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Foley NM, Mason VC, Harris AJ, Bredemeyer KR, Damas J, Lewin HA, Eizirik E, Gatesy J, Karlsson EK, Lindblad-Toh K, Springer MS, Murphy WJ, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. A genomic timescale for placental mammal evolution. Science 2023; 380:eabl8189. [PMID: 37104581 DOI: 10.1126/science.abl8189] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis of genetic variation across an alignment of 241 placental mammal genome assemblies, addressing prior concerns regarding limited genomic sampling across species. We compared neutral genome-wide phylogenomic signals using concatenation and coalescent-based approaches, interrogated phylogenetic variation across chromosomes, and analyzed extensive catalogs of structural variants. Interordinal relationships exhibit relatively low rates of phylogenomic conflict across diverse datasets and analytical methods. Conversely, X-chromosome versus autosome conflicts characterize multiple independent clades that radiated during the Cenozoic. Genomic time trees reveal an accumulation of cladogenic events before and immediately after the Cretaceous-Paleogene (K-Pg) boundary, implying important roles for Cretaceous continental vicariance and the K-Pg extinction in the placental radiation.
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Affiliation(s)
- Nicole M Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Victor C Mason
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Andrew J Harris
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA
| | - Kevin R Bredemeyer
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA
| | - Joana Damas
- The Genome Center, University of California, Davis, CA, USA
| | - Harris A Lewin
- The Genome Center, University of California, Davis, CA, USA
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - Eduardo Eizirik
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Elinor K Karlsson
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Program in Molecular Medicine, University of Massachussetts Chan Medical School, Worcester, MA 01605, USA
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
| | - Mark S Springer
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA
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Goswami A, Noirault E, Coombs EJ, Clavel J, Fabre AC, Halliday TJD, Churchill M, Curtis A, Watanabe A, Simmons NB, Beatty BL, Geisler JH, Fox DL, Felice RN. Attenuated evolution of mammals through the Cenozoic. Science 2022; 378:377-383. [DOI: 10.1126/science.abm7525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The Cenozoic diversification of placental mammals is the archetypal adaptive radiation. Yet, discrepancies between molecular divergence estimates and the fossil record fuel ongoing debate around the timing, tempo, and drivers of this radiation. Analysis of a three-dimensional skull dataset for living and extinct placental mammals demonstrates that evolutionary rates peak early and attenuate quickly. This long-term decline in tempo is punctuated by bursts of innovation that decreased in amplitude over the past 66 million years. Social, precocial, aquatic, and herbivorous species evolve fastest, especially whales, elephants, sirenians, and extinct ungulates. Slow rates in rodents and bats indicate dissociation of taxonomic and morphological diversification. Frustratingly, highly similar ancestral shape estimates for placental mammal superorders suggest that their earliest representatives may continue to elude unequivocal identification.
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Affiliation(s)
- Anjali Goswami
- Department of Life Sciences, Natural History Museum, London, UK
- Department of Genetics, Evolution, and Environment, University College London, London, UK
| | - Eve Noirault
- Department of Life Sciences, Natural History Museum, London, UK
| | - Ellen J. Coombs
- Department of Life Sciences, Natural History Museum, London, UK
- Department of Genetics, Evolution, and Environment, University College London, London, UK
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Julien Clavel
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
| | - Anne-Claire Fabre
- Department of Life Sciences, Natural History Museum, London, UK
- Naturhistorisches Museum Bern, Bern, Switzerland
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Thomas J. D. Halliday
- Department of Life Sciences, Natural History Museum, London, UK
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Morgan Churchill
- Department of Biology, University of Wisconsin Oshkosh, Oshkosh, WI, USA
| | - Abigail Curtis
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Akinobu Watanabe
- Department of Life Sciences, Natural History Museum, London, UK
- Department of Anatomy, New York Institute of Technology College of Osteopathic Medicine, Old Westbury, New York, NY, USA
- Division of Paleontology, American Museum of Natural History, New York, NY, USA
| | - Nancy B. Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Brian L. Beatty
- Department of Anatomy, New York Institute of Technology College of Osteopathic Medicine, Old Westbury, New York, NY, USA
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Jonathan H. Geisler
- Department of Anatomy, New York Institute of Technology College of Osteopathic Medicine, Old Westbury, New York, NY, USA
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - David L. Fox
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Ryan N. Felice
- Department of Life Sciences, Natural History Museum, London, UK
- Department of Genetics, Evolution, and Environment, University College London, London, UK
- Centre for Integrative Anatomy, Department of Cell and Developmental Biology, University College London, London, UK
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3
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Černý D, Natale R. Comprehensive taxon sampling and vetted fossils help clarify the time tree of shorebirds (Aves, Charadriiformes). Mol Phylogenet Evol 2022; 177:107620. [PMID: 36038056 DOI: 10.1016/j.ympev.2022.107620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 06/03/2022] [Accepted: 08/17/2022] [Indexed: 01/20/2023]
Abstract
Shorebirds (Charadriiformes) are a globally distributed clade of modern birds and, due to their ecological and morphological disparity, a frequent subject of comparative studies. While molecular phylogenies have been key to establishing the suprafamilial backbone of the charadriiform tree, a number of relationships at both deep and shallow taxonomic levels remain poorly resolved. The timescale of shorebird evolution also remains uncertain as a result of extensive disagreements among the published divergence dating studies, stemming largely from different choices of fossil calibrations. Here, we present the most comprehensive non-supertree phylogeny of shorebirds to date, based on a total-evidence dataset comprising 353 ingroup taxa (90% of all extant or recently extinct species), 27 loci (15 mitochondrial and 12 nuclear), and 69 morphological characters. We further clarify the timeline of charadriiform evolution by time-scaling this phylogeny using a set of 14 up-to-date and thoroughly vetted fossil calibrations. In addition, we assemble a taxonomically restricted 100-locus dataset specifically designed to resolve outstanding problems in higher-level charadriiform phylogeny. In terms of tree topology, our results are largely congruent with previous studies but indicate that some of the conflicts among earlier analyses reflect a genuine signal of pervasive gene tree discordance. Monophyly of the plovers (Charadriidae), the position of the ibisbill (Ibidorhyncha), and the relationships among the five subfamilies of the gulls (Laridae) could not be resolved even with greatly increased locus and taxon sampling. Moreover, several localized regions of uncertainty persist in shallower parts of the tree, including the interrelationships of the true auks (Alcinae) and anarhynchine plovers. Our node-dating and macroevolutionary rate analyses find support for a Paleocene origin of crown-group shorebirds, as well as exceptionally rapid recent radiations of Old World oystercatchers (Haematopodidae) and select genera of gulls. Our study underscores the challenges involved in estimating a comprehensively sampled and carefully calibrated time tree for a diverse avian clade, and highlights areas in need of further research.
