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Hand SJ, Maugoust J, Beck RMD, Orliac MJ. A 50-million-year-old, three-dimensionally preserved bat skull supports an early origin for modern echolocation. Curr Biol 2023; 33:4624-4640.e21. [PMID: 37858341 DOI: 10.1016/j.cub.2023.09.043] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 07/24/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023]
Abstract
Bats are among the most recognizable, numerous, and widespread of all mammals. But much of their fossil record is missing, and bat origins remain poorly understood, as do the relationships of early to modern bats. Here, we describe a new early Eocene bat that helps bridge the gap between archaic stem bats and the hyperdiverse modern bat radiation of more than 1,460 living species. Recovered from ∼50 million-year-old cave sediments in the Quercy Phosphorites of southwestern France, Vielasia sigei's remains include a near-complete, three-dimensionally preserved skull-the oldest uncrushed bat cranium yet found. Phylogenetic analyses of a 2,665 craniodental character matrix, with and without 36.8 kb of DNA sequence data, place Vielasia outside modern bats, with total evidence tip-dating placing it sister to the crown clade. Vielasia retains the archaic dentition and skeletal features typical of early Eocene bats, but its inner ear shows specializations found in modern echolocating bats. These features, which include a petrosal only loosely attached to the basicranium, an expanded cochlea representing ∼25% basicranial width, and a long basilar membrane, collectively suggest that the kind of laryngeal echolocation used by most modern bats predates the crown radiation. At least 23 individuals of V. sigei are preserved together in a limestone cave deposit, indicating that cave roosting behavior had evolved in bats by the end of the early Eocene; this period saw the beginning of significant global climate cooling that may have been an evolutionary driver for bats to first congregate in caves.
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Affiliation(s)
- Suzanne J Hand
- ESSRC, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jacob Maugoust
- Institut des Sciences de l'Evolution, UMR 5554 CNRS, IRD, EPHE, Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Robin M D Beck
- School of Science, Engineering and Environment, University of Salford, Manchester M5 4WT, UK.
| | - Maeva J Orliac
- Institut des Sciences de l'Evolution, UMR 5554 CNRS, IRD, EPHE, Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
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Pessoa EM, Ribeiro AC, Christenhusz MJM, Coan AI, Jud NA. Is Santaniella a ranunculid? Reassessment of this enigmatic fossil angiosperm from the Lower Cretaceous (Aptian, Crato Konservat-Lagerstätte, Brazil) provides a new interpretation. AMERICAN JOURNAL OF BOTANY 2023; 110:e16163. [PMID: 37014186 DOI: 10.1002/ajb2.16163] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 03/14/2023] [Accepted: 03/16/2023] [Indexed: 05/05/2023]
Abstract
PREMISE The Lower Cretaceous Crato Konservat-Lagerstätte (CKL) preserves a rich flora that includes early angiosperms from northern Gondwana. From this area, the recently described fossil genus Santaniella was interpreted as a ranunculid (presumably Ranunculaceae). However, based on our examination of an additional specimen and a new phylogenetic analysis, we offer an alternative interpretation. METHODS The new fossil was collected from an active quarry for paving stones in the state of Ceará, northeastern Brazil. We assessed support for alternative phylogenetic hypotheses using a combined analysis of morphological data and DNA sequence data using Bayesian inference. We used a consensus network to visualize the posterior distribution of trees, and we used RoguePlot to illustrate the support for alternative positions on a scaffold tree. RESULTS The new material includes a flower-like structure not present in the original material and also includes follicles preserved at early stages of development. The flower-like structure is a compact terminal cluster of elliptical sterile laminar organs surrounding internal filamentous structures that occur on flexuous axes. Phylogenetic analyses did not support the fossil placement among eudicots. Instead, Santaniella appears to belong in the magnoliid clade. CONCLUSIONS The presence of seeds in a marginal-linear placentation and enclosed in a follicle supports the fossil as an angiosperm. However, even though most characters are clearly recognizable, its combination of characters does not provide strong support for a close relationship to any extant order of flowering plants. Its position in the magnoliid clade is intriguing and, based on plicate carpels, it is definitely a mesangiosperm.
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Affiliation(s)
- Edlley M Pessoa
- Laboratório de Estudos Integrados de Plantas, Departamento de Botânica e Ecologia, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Alexandre C Ribeiro
- Departamento de Biologia e Zoologia, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Maarten J M Christenhusz
- Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia; Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Alessandra Ike Coan
- Departamento de Biodiversidade, Universidade Estadual Paulista "Júlio de Mesquita Filho," Instituto de Biociências, Rio Claro, São Paulo, Brazil
| | - Nathan A Jud
- Department of Biology, William Jewell College, Liberty, Missouri, USA
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3
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Beck RMD, de Vries D, Janiak MC, Goodhead IB, Boubli JP. Total evidence phylogeny of platyrrhine primates and a comparison of undated and tip-dating approaches. J Hum Evol 2023; 174:103293. [PMID: 36493598 DOI: 10.1016/j.jhevol.2022.103293] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 10/21/2022] [Accepted: 10/21/2022] [Indexed: 12/12/2022]
Abstract
There have been multiple published phylogenetic analyses of platyrrhine primates (New World monkeys) using both morphological and molecular data, but relatively few that have integrated both types of data into a total evidence approach. Here, we present phylogenetic analyses of recent and fossil platyrrhines, based on a total evidence data set of 418 morphological characters and 10.2 kilobases of DNA sequence data from 17 nuclear genes taken from previous studies, using undated and tip-dating approaches in a Bayesian framework. We compare the results of these analyses with molecular scaffold analyses using maximum parsimony and Bayesian approaches, and we use a formal information theoretic approach to identify unstable taxa. After a posteriori pruning of unstable taxa, the undated and tip-dating topologies appear congruent with recent molecular analyses and support largely similar relationships, with strong support for Stirtonia as a stem alouattine, Neosaimiri as a stem saimirine, Cebupithecia as a stem pitheciine, and Lagonimico as a stem callitrichid. Both analyses find three Greater Antillean subfossil platyrrhines (Xenothrix, Antillothrix, and Paralouatta) to form a clade that is related to Callicebus, congruent with a single dispersal event by the ancestor of this clade to the Greater Antilles. They also suggest that the fossil Proteropithecia may not be closely related to pitheciines, and that all known platyrrhines older than the Middle Miocene are stem taxa. Notably, the undated analysis found the Early Miocene Panamacebus (currently recognized as the oldest known cebid) to be unstable, and the tip-dating analysis placed it outside crown Platyrrhini. Our tip-dating analysis supports a late Oligocene or earliest Miocene (20.8-27.0 Ma) age for crown Platyrrhini, congruent with recent molecular clock analyses.
