DOCSLIB.ORG

Mammalian Evolution May Not Be Strictly Bifurcating Open Access

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Mammalian Evolution May Not Be Strictly Bifurcating Open Access View metadata, citation and similar papers at core.ac.uk brought to you by CORE Mammalian Evolution May not Be Strictly Bifurcating provided by PubMed Central Bjo¨rn M. Hallstro¨m1 and Axel Janke*,2 1Department of Cell and Organism Biology, Division of Evolutionary Molecular Systematics, University of Lund, Lund, Sweden 2LOEWE—Biodiversita¨t und Klima Forschungszentrum BiK-F, Frankfurt, Germany *Corresponding author: E-mail: [email protected]. Associate editor: Arndt von Haeseler Abstract The massive amount of genomic sequence data that is now available for analyzing evolutionary relationships among 31 placental mammals reduces the stochastic error in phylogenetic analyses to virtually zero. One would expect that this would make it possible to finally resolve controversial branches in the placental mammalian tree. We analyzed a 2,863,797 nucleotide- Research article long alignment (3,364 genes) from 31 placental mammals for reconstructing their evolution. Most placental mammalian relationships were resolved, and a consensus of their evolution is emerging. However, certain branches remain difficult or virtually impossible to resolve. These branches are characterized by short divergence times in the order of 1–4 million years. Computer simulations based on parameters from the real data show that as little as about 12,500 amino acid sites could be sufficient to confidently resolve short branches as old as about 90 million years ago (Ma). Thus, the amount of sequence data should no longer be a limiting factor in resolving the relationships among placental mammals. The timing of the early radiation of placental mammals coincides with a period of climate warming some 100–80 Ma and with continental fragmentation. These global processes may have triggered the rapid diversification of placental mammals. However, the rapid radiations of certain mammalian groups complicate phylogenetic analyses, possibly due to incomplete lineage sorting and introgression. These speciation-related processes led to a mosaic genome and conflicting phylogenetic signals. Split network methods are ideal for visualizing these problematic branches and can therefore depict data conflict and possibly the true evolutionary history better than strictly bifurcating trees. Given the timing of tectonics, of placental mammalian divergences, and the fossil record, a Laurasian rather than Gondwanan origin of placental mammals seems the most parsimonious explanation. Key words: continental drift, Cretaceous warming, genome analysis, hybridization, phylogenomics, split decomposition. Introduction Despite the amount of available data, some branches in the placental mammal tree are only weakly supported and As genomic sequences are the ultimate source of molecular phylogenomic analyses leave some branches as yet com- data for evolutionary studies, the wealth of information pletely unresolved due to the variable and poor support available from the whole-genome sequencing of metazoans has revolutionized evolutionary studies. After publication for different evolutionary scenarios (Hallstro¨m and Janke of the human genome (Lander et al. 2001; Venter et al. 2008). This was unexpected because, theoretically, the 2001), it was decided that low-coverage (2Â) genome se- sheer amount of genomic data should have easily over- quences from additional mammalian species would be come stochastic errors from single and multiple (20) gene beneficial for more accurate sequence annotation and analyses, a problem that vexed molecular phylogenetic for studying the evolution of disease genes. The data from studies before the wealth of information from the genomic these genome projects also enable us to study the evolu- age (Kullberg et al. 2008). tion of mammalian lineages with a previously unimaginable To date, three important but difficult to resolve branch- amount of data, opening the filed of phylogenomics. The ing points in the mammalian tree have been identified. The first phylogenomic study of placental mammals initially in- first