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Affiliation(s)
- David Černý
- Department of the Geophysical Sciences, University of Chicago, Chicago 60637, USA.
| | - Rossy Natale
- Department of Organismal Biology & Anatomy, University of Chicago, Chicago 60637, USA
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Velazco PM, Buczek AJ, Hoffman E, Hoffman DK, O'Leary MA, Novacek MJ. Combined data analysis of fossil and living mammals: a Paleogene sister taxon of Placentalia and the antiquity of Marsupialia. Cladistics 2022; 38:359-373. [PMID: 35098586 DOI: 10.1111/cla.12499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2022] [Indexed: 11/28/2022] Open
Abstract
The Cretaceous-Paleogene (KPg) boundary, one of Earth's five major extinction events, occurred just before the appearance of Placentalia in the fossil record. The Gobi Desert, Mongolia and the Western Interior of North America have important fossil mammals occurring just before and after the KPg boundary (e.g. Prodiacodon, Deltatheridium) that have yet to be phylogenetically tested in a character-rich context with molecular data. We present here phylogenetic analyses of >6000 newly scored anatomical observations drawn from six untested fossils and added to the largest existing morphological matrix for mammals. These data are combined with sequence data from 27 nuclear genes. Results show the existence of a new eutherian sister clade to Placentalia, which we name and characterize. The extinct clade Leptictidae is part of this placental sister clade, indicating that the sister clade survived the KPg event to co-exist in ancient ecosystems during the Paleogene radiation of placentals. Analysing the Cretaceous metatherian Deltatheridium in this character-rich context reveals it is a member of Marsupialia, a finding that extends the minimum age of Marsupialia before the KPg boundary. Numerous shared-derived features from multiple anatomical systems support the assignment of Deltatheridium to Marsupialia. Computed tomography scans of exquisite new specimens better document the marsupial-like dental replacement pattern of Deltatheridium. The new placental sister clade has both Asian and North American species, and is ancestrally characterized by shared derived features such as a hind limb modified for saltatorial locomotion.
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Affiliation(s)
- Paúl M Velazco
- Division of Paleontology, American Museum of Natural History, New York, NY, 10024, USA.,Department of Biology, Arcadia University, Glenside, PA, 19038, USA
| | - Alexandra J Buczek
- Division of Paleontology, American Museum of Natural History, New York, NY, 10024, USA
| | - Eva Hoffman
- Division of Paleontology, American Museum of Natural History, New York, NY, 10024, USA
| | - Devin K Hoffman
- Department of Geosciences, Virginia Tech, Blacksburg, VA, 24060, USA
| | - Maureen A O'Leary
- Division of Paleontology, American Museum of Natural History, New York, NY, 10024, USA.,Department of Anatomical Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Michael J Novacek
- Division of Paleontology, American Museum of Natural History, New York, NY, 10024, USA
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de Vries D, Heritage S, Borths MR, Sallam HM, Seiffert ER. Widespread loss of mammalian lineage and dietary diversity in the early Oligocene of Afro-Arabia. Commun Biol 2021; 4:1172. [PMID: 34621013 PMCID: PMC8497553 DOI: 10.1038/s42003-021-02707-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 09/21/2021] [Indexed: 11/16/2022] Open
Abstract
Diverse lines of geological and geochemical evidence indicate that the Eocene-Oligocene transition (EOT) marked the onset of a global cooling phase, rapid growth of the Antarctic ice sheet, and a worldwide drop in sea level. Paleontologists have established that shifts in mammalian community structure in Europe and Asia were broadly coincident with these events, but the potential impact of early Oligocene climate change on the mammalian communities of Afro-Arabia has long been unclear. Here we employ dated phylogenies of multiple endemic Afro-Arabian mammal clades (anomaluroid and hystricognath rodents, anthropoid and strepsirrhine primates, and carnivorous hyaenodonts) to investigate lineage diversification and loss since the early Eocene. These analyses provide evidence for widespread mammalian extinction in the early Oligocene of Afro-Arabia, with almost two-thirds of peak late Eocene diversity lost in these clades by ~30 Ma. Using homology-free dental topographic metrics, we further demonstrate that the loss of Afro-Arabian rodent and primate lineages was associated with a major reduction in molar occlusal topographic disparity, suggesting a correlated loss of dietary diversity. These results raise new questions about the relative importance of global versus local influences in shaping the evolutionary trajectories of Afro-Arabia's endemic mammals during the Oligocene.
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Affiliation(s)
- Dorien de Vries
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Steven Heritage
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, NY, 11794, USA
- Duke Lemur Center Museum of Natural History, Durham, NC, 27705, USA
| | - Matthew R Borths
- Duke Lemur Center Museum of Natural History, Durham, NC, 27705, USA
| | - Hesham M Sallam
- Duke Lemur Center Museum of Natural History, Durham, NC, 27705, USA
- Mansoura University Vertebrate Paleontology, Department of Geology, Faculty of Science, Mansoura, Egypt
- Institute of Global Health and Human Ecology (I-GHHE), School of Sciences and Engineering, American University in Cairo, New Cairo, Egypt
| | - Erik R Seiffert
- Duke Lemur Center Museum of Natural History, Durham, NC, 27705, USA.
- Department of Integrative Anatomical Sciences, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA.
- Department of Mammalogy, Natural History Museum of Los Angeles County, Los Angeles, CA, 90007, USA.
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Brady PL, Springer MS. The effects of fossil taxa, hypothetical predicted ancestors, and a molecular scaffold on pseudoextinction analyses of extant placental orders. PLoS One 2021; 16:e0257338. [PMID: 34534236 PMCID: PMC8448315 DOI: 10.1371/journal.pone.0257338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/30/2021] [Indexed: 12/02/2022] Open
Abstract
Pseudoextinction analyses, which simulate extinction in extant taxa, use molecular phylogenetics to assess the accuracy of morphological phylogenetics. Previous pseudoextinction analyses have shown a failure of morphological phylogenetics to place some individual placental orders in the correct superordinal clade. Recent work suggests that the inclusion of hypothetical ancestors of extant placental clades, estimated by ancestral state reconstructions of morphological characters, may increase the accuracy of morphological phylogenetic analyses. However, these studies reconstructed direct hypothetical ancestors for each extant taxon based on a well-corroborated molecular phylogeny, which is not possible for extinct taxa that lack molecular data. It remains to be determined if pseudoextinct taxa, and by proxy extinct taxa, can be accurately placed when their immediate hypothetical ancestors are unknown. To investigate this, we employed molecular scaffolds with the largest available morphological data set for placental mammals. Each placental order was sequentially treated as pseudoextinct by exempting it from the molecular scaffold and recoding soft morphological characters as missing for all its constituent species. For each pseudoextinct data set, we omitted the pseudoextinct taxon and performed a parsimony ancestral state reconstruction to obtain hypothetical predicted ancestors. Each pseudoextinct order was then evaluated in seven parsimony analyses that employed combinations of fossil taxa, hypothetical predicted ancestors, and a molecular scaffold. In treatments that included fossils, hypothetical predicted ancestors, and a molecular scaffold, only 8 of 19 pseudoextinct placental orders (42%) retained the same interordinal placement as on the molecular scaffold. In treatments that included hypothetical predicted ancestors but not fossils or a scaffold, only four placental orders (21%) were recovered in positions that are congruent with the scaffold. These results indicate that hypothetical predicted ancestors do not increase the accuracy of pseudoextinct taxon placement when the immediate hypothetical ancestor of the taxon is unknown. Hypothetical predicted ancestors are not a panacea for morphological phylogenetics.
