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Liu G, Pan Q, Dai Y, Wang X, Li M, Zhu P, Zhou X. Phylogenomics of Afrotherian mammals and improved resolution of extant Paenungulata. Mol Phylogenet Evol 2024; 195:108047. [PMID: 38460890 DOI: 10.1016/j.ympev.2024.108047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/19/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
Molecular investigations have gathered a diverse set of mammals-predominantly African natives like elephants, hyraxes, and aardvarks-into a clade known as Afrotheria. Nevertheless, the precise phylogenetic relationships among these species remain contentious. Here, we sourced orthologous markers and ultraconserved elements to discern the interordinal connections among Afrotherian mammals. Our phylogenetic analyses bolster the common origin of Afroinsectiphilia and Paenungulata, and propose Afrosoricida as the closer relative to Macroscelidea rather than Tubulidentata, while also challenging the notion of Sirenia and Hyracoidea as sister taxa. The approximately unbiased test and the gene concordance factor uniformly recognized the alliance of Proboscidea with Hyracoidea as the dominant topology within Paenungulata. Investigation into sites with extremly high phylogenetic signal unveiled their potential to intensify conflicts in the Paenungulata topology. Subsequent exploration suggested that incomplete lineage sorting was predominantly responsible for the observed contentious relationships, whereas introgression exerted a subsidiary influence. The divergence times estimated in our study hint at the Cretaceous-Paleogene (K-Pg) extinction event as a catalyst for Afrotherian diversification. Overall, our findings deliver a tentative but insightful overview of Afrotheria phylogeny and divergence, elucidating these relationships through the lens of phylogenomics.
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Affiliation(s)
- Gaoming Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi Pan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yichen Dai
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiao Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Meng Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Pingfen Zhu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuming Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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Bowman J, Enard D, Lynch VJ. Phylogenomics reveals an almost perfect polytomy among the almost ungulates ( Paenungulata). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570590. [PMID: 38106080 PMCID: PMC10723481 DOI: 10.1101/2023.12.07.570590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Phylogenetic studies have resolved most relationships among Eutherian Orders. However, the branching order of elephants (Proboscidea), hyraxes (Hyracoidea), and sea cows (Sirenia) (i.e., the Paenungulata) has remained uncertain since at least 1758, when Linnaeus grouped elephants and manatees into a single Order (Bruta) to the exclusion of hyraxes. Subsequent morphological, molecular, and large-scale phylogenomic datasets have reached conflicting conclusions on the branching order within Paenungulates. We use a phylogenomic dataset of alignments from 13,388 protein-coding genes across 261 Eutherian mammals to infer phylogenetic relationships within Paenungulates. We find that gene trees almost equally support the three alternative resolutions of Paenungulate relationships and that despite strong support for a Proboscidea+Hyracoidea split in the multispecies coalescent (MSC) tree, there is significant evidence for gene tree uncertainty, incomplete lineage sorting, and introgression among Proboscidea, Hyracoidea, and Sirenia. Indeed, only 8-10% of genes have statistically significant phylogenetic signal to reject the hypothesis of a Paenungulate polytomy. These data indicate little support for any resolution for the branching order Proboscidea, Hyracoidea, and Sirenia within Paenungulata and suggest that Paenungulata may be as close to a real, or at least unresolvable, polytomy as possible.
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Affiliation(s)
- Jacob Bowman
- Department of Biological Sciences, University at Buffalo, SUNY, 551 Cooke Hall, Buffalo, NY, USA
| | - David Enard
- Department of Ecology and Evolutionary Biology. University of Arizona, Tucson, AZ, USA
| | - Vincent J. Lynch
- Department of Biological Sciences, University at Buffalo, SUNY, 551 Cooke Hall, Buffalo, NY, USA
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Szynwelski BE, Kretschmer R, Matzenbacher CA, Ferrari F, Alievi MM, de Freitas TRO. Hybridization in Canids-A Case Study of Pampas Fox ( Lycalopex gymnocercus) and Domestic Dog ( Canis lupus familiaris) Hybrid. Animals (Basel) 2023; 13:2505. [PMID: 37570312 PMCID: PMC10417603 DOI: 10.3390/ani13152505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/25/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
Hybridization between species with different evolutionary trajectories can be a powerful threat to wildlife conservation. Anthropogenic activities, such as agriculture and livestock, have led to the degradation and loss of natural habitats for wildlife. Consequently, the incidence of interspecific hybridization between wild and domestic species has increased, although cases involving species of different genera are rare. In Vacaria, a Southern city in Brazil, a female canid with a strange phenotype, which had characteristics between the phenotype of the domestic dog (Canis familiaris) and that of the pampas fox (Lycalopex gymnocercus), was found. Our analysis suggests that the animal is a hybrid between a domestic dog and a pampas fox, but future studies are necessary to investigate additional cases of this hybridization in nature. This finding worries for the conservation of wild canids in South America, especially concerning Lycalopex species. Hybridization with the domestic dog may have harmful effects on pampas fox populations due to the potential for introgression and disease transmission by the domestic dog. Therefore, future studies to explore the consequences of hybridization on genetics, ecology, and behavior of wild populations will be essential to improve the conservation of this species.
