalex = "W2156451393", references = "doi1011861471214811115" } @article{doi101002evan21400, author = "Gingerich, Philip D.", title = "Species in the primate fossil record", year = "2014", journal = "Evolutionary Anthropology Issues News and Reviews", abstract = "Species in the fossil record are population pools of genetic and phenetic variation at a place and time, morphologically recognizable and distinguishable from others by empirical standards. Change through time can be substantial, requiring subdivision of lineages that becomes more arbitrary as they become more complete. Evolution is about form, space, and time; it is about variation and change. Interpretation of species in the fossil record touches all of these.", url = "https://doi.org/10.1002/evan.21400", doi = "10.1002/evan.21400", openalex = "W1543237746", references = "openalexw201159638" } @article{doi101017s0140525x14000090, author = "Kline, Michelle A.", title = "How to learn about teaching: An evolutionary framework for the study of teaching behavior in humans and other animals", year = "2014", journal = "Behavioral and Brain Sciences", abstract = "The human species is more reliant on cultural adaptation than any other species, but it is unclear how observational learning can give rise to the faithful transmission of cultural adaptations. One possibility is that teaching facilitates accurate social transmission by narrowing the range of inferences that learners make. However, there is wide disagreement about how to define teaching, and how to interpret the empirical evidence for teaching across cultures and species. In this article I argue that disputes about the nature and prevalence of teaching across human societies and nonhuman animals are based on a number of deep-rooted theoretical differences between fields, as well as on important differences in how teaching is defined. To reconcile these disparate bodies of research, I review the three major approaches to the study of teaching - mentalistic, culture-based, and functionalist - and outline the research questions about teaching that each addresses. I then argue for a new, integrated framework that differentiates between teaching types according to the specific adaptive problems that each type solves, and apply this framework to restructure current empirical evidence on teaching in humans and nonhuman animals. This integrative framework generates novel insights, with broad implications for the study of the evolution of teaching, including the roles of cognitive constraints and cooperative dilemmas in how and when teaching evolves. Finally, I propose an explanation for why some types of teaching are uniquely human, and discuss new directions for research motivated by this framework.", url = "https://doi.org/10.1017/s0140525x14000090", doi = "10.1017/s0140525x14000090", openalex = "W2064673991", references = "doi1010160022519364900384, doi1010160022519364900396, doi101016s1090513800000714, doi101017cbo9780511815355, doi101017s0140525x0100396x, doi101017s0140525x05000129, doi101086667653, doi101086668207, doi101126science7466396, doi101371journalpone0045150, doi101515mamm19673111, doi1023071367778, doi1023072804509, openalexw2135943618, openalexw2798374369" } @article{doi101371journalpbio1001853, author = "Benson, Roger and Campione, Nicolás E. and Carrano, Matthew T. and Mannion, Philip D. and Sullivan, Corwin and Upchurch, Paul and Evans, David C.", title = "Rates of Dinosaur Body Mass Evolution Indicate 170 Million Years of Sustained Ecological Innovation on the Avian Stem Lineage", year = "2014", journal = "PLoS Biology", abstract = "Large-scale adaptive radiations might explain the runaway success of a minority of extant vertebrate clades. This hypothesis predicts, among other things, rapid rates of morphological evolution during the early history of major groups, as lineages invade disparate ecological niches. However, few studies of adaptive radiation have included deep time data, so the links between extant diversity and major extinct radiations are unclear. The intensively studied Mesozoic dinosaur record provides a model system for such investigation, representing an ecologically diverse group that dominated terrestrial ecosystems for 170 million years. Furthermore, with 10,000 species, extant dinosaurs (birds) are the most speciose living tetrapod clade. We assembled composite trees of 614-622 Mesozoic dinosaurs/birds, and a comprehensive body mass dataset using the scaling relationship of limb bone robustness. Maximum-likelihood modelling and the node height test reveal rapid evolutionary rates and a predominance of