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Affiliation(s)
- Peggy L. Brady
- Department of Evolution, Ecology, and Evolutionary Biology, University of California, Riverside, Riverside, CA, United States of America
| | - Mark S. Springer
- Department of Evolution, Ecology, and Evolutionary Biology, University of California, Riverside, Riverside, CA, United States of America
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Hu J, Roos C, Lv X, Kuang W, Yu L. Molecular Genetics Supports a Potential Fifth Asian Pangolin Species (Mammalia, Pholidota, Manis). Zoolog Sci 2021; 37:538-543. [PMID: 33269869 DOI: 10.2108/zs200084] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 08/17/2020] [Indexed: 11/17/2022]
Abstract
Recently, two mitochondrial haplotypes, H4 and H8, of Manis sp. were found in two seizures in Hong Kong that do not correspond to Manis javanica, Manis pentadactyla or Manis crassicaudata of Asian pangolin species or any African pangolin species. It was proposed that both haplotypes derived from Manis culionensis, an unknown lineage of M. javanica, or a thus far unidentified Asian pangolin species (Manis sp.). To further investigate these three hypotheses, we used two mitochondrial genes of all eight known extant pangolin species and conducted phylogenetic tree reconstructions, divergence time estimation, and species delimitation analyses. All analyses consistently confirmed that these two haplotypes of Manis sp. constitute a distinct lineage, potentially representing a fifth Asian pangolin species, which originated around the Late Miocene to Early Pliocene (6.95 [4.64-9.85] million years ago). Our study provides genetic support for a potential fifth Asian pangolin species and helps to better understand species diversity of Asian pangolins, which is urgently needed for effective conservation work.
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Affiliation(s)
- Jingyang Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, 650091, Kunming, China
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, D-37077, Göttingen, Germany
| | - Xue Lv
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, 650091, Kunming, China
| | - Weimin Kuang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, 650091, Kunming, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, 650091, Kunming, China,
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Li G, Figueiró HV, Eizirik E, Murphy WJ. Recombination-Aware Phylogenomics Reveals the Structured Genomic Landscape of Hybridizing Cat Species. Mol Biol Evol 2020; 36:2111-2126. [PMID: 31198971 PMCID: PMC6759079 DOI: 10.1093/molbev/msz139] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Current phylogenomic approaches implicitly assume that the predominant phylogenetic signal within a genome reflects the true evolutionary history of organisms, without assessing the confounding effects of postspeciation gene flow that can produce a mosaic of phylogenetic signals that interact with recombinational variation. Here, we tested the validity of this assumption with a phylogenomic analysis of 27 species of the cat family, assessing local effects of recombination rate on species tree inference and divergence time estimation across their genomes. We found that the prevailing phylogenetic signal within the autosomes is not always representative of the most probable speciation history, due to ancient hybridization throughout felid evolution. Instead, phylogenetic signal was concentrated within regions of low recombination, and notably enriched within large X chromosome recombination cold spots that exhibited recurrent patterns of strong genetic differentiation and selective sweeps across mammalian orders. By contrast, regions of high recombination were enriched for signatures of ancient gene flow, and these sequences inflated crown-lineage divergence times by ∼40%. We conclude that existing phylogenomic approaches to infer the Tree of Life may be highly misleading without considering the genomic architecture of phylogenetic signal relative to recombination rate and its interplay with historical hybridization.
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Affiliation(s)
- Gang Li
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX
| | - Henrique V Figueiró
- PUCRS, Escola de Ciências, Laboratory of Genomics and Molecular Biology, Porto Alegre, Brazil.,INCT-EECBio, Brazil
| | - Eduardo Eizirik
- PUCRS, Escola de Ciências, Laboratory of Genomics and Molecular Biology, Porto Alegre, Brazil.,INCT-EECBio, Brazil
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX
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Upham NS, Esselstyn JA, Jetz W. Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation. PLoS Biol 2019; 17:e3000494. [PMID: 31800571 PMCID: PMC6892540 DOI: 10.1371/journal.pbio.3000494] [Citation(s) in RCA: 460] [Impact Index Per Article: 92.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/24/2019] [Indexed: 12/18/2022] Open
Abstract
Big, time-scaled phylogenies are fundamental to connecting evolutionary processes to modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of species involves numerous trade-offs that have limited their utility to comparative biologists. To establish a robust evolutionary timescale for all approximately 6,000 living species of mammals, we developed credible sets of trees that capture root-to-tip uncertainty in topology and divergence times. Our "backbone-and-patch" approach to tree building applies a newly assembled 31-gene supermatrix to two levels of Bayesian inference: (1) backbone relationships and ages among major lineages, using fossil node or tip dating, and (2) species-level "patch" phylogenies with nonoverlapping in-groups that each correspond to one representative lineage in the backbone. Species unsampled for DNA are either excluded ("DNA-only" trees) or imputed within taxonomic constraints using branch lengths drawn from local birth-death models ("completed" trees). Joining time-scaled patches to backbones results in species-level trees of extant Mammalia with all branches estimated under the same modeling framework, thereby facilitating rate comparisons among lineages as disparate as marsupials and placentals. We compare our phylogenetic trees to previous estimates of mammal-wide phylogeny and divergence times, finding that (1) node ages are broadly concordant among studies, and (2) recent (tip-level) rates of speciation are estimated more accurately in our study than in previous "supertree" approaches, in which unresolved nodes led to branch-length artifacts. Credible sets of mammalian phylogenetic history are now available for download at http://vertlife.org/phylosubsets, enabling investigations of long-standing questions in comparative biology.