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Affiliation(s)
- Bruna Elenara Szynwelski
- Laboratório de Citogenética e Evolução, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900, Rio Grande do Sul, Brazil; (B.E.S.); (C.A.M.); (T.R.O.d.F.)
| | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Universidade Federal de Pelotas, Campus Universitário Capão do Leão, Pelotas 96010-900, Rio Grande do Sul, Brazil
| | - Cristina Araujo Matzenbacher
- Laboratório de Citogenética e Evolução, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900, Rio Grande do Sul, Brazil; (B.E.S.); (C.A.M.); (T.R.O.d.F.)
| | - Flávia Ferrari
- Núcleo de Conservação e Reabilitação de Animais Silvestres, Universidade Federal do Rio Grande do Sul, Porto Alegre 90540-000, Rio Grande do Sul, Brazil; (F.F.); (M.M.A.)
| | - Marcelo Meller Alievi
- Núcleo de Conservação e Reabilitação de Animais Silvestres, Universidade Federal do Rio Grande do Sul, Porto Alegre 90540-000, Rio Grande do Sul, Brazil; (F.F.); (M.M.A.)
| | - Thales Renato Ochotorena de Freitas
- Laboratório de Citogenética e Evolução, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900, Rio Grande do Sul, Brazil; (B.E.S.); (C.A.M.); (T.R.O.d.F.)
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Beck RM, Voss RS, Jansa SA. Craniodental Morphology and Phylogeny of Marsupials. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2022. [DOI: 10.1206/0003-0090.457.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Robin M.D. Beck
- School of Science, Engineering and Environment University of Salford, U.K. School of Biological, Earth & Environmental Sciences University of New South Wales, Australia Division of Vertebrate Zoology (Mammalogy) American Museum of Natural History
| | - Robert S. Voss
- Division of Vertebrate Zoology (Mammalogy) American Museum of Natural History
| | - Sharon A. Jansa
- Bell Museum and Department of Ecology, Evolution, and Behavior University of Minnesota
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5
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OUP accepted manuscript. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Iotchev IB, Kubinyi E. Shared and unique features of mammalian sleep spindles - insights from new and old animal models. Biol Rev Camb Philos Soc 2021; 96:1021-1034. [PMID: 33533183 DOI: 10.1111/brv.12688] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 11/29/2022]
Abstract
Sleep spindles are phasic events observed in mammalian non-rapid eye movement sleep. They are relevant today in the study of memory consolidation, sleep quality, mental health and ageing. We argue that our advanced understanding of their mechanisms has not exhausted the utility and need for animal model work. This is both because some topics, like cognitive ageing, have not yet been addressed sufficiently in comparative efforts and because the evolutionary history of this oscillation is still poorly understood. Comparisons across species often are either limited to referencing the classical cat and rodent models, or are over-inclusive, uncritically including reports of sleep spindles in rarely studied animals. In this review, we discuss the emergence of new (dog and sheep) models for sleep spindles and compare the strengths and shortcomings of new and old models based on the three validation criteria for animal models - face, predictive, and construct validity. We conclude that an emphasis on cognitive ageing might dictate the future of comparative sleep spindle studies, a development that is already becoming visible in studies on dogs. Moreover, reconstructing the evolutionary history of sleep spindles will require more stringent criteria for their identification, across more species. In particular, a stronger emphasis on construct and predictive validity can help verify if spindle-like events in other species are actual sleep spindles. Work in accordance with such stricter validation suggests that sleep spindles display more universally shared features, like defining frequency, than previously thought.
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Affiliation(s)
- Ivaylo Borislavov Iotchev
- Department of Ethology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary
| | - Eniko Kubinyi
- Department of Ethology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary
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Lv X, Hu J, Hu Y, Li Y, Xu D, Ryder OA, Irwin DM, Yu L. Diverse phylogenomic datasets uncover a concordant scenario of laurasiatherian interordinal relationships. Mol Phylogenet Evol 2020; 157:107065. [PMID: 33387649 DOI: 10.1016/j.ympev.2020.107065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 12/22/2020] [Accepted: 12/24/2020] [Indexed: 10/22/2022]
Abstract
Resolving the interordinal relationships in the mammalian superorder Laurasiatheria has been among the most intractable problems in higher-level mammalian systematics, with many conflicting hypotheses having been proposed. The present study collected three different sources of genome-scale data with comprehensive taxon sampling of laurasiatherian species, including two protein-coding datasets (4,186 protein-coding genes for an amino acid dataset comprising 2,761,247 amino acid residues and a nucleotide dataset comprising 5,516,340 nucleotides from 1st and 2nd codon positions), an intronic dataset (1,210 introns comprising 1,162,723 nucleotides) and an ultraconserved elements (UCEs) dataset (1,246 UCEs comprising 1,946,472 nucleotides) from 40 species representing all six laurasiatherian orders and 7 non-laurasiatherian outgroups. Remarkably, phylogenetic trees reconstructed with the four datasets using different tree-building methods (RAxML, FastTree, ASTRAL and MP-EST) all supported the relationship (Eulipotyphla, (Chiroptera, ((Carnivora, Pholidota), (Cetartiodactyla, Perissodactyla)))). We find a resolution of interordinal relationships of Laurasiatheria among all types of markers used in the present study, and the likelihood ratio tests for tree comparisons confirmed that the present tree topology is the optimal hypothesis compared to other examined hypotheses. Jackknifing subsampling analyses demonstrate that the results of laurasiatherian tree reconstruction varied with the number of loci and ordinal representatives used, which are likely the two main contributors to phylogenetic disagreements of Laurasiatheria seen in previous studies. Our study provides significant insight into laurasiatherian evolution, and moreover, an important methodological strategy and reference for resolving phylogenies of adaptive radiation, which have been a long-standing challenge in the field of phylogenetics.