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Affiliation(s)
- Robin M D Beck
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK.
| | - Dorien de Vries
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Mareike C Janiak
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Ian B Goodhead
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Jean P Boubli
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
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Monson TA, Brasil MF, Mahaney MC, Schmitt CA, Taylor CE, Hlusko LJ. Keeping 21st Century Paleontology Grounded: Quantitative Genetic Analyses and Ancestral State Reconstruction Re-Emphasize the Essentiality of Fossils. BIOLOGY 2022; 11:1218. [PMID: 36009845 PMCID: PMC9404954 DOI: 10.3390/biology11081218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/10/2022] [Accepted: 08/10/2022] [Indexed: 02/06/2023]
Abstract
Advances in genetics and developmental biology are revealing the relationship between genotype and dental phenotype (G:P), providing new approaches for how paleontologists assess dental variation in the fossil record. Our aim was to understand how the method of trait definition influences the ability to reconstruct phylogenetic relationships and evolutionary history in the Cercopithecidae, the Linnaean Family of monkeys currently living in Africa and Asia. We compared the two-dimensional assessment of molar size (calculated as the mesiodistal length of the crown multiplied by the buccolingual breadth) to a trait that reflects developmental influences on molar development (the inhibitory cascade, IC) and two traits that reflect the genetic architecture of postcanine tooth size variation (defined through quantitative genetic analyses: MMC and PMM). All traits were significantly influenced by the additive effects of genes and had similarly high heritability estimates. The proportion of covariate effects was greater for two-dimensional size compared to the G:P-defined traits. IC and MMC both showed evidence of selection, suggesting that they result from the same genetic architecture. When compared to the fossil record, Ancestral State Reconstruction using extant taxa consistently underestimated MMC and PMM values, highlighting the necessity of fossil data for understanding evolutionary patterns in these traits. Given that G:P-defined dental traits may provide insight to biological mechanisms that reach far beyond the dentition, this new approach to fossil morphology has the potential to open an entirely new window onto extinct paleobiologies. Without the fossil record, we would not be able to grasp the full range of variation in those biological mechanisms that have existed throughout evolution.
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Affiliation(s)
- Tesla A. Monson
- Department of Anthropology, Western Washington University, 516 High Street, Bellingham, WA 98225, USA
| | - Marianne F. Brasil
- Berkeley Geochronology Center, 2455 Ridge Road, Berkeley, CA 94709, USA
- Human Evolution Research Center, Valley Life Sciences Building, University of California Berkeley, MC-3140, Berkeley, CA 94720, USA
| | - Michael C. Mahaney
- Department of Human Genetics, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
| | - Christopher A. Schmitt
- Department of Anthropology, Boston University, 232 Bay State Road, Boston, MA 02115, USA
| | - Catherine E. Taylor
- Human Evolution Research Center, Valley Life Sciences Building, University of California Berkeley, MC-3140, Berkeley, CA 94720, USA
| | - Leslea J. Hlusko
- Human Evolution Research Center, Valley Life Sciences Building, University of California Berkeley, MC-3140, Berkeley, CA 94720, USA
- National Center for Research on Human Evolution (CENIEH), Paseo Sierra de Atapuerca 3, 09002 Burgos, Spain
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5
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Baleka S, Varela L, Tambusso PS, Paijmans JL, Mothé D, Stafford TW, Fariña RA, Hofreiter M. Revisiting proboscidean phylogeny and evolution through total evidence and palaeogenetic analyses including Notiomastodon ancient DNA. iScience 2022; 25:103559. [PMID: 34988402 PMCID: PMC8693454 DOI: 10.1016/j.isci.2021.103559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 10/18/2021] [Accepted: 12/01/2021] [Indexed: 01/13/2023] Open
Abstract
The extinct Gomphotheriidae is the only proboscidean family that colonized South America. The phylogenetic position of the endemic taxa has been through several revisions using morphological comparisons. Morphological studies are enhanced by paleogenetic analyses, a powerful tool to resolve phylogenetic relationships; however, ancient DNA (aDNA) preservation decreases in warmer regions. Despite the poor preservation conditions for aDNA in humid, sub-tropical climates, we recovered ∼3,000 bp of mtDNA of Notiomastodon platensis from the Arroyo del Vizcaíno site, Uruguay. Our calibrated phylogeny places Notiomastodon as a sister taxon to Elephantidae, with a divergence time of ∼13.5 Ma. Additionally, a total evidence analysis combining morphological and paleogenetic data shows that the three most diverse clades within Proboscidea diverged during the early Miocene, coinciding with the formation of a land passage between Africa and Eurasia. Our results are a further step toward aDNA analyses on Pleistocene samples from subtropical regions and provide a framework for proboscidean evolution.
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Affiliation(s)
- Sina Baleka
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
- Faculty of Life and Environmental Sciences, University of Iceland, Sæmundargata 2, 102 Reykjavik, Iceland
| | - Luciano Varela
- Departamento de Paleontología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
- Servicio Académico Universitario y Centro de Estudios Paleontológicos (SAUCE-P), Universidad de la República, Santa Isabel s/n, 91500 Sauce, Departamento de Canelones, Uruguay
| | - P. Sebastián Tambusso
- Departamento de Paleontología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
- Servicio Académico Universitario y Centro de Estudios Paleontológicos (SAUCE-P), Universidad de la República, Santa Isabel s/n, 91500 Sauce, Departamento de Canelones, Uruguay
| | - Johanna L.A. Paijmans
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Dimila Mothé
- Laboratório de Mastozoologia, Instituto de Biociências, Universidade Federal do Estado do Rio de Janeiro, Av. Pasteur, 458/501, 22290-240 Rio de Janeiro, Brazil
- Programa de Pós-graduação em Biodiversidade e Biologia Evolutiva, Centro de Ciências da Saúde, Instituto de Biologia, Campus Ilha do Fundão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Richard A. Fariña
- Departamento de Paleontología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
- Servicio Académico Universitario y Centro de Estudios Paleontológicos (SAUCE-P), Universidad de la República, Santa Isabel s/n, 91500 Sauce, Departamento de Canelones, Uruguay
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
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Chiropteran (Chiroptera; Mammalia) taxonomy in light of modern methods and approaches. RUSSIAN JOURNAL OF THERIOLOGY 2021. [DOI: 10.15298/rusjtheriol.20.2.01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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7
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Asher RJ, Smith MR. Phylogenetic Signal and Bias in Paleontology. Syst Biol 2021; 71:986-1008. [PMID: 34469583 PMCID: PMC9248965 DOI: 10.1093/sysbio/syab072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 08/24/2021] [Accepted: 08/27/2021] [Indexed: 11/12/2022] Open
Abstract
An unprecedented amount of evidence now illuminates the phylogeny of living mammals and birds on the Tree of Life. We use this tree to measure phylogenetic value of data typically used in paleontology (bones and teeth) from six datasets derived from five published studies. We ask three interrelated questions: 1) Can these data adequately reconstruct known parts of the Tree of Life? 2) Is accuracy generally similar for studies using morphology, or do some morphological datasets perform better than others? 3) Does the loss of non-fossilizable data cause taxa to occur in misleadingly basal positions? Adding morphology to DNA datasets usually increases congruence of resulting topologies to the well corroborated tree, but this varies among morphological datasets. Extant taxa with a high proportion of missing morphological characters can greatly reduce phylogenetic resolution when analyzed together with fossils. Attempts to ameliorate this by deleting extant taxa missing morphology are prone to decreased accuracy due to long-branch artefacts. We find no evidence that fossilization causes extinct taxa to incorrectly appear at or near topologically basal branches. Morphology comprises the evidence held in common by living taxa and fossils, and phylogenetic analysis of fossils greatly benefits from inclusion of molecular and morphological data sampled for living taxa, whatever methods are used for phylogeny estimation.