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Affiliation(s)
- Nathan S. Upham
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Center for Biodiversity & Global Change, Yale University, New Haven, Connecticut, United States of America
| | - Jacob A. Esselstyn
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Walter Jetz
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Center for Biodiversity & Global Change, Yale University, New Haven, Connecticut, United States of America
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Springer MS, Foley NM, Brady PL, Gatesy J, Murphy WJ. Evolutionary Models for the Diversification of Placental Mammals Across the KPg Boundary. Front Genet 2019; 10:1241. [PMID: 31850081 PMCID: PMC6896846 DOI: 10.3389/fgene.2019.01241] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 11/08/2019] [Indexed: 01/29/2023] Open
Abstract
Deciphering the timing of the placental mammal radiation is a longstanding problem in evolutionary biology, but consensus on the tempo and mode of placental diversification remains elusive. Nevertheless, an accurate timetree is essential for understanding the role of important events in Earth history (e.g., Cretaceous Terrestrial Revolution, KPg mass extinction) in promoting the taxonomic and ecomorphological diversification of Placentalia. Archibald and Deutschman described three competing models for the diversification of placental mammals, which are the Explosive, Long Fuse, and Short Fuse Models. More recently, the Soft Explosive Model and Trans-KPg Model have emerged as additional hypotheses for the placental radiation. Here, we review molecular and paleontological evidence for each of these five models including the identification of general problems that can negatively impact divergence time estimates. The Long Fuse Model has received more support from relaxed clock studies than any of the other models, but this model is not supported by morphological cladistic studies that position Cretaceous eutherians outside of crown Placentalia. At the same time, morphological cladistics has a poor track record of reconstructing higher-level relationships among the orders of placental mammals including the results of new pseudoextinction analyses that we performed on the largest available morphological data set for mammals (4,541 characters). We also examine the strengths and weaknesses of different timetree methods (node dating, tip dating, and fossilized birth-death dating) that may now be applied to estimate the timing of the placental radiation. While new methods such as tip dating are promising, they also have problems that must be addressed if these methods are to effectively discriminate among competing hypotheses for placental diversification. Finally, we discuss the complexities of timetree estimation when the signal of speciation times is impacted by incomplete lineage sorting (ILS) and hybridization. Not accounting for ILS results in dates that are older than speciation events. Hybridization, in turn, can result in dates than are younger or older than speciation dates. Disregarding this potential variation in "gene" history across the genome can distort phylogenetic branch lengths and divergence estimates when multiple unlinked genomic loci are combined together in a timetree analysis.
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Affiliation(s)
- Mark S. Springer
- Department of Evolution, Ecology, and Evolutionary Biology, University of California, Riverside, Riverside, CA, United States
| | - Nicole M. Foley
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| | - Peggy L. Brady
- Department of Evolution, Ecology, and Evolutionary Biology, University of California, Riverside, Riverside, CA, United States
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, United States
| | - William J. Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
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Du Y, Wu S, Edwards SV, Liu L. The effect of alignment uncertainty, substitution models and priors in building and dating the mammal tree of life. BMC Evol Biol 2019; 19:203. [PMID: 31694538 PMCID: PMC6833305 DOI: 10.1186/s12862-019-1534-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 10/21/2019] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The flood of genomic data to help build and date the tree of life requires automation at several critical junctures, most importantly during sequence assembly and alignment. It is widely appreciated that automated alignment protocols can yield inaccuracies, but the relative impact of various sources error on phylogenomic analysis is not yet known. This study employs an updated mammal data set of 5162 coding loci sampled from 90 species to evaluate the effects of alignment uncertainty, substitution models, and fossil priors on gene tree, species tree, and divergence time estimation. Additionally, a novel coalescent likelihood ratio test is introduced for comparing competing species trees against a given set of gene trees. RESULTS The aligned DNA sequences of 5162 loci from 90 species were trimmed and filtered using trimAL and two filtering protocols. The final dataset contains 4 sets of alignments - before trimming, after trimming, filtered by a recently proposed pipeline, and further filtered by comparing ML gene trees for each locus with the concatenation tree. Our analyses suggest that the average discordance among the coalescent trees is significantly smaller than that among the concatenation trees estimated from the 4 sets of alignments or with different substitution models. There is no significant difference among the divergence times estimated with different substitution models. However, the divergence dates estimated from the alignments after trimming are more recent than those estimated from the alignments before trimming. CONCLUSIONS Our results highlight that alignment uncertainty of the updated mammal data set and the choice of substitution models have little impact on tree topologies yielded by coalescent methods for species tree estimation, whereas they are more influential on the trees made by concatenation. Given the choice of calibration scheme and clock models, divergence time estimates are robust to the choice of substitution models, but removing alignments deemed problematic by trimming algorithms can lead to more recent dates. Although the fossil prior is important in divergence time estimation, Bayesian estimates of divergence times in this data set are driven primarily by the sequence data.
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Affiliation(s)
- Yan Du
- Department of Statistics, University of Georgia, 310 Herty Drive, Athens, GA 30606 USA
| | - Shaoyuan Wu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu 221116 People’s Republic of China
| | - Scott V. Edwards
- Department of Organismic & Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138 USA
| | - Liang Liu
- Liang Liu, Department of Statistics and Institute of Bioinformatics, University of Georgia, 310 Herty Drive, Athens, GA 30606 USA
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12
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Sato JJ, Bradford TM, Armstrong KN, Donnellan SC, Echenique-Diaz LM, Begué-Quiala G, Gámez-Díez J, Yamaguchi N, Nguyen ST, Kita M, Ohdachi SD. Post K-Pg diversification of the mammalian order Eulipotyphla as suggested by phylogenomic analyses of ultra-conserved elements. Mol Phylogenet Evol 2019; 141:106605. [PMID: 31479732 DOI: 10.1016/j.ympev.2019.106605] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 11/26/2022]
Abstract
The origin of the mammalian order Eulipotyphla has been debated intensively with arguments around whether they began diversifying before or after the Cretaceous-Palaeogene (K-Pg) boundary at 66 Ma. Here, we used an in-solution nucleotide capture method and next generation DNA sequencing to determine the sequence of hundreds of ultra-conserved elements (UCEs), and conducted phylogenomic and molecular dating analyses for the four extant eulipotyphlan lineages-Erinaceidae, Solenodontidae, Soricidae, and Talpidae. Concatenated maximum-likelihood analyses with single or partitioned models and a coalescent species-tree analysis showed that divergences among the four major eulipotyphlan lineages occurred within a short period of evolutionary time, but did not resolve the interrelationships among them. Alternative suboptimal phylogenetic hypotheses received consistently the same amount of support from different UCE loci, and were not significantly different from the maximum likelihood tree topology, suggesting the prevalence of stochastic lineage sorting. Molecular dating analyses that incorporated among-lineage evolutionary rate differences supported a scenario where the four eulipotyphlan families diversified between 57.8 and 63.2 Ma. Given short branch lengths with low support values, traces of rampant genome-wide stochastic lineage sorting, and post K-Pg diversification, we concluded that the crown eulipotyphlan lineages arose through a rapid diversification after the K-Pg boundary when novel niches were created by the mass extinction of species.