is the primary branching among placental mammals, volved some 200,000 nucleotides (nt) of protein-coding that is, between the superorders Xenarthra (in this study: sequences (Nikolaev et al. 2007). Improving the sequence sloth and armadillo), Afrotheria (elephant, tenrec, and hy- and taxon coverage, phylogenomic analyses of mammals rax), and Boreoplacentalia (all remaining species used in included 2.2 million nucleotides (Mnt) from about 2,840 this study). Previous resolutions of their divergences de- protein-coding genes (Hallstro¨m et al. 2007) or some pended on the choice of analytical methodology and type 1,700 conserved genome loci (Wildman et al. 2007). The of data but did not enable the rejection of alternative hy- largest and most complete data set so far analyzed more potheses (Nishihara et al. 2007; Hallstro¨m and Janke 2008). than 2.8 Mnt from 3,012 protein-coding genes (Hallstro¨m Even the analyses of retroposon insertions, otherwise gen- and Janke 2008). However, phylogenomics has failed to re- erally regarded as a solid phylogenetic marker system, failed liably resolve certain branches of the placental mammal to resolve a clear bifurcation in the most basal divergences tree, thereby posing new problems and questions in animal among placental mammals (Churakov et al. 2009; Nishihara evolution (Hallstro¨m and Janke 2008). et al. 2009), thus, supporting the original sequence-based © The Author(s) 2010. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. Open Access 2804 Mol. Biol. Evol. 27(12):2804–2816. 2010 doi:10.1093/molbev/msq166 Advance Access publication June 29, 2010 Mammalian Phylogenomics · doi:10.1093/molbev/msq166 MBE findings (Hallstro¨m and Janke 2008). Retroposon insertions branches in the mammalian tree and to study the tree like- are, with a few exceptions (Cantrell et al. 2001; van de ness of the mammalian genome data. The number of pla- Lagemaat et al. 2005), free of homoplasies (Steel and Penny cental mammals included in this study has been increased 2000). Therefore, the apparently contradicting results from to 31, 12 (63%) more than in a previous phylogenomic anal- sequence data and retroposon insertion analyses require ysis (Hallstro¨m and Janke 2008), and the genome data from a natural explanation. Similar observations have also been six outgroup species were included to ensure a solid root of made for the other two poorly or unresolved mammalian the tree from a maximal taxon sampling. The previously phylogenetic branches. The detection of apparently con- unresolved branchings inside the Laurasiaplacentalia, flicting phylogenetic signals for the position of the Scan- which include Perissodactyla, Carnivora, Artiodactyla, dentia (tree shrews) relative to Primates and Glires Cetacea, Chiroptera, and Lipotyphla (Arnason et al. (rodents and lagomorphs) within the Euarchontoglires 2008), may be clarified by the new genome data of a peris- clade, and the position of Chiroptera (bats) relative to sodactyl (horse), a second chiropteran (mega bat), a ceta- Artiodactyla (even-toed ungulates), Carnivora, Lipothypla cean (dolphin), and an artiodactylan (alpaca). The genome (hedghog, common shrew, and allies), and Perissodactyla data from a hyracoid (hyrax) and a second xenarthran (odd-toed ungulates) within the Laurasiaplacentalia, leave (sloth) are invaluable additions to the hitherto long and both controversial and poorly supported (Nishihara et al. undivided branches of Afrotheria and Xenarthra, allowing 2006; Janecka et al. 2007; Kriegs et al. 2007; Hallstro¨m and the basal divergences among placental mammals to be ex- Janke 2008). amined in more detail. Computer simulations were made A common feature of these three problematic divergen- to estimate the amount of data needed to resolve short ces is the divergence of groups within 1–4 million years branches, and finally, split decomposition methods (Huson (My) of one another (Hallstro¨m and Janke 2008). Such time and Bryant 2006) were used for visualizing conflict in the intervals may have been too short for the respective ge- tree. nomes to gather enough substitutions to resolve rapid di- vergences some 100 My later or limited taxon sampling Materials and Methods may impede such