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Affiliation(s)
- Robert J Asher
- Department of Zoology, Downing St., University of Cambridge CB2 3EJ, UK
| | - Martin R Smith
- Department of Earth Sciences, Lower Mount Joy, Durham University, Durham DH1 3LE, UK
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8
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Bastide P, Ho LST, Baele G, Lemey P, Suchard MA. Efficient Bayesian inference of general Gaussian models on large phylogenetic trees. Ann Appl Stat 2021. [DOI: 10.1214/20-aoas1419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
| | - Lam Si Tung Ho
- Department of Mathematics and Statistics, Dalhousie University
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven
| | - Marc A. Suchard
- Departments of Biostatistics, Biomathematics, and Human Genetics, University of California, Los Angeles
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9
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Chatterji RM, Hutchinson MN, Jones MEH. Redescription of the skull of the Australian flatback sea turtle, Natator depressus, provides new morphological evidence for phylogenetic relationships among sea turtles (Chelonioidea). Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlaa071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Abstract
Chelonioidea (sea turtles) are a group where available morphological evidence for crown-group relationships are incongruent with those established using molecular data. However, morphological surveys of crown-group taxa tend to focus on a recurring subset of the extant species. The Australian flatback sea turtle, Natator depressus, is often excluded from comparisons and it is the most poorly known of the seven extant species of Chelonioidea. Previous descriptions of its skull morphology are limited and conflict. Here we describe three skulls of adult N. depressus and re-examine the phylogenetic relationships according to morphological character data. Using X-ray micro Computed Tomography we describe internal structures of the braincase and identify new phylogenetically informative characters not previously reported. Phylogenetic analysis using a Bayesian approach strongly supports a sister-group relationship between Chelonia mydas and N. depressus, a topology that was not supported by previous analyses of morphological data but one that matches the topology supported by analysis of molecular data. Our results highlight the general need to sample the morphological anatomy of crown-group taxa more thoroughly before concluding that morphological and molecular evidence are incongruous.
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Affiliation(s)
- Ray M Chatterji
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, SA, Australia
- South Australian Museum, Adelaide, Adelaide, South Australia, SA, Australia
| | - Mark N Hutchinson
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, SA, Australia
- South Australian Museum, Adelaide, Adelaide, South Australia, SA, Australia
| | - Marc E H Jones
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, SA, Australia
- South Australian Museum, Adelaide, Adelaide, South Australia, SA, Australia
- Earth Sciences, Natural History Museum, London, UK
- Cell and Developmental Biology, UCL, University College London, London, UK
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10
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Bapst DW, Schreiber HA, Carlson SJ. Combined Analysis of Extant Rhynchonellida (Brachiopoda) using Morphological and Molecular Data. Syst Biol 2018; 67:32-48. [PMID: 28482055 PMCID: PMC5790130 DOI: 10.1093/sysbio/syx049] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 04/28/2017] [Indexed: 01/14/2023] Open
Abstract
Independent molecular and morphological phylogenetic analyses have often produced discordant results for certain groups which, for fossil-rich groups, raises the possibility that morphological data might mislead in those groups for which we depend upon morphology the most. Rhynchonellide brachiopods, with more than 500 extinct genera but only 19 extant genera represented today, provide an opportunity to explore the factors that produce contentious phylogenetic signal across datasets, as previous phylogenetic hypotheses generated from molecular sequence data bear little agreement with those constructed using morphological characters. Using a revised matrix of 66 morphological characters, and published ribosomal DNA sequences, we performed a series of combined phylogenetic analyses to identify conflicting phylogenetic signals. We completed a series of parsimony-based and Bayesian analyses, varying the data used, the taxa included, and the models used in the Bayesian analyses. We also performed simulation-based sensitivity analyses to assess whether the small size of the morphological data partition relative to the molecular data influenced the results of the combined analyses. In order to compare and contrast a large number of phylogenetic analyses and their resulting summary trees, we developed a measure for the incongruence between two topologies and simultaneously ignore any differences in phylogenetic resolution. Phylogenetic hypotheses generated using only morphological characters differed among each other, and with previous analyses, whereas molecular-only and combined Bayesian analyses produced extremely similar topologies. Characters historically associated with traditional classification in the Rhynchonellida have very low consistency indices on the topology preferred by the combined Bayesian analyses. Overall, this casts doubt on the use of morphological systematics to resolve relationships among the crown rhynchonellide brachiopods. However, expanding our dataset to a larger number of extinct taxa with intermediate morphologies is necessary to exclude the possibility that the morphology of extant taxa is not dominated by convergence along long branches.
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Affiliation(s)
- David W Bapst
- Department of Earth and Planetary Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Holly A Schreiber
- Department of Earth and Planetary Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA.,Penn Dixie Fossil Park and Nature Reserve, 3556 Lakeshore Rd, Ste. 210 Blasdell, NY 14219, USA
| | - Sandra J Carlson
- Department of Earth and Planetary Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
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Kealy S, Beck R. Total evidence phylogeny and evolutionary timescale for Australian faunivorous marsupials (Dasyuromorphia). BMC Evol Biol 2017; 17:240. [PMID: 29202687 PMCID: PMC5715987 DOI: 10.1186/s12862-017-1090-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/22/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The order Dasyuromorphia is a diverse radiation of faunivorous marsupials, comprising >80 modern species in Australia and New Guinea. It includes dasyurids, the numbat (the myrmecobiid Myrmecobius fasciatus) and the recently extinct thylacine (the thylacinid Thylacinus cyncocephalus). There is also a diverse fossil record of dasyuromorphians and "dasyuromorphian-like" taxa known from Australia. We present the first total evidence phylogenetic analyses of the order, based on combined morphological and molecular data (including a novel set of 115 postcranial characters), to resolve relationships and calculate divergence dates. We use this information to analyse the diversification dynamics of modern dasyuromorphians. RESULTS Our morphology-only analyses are poorly resolved, but our molecular and total evidence analyses confidently resolve most relationships within the order, and are strongly congruent with recent molecular studies. Thylacinidae is the first family to diverge within the order, and there is strong support for four tribes within Dasyuridae (Dasyurini, Phascogalini, Planigalini and Sminthopsini). Among fossil taxa, Ankotarinja and Keeuna do not appear to be members of Dasyuromorphia, whilst Barinya and Mutpuracinus are of uncertain relationships within the order. Divergence dates calculated using total evidence tip-and-node dating are younger than both molecular node-dating and total evidence tip-dating, but appear more congruent with the fossil record and are relatively insensitive to calibration strategy. The tip-and-node divergence dates indicate that Dasyurini, Phascogalini and Sminthopsini began to radiate almost simultaneously during the middle-to-late Miocene (11.5-13.1 MYA; composite 95% HPD: 9.5-15.9 MYA); the median estimates for these divergences are shortly after a drop in global temperatures (the middle Miocene Climatic Transition), and coincide with a faunal turnover event in the mammalian fossil record of Australia. Planigalini radiated much later, during the latest Miocene to earliest Pliocene (6.5 MYA; composite 95% HPD: 4.4-8.9 MYA); the median estimates for these divergences coincide with an increase in grass pollen in the Australian palynological record that suggests the development of more open habitats, which are preferred by modern planigale species. CONCLUSIONS Our results provide a phylogenetic and temporal framework for interpreting the evolution of modern and fossil dasyuromorphians, but future progress will require a much improved fossil record.