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Affiliation(s)
- Jun J Sato
- Laboratory of Animal Cell Technology, Faculty of Life Science and Technology, Fukuyama University, Higashimuracho, Aza, Sanzo, 985, Fukuyama 729-0292, Japan; School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia.
| | - Tessa M Bradford
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia; South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Kyle N Armstrong
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia; South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Stephen C Donnellan
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia; South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Lazaro M Echenique-Diaz
- Environmental Education Center, Miyagi University of Education, Aramaki Aza-Aoba, Aoba-ku, Sendai 980-0845, Japan
| | - Gerardo Begué-Quiala
- Unidad Presupuestada Parque Nacional Alejandro de Humboldt (CITMA), Calle Abogado 14 e/12 y 13 Norte, Guantanamo 95200, Cuba
| | - Jorgelino Gámez-Díez
- Estación Ecológica La Melba, Unidad Presupuestada Parque Nacional Alejandro de Humboldt, CITMA-Guantánamo, Cuba
| | - Nobuyuki Yamaguchi
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, PO Box 2713, Doha, Qatar
| | - Son Truong Nguyen
- Institute of Ecology and Biological Resources and Graduate University of Science and Technology, Vietnam Academy of Sciences and Technology, 18 Hoang Quoc Viet, Hanoi, Viet Nam
| | - Masaki Kita
- Graduate School of Bioagricultural Sciences, Nagoya University Furo-cho, Chikusa, Nagoya 464-8601, Japan
| | - Satoshi D Ohdachi
- Institute of Low Temperature Science, Hokkaido University, Kita-19 Nishi-8, Kita-ku, Sapporo 060-0819, Japan
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13
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Morgan CC, Hart MW. Molecular evolution of mammalian genes with epistatic interactions in fertilization. BMC Evol Biol 2019; 19:154. [PMID: 31345177 PMCID: PMC6659299 DOI: 10.1186/s12862-019-1480-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 07/16/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Genes that encode proteins associated with sperm competition, fertilization, and sexual conflicts of interest are often among the most rapidly evolving parts of animal genomes. One family of sperm-expressed genes (Zp3r, C4bpa) in the mammalian gene cluster called the regulator of complement activation (RCA) encodes proteins that bind eggs and mediate reproductive success, and are therefore expected to show high relative rates of nonsynonymous nucleotide substitution in response to sexual selection in comparison to other genes not involved in gamete binding at fertilization. We tested that working hypothesis by using phylogenetic models of codon evolution to identify episodes of diversifying positive selection. We used a comparative approach to quantify the evidence for episodic diversifying selection acting on RCA genes with known functions in fertilization (and sensitivity to sexual selection), and contrast them with other RCA genes in the same gene family that function in innate immunity (and are not sensitive to sexual selection). RESULTS We expected but did not find evidence for more episodes of positive selection on Zp3r in Glires (the rodents and lagomorphs) or on C4BPA in Primates, in comparison to other paralogous RCA genes in the same taxon, or in comparison to the same orthologous RCA gene in the other taxon. That result was not unique to RCA genes: we also found little evidence for more episodes of diversifying selection on genes that encode selective sperm-binding molecules in the egg coat or zona pellucida (Zp2, Zp3) in comparison to members of the same gene family that encode structural elements of the egg coat (Zp1, Zp4). Similarly, we found little evidence for episodic diversifying selection acting on two other recently discovered genes (Juno, Izumo1) that encode essential molecules for sperm-egg fusion. CONCLUSIONS These negative results help to illustrate the importance of a comparative context for this type of codon model analysis. The results may also point to other phylogenetic contexts in which the effects of selection acting on these fertilization proteins might be more readily discovered and documented in mammals and other taxa.
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Affiliation(s)
- Claire C. Morgan
- Department of Medicine, Imperial College London, London, W12 0NN UK
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Michael W. Hart
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia V5A 1S6 Canada
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Grossnickle DM, Smith SM, Wilson GP. Untangling the Multiple Ecological Radiations of Early Mammals. Trends Ecol Evol 2019; 34:936-949. [PMID: 31229335 DOI: 10.1016/j.tree.2019.05.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/14/2019] [Accepted: 05/21/2019] [Indexed: 11/16/2022]
Abstract
The ecological diversification of early mammals is one of the most globally transformative events in Earth's history and the Cretaceous Terrestrial Revolution (KTR) and end-Cretaceous mass extinction are commonly hailed as catalysts. However, a confounding issue when examining this diversification is that it comprised nested radiations of mammalian subclades within the broader scope of mammalian evolution. In the past 200 million years, various independent groups experienced large-scale radiations, each involving ecological diversification from ancestral lineages of small insectivores; examples include Jurassic mammaliaforms, Late Cretaceous metatherians, and Cenozoic placentals. Here, we review these ecological radiations, highlighting the nuanced complexity of early mammal evolution, the value of ecomorphological fossil data, and the importance of phylogenetic context in macroevolutionary studies.
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Affiliation(s)
| | - Stephanie M Smith
- Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA
| | - Gregory P Wilson
- Department of Biology, University of Washington, Seattle, WA, USA
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15
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Beck RMD, Baillie C. Improvements in the fossil record may largely resolve current conflicts between morphological and molecular estimates of mammal phylogeny. Proc Biol Sci 2018; 285:20181632. [PMID: 30963896 PMCID: PMC6304057 DOI: 10.1098/rspb.2018.1632] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/23/2018] [Indexed: 01/16/2023] Open
Abstract
Phylogenies of mammals based on morphological data continue to show several major areas of conflict with the current consensus view of their relationships, which is based largely on molecular data. This raises doubts as to whether current morphological character sets are able to accurately resolve mammal relationships. We tested this under a hypothetical 'best case scenario' by using ancestral state reconstruction (under both maximum parsimony and maximum likelihood) to infer the morphologies of fossil ancestors for all clades present in a recent comprehensive DNA sequence-based phylogeny of mammals, and then seeing what effect the subsequent inclusion of these predicted ancestors had on unconstrained phylogenetic analyses of morphological data. We found that this resulted in topologies that are highly congruent with the current consensus phylogeny, at least when the predicted ancestors are assumed to be well preserved and densely sampled. Most strikingly, several analyses recovered the monophyly of clades that have never been found in previous morphology-only studies, such as Afrotheria and Laurasiatheria. Our results suggest that, at least in principle, improvements in the fossil record-specifically the discovery of fossil taxa that preserve the ancestral or near-ancestral morphologies of the nodes in the current consensus-may be sufficient to largely reconcile morphological and molecular estimates of mammal phylogeny, even using current morphological character sets.