phylogenetic analyses. Another possible Data reason for the problems involved in clearly resolving short Predicted cDNA sequences from all tetrapods with assem- central branches of the placental mammalian tree by se- blies and gene builds in release 54 of ENSEMBL were down- quence and retroposon data may be speciation-associated loaded from ftp://ftp.ensembl.org/pub/current_fasta/. In processes, such as species hybridization and incomplete lin- total, 37 species (table 1) were included in the data build. eage sorting (Nei 1987). Species hybridization leads to in- The taxon sampling represents 16 of the 21 extant euthe- trogression, the incorporation of genes from one species rian orders. The sequence data from metatherian (marsu- into the gene pool of another species, whereas incomplete pials), prototherian (monotremes), avian (bird), reptile, and lineage sorting produces a pattern of allele fixations from amphibian species were collected for rooting the placental ancestral
Load more

Recommended publications
  • Ecological Causes of Uneven Diversification and Richness in the Mammal Tree of Life
    bioRxiv preprint doi: https://doi.org/10.1101/504803; this version posted March 28, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Ecological causes of uneven diversification and richness in the mammal tree of life 2 Short title: Ecological causes of diversification in mammals 3 4 Nathan S. Upham1*, Jacob A. Esselstyn2, and Walter Jetz1* 5 6 Author affiliations: 1Department of Ecology & Evolutionary Biology, Yale University, New 7 Haven, CT 06511 USA. 2Department of Biological Sciences and Museum of Natural Science, 8 Louisiana State University, Baton Rouge, LA 70803 USA. 9 10 *Corresponding authors: 165 Prospect St., OML 122, New Haven, CT 06511 USA; 11 [email protected]; [email protected] 12 bioRxiv preprint doi: https://doi.org/10.1101/504803; this version posted March 28, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 13 Abstract 14 The uneven distribution of species in the tree of life is rooted in unequal speciation and 15 extinction among groups. Yet the causes of differential diversification are little known despite 16 their relevance for sustaining biodiversity into the future. Here we investigate rates of species 17 diversification across extant Mammalia, a compelling system that includes our own closest 18 relatives.
    [Show full text]
  • Molecular Evolution and Phylogenetic Importance of a Gamete Recognition Gene Zan Reveals a Unique Contribution to Mammalian Speciation
    Molecular evolution and phylogenetic importance of a gamete recognition gene Zan reveals a unique contribution to mammalian speciation. by Emma K. Roberts A Dissertation In Biological Sciences Submitted to the Graduate Faculty of Texas Tech University in Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY Approved Robert D. Bradley Chair of Committee Daniel M. Hardy Llewellyn D. Densmore Caleb D. Phillips David A. Ray Mark Sheridan Dean of the Graduate School May, 2020 Copyright 2020, Emma K. Roberts Texas Tech University, Emma K. Roberts, May 2020 ACKNOWLEDGMENTS I would like to thank numerous people for support, both personally and professionally, throughout the course of my degree. First, I thank Dr. Robert D. Bradley for his mentorship, knowledge, and guidance throughout my tenure in in PhD program. His ‘open door policy’ helped me flourish and grow as a scientist. In addition, I thank Dr. Daniel M. Hardy for providing continued support, knowledge, and exciting collaborative efforts. I would also like to thank the remaining members of my advisory committee, Drs. Llewellyn D. Densmore III, Caleb D. Phillips, and David A. Ray for their patience, guidance, and support. The above advisors each helped mold me into a biologist and I am incredibly gracious for this gift. Additionally, I would like to thank numerous mentors, friends and colleagues for their advice, discussions, experience, and friendship. For these reasons, among others, I thank Dr. Faisal Ali Anwarali Khan, Dr. Sergio Balaguera-Reina, Dr. Ashish Bashyal, Joanna Bateman, Karishma Bisht, Kayla Bounds, Sarah Candler, Dr. Juan P. Carrera-Estupiñán, Dr. Megan Keith, Christopher Dunn, Moamen Elmassry, Dr.