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Affiliation(s)
- Xue Lv
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China; School of Life Sciences, Yunnan University, Kunming, China
| | - Jingyang Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China; School of Life Sciences, Yunnan University, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Yiwen Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China; School of Life Sciences, Yunnan University, Kunming, China
| | - Yitian Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China; School of Life Sciences, Yunnan University, Kunming, China
| | - Dongming Xu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming, China
| | - Oliver A Ryder
- Institute for Conservation Research, San Diego Zoo Global, Escondido, CA, USA
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.
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Magnadóttir B, Uysal-Onganer P, Kraev I, Svansson V, Hayes P, Lange S. Deiminated proteins and extracellular vesicles - Novel serum biomarkers in whales and orca. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 34:100676. [PMID: 32114311 DOI: 10.1016/j.cbd.2020.100676] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/16/2020] [Accepted: 02/17/2020] [Indexed: 02/06/2023]
Abstract
Peptidylarginine deiminases (PADs) are a family of phylogenetically conserved calcium-dependent enzymes which cause post-translational protein deimination. This can result in neoepitope generation, affect gene regulation and allow for protein moonlighting via functional and structural changes in target proteins. Extracellular vesicles (EVs) carry cargo proteins and genetic material and are released from cells as part of cellular communication. EVs are found in most body fluids where they can be useful biomarkers for assessment of health status. Here, serum-derived EVs were profiled, and post-translationally deiminated proteins and EV-related microRNAs are described in 5 ceataceans: minke whale, fin whale, humpback whale, Cuvier's beaked whale and orca. EV-serum profiles were assessed by transmission electron microscopy and nanoparticle tracking analysis. EV profiles varied between the 5 species and were identified to contain deiminated proteins and selected key inflammatory and metabolic microRNAs. A range of proteins, critical for immune responses and metabolism were identified to be deiminated in cetacean sera, with some shared KEGG pathways of deiminated proteins relating to immunity and physiology, while some KEGG pathways were species-specific. This is the first study to characterise and profile EVs and to report deiminated proteins and putative effects of protein-protein interaction networks via such post-translationald deimination in cetaceans, revealing key immune and metabolic factors to undergo this post-translational modification. Deiminated proteins and EVs profiles may possibly be developed as new biomarkers for assessing health status of sea mammals.
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Affiliation(s)
- Bergljót Magnadóttir
- Institute for Experimental Pathology, University of Iceland, Keldur v. Vesturlandsveg, 112 Reykjavik, Iceland.
| | - Pinar Uysal-Onganer
- Cancer Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK.
| | - Igor Kraev
- Electron Microscopy Suite, Faculty of Science, Technology, Engineering and Mathematics, Open University, Milton Keynes MK7 6AA, UK.
| | - Vilhjálmur Svansson
- Institute for Experimental Pathology, University of Iceland, Keldur v. Vesturlandsveg, 112 Reykjavik, Iceland
| | - Polly Hayes
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK.
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK.
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9
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Nyakatura JA. Early primate evolution: insights into the functional significance of grasping from motion analyses of extant mammals. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz057] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- John A Nyakatura
- AG Morphologie und Formengeschichte, Institut für Biologie, Humboldt Universität, Philippstraße, Berlin, Germany
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11
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Steyn C, Soley JT, Crole MR. Osteology and Radiological Anatomy of the Thoracic Limbs of Temminck's Ground Pangolin (Smutsia temminckii
). Anat Rec (Hoboken) 2017; 301:624-635. [DOI: 10.1002/ar.23733] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/14/2017] [Accepted: 08/27/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Christine Steyn
- Department of Anatomy and Physiology, Faculty of Veterinary Science; University of Pretoria; Onderstepoort South Africa
| | - John T. Soley
- Department of Anatomy and Physiology, Faculty of Veterinary Science; University of Pretoria; Onderstepoort South Africa
| | - Martina R. Crole
- Department of Anatomy and Physiology, Faculty of Veterinary Science; University of Pretoria; Onderstepoort South Africa
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12
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Phylogeny mandalas for illustrating the Tree of Life. Mol Phylogenet Evol 2017; 117:168-178. [DOI: 10.1016/j.ympev.2016.11.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 10/12/2016] [Accepted: 11/01/2016] [Indexed: 01/01/2023]
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13
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Abstract
BACKGROUND Gene order changes, under rearrangements, insertions, deletions and duplications, have been used as a new type of data source for phylogenetic reconstruction. Because these changes are rare compared to sequence mutations, they allow the inference of phylogeny further back in evolutionary time. There exist many computational methods for the reconstruction of gene-order phylogenies, including widely used maximum parsimonious methods and maximum likelihood methods. However, both methods face challenges in handling large genomes with many duplicated genes, especially in the presence of whole genome duplication. METHODS In this paper, we present three simple yet powerful methods based on maximum-likelihood (ML) approaches that encode multiplicities of both gene adjacency and gene content information for phylogenetic reconstruction. RESULTS Extensive experiments on simulated data sets show that our new method achieves the most accurate phylogenies compared to existing approaches. We also evaluate our method on real whole-genome data from eleven mammals. The package is publicly accessible at http://www.geneorder.org . CONCLUSIONS Our new encoding schemes successfully incorporate the multiplicity information of gene adjacencies and gene content into an ML framework, and show promising results in reconstruct phylogenies for whole-genome data in the presence of massive duplications.