rapid shifts among size classes in early (Triassic) dinosaurs. This indicates an early burst niche-filling pattern and contrasts with previous studies that favoured gradualistic rates. Subsequently, rates declined in most lineages, which rarely exploited new ecological niches. However, feathered maniraptoran dinosaurs (including Mesozoic birds) sustained rapid evolution from at least the Middle Jurassic, suggesting that these taxa evaded the effects of niche saturation. This indicates that a long evolutionary history of continuing ecological innovation paved the way for a second great radiation of dinosaurs, in birds. We therefore demonstrate links between the predominantly extinct deep time adaptive radiation of non-avian dinosaurs and the phenomenal diversification of birds, via continuing rapid rates of evolution along the phylogenetic stem lineage. This raises the possibility that the uneven distribution of biodiversity results not just from large-scale extrapolation of the process of adaptive radiation in a few extant clades, but also from the maintenance of evolvability on vast time scales across the history of life, in key lineages.", url = "https://doi.org/10.1371/journal.pbio.1001853", doi = "10.1371/journal.pbio.1001853", openalex = "W2155522161", references = "doi101007b97636, doi101017s009483730001263x, doi101017s009483730001280x, doi10103835086500, doi10103844766, doi101038nature11631, doi10108010635150490445706, doi101086284325, doi101093bioinformaticsbtm538, doi101093oso97801985052350010001, doi101093oso97801985404720010001, doi101098rspb20122526, doi101111j001438202003tb00285x, doi101111j1469185x201000137x, doi101111j15585646201201723x, doi101126science1144066, doi101126science1161833, doi101146annurevecolsys39110707173447, doi101159000452856, doi101186174170071060, doi101198tech2003s146, doi101371journalpbio1001853, doi101371journalpone0007390, doi101371journalpone0044318, doi10166612041, martinsander2006bone, openalexw2145250129" } @article{doi1011112041210x12420, author = "Clavel, Julien and Escarguel, Gilles and Merceron, Gildas", title = "mv morph: an r package for fitting multivariate evolutionary models to morphometric data", year = "2015", journal = "Methods in Ecology and Evolution", abstract = "Summary We present mv morph, a package of multivariate phylogenetic comparative methods for the r statistical environment. mv morph is freely available on the cran package repository (http://cran.r-project.org/web/packages/mvMORPH/). mv morph allows fitting a range of multivariate evolutionary models under a maximum‐likelihood criterion. Initially developed in the context of phylogenetic analysis of multiple morphometric traits, its use can be extended to any biological data set with one or multiple covarying continuous traits. All the fitting models include the possibility to use simmap ‐like mapping, which may be useful for fitting changes along lineages at a given point in time. All models provide diagnostic metrics for convergence and reliability of estimates, as well as the possibility to include trait measurement errors in model estimates. New features provided by the mv morph package include the possibility of fitting models with changes in the mode of evolution along the phylogeny, which will be particularly meaningful in comparative analyses that include extinct taxa, for example when testing changes in evolutionary mode associated with global biotic/abiotic events. We briefly describe the models already included in mv morph and provide some demonstration of the use of the package with two simulated worked examples.", url = "https://doi.org/10.1111/2041-210x.12420", doi = "10.1111/2041-210x.12420", openalex = "W1527504944", references = "doi1010079783662024522, doi1010079783662053898, doi10103844766, doi101086284325, doi101086383584, doi1011112041210x12035, doi101111j001438202003tb00285x, doi101111j155856461979tb04694x, doi101111j155856461983tb00236x, doi101111j15585646201201723x, doi101111j2041210x201100169x, doi10118614712105788, doi1023073802723" } @article{doi101186s129180150149z, author = "Tendler, Avichai and Mayo, Avi and Alon, Uri", title = "Evolutionary tradeoffs, Pareto optimality and the morphology of ammonite shells", year = "2015", journal = "BMC Systems Biology", abstract = "These results support Pareto optimality theory as an approach to study evolutionary tradeoffs, and demonstrate how this approach can be used to infer the putative tasks that may shape the natural selection of phenotypes.", url = "https://doi.org/10.1186/s12918-015-0149-z", doi = "10.1186/s12918-015-0149-z", openalex = "W2061815181", references = "doi101007978147579153216, doi101111jzo12118, doi1011861471214811115, doi101666100271" } @article{doi1026879424, author = "Benton, Michael J. and Donoghue, PCJ and Vinther, Jakob and Asher, RJ and Friedman, Mary M. and Near, Thomas J.", title = "Constraints on the timescale of animal evolutionary history", year = "2015", journal = "Palaeontologia Electronica", abstract = "Dating the tree of life is a core endeavor in evolutionary biology. Rates of evolution are fundamental to nearly every evolutionary model and process. Rates need dates. There is much debate on the most appropriate and reasonable ways in which to date the tree of life, and recent work has highlighted some confusions and complexities that can be avoided. Whether phylogenetic trees are dated after they have been established, or as part of the process of tree finding, practitioners need to know which calibrations to use. We emphasize the importance of identifying crown (not stem) fossils, levels of confidence in their attribution to the crown, current chronostratigraphic precision, the primacy of the host geological formation and asymmetric confidence intervals. Here we present calibrations for 88 key nodes across the phylogeny of animals, ranging from the root of Metazoa to the last common ancestor of Homo sapiens. Close attention to detail is constantly required: for example, the classic bird-mammal date (base of crown Amniota) has often been given as 310-315 Ma; the 2014 international time scale indicates a minimum age of 318 Ma.", url = "https://doi.org/10.26879/424", doi = "10.26879/424", openalex = "W1962669040", references = "doi10100703064746897, doi101007978146139246016, doi101007bf02101694, doi101016b9780126709506500187, doi101016b9780444594259000196, doi101016b9780444594259000202, doi101016b9780444594259000214, doi101016b9780444594259000238, doi101016b9780444594259000287, doi101016jpalaeo200703046, doi101016jpalwor200911007, doi101016s0301926899000777, doi101016s096098220900431x, doi101017s0006323199005472, doi101017s0016756811000720, doi101017s1464793102006103, doi101017s1464793105006779, doi101017s1477201906002008, doi101023a1018471324332, doi101038377720a0, doi101038nature01264, doi101038nature03150, doi101038nature05634, doi101038nature06134, doi101038nature06277, doi101038nature06614, doi101038nature07855, doi101038nature08322, doi101038nature09810, doi101038nature09864, doi101038nature10291, doi101038nature13718, doi101073pnas1010350107, doi101073pnas1110395108, doi101073pnas9794469, doi10108002724634198110011886, doi10108002724634199710010948, doi10108002724634199810011114, doi10108010635150590950326, doi10108010635150600755396, doi10108010635150701397635, doi101098rstb19790006, doi101098rstb19990489, doi101111j109636421995tb00932x, doi101111j10963642200600293x, doi101111j1469185x1999tb00046x, doi101111j1469185x200900094x, doi101111j1469185x201200220x, doi101111j14754983201001019x, doi101111j14754983201201165x, doi101111pala12125, doi101111zoj12111, doi101126science1157704, doi101139e87124, doi1011861471214813208, doi1012060003009020062970001tatol20co2, doi1012066231, doi101242dev066712, doi101371journalpone0009586, doi101643004585112002002053220co2, doi1016660022336020030770822mbatho20co2, doi102307jctt1xp3v3r, doi105252g2010n4a1, doi105281zenodo18028696, doi105860choice320949, doi105860choice355657, doi105860choice405235, doi105860choice432801, doi105860choice503272, doi107312kiel11918, gardiner1989interrelationships, openalexw2898156694, openalexw78894702" } @article{doi105751es07634200234, author = "Waring, Timothy M. and Kline, Michelle A. and Brooks, Jeremy and Goff, Sandra and Gowdy, John M. and Janssen, Marco A. and Smaldino, Paul E. and Jacquet, Jennifer", title = "A multilevel evolutionary framework for sustainability analysis", year = "2015", journal = "Ecology and Society", abstract = "Waring, T. M., M. A. Kline, J. S. Brooks, S. H. Goff, J. Gowdy, M. A. Janssen, P. E. Smaldino, and J. Jacquet. 