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Affiliation(s)
- Robin M. D. Beck
- School of Environment and Life Sciences, University of Salford, Manchester M5 4WT, UK
| | - Charles Baillie
- School of Environment and Life Sciences, University of Salford, Manchester M5 4WT, UK
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16
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Phillips MJ, Fruciano C. The soft explosive model of placental mammal evolution. BMC Evol Biol 2018; 18:104. [PMID: 29969980 PMCID: PMC6029115 DOI: 10.1186/s12862-018-1218-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 06/19/2018] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Recent molecular dating estimates for placental mammals echo fossil inferences for an explosive interordinal diversification, but typically place this event some 10-20 million years earlier than the Paleocene fossils, among apparently more "primitive" mammal faunas. RESULTS However, current models of molecular evolution do not adequately account for parallel rate changes, and result in dramatic divergence underestimates for large, long-lived mammals such as whales and hominids. Calibrating among these taxa shifts the rate model errors deeper in the tree, inflating interordinal divergence estimates. We employ simulations based on empirical rate variation, which show that this "error-shift inflation" can explain previous molecular dating overestimates relative to fossil inferences. Molecular dating accuracy is substantially improved in the simulations by focusing on calibrations for taxa that retain plesiomorphic life-history characteristics. Applying this strategy to the empirical data favours the soft explosive model of placental evolution, in line with traditional palaeontological interpretations - a few Cretaceous placental lineages give rise to a rapid interordinal diversification following the 66 Ma Cretaceous-Paleogene boundary mass extinction. CONCLUSIONS Our soft explosive model for the diversification of placental mammals brings into agreement previously incongruous molecular, fossil, and ancestral life history estimates, and closely aligns with a growing consensus for a similar model for bird evolution. We show that recent criticism of the soft explosive model relies on ignoring both experimental controls and statistical confidence, as well as misrepresentation, and inconsistent interpretations of morphological phylogeny. More generally, we suggest that the evolutionary properties of adaptive radiations may leave current molecular dating methods susceptible to overestimating the timing of major diversification events.
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Affiliation(s)
- Matthew J. Phillips
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Australia
| | - Carmelo Fruciano
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Australia
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17
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Kijpornyongpan T, Mondo SJ, Barry K, Sandor L, Lee J, Lipzen A, Pangilinan J, LaButti K, Hainaut M, Henrissat B, Grigoriev IV, Spatafora JW, Aime MC. Broad Genomic Sampling Reveals a Smut Pathogenic Ancestry of the Fungal Clade Ustilaginomycotina. Mol Biol Evol 2018; 35:1840-1854. [DOI: 10.1093/molbev/msy072] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
| | - Stephen J Mondo
- US Department of Energy Joint Genome Institute, Walnut Creek, CA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Walnut Creek, CA
| | - Laura Sandor
- US Department of Energy Joint Genome Institute, Walnut Creek, CA
| | - Juna Lee
- US Department of Energy Joint Genome Institute, Walnut Creek, CA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek, CA
| | | | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Walnut Creek, CA
| | - Matthieu Hainaut
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France
- INRA, USC 1408 AFMB, Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France
- INRA, USC 1408 AFMB, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA
| | - Joseph W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR
| | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN
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18
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Emerling CA, Delsuc F, Nachman MW. Chitinase genes ( CHIAs) provide genomic footprints of a post-Cretaceous dietary radiation in placental mammals. SCIENCE ADVANCES 2018; 4:eaar6478. [PMID: 29774238 PMCID: PMC5955627 DOI: 10.1126/sciadv.aar6478] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 03/30/2018] [Indexed: 05/21/2023]
Abstract
The end-Cretaceous extinction led to a massive faunal turnover, with placental mammals radiating in the wake of nonavian dinosaurs. Fossils indicate that Cretaceous stem placentals were generally insectivorous, whereas their earliest Cenozoic descendants occupied a variety of dietary niches. It is hypothesized that this dietary radiation resulted from the opening of niche space, following the extinction of dinosaurian carnivores and herbivores. We provide the first genomic evidence for the occurrence and timing of this dietary radiation in placental mammals. By comparing the genomes of 107 placental mammals, we robustly infer that chitinase genes (CHIAs), encoding enzymes capable of digesting insect exoskeletal chitin, were present as five functional copies in the ancestor of all placental mammals, and the number of functional CHIAs in the genomes of extant species positively correlates with the percentage of invertebrates in their diets. The diverse repertoire of CHIAs in early placental mammals corroborates fossil evidence of insectivory in Cretaceous eutherians, with descendant lineages repeatedly losing CHIAs beginning at the Cretaceous/Paleogene (K/Pg) boundary as they radiated into noninsectivorous niches. Furthermore, the timing of gene loss suggests that interordinal diversification of placental mammals in the Cretaceous predates the dietary radiation in the early Cenozoic, helping to reconcile a long-standing debate between molecular timetrees and the fossil record. Our results demonstrate that placental mammal genomes, including humans, retain a molecular record of the post-K/Pg placental adaptive radiation in the form of numerous chitinase pseudogenes.
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Affiliation(s)
- Christopher A. Emerling
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Institut des Sciences de l’Évolution de Montpellier (ISEM), Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
- Corresponding author.
| | - Frédéric Delsuc
- Institut des Sciences de l’Évolution de Montpellier (ISEM), Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Michael W. Nachman
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
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19
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The interplay of past diversification and evolutionary isolation with present imperilment across the amphibian tree of life. Nat Ecol Evol 2018; 2:850-858. [DOI: 10.1038/s41559-018-0515-5] [Citation(s) in RCA: 273] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 02/21/2018] [Indexed: 02/02/2023]
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Garland T, Albuquerque RL. Locomotion, Energetics, Performance, and Behavior: A Mammalian Perspective on Lizards, and Vice Versa. Integr Comp Biol 2018; 57:252-266. [PMID: 28859413 DOI: 10.1093/icb/icx059] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
SYNOPSIS Animals are constrained by their abilities and by interactions with environmental factors, such as low ambient temperatures. These constraints range from physical impossibilities to energetic inefficiencies, and may entail trade-offs. Some of the constraints related to locomotion and activity metabolism can be illustrated through allometric comparisons of mammals and lizards, as representative terrestrial vertebrate endotherms and ectotherms, respectively, because these lineages differ greatly in aerobic metabolic capacities, resting energetic costs, and thermoregulatory patterns. Allometric comparisons are both useful and unavoidable, but "outlier" species (unusual for their clade) can also inform evolutionary scenarios, as they help indicate extremes of possible adaptation within mammalian and saurian levels of organization. We compared mammals and lizards for standard metabolic rate (SMR), maximal oxygen consumption during forced exercise (VO2max), net (incremental) cost of transport (NCT), maximal aerobic speed (MAS), daily movement distance (DMD), daily energy expenditure (DEE) during the active season, and the ecological cost of transport (ECT = percentage of DEE attributable to locomotion). (Snakes were excluded because their limbless locomotion has no counterpart in terrestrial mammals.) We only considered lizard SMR, VO2max, NCT, MAS, and sprint speed data if measured at 35-40 °C. On average, MAS is ∼7.4-fold higher in mammals, whereas SMR and VO2max are ∼6-fold greater, but values for all three of these traits overlap (or almost overlap) between mammals and lizards, a fact that has not previously been appreciated. Previous studies show that sprint speeds are similar for smaller mammals and lizards, but at larger sizes lizards are not as fast as some mammals. Mammals move ∼6-fold further each day than lizards, and DMD is by far the most variable trait considered here, but their NCT is similar. Mammals exceed lizards by ∼11.4-fold for DEE. On average for both lineages, the ECT is surprisingly low, somewhat higher for lizards, and positively allometric. If a lizard and mammal of 100 g body mass were both to move their entire DMD at their MAS, they could do so in ∼21 and 17 min, respectively, thus de-emphasizing the possible importance of time constraints. We conclude that ecological-energetic constraints related to locomotion are relatively more likely to occur in large, carnivorous lizards. Overall, our comparisons support the idea that the (gradual) evolution of mammalian endothermy did not necessarily require major changes in locomotor energetics, performance, or associated behaviors. Instead, we speculate that the evolution of thermoregulatory responses to low temperatures (e.g., shivering) may have been a key and "difficult" step in this transition.