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Affiliation(s)
- Lingxi Zhou
- Department of Computer Science and Engineering, University of South Carolina, Columbia, 29208 South Carolina USA
| | - Yu Lin
- Research School of Computer Science, Australian National University, Canberra, 2601 ACT Australia
| | - Bing Feng
- Department of Computer Science and Engineering, University of South Carolina, Columbia, 29208 South Carolina USA
| | - Jieyi Zhao
- University of Texas School of Biomedical Informatics at Houston, Houston, 77030 Texas USA
| | - Jijun Tang
- School of Computer Science and Engineering, Tianjin University, Tianjin, 300072 China
- Department of Computer Science and Engineering, University of South Carolina, Columbia, 29208 South Carolina USA
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14
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Roles of APOBEC3A and APOBEC3B in Human Papillomavirus Infection and Disease Progression. Viruses 2017; 9:v9080233. [PMID: 28825669 PMCID: PMC5580490 DOI: 10.3390/v9080233] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 08/16/2017] [Accepted: 08/16/2017] [Indexed: 02/06/2023] Open
Abstract
The apolipoprotein B messenger RNA-editing, enzyme-catalytic, polypeptide-like 3 (APOBEC3) family of cytidine deaminases plays an important role in the innate immune response to viral infections by editing viral genomes. However, the cytidine deaminase activity of APOBEC3 enzymes also induces somatic mutations in host genomes, which may drive cancer progression. Recent studies of human papillomavirus (HPV) infection and disease outcome highlight this duality. HPV infection is potently inhibited by one family member, APOBEC3A. Expression of APOBEC3A and APOBEC3B is highly elevated by the HPV oncoproteins E6 and E7 during persistent virus infection and disease progression. Furthermore, there is a high prevalence of APOBEC3A and APOBEC3B mutation signatures in HPV-associated cancers. These findings suggest that induction of an APOBEC3-mediated antiviral response during HPV infection may inadvertently contribute to cancer mutagenesis and virus evolution. Here, we discuss current understanding of APOBEC3A and APOBEC3B biology in HPV restriction, evolution, and associated cancer mutagenesis.
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15
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Time scaled phylogeography and demography of Bradypus torquatus (Pilosa: Bradypodidae). Glob Ecol Conserv 2017. [DOI: 10.1016/j.gecco.2017.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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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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17
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Schweizer RM, Robinson J, Harrigan R, Silva P, Galverni M, Musiani M, Green RE, Novembre J, Wayne RK. Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in grey wolves. Mol Ecol 2015; 25:357-79. [DOI: 10.1111/mec.13467] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 11/04/2015] [Accepted: 11/06/2015] [Indexed: 12/29/2022]
Affiliation(s)
- Rena M. Schweizer
- Department of Ecology and Evolutionary Biology University of California, Los Angeles 610 Charles E Young Dr East Los Angeles CA 90095 USA
| | - Jacqueline Robinson
- Department of Ecology and Evolutionary Biology University of California, Los Angeles 610 Charles E Young Dr East Los Angeles CA 90095 USA
| | - Ryan Harrigan
- Center for Tropical Research Institute of the Environment and Sustainability University of California 619 Charles E. Young Drive East Los Angeles CA 90095 USA
| | - Pedro Silva
- CIBIO/InBio – Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Campus Agrário de Vairão 4485‐661 Vairão Portugal
- Departamento de Biologia Faculdade de Ciências Universidade do Porto Rua do Campo Alegre s/n. 4169‐007 Porto Portugal
| | - Marco Galverni
- Laboratory of Genetics ISPRA (Istituto Superiore per la Protezione e Ricerca Ambientale) Via Cà Fornacetta 9 40064 Ozzano dell'Emilia BO Italy
| | - Marco Musiani
- Faculties of Environmental Design and Veterinary Medicine (Joint Appointment) EVDS University of Calgary 2500 University Dr NW Calgary Alberta Canada T2N 1N4
| | - Richard E. Green
- Department of Biomolecular Engineering University of California Santa Cruz CA 95060 USA
| | - John Novembre
- Department of Human Genetics University of Chicago 920 E. 58th Street Chicago IL 60637 USA
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology University of California, Los Angeles 610 Charles E Young Dr East Los Angeles CA 90095 USA
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Gibb GC, Condamine FL, Kuch M, Enk J, Moraes-Barros N, Superina M, Poinar HN, Delsuc F. Shotgun Mitogenomics Provides a Reference Phylogenetic Framework and Timescale for Living Xenarthrans. Mol Biol Evol 2015; 33:621-42. [PMID: 26556496 PMCID: PMC4760074 DOI: 10.1093/molbev/msv250] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Xenarthra (armadillos, sloths, and anteaters) constitutes one of the four major clades of placental mammals. Despite their phylogenetic distinctiveness in mammals, a reference phylogeny is still lacking for the 31 described species. Here we used Illumina shotgun sequencing to assemble 33 new complete mitochondrial genomes, establishing Xenarthra as the first major placental clade to be fully sequenced at the species level for mitogenomes. The resulting data set allowed the reconstruction of a robust phylogenetic framework and timescale that are consistent with previous studies conducted at the genus level using nuclear genes. Incorporating the full species diversity of extant xenarthrans points to a number of inconsistencies in xenarthran systematics and species definition. We propose to split armadillos into two distinct families Dasypodidae (dasypodines) and Chlamyphoridae (euphractines, chlamyphorines, and tolypeutines) to better reflect their ancient divergence, estimated around 42 Ma. Species delimitation within long-nosed armadillos (genus Dasypus) appeared more complex than anticipated, with the discovery of a divergent lineage in French Guiana. Diversification analyses showed Xenarthra to be an ancient clade with a constant diversification rate through time with a species turnover driven by high but constant extinction. We also detected a significant negative correlation between speciation rate and past temperature fluctuations with an increase in speciation rate corresponding to the general cooling observed during the last 15 My. Biogeographic reconstructions identified the tropical rainforest biome of Amazonia and the Guiana Shield as the cradle of xenarthran evolutionary history with subsequent dispersions into more open and dry habitats.