2015. A multilevel evolutionary framework for sustainability analysis. Ecology and Society 20(2): 34. https://doi.org/10.5751/ES-07634-200234", url = "https://doi.org/10.5751/es-07634-200234", doi = "10.5751/es-07634-200234", openalex = "W2471972841", references = "doi101371journalpone0045150" } @article{doi101002evan21526, author = "Silcox, Mary and Bloch, Jonathan I. and Boyer, Douglas and Chester, Stephen G. B. and López‐Torres, Sergi", title = "The evolutionary radiation of plesiadapiforms", year = "2017", journal = "Evolutionary Anthropology Issues News and Reviews", abstract = "Very shortly after the disappearance of the non-avian dinosaurs, the first mammals that had features similar to those of primates started appearing. These first primitive forms went on to spawn a rich diversity of plesiadapiforms, often referred to as archaic primates. Like many living primates, plesiadapiforms were small arboreal animals that generally ate fruit, insects, and, occasionally, leaves. However, this group lacked several diagnostic features of euprimates. They also had extraordinarily diverse specializations, represented in eleven families and more than 140 species, which, in some cases, were like nothing seen since in the primate order. Plesiadapiforms are known from all three Northern continents, with representatives that persisted until at least 37 million years ago. In this article we provide a summary of the incredible diversity of plesiadapiform morphology and adaptations, reviewing our knowledge of all eleven families. We also discuss the challenges that remain in our understanding of their ecology and evolution.", url = "https://doi.org/10.1002/evan.21526", doi = "10.1002/evan.21526", openalex = "W2607369018", references = "doi101002ajpa22724, doi101098rspb20132792, doi101126science1503697743, doi105281zenodo13648988, openalexw16475780" } @article{doi101016jcub201701027, author = "Peters, Ralph S. and Krogmann, Lars and Mayer, Christoph and Donath, Alexander and Gunkel, Simon and Meusemann, Karen and Kozlov, Alexey M. and Podsiadłowski, Lars and Petersen, Malte and Lanfear, Robert and Diez, Patricia A. and Heraty, John M. and Kjer, Karl M. and Klopfstein, Seraina and Meier, Rudolf and Polidori, Carlo and Schmitt, Thomas and Liu, Shanlin and Zhou, Xin and Wappler, Torsten and Rust, Jes and Misof, Bernhard and Niehuis, Oliver", title = "Evolutionary History of the Hymenoptera", year = "2017", journal = "Current Biology", url = "https://doi.org/10.1016/j.cub.2017.01.027", doi = "10.1016/j.cub.2017.01.027", openalex = "W2602840959", references = "doi101016jympev201104003, doi101093sysbiosyr107, doi101126science1257570, doi101186147121481452, doi107717peerj1719, openalexw1900040508" } @article{doi101016jjebo201709014, author = "Glowacki, Luke and Wilson, Michael L. and Wrangham, Richard W.", title = "The evolutionary anthropology of war", year = "2017", journal = "Journal of Economic Behavior \& Organization", url = "https://doi.org/10.1016/j.jebo.2017.09.014", doi = "10.1016/j.jebo.2017.09.014", openalex = "W2757278824", references = "doi101038nature16477, doi101086409471, doi101086667653, doi101371journalpone0045150" } @article{doi101038nature21074, author = "Cooney, Christopher R. and Bright, Jen A. and Capp, Elliot J. R. and Chira, Angela M. and Hughes, Emma C. and Moody, Christopher J. and Nouri, L. O. and Varley, Zoë K. and Thomas, Gavin H.", title = "Mega-evolutionary dynamics of the adaptive radiation of birds", year = "2017", journal = "Nature", url = "https://doi.org/10.1038/nature21074", doi = "10.1038/nature21074", openalex = "W2585565608", references = "doi10100703064746897, doi101016c20100662092, doi101016jcub201508003, doi101038nature10516, doi101038nature11631, doi101038nature15697, doi101073pnas1302642110, doi101093molbevmss075, doi1011112041210x12035, doi101111j2041210x201100169x, doi101126science1157704, doi101126science1160662, doi1018637jssv033i02, doi105860choice485062" } @article{doi101098rsbl20180431, author = "Marshall, Charles R. and Finnegan, Seth and Clites, Erica C. and Holroyd, Patricia A. and Bonuso, N. and Cortez, Célia Martins and Davis, Edward and Dietl, Gregory P. and Druckenmiller, Patrick S. and Eng, Ronald and Garcia, Christine and Estes-Smargiassi, Kathryn and Hendy, Austin and Hollis, Kathy and Little, Holly and Nesbitt, Elizabeth A. and Roopnarine, Peter D. and Skibinski, L. and Vendetti, Jann E. and White, Lisa D.", title = "Quantifying the dark data in museum fossil collections as palaeontology undergoes a second digital revolution", year = "2018", journal = "Biology Letters", abstract = "Large-scale analysis of the fossil record requires aggregation of palaeontological data from individual fossil localities. Prior to computers, these synoptic datasets were compiled by hand, a laborious undertaking that took years of effort and forced palaeontologists to make difficult choices about what types of data to tabulate. The advent of desktop computers ushered in palaeontology's first digital revolution-online literature-based databases, such as the Paleobiology Database (PBDB). However, the published literature represents only a small proportion of the palaeontological data housed in museum collections. Although this issue has long been appreciated, the