    [Show full text]
  • Evolution 1 Ecological Causes of Uneven Diversification and Richness
    bioRxiv preprint doi: https://doi.org/10.1101/504803; this version posted January 4, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 BIOLOGICAL SCIENCES: Evolution 2 Ecological causes of uneven diversification and richness in the mammal tree of life 3 Short title: Ecological causes of diversification in mammals 4 5 Nathan S. Upham1*, Jacob A. Esselstyn2, and Walter Jetz1* 6 7 Author affiliations: 1Department of Ecology & Evolutionary Biology, Yale University, New 8 Haven, CT 06511 USA. 2Department of Biological Sciences and Museum of Natural Science, 9 Louisiana State University, Baton Rouge, LA 70803 USA. 10 11 *Corresponding author: Nathan S. Upham; address: 165 Prospect St., OML 122, New Haven, CT 12 06511 USA; phone: 773-263-1533; email: [email protected]. bioRxiv preprint doi: https://doi.org/10.1101/504803; this version posted January 4, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 13 Abstract 14 The uneven distribution of species in the tree of life is rooted in unequal speciation and 15 extinction among groups. Yet the causes of differential diversification are little known despite 16 their relevance for sustaining biodiversity into the future. Here we investigate rates of species 17 diversification across extant Mammalia, a compelling system that includes our own closest 18 relatives.
    [Show full text]
  • Discovery of Prosimian and Afrotherian Foamy Viruses And
    Katzourakis et al. Retrovirology 2014, 11:61 http://www.retrovirology.com/content/11/1/61 RESEARCH Open Access Discovery of prosimian and afrotherian foamy viruses and potential cross species transmissions amidst stable and ancient mammalian co-evolution Aris Katzourakis1*†, Pakorn Aiewsakun1†, Hongwei Jia2, Nathan D Wolfe3,4,5, Matthew LeBreton6, Anne D Yoder7 and William M Switzer2* Abstract Background: Foamy viruses (FVs) are a unique subfamily of retroviruses that are widely distributed in mammals. Owing to the availability of sequences from diverse mammals coupled with their pattern of codivergence with their hosts, FVs have one of the best-understood viral evolutionary histories ever documented, estimated to have an ancient origin. Nonetheless, our knowledge of some parts of FV evolution, notably that of prosimian and afrotherian FVs, is far from complete due to the lack of sequence data. Results: Here, we report the complete genome of the first extant prosimian FV (PSFV) isolated from a lorisiforme galago (PSFVgal), and a novel partial endogenous viral element with high sequence similarity to FVs, present in the afrotherian Cape golden mole genome (ChrEFV). We also further characterize a previously discovered endogenous PSFV present in the aye-aye genome (PSFVaye). Using phylogenetic methods and available FV sequence data, we show a deep divergence and stable co-evolution of FVs in eutherian mammals over 100 million years. Nonetheless, we found that the evolutionary histories of bat, aye-aye, and New World monkey FVs conflict with the evolutionary histories of their hosts. By combining sequence analysis and biogeographical knowledge, we propose explanations for these mismatches in FV-host evolutionary history.
    [Show full text]
  • Life-History Traits Drive the Evolutionary Rates of Mammalian Coding and Noncoding Genomic Elements
    Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements Sergey I. Nikolaev*†, Juan I. Montoya-Burgos‡, Konstantin Popadin§, Leila Parand*, Elliott H. Margulies¶, National Institutes of Health Intramural Sequencing Center Comparative Sequencing Program¶ʈ**, and Stylianos E. Antonarakis* *Department of Genetic Medicine and Development, University of Geneva Medical School, 1 Rue Michel-Servet, 1211 Geneva, Switzerland; ‡Department of Animal Biology, University of Geneva, 30 Quai Ansermet, 1211 Geneva, Switzerland; §Institute for Information Transmission Problems RAS, Bolshoi Karetny Pereulok 19, Moscow 127994, Russia; and ¶Genome Technology Branch and ʈIntramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 Edited by Morris Goodman, Wayne State University School of Medicine, Detroit, MI, and approved October 23, 2007 (received for review June 19, 2007) A comprehensive phylogenetic framework is indispensable for spread throughout the population because of random genetic investigating the evolution of genomic features in mammals as a drift (17). Because the effect of positive selection is negligible whole, and particularly in humans. Using the ENCODE sequence (i.e., most new mutations have s Ͻ 0), the nearly neutral theory data, we estimated mammalian neutral evolutionary rates and deals mainly with slightly deleterious mutations. Given that the selective pressures acting on conserved coding and noncoding probability of fixation of slightly deleterious mutations depends elements. We show that neutral evolutionary rates can be ex- on the effective population size, there is a class of these plained by the generation time (GT) hypothesis. Accordingly, mutations that can be fixed in small populations because of primates (especially humans), having longer GTs than other mam- random drift but are counter-selected, through purifying selec- mals, display slower rates of neutral evolution.