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Affiliation(s)
- Gillian C Gibb
- Institut des Sciences de l'Evolution, UMR 5554, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France Ecology Group, Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Fabien L Condamine
- Institut des Sciences de l'Evolution, UMR 5554, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden Department of Biological Sciences, University of Alberta, Edmonton, AL, Canada
| | - Melanie Kuch
- McMaster Ancient DNA Centre, Department of Anthropology and Biology, McMaster University, Hamilton, ON, Canada
| | - Jacob Enk
- McMaster Ancient DNA Centre, Department of Anthropology and Biology, McMaster University, Hamilton, ON, Canada
| | - Nadia Moraes-Barros
- Cibio/Inbio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal Laboratório de Biologia Evolutiva e Conservação de Vertebrados (Labec), Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Mariella Superina
- Laboratorio de Endocrinología de la Fauna Silvestre, IMBECU, CCT CONICET Mendoza, Mendoza, Argentina
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, Department of Anthropology and Biology, McMaster University, Hamilton, ON, Canada
| | - Frédéric Delsuc
- Institut des Sciences de l'Evolution, UMR 5554, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
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Doronina L, Churakov G, Shi J, Brosius J, Baertsch R, Clawson H, Schmitz J. Exploring Massive Incomplete Lineage Sorting in Arctoids (Laurasiatheria, Carnivora). Mol Biol Evol 2015; 32:3194-204. [PMID: 26337548 DOI: 10.1093/molbev/msv188] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Freed from the competition of large raptors, Paleocene carnivores could expand their newly acquired habitats in search of prey. Such changing conditions might have led to their successful distribution and rapid radiation. Today, molecular evolutionary biologists are faced, however, with the consequences of such accelerated adaptive radiations, because they led to sequential speciation more rapidly than phylogenetic markers could be fixed. The repercussions being that current genealogies based on such markers are incongruent with species trees.Our aim was to explore such conflicting phylogenetic zones of evolution during the early arctoid radiation, especially to distinguish diagnostic from misleading phylogenetic signals, and to examine other carnivore-related speciation events. We applied a combination of high-throughput computational strategies to screen carnivore and related genomes in silico for randomly inserted retroposed elements that we then used to identify inconsistent phylogenetic patterns in the Arctoidea group, which is well known for phylogenetic discordances.Our combined retrophylogenomic and in vitro wet lab approach detected hundreds of carnivore-specific insertions, many of them confirming well-established splits or identifying and solving conflicting species distributions. Our systematic genome-wide screens for Long INterspersed Elements detected homoplasy-free markers with insertion-specific truncation points that we used to distinguish phylogenetically informative markers from conflicting signals. The results were independently confirmed by phylogenetic diagnostic Short INterspersed Elements. As statistical analysis ruled out ancestral hybridization, these doubly verified but still conflicting patterns were statistically determined to be genomic remnants from a time of ancestral incomplete lineage sorting that especially accompanied large parts of Arctoidea evolution.
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Affiliation(s)
- Liliya Doronina
- Institute of Experimental Pathology, ZMBE, University of Münster, Münster, Germany
| | - Gennady Churakov
- Institute of Experimental Pathology, ZMBE, University of Münster, Münster, Germany Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Jingjing Shi
- Institute of Experimental Pathology, ZMBE, University of Münster, Münster, Germany
| | - Jürgen Brosius
- Institute of Experimental Pathology, ZMBE, University of Münster, Münster, Germany Institute of Evolutionary and Medical Genomics, Brandenburg Medical School (MHB), Neuruppin, Germany
| | - Robert Baertsch
- Department of Biomolecular Engineering, University of California, Santa Cruz
| | - Hiram Clawson
- Department of Biomolecular Engineering, University of California, Santa Cruz
| | - Jürgen Schmitz
- Institute of Experimental Pathology, ZMBE, University of Münster, Münster, Germany
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20
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Abstract
Species tree reconstruction has been a subject of substantial research due to its central role across biology and medicine. A species tree is often reconstructed using a set of gene trees or by directly using sequence data. In either of these cases, one of the main confounding phenomena is the discordance between a species tree and a gene tree due to evolutionary events such as duplications and losses. Probabilistic methods can resolve the discordance by coestimating gene trees and the species tree but this approach poses a scalability problem for larger data sets. We present MixTreEM-DLRS: A two-phase approach for reconstructing a species tree in the presence of gene duplications and losses. In the first phase, MixTreEM, a novel structural expectation maximization algorithm based on a mixture model is used to reconstruct a set of candidate species trees, given sequence data for monocopy gene families from the genomes under study. In the second phase, PrIME-DLRS, a method based on the DLRS model (Åkerborg O, Sennblad B, Arvestad L, Lagergren J. 2009. Simultaneous Bayesian gene tree reconstruction and reconciliation analysis. Proc Natl Acad Sci U S A. 106(14):5714-5719), is used for selecting the best species tree. PrIME-DLRS can handle multicopy gene families since DLRS, apart from modeling sequence evolution, models gene duplication and loss using a gene evolution model (Arvestad L, Lagergren J, Sennblad B. 2009. The gene evolution model and computing its associated probabilities. J ACM. 56(2):1-44). We evaluate MixTreEM-DLRS using synthetic and biological data, and compare its performance with a recent genome-scale species tree reconstruction method PHYLDOG (Boussau B, Szöllősi GJ, Duret L, Gouy M, Tannier E, Daubin V. 2013. Genome-scale coestimation of species and gene trees. Genome Res. 23(2):323-330) as well as with a fast parsimony-based algorithm Duptree (Wehe A, Bansal MS, Burleigh JG, Eulenstein O. 2008. Duptree: a program for large-scale phylogenetic analyses using gene tree parsimony. Bioinformatics 24(13):1540-1541). Our method is competitive with PHYLDOG in terms of accuracy and runs significantly faster and our method outperforms Duptree in accuracy. The analysis constituted by MixTreEM without DLRS may also be used for selecting the target species tree, yielding a fast and yet accurate algorithm for larger data sets. MixTreEM is freely available at http://prime.scilifelab.se/mixtreem/.