magnitude, and thus potential significance, of these so-called 'dark data' has been difficult to determine. Here, in the early phases of a second digital revolution in palaeontology--the digitization of museum collections-we provide an estimate of the magnitude of palaeontology's dark data. Digitization of our nine institutions' holdings of Cenozoic marine invertebrate collections from California, Oregon and Washington in the USA reveals that they represent 23 times the number of unique localities than are currently available in the PBDB. These data, and the vast quantity of similarly untapped dark data in other museum collections, will, when digitally mobilized, enhance palaeontologists' ability to make inferences about the patterns and processes of past evolutionary and ecological changes.", url = "https://doi.org/10.1098/rsbl.2018.0431", doi = "10.1098/rsbl.2018.0431", openalex = "W2890070252", references = "crossref1977patterns, doi101080027246342012716114, doi101093bioscibiv104, doi101126science3526287762, doi101126scienceaah4787, doi105860choice500902, doi105962bhltitle22153, openalexw1599677799, openalexw45809738, simpson1978patterns" } @article{doi101098rsos191394, author = "Valenzuela‐Toro, Ana M. and Pyenson, Nicholas D.", title = "What do we know about the fossil record of pinnipeds? A historiographical investigation", year = "2019", journal = "Royal Society Open Science", abstract = "The fossil record of pinnipeds (seals, fur seals and walruses) is globally distributed, spanning from the late Oligocene to the Holocene. This record shows a complex evolutionary history that could not otherwise be inferred from their extant relatives, including multiple radiations and iterative ecomorphological specializations among different lineages, many of which are extinct. The fossil record of pinnipeds is not uniformly represented in space and time, however, leaving some gaps in our knowledge. We performed a historiographical investigation of the published fossil record of pinnipeds based on the information available in the Paleobiology Database, with the aim to broadly characterize and evaluate it from a taxonomic, geographical and temporal perspective. We identified major trends, strengths and weaknesses of the pinniped fossil record, including potential biases that may affect our interpretations. We found that 39\% of the record corresponds to extant taxa, which are essentially from the Pleistocene and Holocene. There is a larger record from the Northern Hemisphere, suggesting biases in sampling and collection effort. The record is not strongly biased by sedimentary outcrop bias. Specifically, for extinct species, nearly half of them are represented by a single occurrence and a large proportion have type specimens consisting of single isolated postcranial elements. While the pinniped fossil record may have adequate temporal and taxonomic coverage, it has a strong geographical bias and its comparability is hindered by the incompleteness of type specimens. These results should be taken into account when addressing patterns of their past diversity, evolutionary history and paleoecology.", url = "https://doi.org/10.1098/rsos.191394", doi = "10.1098/rsos.191394", openalex = "W2990272826", references = "doi101017s0094837300006060, doi101098rsbl20180431" } @article{doi101371journalpcbi1006650, author = "Bouckaert, Remco and Vaughan, Timothy G. and Barido‐Sottani, Joëlle and Duchêne, Sebastián and Fourment, Mathieu and Gavryushkina, Alexandra and Heled, Joseph and Jones, Graham and Kühnert, Denise and Maio, Nicola De and Matschiner, Michael and Mendes, Fábio K. and Müller, Nicola F. and Ogilvie, Huw A. and du Plessis, Louis and Popinga, Alex and Rambaut, Andrew and Rasmussen, David A. and Siveroni, Igor and Suchard, Marc A. and Wu, Chieh‐Hsi and Xie, Dong and Zhang, Chi and Stadler, Tanja and Drummond, Alexei J.", title = "BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis", year = "2019", journal = "PLoS Computational Biology", abstract = "Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. It is increasingly appreciated that some evolutionary questions can only be adequately answered by combining evidence from multiple independent sources of data, including genome sequences, sampling dates, phenotypic data, radiocarbon dates, fossil occurrences, and biogeographic range information among others. Including all relevant data into a single joint model is very challenging both conceptually and computationally. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing such software frameworks is increasingly a major scientific activity in its own right, and comes with specific challenges, from practical software design, development and engineering challenges to statistical and conceptual modelling challenges. BEAST 2 is one such computational software platform, and was first announced over 4 years ago. Here we describe a series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release.", url = "https://doi.org/10.1371/journal.pcbi.1006650", doi = "10.1371/journal.pcbi.1006650", openalex = "W2901954177", references = "doi101016jtree200901009, doi101038nature10231, doi101038nature13726, doi101073pnas1319091111, doi101073pnas89178322, doi101080106351501753462876, doi101093acprofoso97801985670280010001, doi101093genetics1551431, doi101093molbevmsp274, doi101093sysbiosyq085, doi101093sysbiosyr047, doi101093sysbiosyv080, doi101093vevey016, doi101098rspa19270118, doi101186147121487214, doi101186s1286201708906, doi1012019780429258411, doi101371journalpbio0040088, doi101371journalpcbi1003537" } @article{doi103389fgene201901049, author = "Marshall, Charles R.", title = "Using the Fossil Record to Evaluate Timetree Timescales", year = "2019", journal = "Frontiers in Genetics", abstract = "The fossil and geologic records provide the primary data used to established absolute timescales for timetrees. For the paleontological evaluation of proposed timetree timescales, and for node-based methods for constructing timetrees, the fossil record is used to bracket divergence times. Minimum brackets (minimum ages) can be established robustly using well-dated fossils that can be reliably assigned to lineages based on positive morphological evidence. Maximum brackets are much harder to establish, largely because it is difficult to establish definitive evidence that the absence of a taxon in the fossil record is real and not just due to the incompleteness of the fossil and rock records. Five primary methods have been developed to estimate maximum age brackets, each of which is discussed. The fact that the fossilization potential of a group typically decreases the closer one approaches its time of origin increases the challenge of estimating maximum age brackets. Additional complications arise: 1) because fossil data actually bracket the time of origin of the first relevant fossilizable morphology (apomorphy), not the divergence time itself; 2) due to the phylogenetic uncertainty in the placement of fossils; 3) because of idiosyncratic temporal and geographic gaps in the rock and fossil records; and 4) if the preservation potential of a group changed significantly during its history. In contrast, uncertainties in the absolute ages of fossils are typically relatively unimportant, even though the vast majority of fossil cannot be dated directly. These issues and relevant quantitative methods are reviewed, and their relative magnitudes assessed, which typically correlate with the age of the group, its geographic range, and species richness.", url = "https://doi.org/10.3389/fgene.2019.01049", doi = "10.3389/fgene.2019.01049", openalex = "W2983202100", references = "doi101016jympev201705008, doi101098rsbl20180431" } @article{doi104039tce201961, author = "Archibald, S. Bruce and Cannings, Robert A.", title = "Fossil dragonflies (Odonata: Anisoptera) from the early Eocene Okanagan Highlands, western North America", year = "2019", journal = "The Canadian Entomologist", abstract = "Abstract We describe the first dragonflies (Odonata: Anisoptera) from the early Eocene Okanagan Highlands of far-western North America from nine fossils. Six are assigned to five species in four new, named genera of Aeshnidae: Antiquiala snyderae new genus and species, Idemlinea versatilis new genus and species, Ypshna brownleei new genus and species, Ypshna latipennata new genus and species, and Eoshna thompsonensis new genus and species; we treat one as Aeshnidae genus A, species A; one is assigned to Gomphidae: Auroradraco eos new genus and species; and we treat a ninth, fragmentary fossil of unknown family affinity as Anisoptera indeterminate genus A, species A, which represents a seventh genus and eighth species. The dominance of Aeshnidae is consistent with other Paleocene and Eocene fossil localities. Auroradraco eos is the only fossil Gomphidae in the roughly 66-million-year gap between occurrences in mid-Cretaceous Burmese amber and the early Oligocene of France. Ypshna appears close to Parabaissaeshna ejerslevense from the early Eocene Fur Formation of Denmark; this is not surprising given Holarctic intercontinental connections at this time and a growing list of insect taxa shared between the Okanagan Highlands and the Fur Formation.", url = "https://doi.org/10.4039/tce.2019.61", doi = "10.4039/tce.2019.61", openalex = "W2981968678", references = "doi104039tce201759" } @article{doi101111pala12496, author = "Cashmore, Daniel D. and Mannion, Philip D. and Upchurch, Paul and Butler, Richard J.", title = "Ten more years of discovery: revisiting the quality of the sauropodomorph dinosaur fossil record", year = "2020", journal = "Palaeontology", abstract = "Abstract Spatiotemporal changes in fossil specimen completeness can bias our understanding of a group's evolutionary history. The quality of the sauropodomorph fossil record was assessed a decade ago, but the number of valid species has since increased by 60\%, and 17\% of the taxa from that study have since undergone taxonomic revision. Here, we assess how 10 years of additional research has changed our outlook on the group's fossil record. We quantified the completeness of all 307 sauropodomorph species currently considered valid using the skeletal completeness metric, which calculates the proportion of a complete skeleton preserved for each taxon. Taxonomic and stratigraphic age revisions, rather than new species, are the drivers of the most significant differences between the current results and those of the previous assessment. No statistical differences appeared when we use our new dataset to generate temporal completeness curves based solely on taxa known in 2009 or 1999. We now observe a severe drop in mean completeness values across the Jurassic–Cretaceous boundary that never recovers to pre‐Cretaceous levels. Explaining this pattern is difficult, as we find no convincing evidence that it is related to environmental preferences or body size changes. Instead, it might result from: (1) reduction of terrestrial fossil preservation space due to sea level rise; (2) ecological specificities and relatively high diagnosability of Cretaceous species; and/or (3) increased sampling of newly explored sites with many previously unknown taxa. Revisiting patterns in this manner allows us to test the longevity of conclusions made in previous quantitative studies.", url = "https://doi.org/10.1111/pala.12496", doi = "10.1111/pala.12496", openalex = "W3017772092", references = "doi1010079780387981413, doi1010079783319242774, doi101016jjsames201411008, doi101016jpalaeo200901002, doi101016jpalaeo200906004, doi101016s0016787876800077, doi101038s41467018051281, doi101038s41467019089972, doi101046j14209101200200472x, doi101073pnas1521478113, doi10108008912969009386535, doi101093bioinformaticsbty633, doi101093zoolinneanzlx103, doi101093zoolinneanzly009, doi101093zoolinneanzly068, doi101098rsbl20180431, doi101098rspb20122526, doi101111brv12255, doi101111j2041210x201100169x, doi101111j2041210x201200196x, doi101111j251761611995tb02031x, doi101126science1105113, doi101126science23547931156, doi101371journalpone0078573, openalexw2611511275" } @article{doi101038s41467022305070, author = "Flannery‐Sutherland, Joseph T. and Silvestro, Daniele and Benton, Michael J.", title = "Global diversity dynamics in the fossil record are regionally heterogeneous", year = "2022", journal = "Nature Communications", abstract = "Global diversity patterns in the fossil record comprise a mosaic of regional trends, underpinned by spatially non-random drivers and distorted by variation in sampling intensity through time and across space. Sampling-corrected diversity estimates from spatially-standardised fossil datasets retain their regional biogeographic nuances and avoid these biases, yet diversity-through-time arises from the interplay of origination and extinction, the processes that shape macroevolutionary history. Here we present a subsampling algorithm to eliminate spatial sampling bias, coupled with advanced probabilistic methods for estimating origination and extinction rates and a Bayesian method for estimating sampling-corrected diversity. We then re-examine the Late Permian to Early Jurassic marine fossil record, an interval spanning several global biotic upheavals that shaped the origins of the modern marine biosphere. We find that origination and extinction rates are regionally heterogenous even during events that manifested globally, highlighting the need for spatially explicit views of macroevolutionary processes through geological time.", url = "https://doi.org/10.1038/s41467-022-30507-0", doi = "10.1038/s41467-022-30507-0", openalex = "W4280565279", references = "doi101016jcub202107071, doi101016jearscirev2020103282, doi101038s41467021237540, doi101038s41559021016088, doi101073pnas2020778118, doi101093sysbiosyab045, doi101126sciadvaba0099, doi101130g479071" }