    [Show full text]
  • A Radiation of Arboreal Basal Eutherian Mammals Beginning in the Late Cretaceous of India
    A radiation of arboreal basal eutherian mammals beginning in the Late Cretaceous of India Anjali Goswamia,b,1, Guntupalli V. R. Prasadc, Paul Upchurchb, Doug M. Boyerd, Erik R. Seifferte, Omkar Vermaf, Emmanuel Gheerbrantg, and John J. Flynnh aDepartment of Genetics, Evolution, and Environment, bDepartment of Earth Sciences, University College London, London WC1E 6BT, United Kingdom; cDepartment of Geology, Centre for Advanced Studies, University of Delhi, Delhi 110 007, India; dDepartment of Anthropology and Archaeology, Brooklyn College, City University of New York, Brooklyn, NY 11210; eDepartment of Anatomical Sciences, Stony Brook University, Stony Brook, NY 11794-8081; fSchool of Sciences, Indira Gandhi National Open University, New Delhi 110 068, India; gUnité Mixte de Recherche 7207 du Centre National de la Recherche Scientifique (CR2P), Département Histoire de la Terre, Muséum National d’Histoire Naturelle, 75005 Paris, France; and hDivision of Paleontology and Richard Gilder Graduate School, American Museum of Natural History, New York, NY 10024 Edited* by Elwyn L. Simons, Duke University, Durham, NC, and approved August 15, 2011 (received for review June 6, 2011) India’s Late Cretaceous fossil mammals include the only undis- cluding placentals and their stem relatives) are known from the puted pre-Tertiary Gondwanan eutherians, such as Deccanolestes. Late Cretaceous of Laurasia (North America, Europe, and Asia) Recent studies have suggested a relationship between Deccano- (9), and although a few have been suggested as possible pla- lestes and African and European Paleocene adapisoriculids, which centals [e.g., Protungulatum (10)], none are unequivocally sup- have been variably identified as stem euarchontans, stem pri- ported as a Cretaceous placental mammal (2).
    [Show full text]
  • Massive Loss of Transcription Factors and the Initial Diversification of Placental Mammals
    bioRxiv preprint doi: https://doi.org/10.1101/2021.03.26.436744; this version posted March 26, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Massive loss of transcription factors and the initial diversification of placental mammals Xin-Wei Zhao1*†, Jiaqi Wu2†, Hirohisa Kishino1 1Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan. 2School of Life Science and Technology, Tokyo Institute of Technology, Meguro Ward, Tokyo 152- 8550, Japan. *Correspondence to: [email protected] (X.-W.Z.) †These authors contributed equally to this work. ABSTRACT As one of the most successful categories of organisms, mammals occupy a variety of niches on earth as a result of macroevolution. Transcription factors (TFs), the basic regulators of gene expression, may also evolve during mammalian phenotypic diversification and macroevolution. To examine the relationship between TFs and mammalian macroevolution, we analyzed 140,821 de novo-identified TFs and their birth and death histories from 96 mammalian species. Gene tree vs. species tree reconciliation revealed that mammals experienced an upsurge in TF losses around 100 million years ago and also near the K–Pg boundary, thus implying a relationship with the divergence of placental animals. From approximately 100 million years ago to the present, losses dominated TF events without a significant change in TF gains. To quantify the effects of this TF pruning on mammalian macroevolution, we analyzed rates of molecular evolution and expression profiles of regulated target genes.