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Affiliation(s)
- Shimona Kealy
- Archaeology and Natural History, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Acton, ACT Australia
| | - Robin Beck
- School of Environment and Life Sciences, University of Salford, Salford, M5 4WT UK
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12
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Chani-Posse MR, Brunke AJ, Chatzimanolis S, Schillhammer H, Solodovnikov A. Phylogeny of the hyper-diverse rove beetle subtribe Philonthina with implications for classification of the tribe Staphylinini (Coleoptera: Staphylinidae). Cladistics 2017. [DOI: 10.1111/cla.12188] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Mariana R. Chani-Posse
- Laboratorio de Entomología; Instituto Argentino de Investigaciones de las Zonas Aridas (IADIZA, CCT CONICET, Mendoza); Casilla de Correo 507 5500 Mendoza Argentina
- BioSystematics; Natural History Museum of Denmark; Universitetsparken 15 2100 Copenhagen Denmark
| | - Adam James Brunke
- Natural History Museum Vienna; International Research Institute for Entomology; Burgring 7 A-1010 Vienna Austria
- Canadian National Collection of Insects, Arachnids and Nematodes; Agriculture and Agri-Food Canada; 960 Carling Avenue K.W. Neatby Building Ottawa ON K1A 0C6 Canada
| | - Stylianos Chatzimanolis
- Department of Biology, Geology and Environmental Science; University of Tennessee at Chattanooga; 615 McCallie Ave., Dept. 2653 Chattanooga TN USA
| | - Harald Schillhammer
- Natural History Museum Vienna; International Research Institute for Entomology; Burgring 7 A-1010 Vienna Austria
| | - Alexey Solodovnikov
- BioSystematics; Natural History Museum of Denmark; Universitetsparken 15 2100 Copenhagen Denmark
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13
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Ware JL, Barden P. Incorporating fossils into hypotheses of insect phylogeny. CURRENT OPINION IN INSECT SCIENCE 2016; 18:69-76. [PMID: 27939713 DOI: 10.1016/j.cois.2016.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 10/12/2016] [Indexed: 06/06/2023]
Abstract
Fossils represent stem and crown lineages, and their inclusion in phylogenetic reconstruction influences branch lengths, topology, and divergence time estimation. In addition, paleontological data may inform trends in morphological evolution as well as biogeographic history. Here we review the incorporation of fossils in studies of insect evolution, from morphological analyses to combined 'total evidence' node dating analyses. We discuss challenges associated with fossil based phylogenetics, and suggest best practices for use in tree reconstruction.
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Affiliation(s)
- Jessica L Ware
- Rutgers University, 195 University Ave, Newark, NJ 07102, United States.
| | - Phillip Barden
- Rutgers University, 195 University Ave, Newark, NJ 07102, United States
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Marx FG, Kohno N. A new Miocene baleen whale from the Peruvian desert. ROYAL SOCIETY OPEN SCIENCE 2016; 3:160542. [PMID: 27853573 PMCID: PMC5098998 DOI: 10.1098/rsos.160542] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 09/05/2016] [Indexed: 05/13/2023]
Abstract
The Pisco-Ica and Sacaco basins of southern Peru are renowned for their abundance of exceptionally preserved fossil cetaceans, several of which retain traces of soft tissue and occasionally even stomach contents. Previous work has mostly focused on odontocetes, with baleen whales currently being restricted to just three described taxa. Here, we report a new Late Miocene rorqual (family Balaenopteridae), Incakujira anillodefuego gen. et sp. nov., based on two exceptionally preserved specimens from the Pisco Formation exposed at Aguada de Lomas, Sacaco Basin, southern Peru. Incakujira overall closely resembles modern balaenopterids, but stands out for its unusually gracile ascending process of the maxilla, as well as a markedly twisted postglenoid process of the squamosal. The latter likely impeded lateral (omega) rotation of the mandible, in stark contrast with the highly flexible craniomandibular joint of extant lunge-feeding rorquals. Overall, Incakujira expands the still meagre Miocene record of balaenopterids and reveals a previously underappreciated degree of complexity in the evolution of their iconic lunge-feeding strategy.
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Affiliation(s)
- Felix G. Marx
- Department of Geology and Palaeontology, National Museum of Nature and Science, Tsukuba, Japan
- School of Biological Sciences, Monash University, 25 Rainforest Walk, Clayton, Victoria 3800, Australia
- Geosciences, Museum Victoria, Melbourne, Australia
- Directorate of Earth and History of Life, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Author for correspondence: Felix G. Marx e-mail:
| | - Naoki Kohno
- Department of Geology and Palaeontology, National Museum of Nature and Science, Tsukuba, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
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15
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Serb JM. Reconciling Morphological and Molecular Approaches in Developing a Phylogeny for the Pectinidae (Mollusca: Bivalvia). SCALLOPS - BIOLOGY, ECOLOGY, AQUACULTURE, AND FISHERIES 2016. [DOI: 10.1016/b978-0-444-62710-0.00001-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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16
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Organ CL, Cooper LN, Hieronymus TL. Macroevolutionary developmental biology: Embryos, fossils, and phylogenies. Dev Dyn 2015; 244:1184-92. [PMID: 26250386 DOI: 10.1002/dvdy.24318] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 06/16/2015] [Accepted: 06/17/2015] [Indexed: 12/23/2022] Open
Abstract
The field of evolutionary developmental biology is broadly focused on identifying the genetic and developmental mechanisms underlying morphological diversity. Connecting the genotype with the phenotype means that evo-devo research often considers a wide range of evidence, from genetics and morphology to fossils. In this commentary, we provide an overview and framework for integrating fossil ontogenetic data with developmental data using phylogenetic comparative methods to test macroevolutionary hypotheses. We survey the vertebrate fossil record of preserved embryos and discuss how phylogenetic comparative methods can integrate data from developmental genetics and paleontology. Fossil embryos provide limited, yet critical, developmental data from deep time. They help constrain when developmental innovations first appeared during the history of life and also reveal the order in which related morphologies evolved. Phylogenetic comparative methods provide a powerful statistical approach that allows evo-devo researchers to infer the presence of nonpreserved developmental traits in fossil species and to detect discordant evolutionary patterns and processes across levels of biological organization.