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Affiliation(s)
- Ikram Ullah
- School of Computer Science and Communication, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Pekka Parviainen
- Department of Computer Science, Helsinki Institute for Information Technology HIIT, Aalto University, Espoo, Finland
| | - Jens Lagergren
- School of Computer Science and Communication, Science for Life Laboratory, Swedish e-Science Research Center (SeRC), KTH Royal Institute of Technology, Stockholm, Sweden
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21
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Averianov AO, Lopatin AV. High-level systematics of placental mammals: Current status of the problem. BIOL BULL+ 2014. [DOI: 10.1134/s1062359014090039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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22
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Anthracobunids from the middle eocene of India and pakistan are stem perissodactyls. PLoS One 2014; 9:e109232. [PMID: 25295875 PMCID: PMC4189980 DOI: 10.1371/journal.pone.0109232] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 08/20/2014] [Indexed: 11/19/2022] Open
Abstract
Anthracobunidae is an Eocene family of large mammals from south Asia that is commonly considered to be part of the radiation that gave rise to elephants (proboscideans) and sea cows (sirenians). We describe a new collection of anthracobunid fossils from Middle Eocene rocks of Indo-Pakistan that more than doubles the number of known anthracobunid fossils and challenges their putative relationships, instead implying that they are stem perissodactyls. Cranial, dental, and postcranial elements allow a revision of species and the recognition of a new anthracobunid genus. Analyses of stable isotopes and long bone geometry together suggest that most anthracobunids fed on land, but spent a considerable amount of time near water. This new evidence expands our understanding of stem perissodactyl diversity and sheds new light on perissodactyl origins.
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Nunome M, Kinoshita G, Tomozawa M, Torii H, Matsuki R, Yamada F, Matsuda Y, Suzuki H. Lack of association between winter coat colour and genetic population structure in the Japanese hare,Lepus brachyurus(Lagomorpha: Leporidae). Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12245] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mitsuo Nunome
- Laboratory of Animal Genetics; Department of Applied Molecular Biosciences; Graduate School of Bioagricultural Sciences; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8601 Japan
| | - Gohta Kinoshita
- Laboratory of Ecology and Genetics; Faculty of Environmental Earth Science; Hokkaido University; Kita-ku Sapporo 060-0810 Japan
| | | | - Harumi Torii
- Center for Natural Environment Education; Nara University of Education; Takabatake-cho Nara 630-8528 Japan
| | - Rikyu Matsuki
- Environmental Science Research Laboratory; Central Research Institute of Electric Power Industry; 1646 Abiko Chiba 270-1194 Japan
| | - Fumio Yamada
- Forestry and Forest Products Research Institute; PO Box 16 Tsukuba Norin Ibaraki 305-8687 Japan
| | - Yoichi Matsuda
- Laboratory of Animal Genetics; Department of Applied Molecular Biosciences; Graduate School of Bioagricultural Sciences; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8601 Japan
| | - Hitoshi Suzuki
- Laboratory of Ecology and Genetics; Faculty of Environmental Earth Science; Hokkaido University; Kita-ku Sapporo 060-0810 Japan
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Abstract
Nuclear rDNA Internal Transcribed Spacers, ITS1 and ITS2, are widely used for eukaryote phylogenetic studies from the ordinal level to the species level, and there is even a database for ITS2 sequences. However, ITS regions have been ignored in mammalian phylogenetic studies, and only a few rodent and ape sequences are represented in GenBank. The reasons for this dearth, and the remedies, are described here. We have recovered these sequences, mostly >1 kb in length, for 36 mammalian species. Sequence alignment and transcript folding comparisons reveal the rRNA transcript secondary structure. Mammalian ITS regions, though quite long, still fold into the recognizable secondary structure of other eukaryotes. The ITS2 in particular bears the four standard helix loops, and loops II and III have the hallmark characters universal to eukaryotes. Both sequence and insertions/deletions of transcript secondary structure helices observed here support the four superorder taxonomy of Placentalia. On the family level, major unique indels, neatly excising entire helices, will be useful when additional species are represented, resulting in significant further understanding of the details of mammalian evolutionary history. Furthermore, the identification of a highly conserved element of ITS1 common to warm-blooded vertebrates may aid in deciphering the complex mechanism of RNA transcript processing. This is the last major group of terrestrial vertebrates for which rRNA ITS secondary structure has been resolved.