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Affiliation(s)
- Theodore Garland
- Department of Biology, University of California, Riverside, CA 92506, USA
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21
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Springer MS, Murphy WJ, Roca AL. Appropriate fossil calibrations and tree constraints uphold the Mesozoic divergence of solenodons from other extant mammals. Mol Phylogenet Evol 2018; 121:158-165. [PMID: 29331683 DOI: 10.1016/j.ympev.2018.01.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 12/27/2017] [Accepted: 01/09/2018] [Indexed: 11/30/2022]
Abstract
The mammalian order Eulipotyphla includes four extant families of insectivorans: Solenodontidae (solenodons); Talpidae (moles); Soricidae (shrews); and Erinaceidae (hedgehogs). Of these, Solenodontidae includes only two extant species, which are endemic to the largest islands of the Greater Antilles: Cuba and Hispaniola. Most molecular studies suggest that eulipotyphlan families diverged from each other across several million years, with the basal split between Solenodontidae and other families occurring in the Late Cretaceous. By contrast, Sato et al. (2016) suggest that eulipotyphlan families diverged from each other in a polytomy ∼58.6 million years ago (Mya). This more recent divergence estimate for Solenodontidae versus other extant eulipotyphlans suggests that solenodons must have arrived in the Greater Antilles via overwater dispersal rather than vicariance. Here, we show that the young timetree estimates for eulipotyphlan families and the polytomy are due to an inverted ingroup-outgroup arrangement of the tree, the result of using Tracer rather than TreeAnnotator to compile interfamilial divergence times, and of not enforcing the monophly of well-established clades such as Laurasiatheria and Eulipotyphla. Finally, Sato et al.'s (2016) timetree includes several zombie lineages where estimated divergence times are much younger than minimum ages that are implied by the fossil record. We reanalyzed Sato et al.'s (2016) original data with enforced monophyly for well-established clades and updated fossil calibrations that eliminate the inference of zombie lineages. Our resulting timetrees, which were compiled with TreeAnnotator rather than Tracer, produce dates that are in good agreement with other recent studies and place the basal split between Solenodontidae and other eulipotyphlans in the Late Cretaceous.
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Affiliation(s)
- Mark S Springer
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA 92521, USA.
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Alfred L Roca
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA
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Abstract
Brown adipose tissue (BAT), the specialized heat-producing organ found in many placental mammals including humans, may be accessible for clinical drug intervention to help combat metabolic diseases. Understanding the biology of BAT and its thermogenic uncoupling protein 1 (UCP1) will benefit from an assessment of its evolution, answering where UCP1 originated and how it has been modified and integrated into cellular energy metabolism. Here, we review topical insights regarding the molecular evolution of UCP1-also reconstructing the proximate and ultimate factors selecting for brown fat thermogenesis in placental mammals. This new thinking on "old" events will assist our understanding of how thermogenic mitochondrial uncoupling was integrated into the physiology of the brown adipocyte. Recent comparative studies examining the occurrence of UCP1 in vertebrates not only identified the ancient (pre-mammal) rise of UCP1 but also its repeated downfall during mammalian evolution as evidenced by multiple independent gene loss and/or inactivation events. Together with the comparative physiology of various species, we may be able to find conditions that favor UCP1 thermogenesis and, learning from these insights, identify molecular networks that will be useful to pharmacologically stimulate the tissue.
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Affiliation(s)
- Michael J Gaudry
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Kevin L Campbell
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Martin Jastroch
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center at Helmholtz Zentrum München, Neuherberg, Germany. .,German Center for Diabetes Research (DZD), München-Neuherberg, Germany.
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Gatesy J, Springer MS. Phylogenomic red flags: Homology errors and zombie lineages in the evolutionary diversification of placental mammals. Proc Natl Acad Sci U S A 2017; 114:E9431-E9432. [PMID: 29078405 PMCID: PMC5692601 DOI: 10.1073/pnas.1715318114] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024;
| | - Mark S Springer
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA 92521
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Dornburg A, Townsend JP, Wang Z. Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big Data. ADVANCES IN GENETICS 2017; 100:1-47. [PMID: 29153398 DOI: 10.1016/bs.adgen.2017.09.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Since its original inception over 150 years ago by Darwin, we have made tremendous progress toward the reconstruction of the Tree of Life. In particular, the transition from analyzing datasets comprised of small numbers of loci to those comprised of hundreds of loci, if not entire genomes, has aided in resolving some of the most vexing of evolutionary problems while giving us a new perspective on biodiversity. Correspondingly, phylogenetic trees have taken a central role in fields that span ecology, conservation, and medicine. However, the rise of big data has also presented phylogenomicists with a new set of challenges to experimental design, quantitative analyses, and computation. The sequencing of a number of very first genomes presented significant challenges to phylogenetic inference, leading fungal phylogenomicists to begin addressing pitfalls and postulating solutions to the issues that arise from genome-scale analyses relevant to any lineage across the Tree of Life. Here we highlight insights from fungal phylogenomics for topics including systematics and species delimitation, ecological and phenotypic diversification, and biogeography while providing an overview of progress made on the reconstruction of the fungal Tree of Life. Finally, we provide a review of considerations to phylogenomic experimental design for robust tree inference. We hope that this special issue of Advances in Genetics not only excites the continued progress of fungal evolutionary biology but also motivates the interdisciplinary development of new theory and methods designed to maximize the power of genomic scale data in phylogenetic analyses.