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Affiliation(s)
- Chris L Organ
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana.,Department of Earth Sciences, Montana State University, Bozeman, Montana
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17
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Arcila D, Alexander Pyron R, Tyler JC, Ortí G, Betancur-R R. An evaluation of fossil tip-dating versus node-age calibrations in tetraodontiform fishes (Teleostei: Percomorphaceae). Mol Phylogenet Evol 2014; 82 Pt A:131-45. [PMID: 25462998 DOI: 10.1016/j.ympev.2014.10.011] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 10/14/2014] [Indexed: 10/24/2022]
Abstract
Time-calibrated phylogenies based on molecular data provide a framework for comparative studies. Calibration methods to combine fossil information with molecular phylogenies are, however, under active development, often generating disagreement about the best way to incorporate paleontological data into these analyses. This study provides an empirical comparison of the most widely used approach based on node-dating priors for relaxed clocks implemented in the programs BEAST and MrBayes, with two recently proposed improvements: one using a new fossilized birth-death process model for node dating (implemented in the program DPPDiv), and the other using a total-evidence or tip-dating method (implemented in MrBayes and BEAST). These methods are applied herein to tetraodontiform fishes, a diverse group of living and extinct taxa that features one of the most extensive fossil records among teleosts. Previous estimates of time-calibrated phylogenies of tetraodontiforms using node-dating methods reported disparate estimates for their age of origin, ranging from the late Jurassic to the early Paleocene (ca. 150-59Ma). We analyzed a comprehensive dataset with 16 loci and 210 morphological characters, including 131 taxa (95 extant and 36 fossil species) representing all families of fossil and extant tetraodontiforms, under different molecular clock calibration approaches. Results from node-dating methods produced consistently younger ages than the tip-dating approaches. The older ages inferred by tip dating imply an unlikely early-late Jurassic (ca. 185-119Ma) origin for this order and the existence of extended ghost lineages in their fossil record. Node-based methods, by contrast, produce time estimates that are more consistent with the stratigraphic record, suggesting a late Cretaceous (ca. 86-96Ma) origin. We show that the precision of clade age estimates using tip dating increases with the number of fossils analyzed and with the proximity of fossil taxa to the node under assessment. This study suggests that current implementations of tip dating may overestimate ages of divergence in calibrated phylogenies. It also provides a comprehensive phylogenetic framework for tetraodontiform systematics and future comparative studies.
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Affiliation(s)
- Dahiana Arcila
- Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, DC 20052, United States; Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, MRC 159, Washington, DC 20013, United States.
| | - R Alexander Pyron
- Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, DC 20052, United States
| | - James C Tyler
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, MRC 159, Washington, DC 20013, United States
| | - Guillermo Ortí
- Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, DC 20052, United States
| | - Ricardo Betancur-R
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, MRC 159, Washington, DC 20013, United States; Department of Biology, University of Puerto Rico - Río Piedras, P.O. Box 23360, San Juan 00931, Puerto Rico
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Hipsley CA, Müller J. Beyond fossil calibrations: realities of molecular clock practices in evolutionary biology. Front Genet 2014; 5:138. [PMID: 24904638 PMCID: PMC4033271 DOI: 10.3389/fgene.2014.00138] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 04/27/2014] [Indexed: 01/22/2023] Open
Abstract
Molecular-based divergence dating methods, or molecular clocks, are the primary neontological tool for estimating the temporal origins of clades. While the appropriate use of vertebrate fossils as external clock calibrations has stimulated heated discussions in the paleontological community, less attention has been given to the quality and implementation of other calibration types. In lieu of appropriate fossils, many studies rely on alternative sources of age constraints based on geological events, substitution rates and heterochronous sampling, as well as dates secondarily derived from previous analyses. To illustrate the breadth and frequency of calibration types currently employed, we conducted a literature survey of over 600 articles published from 2007 to 2013. Over half of all analyses implemented one or more fossil dates as constraints, followed by geological events and secondary calibrations (15% each). Vertebrate taxa were subjects in nearly half of all studies, while invertebrates and plants together accounted for 43%, followed by viruses, protists and fungi (3% each). Current patterns in calibration practices were disproportionate to the number of discussions on their proper use, particularly regarding plants and secondarily derived dates, which are both relatively neglected in methodological evaluations. Based on our survey, we provide a comprehensive overview of the latest approaches in clock calibration, and outline strengths and weaknesses associated with each. This critique should serve as a call to action for researchers across multiple communities, particularly those working on clades for which fossil records are poor, to develop their own guidelines regarding selection and implementation of alternative calibration types. This issue is particularly relevant now, as time-calibrated phylogenies are used for more than dating evolutionary origins, but often serve as the backbone of investigations into biogeography, diversity dynamics and rates of phenotypic evolution.
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Affiliation(s)
- Christy A. Hipsley
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und BiodiversitätsforschungBerlin, Germany
| | - Johannes Müller
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und BiodiversitätsforschungBerlin, Germany
- Berlin-Brandenburg Institute of Avanced Biodiversity ResearchBerlin, Germany
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Dávalos LM, Velazco PM, Warsi OM, Smits PD, Simmons NB. Integrating Incomplete Fossils by Isolating Conflicting Signal in Saturated and Non-Independent Morphological Characters. Syst Biol 2014; 63:582-600. [DOI: 10.1093/sysbio/syu022] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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20
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Ruhfel BR, Gitzendanner MA, Soltis PS, Soltis DE, Burleigh JG. From algae to angiosperms-inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes. BMC Evol Biol 2014; 14:23. [PMID: 24533922 PMCID: PMC3933183 DOI: 10.1186/1471-2148-14-23] [Citation(s) in RCA: 322] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 01/13/2014] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Next-generation sequencing has provided a wealth of plastid genome sequence data from an increasingly diverse set of green plants (Viridiplantae). Although these data have helped resolve the phylogeny of numerous clades (e.g., green algae, angiosperms, and gymnosperms), their utility for inferring relationships across all green plants is uncertain. Viridiplantae originated 700-1500 million years ago and may comprise as many as 500,000 species. This clade represents a major source of photosynthetic carbon and contains an immense diversity of life forms, including some of the smallest and largest eukaryotes. Here we explore the limits and challenges of inferring a comprehensive green plant phylogeny from available complete or nearly complete plastid genome sequence data. RESULTS We assembled protein-coding sequence data for 78 genes from 360 diverse green plant taxa with complete or nearly complete plastid genome sequences available from GenBank. Phylogenetic analyses of the plastid data recovered well-supported backbone relationships and strong support for relationships that were not observed in previous analyses of major subclades within Viridiplantae. However, there also is evidence of systematic error in some analyses. In several instances we obtained strongly supported but conflicting topologies from analyses of nucleotides versus amino acid characters, and the considerable variation in GC content among lineages and within single genomes affected the phylogenetic placement of several taxa. CONCLUSIONS Analyses of the plastid sequence data recovered a strongly supported framework of relationships for green plants. This framework includes: i) the placement of Zygnematophyceace as sister to land plants (Embryophyta), ii) a clade of extant gymnosperms (Acrogymnospermae) with cycads + Ginkgo sister to remaining extant gymnosperms and with gnetophytes (Gnetophyta) sister to non-Pinaceae conifers (Gnecup trees), and iii) within the monilophyte clade (Monilophyta), Equisetales + Psilotales are sister to Marattiales + leptosporangiate ferns. Our analyses also highlight the challenges of using plastid genome sequences in deep-level phylogenomic analyses, and we provide suggestions for future analyses that will likely incorporate plastid genome sequence data for thousands of species. We particularly emphasize the importance of exploring the effects of different partitioning and character coding strategies.