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Affiliation(s)
- Annette W Coleman
- Division of Biology and Medicine, Brown University, Providence, Rhode Island, United States of America
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25
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Hu JY, Zhang YP, Yu L. Summary of Laurasiatheria (mammalia) phylogeny. DONG WU XUE YAN JIU = ZOOLOGICAL RESEARCH 2013; 33:E65-74. [PMID: 23266984 DOI: 10.3724/sp.j.1141.2012.e05-06e65] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Laurasiatheria is one of the richest and most diverse superorders of placental mammals. Because this group had a rapid evolutionary radiation, the phylogenetic relationships among the six orders of Laurasiatheria remain a subject of heated debate and several issues related to its phylogeny remain open. Reconstructing the true phylogenetic relationships of Laurasiatheria is a significant case study in evolutionary biology due to the diversity of this suborder and such research will have significant implications for biodiversity conservation. We review the higher-level (inter-ordinal) phylogenies of Laurasiatheria based on previous cytogenetic, morphological and molecular data, and discuss the controversies of its phylogenetic relationship. This review aims to outline future researches on Laurasiatheria phylogeny and adaptive evolution.
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Evolutionary Plasticity in Coccidia – Striking Morphological Similarity of Unrelated Coccidia (Apicomplexa) from Related Hosts: Eimeria spp. from African and Asian Pangolins (Mammalia: Pholidota). Protist 2013; 164:470-81. [DOI: 10.1016/j.protis.2013.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Revised: 02/14/2013] [Accepted: 04/10/2013] [Indexed: 11/18/2022]
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27
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Ekdale EG. Comparative Anatomy of the Bony Labyrinth (Inner Ear) of Placental Mammals. PLoS One 2013; 8:e66624. [PMID: 23805251 PMCID: PMC3689836 DOI: 10.1371/journal.pone.0066624] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 05/07/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Variation is a naturally occurring phenomenon that is observable at all levels of morphology, from anatomical variations of DNA molecules to gross variations between whole organisms. The structure of the otic region is no exception. The present paper documents the broad morphological diversity exhibited by the inner ear region of placental mammals using digital endocasts constructed from high-resolution X-ray computed tomography (CT). Descriptions cover the major placental clades, and linear, angular, and volumetric dimensions are reported. PRINCIPAL FINDINGS The size of the labyrinth is correlated to the overall body mass of individuals, such that large bodied mammals have absolutely larger labyrinths. The ratio between the average arc radius of curvature of the three semicircular canals and body mass of aquatic species is substantially lower than the ratios of related terrestrial taxa, and the volume percentage of the vestibular apparatus of aquatic mammals tends to be less than that calculated for terrestrial species. Aspects of the bony labyrinth are phylogenetically informative, including vestibular reduction in Cetacea, a tall cochlear spiral in caviomorph rodents, a low position of the plane of the lateral semicircular canal compared to the posterior canal in Cetacea and Carnivora, and a low cochlear aspect ratio in Primatomorpha. SIGNIFICANCE The morphological descriptions that are presented add a broad baseline of anatomy of the inner ear across many placental mammal clades, for many of which the structure of the bony labyrinth is largely unknown. The data included here complement the growing body of literature on the physiological and phylogenetic significance of bony labyrinth structures in mammals, and they serve as a source of data for future studies on the evolution and function of the vertebrate ear.
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Affiliation(s)
- Eric G. Ekdale
- Department of Biology, San Diego State University, San Diego, California, United States of America
- Department of Paleontology, San Diego Natural History Museum, San Diego, California, United States of America
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28
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Wu LT, Hui JHL, Chu KH. Origin and evolution of yolk proteins: expansion and functional diversification of large lipid transfer protein superfamily. Biol Reprod 2013; 88:102. [PMID: 23426435 DOI: 10.1095/biolreprod.112.104752] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Vitellogenin (VTG) and apolipoprotein (APO) play a central role in animal reproduction and lipid circulation, respectively. Although previous studies have examined the structural and functional relationships of these large lipid transfer proteins (LLTPs) from an evolutionary perspective, the mechanism in generating these different families have not been addressed in invertebrates. In this study, the most comprehensive phylogenetic and genomic analysis of the LLTP superfamily genes is carried out. We propose the expansion and diversification of LLTPs in invertebrates are mediated via retrotransposon-mediated duplications, followed by either subfunctionalization or neofunctionalization in different lineages. In agreement with a previous hypothesis, our analysis suggests that all LLTPs originate from a series of duplications of a primitive yolk protein gene similar to VTG. Two early consecutive duplications of the yolk protein genes resulted in the formation of microsomal triglyceride transfer protein (MTP) and the APO gene ancestor. Gains and losses of domains and genes occurred in each of these families in different animal lineages, with MTP becoming truncated. MTP maintained only the components stabilizing the huge lipoprotein particle. Surprisingly, for the first time, two VTG-like protein families were found to independently arise in the lineages of insects. This work consolidates the reconstruction of the evolutionary roadmap of the LLTP superfamily and provides the first mechanistic explanation on the expansion of family members via retrotransposition in invertebrates.