    [Show full text]
  • Confirming the Phylogeny of Mammals by Use of Large
    RESEARCH ARTICLES Confirming the Phylogeny of Mammals by Use of Large Comparative Sequence Data Sets Arjun B. Prasad,*à Marc W. Allard,§ NISC Comparative Sequencing Program* and Eric D. Green* *Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD; NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD; àIntegrated Biosciences Program, George Washington University; and §Department of Biological Sciences, George Washington University The ongoing generation of prodigious amounts of genomic sequence data from myriad vertebrates is providing unparalleled opportunities for establishing definitive phylogenetic relationships among species. The size and complexities of such comparative sequence data sets not only allow smaller and more difficult branches to be resolved but also present unique challenges, including large computational requirements and the negative consequences of systematic biases. To explore these issues and to clarify the phylogenetic relationships among mammals, we have analyzed a large data set of over 60 megabase pairs (Mb) of high-quality genomic sequence, which we generated from 41 mammals and 3 other vertebrates. All sequences are orthologous to a 1.9-Mb region of the human genome that encompasses the cystic fibrosis transmembrane conductance regulator gene (CFTR). To understand the characteristics and challenges associated with phylogenetic analyses of such a large data set, we partitioned the sequence
    [Show full text]
  • Retroposon Analysis and Recent Geological Data Suggest Near-Simultaneous Divergence of the Three Superorders of Mammals
    Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals Hidenori Nishiharaa, Shigenori Maruyamab, and Norihiro Okadaa,1 aDepartment of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B-21 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan; and bDepartment of Earth and Planetary Sciences, Graduate School of Science and Engineering, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan Edited by Masatoshi Nei, Pennsylvania State University, University Park, PA, and approved February 13, 2009 (received for review September 17, 2008) As a consequence of recent developments in molecular phylog- (9). They estimated molecular divergence times among many enomics, all extant orders of placental mammals have been mammalian orders to be Ϸ100 Ma, which is inconsistent with grouped into 3 lineages: Afrotheria, Xenarthra, and Boreotheria, fossil records suggesting that most mammals had diverged after which originated in Africa, South America, and Laurasia, respec- 65 Ma. One of their interpretations was that the early divergence tively. Despite this advancement, the order of divergence of these of mammals occurred because of several continental fissions. 3 lineages remains unresolved. Here, we performed extensive This hypothesis prompted many biologists to consider available retroposon analysis with mammalian genomic data. Surprisingly, geological data when estimating lineage divergence. One of the we identified a similar number of informative retroposon loci that outcomes of this idea is Afrotheria, which is a good represen- support each of 3 possible phylogenetic hypotheses: the basal tative case for the association between continental drift and position for Afrotheria (22 loci), Xenarthra (25 loci), and Boreoth- mammalian evolution (10, 11).
    [Show full text]
  • Nomenclature and Placental Mammal Phylogeny Robert J Asher1*, Kristofer M Helgen2
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central Asher and Helgen BMC Evolutionary Biology 2010, 10:102 http://www.biomedcentral.com/1471-2148/10/102 CORRESPONDENCE Open Access Nomenclature and placental mammal phylogeny Robert J Asher1*, Kristofer M Helgen2 Abstract An issue arising from recent progress in establishing the placental mammal Tree of Life concerns the nomenclature of high-level clades. Fortunately, there are now several well-supported clades among extant mammals that require unambiguous, stable names. Although the International Code of Zoological Nomenclature does not apply above the Linnean rank of family, and while consensus on the adoption of competing systems of nomenclature does not yet exist, there is a clear, historical basis upon which to arbitrate among competing names for high-level mamma- lian clades. Here, we recommend application of the principles of priority and stability, as laid down by G.G. Simp- son in 1945, to discriminate among proposed names for high-level taxa. We apply these principles to specific cases among placental mammals with broad relevance for taxonomy, and close with particular emphasis on the Afrotherian family Tenrecidae. We conclude that no matter how reconstructions of the Tree of Life change in years to come, systematists should apply new names reluctantly, deferring to those already published and maximizing consistency with existing nomenclature. Background At the family level and below, Linnean categories The last decade has witnessed an unprecedented increase require types (genera for families, species for genera, in the stability of the mammalian Tree of Life [e.g., specimens for species).