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Affiliation(s)
- Brad R Ruhfel
- Department of Biological Sciences, Eastern Kentucky University, Richmond, KY 40475, USA
| | - Matthew A Gitzendanner
- Department of Biology, University of Florida, Gainesville, FL 32611-8525, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611-7800, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611-7800, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL 32611-8525, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611-7800, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - J Gordon Burleigh
- Department of Biology, University of Florida, Gainesville, FL 32611-8525, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
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21
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Guil N, Machordom A, Guidetti R. High level of phenotypic homoplasy amongst eutardigrades (Tardigrada) based on morphological and total evidence phylogenetic analyses. Zool J Linn Soc 2013. [DOI: 10.1111/zoj.12046] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Noemi Guil
- Department of Biodiversity and Evolutionary Biology; Museo Nacional de Ciencias Naturales de Madrid (MNCN-CSIC); José Gutiérrez Abascal 2; Madrid; 28006; Spain
| | - Annie Machordom
- Department of Biodiversity and Evolutionary Biology; Museo Nacional de Ciencias Naturales de Madrid (MNCN-CSIC); José Gutiérrez Abascal 2; Madrid; 28006; Spain
| | - Roberto Guidetti
- Department of Life Sciences; University of Modena and Reggio Emilia; Via Campi 213/d; Modena; 41125; Italy
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22
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Wolfe JM, Hegna TA. Testing the phylogenetic position of Cambrian pancrustacean larval fossils by coding ontogenetic stages. Cladistics 2013; 30:366-390. [DOI: 10.1111/cla.12051] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/22/2013] [Indexed: 01/14/2023] Open
Affiliation(s)
- Joanna M. Wolfe
- Department of Geology and Geophysics; Yale University; 210 Whitney Avenue New Haven CT 06520 USA
- Division of Invertebrate Zoology & Sackler Institute of Comparative Genomics; American Museum of Natural History; Central Park West at 79th Street New York NY 10024 USA
| | - Thomas A. Hegna
- Department of Geology and Geophysics; Yale University; 210 Whitney Avenue New Haven CT 06520 USA
- Department of Geology; Western Illinois University; Tillman Hall 1 University Circle Macomb IL 61455 USA
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23
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Hammesfahr B, Odronitz F, Mühlhausen S, Waack S, Kollmar M. GenePainter: a fast tool for aligning gene structures of eukaryotic protein families, visualizing the alignments and mapping gene structures onto protein structures. BMC Bioinformatics 2013; 14:77. [PMID: 23496949 PMCID: PMC3605371 DOI: 10.1186/1471-2105-14-77] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 02/24/2013] [Indexed: 11/10/2022] Open
Abstract
Background All sequenced eukaryotic genomes have been shown to possess at least a few introns. This includes those unicellular organisms, which were previously suspected to be intron-less. Therefore, gene splicing must have been present at least in the last common ancestor of the eukaryotes. To explain the evolution of introns, basically two mutually exclusive concepts have been developed. The introns-early hypothesis says that already the very first protein-coding genes contained introns while the introns-late concept asserts that eukaryotic genes gained introns only after the emergence of the eukaryotic lineage. A very important aspect in this respect is the conservation of intron positions within homologous genes of different taxa. Results GenePainter is a standalone application for mapping gene structure information onto protein multiple sequence alignments. Based on the multiple sequence alignments the gene structures are aligned down to single nucleotides. GenePainter accounts for variable lengths in exons and introns, respects split codons at intron junctions and is able to handle sequencing and assembly errors, which are possible reasons for frame-shifts in exons and gaps in genome assemblies. Thus, even gene structures of considerably divergent proteins can properly be compared, as it is needed in phylogenetic analyses. Conserved intron positions can also be mapped to user-provided protein structures. For their visualization GenePainter provides scripts for the molecular graphics system PyMol. Conclusions GenePainter is a tool to analyse gene structure conservation providing various visualization options. A stable version of GenePainter for all operating systems as well as documentation and example data are available at http://www.motorprotein.de/genepainter.html.
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Affiliation(s)
- Björn Hammesfahr
- Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, 37077, Germany
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Dávalos LM, Cirranello AL, Geisler JH, Simmons NB. Understanding phylogenetic incongruence: lessons from phyllostomid bats. Biol Rev Camb Philos Soc 2012; 87:991-1024. [PMID: 22891620 PMCID: PMC3573643 DOI: 10.1111/j.1469-185x.2012.00240.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 07/04/2012] [Accepted: 07/18/2012] [Indexed: 12/25/2022]
Abstract
All characters and trait systems in an organism share a common evolutionary history that can be estimated using phylogenetic methods. However, differential rates of change and the evolutionary mechanisms driving those rates result in pervasive phylogenetic conflict. These drivers need to be uncovered because mismatches between evolutionary processes and phylogenetic models can lead to high confidence in incorrect hypotheses. Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species. For more than a decade, evolutionary relationships among members of the New World bat family Phyllostomidae inferred from morphological and molecular data have been in conflict. Here, we develop and apply methods to minimize systematic biases, uncover the biological mechanisms underlying phylogenetic conflict, and outline data requirements for future phylogenomic and morphological data collection. We introduce new morphological data for phyllostomids and outgroups and expand previous molecular analyses to eliminate methodological sources of phylogenetic conflict such as taxonomic sampling, sparse character sampling, or use of different algorithms to estimate the phylogeny. We also evaluate the impact of biological sources of conflict: saturation in morphological changes and molecular substitutions, and other processes that result in incongruent trees, including convergent morphological and molecular evolution. Methodological sources of incongruence play some role in generating phylogenetic conflict, and are relatively easy to eliminate by matching taxa, collecting more characters, and applying the same algorithms to optimize phylogeny. The evolutionary patterns uncovered are consistent with multiple biological sources of conflict, including saturation in morphological and molecular changes, adaptive morphological convergence among nectar-feeding lineages, and incongruent gene trees. Applying methods to account for nucleotide sequence saturation reduces, but does not completely eliminate, phylogenetic conflict. We ruled out paralogy, lateral gene transfer, and poor taxon sampling and outgroup choices among the processes leading to incongruent gene trees in phyllostomid bats. Uncovering and countering the possible effects of introgression and lineage sorting of ancestral polymorphism on gene trees will require great leaps in genomic and allelic sequencing in this species-rich mammalian family. We also found evidence for adaptive molecular evolution leading to convergence in mitochondrial proteins among nectar-feeding lineages. In conclusion, the biological processes that generate phylogenetic conflict are ubiquitous, and overcoming incongruence requires better models and more data than have been collected even in well-studied organisms such as phyllostomid bats.