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Affiliation(s)
- Alex Dornburg
- North Carolina Museum of Natural Sciences, Raleigh, NC, United States
| | | | - Zheng Wang
- Yale University, New Haven, CT, United States.
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25
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Temporal niche expansion in mammals from a nocturnal ancestor after dinosaur extinction. Nat Ecol Evol 2017; 1:1889-1895. [DOI: 10.1038/s41559-017-0366-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 10/05/2017] [Indexed: 11/08/2022]
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26
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Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary. Proc Natl Acad Sci U S A 2017; 114:E7282-E7290. [PMID: 28808022 DOI: 10.1073/pnas.1616744114] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The timing of the diversification of placental mammals relative to the Cretaceous-Paleogene (KPg) boundary mass extinction remains highly controversial. In particular, there have been seemingly irreconcilable differences in the dating of the early placental radiation not only between fossil-based and molecular datasets but also among molecular datasets. To help resolve this discrepancy, we performed genome-scale analyses using 4,388 loci from 90 taxa, including representatives of all extant placental orders and transcriptome data from flying lemurs (Dermoptera) and pangolins (Pholidota). Depending on the gene partitioning scheme, molecular clock model, and genic deviation from molecular clock assumptions, extensive sensitivity analyses recovered widely varying diversification scenarios for placental mammals from a given gene set, ranging from a deep Cretaceous origin and diversification to a scenario spanning the KPg boundary, suggesting that the use of suboptimal molecular clock markers and methodologies is a major cause of controversies regarding placental diversification timing. We demonstrate that reconciliation between molecular and paleontological estimates of placental divergence times can be achieved using the appropriate clock model and gene partitioning scheme while accounting for the degree to which individual genes violate molecular clock assumptions. A birth-death-shift analysis suggests that placental mammals underwent a continuous radiation across the KPg boundary without apparent interruption by the mass extinction, paralleling a genus-level radiation of multituberculates and ecomorphological diversification of both multituberculates and therians. These findings suggest that the KPg catastrophe evidently played a limited role in placental diversification, which, instead, was likely a delayed response to the slightly earlier radiation of angiosperms.
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27
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Irisarri I, Baurain D, Brinkmann H, Delsuc F, Sire JY, Kupfer A, Petersen J, Jarek M, Meyer A, Vences M, Philippe H. Phylotranscriptomic consolidation of the jawed vertebrate timetree. Nat Ecol Evol 2017; 1:1370-1378. [PMID: 28890940 PMCID: PMC5584656 DOI: 10.1038/s41559-017-0240-5] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Phylogenomics is extremely powerful but introduces new challenges as no agreement exists on "standards" for data selection, curation and tree inference. We use jawed vertebrates (Gnathostomata) as model to address these issues. Despite considerable efforts in resolving their evolutionary history and macroevolution, few studies have included a full phylogenetic diversity of gnathostomes and some relationships remain controversial. We tested a novel bioinformatic pipeline to assemble large and accurate phylogenomic datasets from RNA sequencing and find this phylotranscriptomic approach successful and highly cost-effective. Increased sequencing effort up to ca. 10Gbp allows recovering more genes, but shallower sequencing (1.5Gbp) is sufficient to obtain thousands of full-length orthologous transcripts. We reconstruct a robust and strongly supported timetree of jawed vertebrates using 7,189 nuclear genes from 100 taxa, including 23 new transcriptomes from previously unsampled key species. Gene jackknifing of genomic data corroborates the robustness of our tree and allows calculating genome-wide divergence times by overcoming gene sampling bias. Mitochondrial genomes prove insufficient to resolve the deepest relationships because of limited signal and among-lineage rate heterogeneity. Our analyses emphasize the importance of large curated nuclear datasets to increase the accuracy of phylogenomics and provide a reference framework for the evolutionary history of jawed vertebrates.
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Affiliation(s)
- Iker Irisarri
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78464, Germany. .,Systematic Biology Program, Department of Organismal Biology, Univeristy of Uppsala, Norbyvägen 18D, Uppsala, 75236, Sweden.
| | - Denis Baurain
- InBioS-Eukaryotic Phylogenomics, Department of Life Sciences and PhytoSYSTEMS, University of Liège, Liège, 4000, Belgium
| | - Henner Brinkmann
- Leibniz-Institut DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, 38124, Germany
| | - Frédéric Delsuc
- Institut des Sciences de l'Evolution, UMR 5554, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, 34095, France
| | - Jean-Yves Sire
- Institut de Biologie Paris-Seine, UMR7138, Sorbonne Universities, Paris, 75005, France
| | - Alexander Kupfer
- Department of Zoology, Stuttgart State Museum of Natural History, Stuttgart, 70191, Germany
| | - Jörn Petersen
- Leibniz-Institut DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, 38124, Germany
| | - Michael Jarek
- Department of Genome Analytics, Helmholtz Centre for Infection Research, Braunschweig, 38124, Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78464, Germany
| | - Miguel Vences
- Zoological Institute, Braunschweig University of Technology, Braunschweig, 38106, Germany
| | - Hervé Philippe
- Centre for Biodiversity Theory and Modelling, UMR CNRS 5321, Station of Theoretical and Experimental Ecology, Moulis, 09200, France. .,Departement de Biochimie, Université de Montréal, Montréal, QC, H3C3J7, Canada.
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28
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Foley NM, Springer MS, Teeling EC. Mammal madness: is the mammal tree of life not yet resolved? Philos Trans R Soc Lond B Biol Sci 2016; 371:20150140. [PMID: 27325836 PMCID: PMC4920340 DOI: 10.1098/rstb.2015.0140] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2016] [Indexed: 11/12/2022] Open
Abstract
Most molecular phylogenetic studies place all placental mammals into four superordinal groups, Laurasiatheria (e.g. dogs, bats, whales), Euarchontoglires (e.g. humans, rodents, colugos), Xenarthra (e.g. armadillos, anteaters) and Afrotheria (e.g. elephants, sea cows, tenrecs), and estimate that these clades last shared a common ancestor 90-110 million years ago. This phylogeny has provided a framework for numerous functional and comparative studies. Despite the high level of congruence among most molecular studies, questions still remain regarding the position and divergence time of the root of placental mammals, and certain 'hard nodes' such as the Laurasiatheria polytomy and Paenungulata that seem impossible to resolve. Here, we explore recent consensus and conflict among mammalian phylogenetic studies and explore the reasons for the remaining conflicts. The question of whether the mammal tree of life is or can be ever resolved is also addressed.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.
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Affiliation(s)
- Nicole M Foley
- School of Biology and Environmental Science, Science Centre East, University College Dublin, Dublin 4, Ireland
| | - Mark S Springer
- Department of Biology, University of California, Riverside, CA 92521, USA
| | - Emma C Teeling
- School of Biology and Environmental Science, Science Centre East, University College Dublin, Dublin 4, Ireland
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