    [Show full text]
  • A Radiation of Arboreal Basal Eutherian Mammals Beginning in the Late Cretaceous of India
    A radiation of arboreal basal eutherian mammals beginning in the Late Cretaceous of India Anjali Goswamia,b,1, Guntupalli V. R. Prasadc, Paul Upchurchb, Doug M. Boyerd, Erik R. Seifferte, Omkar Vermaf, Emmanuel Gheerbrantg, and John J. Flynnh aDepartment of Genetics, Evolution, and Environment, bDepartment of Earth Sciences, University College London, London WC1E 6BT, United Kingdom; cDepartment of Geology, Centre for Advanced Studies, University of Delhi, Delhi 110 007, India; dDepartment of Anthropology and Archaeology, Brooklyn College, City University of New York, Brooklyn, NY 11210; eDepartment of Anatomical Sciences, Stony Brook University, Stony Brook, NY 11794-8081; fSchool of Sciences, Indira Gandhi National Open University, New Delhi 110 068, India; gUnité Mixte de Recherche 7207 du Centre National de la Recherche Scientifique (CR2P), Département Histoire de la Terre, Muséum National d’Histoire Naturelle, 75005 Paris, France; and hDivision of Paleontology and Richard Gilder Graduate School, American Museum of Natural History, New York, NY 10024 Edited* by Elwyn L. Simons, Duke University, Durham, NC, and approved August 15, 2011 (received for review June 6, 2011) India’s Late Cretaceous fossil mammals include the only undis- cluding placentals and their stem relatives) are known from the puted pre-Tertiary Gondwanan eutherians, such as Deccanolestes. Late Cretaceous of Laurasia (North America, Europe, and Asia) Recent studies have suggested a relationship between Deccano- (9), and although a few have been suggested as possible pla- lestes and African and European Paleocene adapisoriculids, which centals [e.g., Protungulatum (10)], none are unequivocally sup- have been variably identified as stem euarchontans, stem pri- ported as a Cretaceous placental mammal (2).
    [Show full text]
  • Mammalian Evolution May Not Be Strictly Bifurcating Open Access Research Article
    Mammalian Evolution May not Be Strictly Bifurcating Bjo¨rn M. Hallstro¨m1 and Axel Janke*,2 1Department of Cell and Organism Biology, Division of Evolutionary Molecular Systematics, University of Lund, Lund, Sweden 2LOEWE—Biodiversita¨t und Klima Forschungszentrum BiK-F, Frankfurt, Germany *Corresponding author: E-mail: [email protected]. Associate editor: Arndt von Haeseler Abstract The massive amount of genomic sequence data that is now available for analyzing evolutionary relationships among 31 placental mammals reduces the stochastic error in phylogenetic analyses to virtually zero. One would expect that this would make it possible to finally resolve controversial branches in the placental mammalian tree. We analyzed a 2,863,797 nucleotide- Research article long alignment (3,364 genes) from 31 placental mammals for reconstructing their evolution. Most placental mammalian relationships were resolved, and a consensus of their evolution is emerging. However, certain branches remain difficult or virtually impossible to resolve. These branches are characterized by short divergence times in the order of 1–4 million years. Computer simulations based on parameters from the real data show that as little as about 12,500 amino acid sites could be sufficient to confidently resolve short branches as old as about 90 million years ago (Ma). Thus, the amount of sequence data should no longer be a limiting factor in resolving the relationships among placental mammals. The timing of the early radiation of placental mammals coincides with a period of climate warming some 100–80 Ma and with continental fragmentation. These global processes may have triggered the rapid diversification of placental mammals. However, the rapid radiations of certain mammalian groups complicate phylogenetic analyses, possibly due to incomplete lineage sorting and introgression.
    [Show full text]