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Affiliation(s)
- Liliana M Dávalos
- Department of Ecology and Evolution, and Consortium for Inter-Disciplinary Environmental Research, State University of New York at Stony BrookStony Brook, NY 11794, USA
| | - Andrea L Cirranello
- Division of Vertebrate Zoology (Mammalogy), American Museum of Natural HistoryNew York, NY 10024, USA
- Department of Anatomical Sciences, State University of New York at Stony BrookStony Brook, NY 11794, USA
| | - Jonathan H Geisler
- Department of Anatomy, New York College of Osteopathic MedicineOld Westbury, NY 11568, USA
| | - Nancy B Simmons
- Division of Vertebrate Zoology (Mammalogy), American Museum of Natural HistoryNew York, NY 10024, USA
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Gatesy J, Geisler JH, Chang J, Buell C, Berta A, Meredith RW, Springer MS, McGowen MR. A phylogenetic blueprint for a modern whale. Mol Phylogenet Evol 2012; 66:479-506. [PMID: 23103570 DOI: 10.1016/j.ympev.2012.10.012] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 10/10/2012] [Accepted: 10/12/2012] [Indexed: 11/16/2022]
Abstract
The emergence of Cetacea in the Paleogene represents one of the most profound macroevolutionary transitions within Mammalia. The move from a terrestrial habitat to a committed aquatic lifestyle engendered wholesale changes in anatomy, physiology, and behavior. The results of this remarkable transformation are extant whales that include the largest, biggest brained, fastest swimming, loudest, deepest diving mammals, some of which can detect prey with a sophisticated echolocation system (Odontoceti - toothed whales), and others that batch feed using racks of baleen (Mysticeti - baleen whales). A broad-scale reconstruction of the evolutionary remodeling that culminated in extant cetaceans has not yet been based on integration of genomic and paleontological information. Here, we first place Cetacea relative to extant mammalian diversity, and assess the distribution of support among molecular datasets for relationships within Artiodactyla (even-toed ungulates, including Cetacea). We then merge trees derived from three large concatenations of molecular and fossil data to yield a composite hypothesis that encompasses many critical events in the evolutionary history of Cetacea. By combining diverse evidence, we infer a phylogenetic blueprint that outlines the stepwise evolutionary development of modern whales. This hypothesis represents a starting point for more detailed, comprehensive phylogenetic reconstructions in the future, and also highlights the synergistic interaction between modern (genomic) and traditional (morphological+paleontological) approaches that ultimately must be exploited to provide a rich understanding of evolutionary history across the entire tree of Life.
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Affiliation(s)
- John Gatesy
- Department of Biology, University of California, Riverside, CA 92521, USA.
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26
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Wiens JJ, Tiu J. Highly incomplete taxa can rescue phylogenetic analyses from the negative impacts of limited taxon sampling. PLoS One 2012; 7:e42925. [PMID: 22900065 PMCID: PMC3416753 DOI: 10.1371/journal.pone.0042925] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 07/16/2012] [Indexed: 11/18/2022] Open
Abstract
Background Phylogenies are essential to many areas of biology, but phylogenetic methods may give incorrect estimates under some conditions. A potentially common scenario of this type is when few taxa are sampled and terminal branches for the sampled taxa are relatively long. However, the best solution in such cases (i.e., sampling more taxa versus more characters) has been highly controversial. A widespread assumption in this debate is that added taxa must be complete (no missing data) in order to save analyses from the negative impacts of limited taxon sampling. Here, we evaluate whether incomplete taxa can also rescue analyses under these conditions (empirically testing predictions from an earlier simulation study). Methodology/Principal Findings We utilize DNA sequence data from 16 vertebrate species with well-established phylogenetic relationships. In each replicate, we randomly sample 4 species, estimate their phylogeny (using Bayesian, likelihood, and parsimony methods), and then evaluate whether adding in the remaining 12 species (which have 50, 75, or 90% of their data replaced with missing data cells) can improve phylogenetic accuracy relative to analyzing the 4 complete taxa alone. We find that in those cases where sampling few taxa yields an incorrect estimate, adding taxa with 50% or 75% missing data can frequently (>75% of relevant replicates) rescue Bayesian and likelihood analyses, recovering accurate phylogenies for the original 4 taxa. Even taxa with 90% missing data can sometimes be beneficial. Conclusions We show that adding taxa that are highly incomplete can improve phylogenetic accuracy in cases where analyses are misled by limited taxon sampling. These surprising empirical results confirm those from simulations, and show that the benefits of adding taxa may be obtained with unexpectedly small amounts of data. These findings have important implications for the debate on sampling taxa versus characters, and for studies attempting to resolve difficult phylogenetic problems.
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Affiliation(s)
- John J Wiens
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, United States of America.
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Paredes UM, Prys-Jones R, Adams M, Groombridge J, Kundu S, Agapow PM, Abel RL. Micro-CT X-rays do not fragment DNA in preserved bird skins. J ZOOL SYST EVOL RES 2012. [DOI: 10.1111/j.1439-0469.2012.00657.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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28
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GIRIBET GONZALO, SHARMA PRASHANTP, BENAVIDES LIGIAR, BOYER SARAHL, CLOUSE RONALDM, DE BIVORT BENJAMINL, DIMITROV DIMITAR, KAWAUCHI GISELEY, MURIENNE JEROME, SCHWENDINGER PETERJ. Evolutionary and biogeographical history of an ancient and global group of arachnids (Arachnida: Opiliones: Cyphophthalmi) with a new taxonomic arrangement. Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2011.01774.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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29
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Pyron RA. Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia. Syst Biol 2011; 60:466-81. [PMID: 21540408 DOI: 10.1093/sysbio/syr047] [Citation(s) in RCA: 223] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Were molecular data available for extinct taxa, questions regarding the origins of many groups could be settled in short order. As this is not the case, various strategies have been proposed to combine paleontological and neontological data sets. The use of fossil dates as node age calibrations for divergence time estimation from molecular phylogenies is commonplace. In addition, simulations suggest that the addition of morphological data from extinct taxa may improve phylogenetic estimation when combined with molecular data for extant species, and some studies have merged morphological and molecular data to estimate combined evidence phylogenies containing both extinct and extant taxa. However, few, if any, studies have attempted to estimate divergence times using phylogenies containing both fossil and living taxa sampled for both molecular and morphological data. Here, I infer both the phylogeny and the time of origin for Lissamphibia and a number of stem tetrapods using Bayesian methods based on a data set containing morphological data for extinct taxa, molecular data for extant taxa, and molecular and morphological data for a subset of extant taxa. The results suggest that Lissamphibia is monophyletic, nested within Lepospondyli, and originated in the late Carboniferous at the earliest. This research illustrates potential pitfalls for the use of fossils as post hoc age constraints on internal nodes and highlights the importance of explicit phylogenetic analysis of extinct taxa. These results suggest that the application of fossils as minima or maxima on molecular phylogenies should be supplemented or supplanted by combined evidence analyses whenever possible.
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Affiliation(s)
- R Alexander Pyron
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA.
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Phylogenetic structure and species boundaries in the mountain pitviper Ovophis monticola (Serpentes: Viperidae: Crotalinae) in Asia. Mol Phylogenet Evol 2011; 59:444-57. [DOI: 10.1016/j.ympev.2011.02.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Revised: 02/04/2011] [Accepted: 02/05/2011] [Indexed: 11/23/2022]
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Smith NA. Taxonomic revision and phylogenetic analysis of the flightless Mancallinae (Aves, Pan-Alcidae). Zookeys 2011; 91:1-116. [PMID: 21594108 PMCID: PMC3084493 DOI: 10.3897/zookeys.91.709] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2010] [Accepted: 03/18/2011] [Indexed: 11/12/2022] Open
Abstract
Although flightless alcids from the Miocene and Pliocene of the eastern Pacific Ocean have been known for over 100 years, there is no detailed evaluation of diversity and systematic placement of these taxa. This is the first combined analysis of morphological and molecular data to include all extant alcids, the recently extinct Great Auk Pinguinus impennis, the mancalline auks, and a large outgroup sampling of 29 additional non-alcid charadriiforms. Based on the systematic placement of Mancallinae outside of crown clade Alcidae, the clade name Pan-Alcidae is proposed to include all known alcids. An extensive review of the Mancallinae fossil record resulted in taxonomic revision of the clade, and identification of three new species. In addition to positing the first hypothesis of inter-relationships between Mancallinae species, phylogenetic results support placement of Mancallinae as the sister taxon to all other Alcidae, indicating that flightlessness evolved at least twice in the alcid lineage. Convergent osteological characteristics of Mancallinae, the flightless Great Auk, and Spheniscidae are summarized, and implications of Mancallinae diversity, radiation, and extinction in the context of paleoclimatic changes are discussed.
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Affiliation(s)
- Neil Adam Smith
- Department of Entomology, University of Arizona, Tucson, Arizona 85721-0036, USA
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Wiens JJ, Morrill MC. Missing data in phylogenetic analysis: reconciling results from simulations and empirical data. Syst Biol 2011; 60:719-31. [PMID: 21447483 DOI: 10.1093/sysbio/syr025] [Citation(s) in RCA: 338] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- John J Wiens
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA.
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Tarver JE, Donoghue PCJ. The Trouble with Topology: Phylogenies without Fossils Provide a Revisionist Perspective of Evolutionary History in Topological Analyses of Diversity. Syst Biol 2011; 60:700-12. [DOI: 10.1093/sysbio/syr018] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- James E. Tarver
- School of Earth Sciences, University of Bristol, Wills Memorial Building, Queen's Road, Bristol, BS8 1RJ, UK
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Philip C. J. Donoghue
- School of Earth Sciences, University of Bristol, Wills Memorial Building, Queen's Road, Bristol, BS8 1RJ, UK
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Ruhfel BR, Bittrich V, Bove CP, Gustafsson MHG, Philbrick CT, Rutishauser R, Xi Z, Davis CC. Phylogeny of the clusioid clade (Malpighiales): evidence from the plastid and mitochondrial genomes. AMERICAN JOURNAL OF BOTANY 2011; 98:306-325. [PMID: 21613119 DOI: 10.3732/ajb.1000354] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
PREMISE OF THE STUDY The clusioid clade includes five families (i.e., Bonnetiaceae, Calophyllaceae, Clusiaceae s.s., Hypericaceae, and Podostemaceae) represented by 94 genera and ≈1900 species. Species in this clade form a conspicuous element of tropical forests worldwide and are important in horticulture, timber production, and pharmacology. We conducted a taxon-rich multigene phylogenetic analysis of the clusioids to clarify phylogenetic relationships in this clade. METHODS We analyzed plastid (matK, ndhF, and rbcL) and mitochondrial (matR) nucleotide sequence data using parsimony, maximum likelihood, and Bayesian inference. Our combined data set included 194 species representing all major clusioid subclades, plus numerous species spanning the taxonomic, morphological, and biogeographic breadth of the clusioid clade. KEY RESULTS Our results indicate that Tovomita (Clusiaceae s.s.), Harungana and Hypericum (Hypericaceae), and Ledermanniella s.s. and Zeylanidium (Podostemaceae) are not monophyletic. In addition, we place four genera that have not been included in any previous molecular study: Ceratolacis, Diamantina, and Griffithella (Podostemaceae), and Santomasia (Hypericaceae). Finally, our results indicate that Lianthus, Santomasia, Thornea, and Triadenum can be safely merged into Hypericum (Hypericaceae). CONCLUSIONS We present the first well-resolved, taxon-rich phylogeny of the clusioid clade. Taxon sampling and resolution within the clade are greatly improved compared to previous studies and provide a strong basis for improving the classification of the group. In addition, our phylogeny will form the foundation for our future work investigating the biogeography of tropical angiosperms that exhibit Gondwanan distributions.
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Affiliation(s)
- Brad R Ruhfel
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, Massachusetts 02138, USA.
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RUANE S, PYRON RA, BURBRINK FT. Phylogenetic relationships of the Cretaceous frog Beelzebufo from Madagascar and the placement of fossil constraints based on temporal and phylogenetic evidence. J Evol Biol 2010; 24:274-85. [DOI: 10.1111/j.1420-9101.2010.02164.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Wiens JJ, Kuczynski CA, Townsend T, Reeder TW, Mulcahy DG, Sites JW. Combining Phylogenomics and Fossils in Higher-Level Squamate Reptile Phylogeny: Molecular Data Change the Placement of Fossil Taxa. Syst Biol 2010; 59:674-88. [PMID: 20930035 DOI: 10.1093/sysbio/syq048] [Citation(s) in RCA: 180] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- John J. Wiens
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA
| | - Caitlin A. Kuczynski
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA
| | - Ted Townsend
- Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA
| | - Tod W. Reeder
- Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA
| | - Daniel G. Mulcahy
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Jack W. Sites
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
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Pyron RA. A likelihood method for assessing molecular divergence time estimates and the placement of fossil calibrations. Syst Biol 2009; 59:185-94. [PMID: 20525629 DOI: 10.1093/sysbio/syp090] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Estimating divergence times using molecular sequence data has become a common application of statistical phylogenetics. However, disparities between estimated ages for clades produced in different studies have become equally commonplace. Here, I propose a method for the objective assessment of the likelihood of inferred divergence times to evaluate the placement of fossil constraints using information from the broader fossil record. The inclusion of nodes from the Tree of Life for which credible age ranges are known, in addition to the fossil constraints used in the ingroup, will allow for the comparison of alternate fossil placements when the phylogenetic affinity of a fossil is ambiguous as well as provide a heuristic assessment of the global likelihood of estimated divergence times. The use of these "likelihood checkpoints" will allow for the comparison of inferred dates across data sets and across taxonomic groups to place divergence time estimates into a broader evolutionary timescale. The method is illustrated with an example using an expanded phylogenetic estimate of the Gnathostomata, inferred with relaxed-clock molecular dating methods.
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Affiliation(s)
- R Alexander Pyron
- The Graduate School and University Center, The City University of New York, 365 Fifth Avenue, New York, NY 10016, USA.
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LEE MSY, CAMENS AB. Strong morphological support for the molecular evolutionary tree of placental mammals. J Evol Biol 2009; 22:2243-57. [DOI: 10.1111/j.1420-9101.2009.01843.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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