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Affiliation(s)
- Long Tao Wu
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
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29
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Bornholdt R, Helgen K, Koepfli KP, Oliveira L, Lucherini M, Eizirik E. Taxonomic revision of the genusGalictis(Carnivora: Mustelidae): species delimitation, morphological diagnosis, and refined mapping of geographical distribution. Zool J Linn Soc 2013. [DOI: 10.1111/j.1096-3642.2012.00859.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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30
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O'Leary MA, Bloch JI, Flynn JJ, Gaudin TJ, Giallombardo A, Giannini NP, Goldberg SL, Kraatz BP, Luo ZX, Meng J, Ni X, Novacek MJ, Perini FA, Randall ZS, Rougier GW, Sargis EJ, Silcox MT, Simmons NB, Spaulding M, Velazco PM, Weksler M, Wible JR, Cirranello AL. The placental mammal ancestor and the post-K-Pg radiation of placentals. Science 2013; 339:662-7. [PMID: 23393258 DOI: 10.1126/science.1229237] [Citation(s) in RCA: 622] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
To discover interordinal relationships of living and fossil placental mammals and the time of origin of placentals relative to the Cretaceous-Paleogene (K-Pg) boundary, we scored 4541 phenomic characters de novo for 86 fossil and living species. Combining these data with molecular sequences, we obtained a phylogenetic tree that, when calibrated with fossils, shows that crown clade Placentalia and placental orders originated after the K-Pg boundary. Many nodes discovered using molecular data are upheld, but phenomic signals overturn molecular signals to show Sundatheria (Dermoptera + Scandentia) as the sister taxon of Primates, a close link between Proboscidea (elephants) and Sirenia (sea cows), and the monophyly of echolocating Chiroptera (bats). Our tree suggests that Placentalia first split into Xenarthra and Epitheria; extinct New World species are the oldest members of Afrotheria.
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Affiliation(s)
- Maureen A O'Leary
- Department of Anatomical Sciences, School of Medicine, HSC T-8 (040), Stony Brook University, Stony Brook, NY 11794-8081, USA.
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31
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Fabre PH, Galewski T, Tilak MK, Douzery EJP. Diversification of South American spiny rats (Echimyidae): a multigene phylogenetic approach. ZOOL SCR 2012. [DOI: 10.1111/j.1463-6409.2012.00572.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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32
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Lin Y, Rajan V, Moret BME. Bootstrapping phylogenies inferred from rearrangement data. Algorithms Mol Biol 2012; 7:21. [PMID: 22931958 PMCID: PMC3487984 DOI: 10.1186/1748-7188-7-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 07/26/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Large-scale sequencing of genomes has enabled the inference of phylogenies based on the evolution of genomic architecture, under such events as rearrangements, duplications, and losses. Many evolutionary models and associated algorithms have been designed over the last few years and have found use in comparative genomics and phylogenetic inference. However, the assessment of phylogenies built from such data has not been properly addressed to date. The standard method used in sequence-based phylogenetic inference is the bootstrap, but it relies on a large number of homologous characters that can be resampled; yet in the case of rearrangements, the entire genome is a single character. Alternatives such as the jackknife suffer from the same problem, while likelihood tests cannot be applied in the absence of well established probabilistic models. RESULTS We present a new approach to the assessment of distance-based phylogenetic inference from whole-genome data; our approach combines features of the jackknife and the bootstrap and remains nonparametric. For each feature of our method, we give an equivalent feature in the sequence-based framework; we also present the results of extensive experimental testing, in both sequence-based and genome-based frameworks. Through the feature-by-feature comparison and the experimental results, we show that our bootstrapping approach is on par with the classic phylogenetic bootstrap used in sequence-based reconstruction, and we establish the clear superiority of the classic bootstrap for sequence data and of our corresponding new approach for rearrangement data over proposed variants. Finally, we test our approach on a small dataset of mammalian genomes, verifying that the support values match current thinking about the respective branches. CONCLUSIONS Our method is the first to provide a standard of assessment to match that of the classic phylogenetic bootstrap for aligned sequences. Its support values follow a similar scale and its receiver-operating characteristics are nearly identical, indicating that it provides similar levels of sensitivity and specificity. Thus our assessment method makes it possible to conduct phylogenetic analyses on whole genomes with the same degree of confidence as for analyses on aligned sequences. Extensions to search-based inference methods such as maximum parsimony and maximum likelihood are possible, but remain to be thoroughly tested.
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Affiliation(s)
- Yu Lin
- Laboratory for Computational Biology and Bioinformatics, EPFL, EPFL-IC-LCBB INJ230, Station 14, CH-1015 Lausanne, Switzerland
| | - Vaibhav Rajan
- Laboratory for Computational Biology and Bioinformatics, EPFL, EPFL-IC-LCBB INJ230, Station 14, CH-1015 Lausanne, Switzerland
| | - Bernard ME Moret
- Laboratory for Computational Biology and Bioinformatics, EPFL, EPFL-IC-LCBB INJ230, Station 14, CH-1015 Lausanne, Switzerland
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Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model. Proc Natl Acad Sci U S A 2012; 109:14942-7. [PMID: 22930817 DOI: 10.1073/pnas.1211733109] [Citation(s) in RCA: 307] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The reconstruction of the Tree of Life has relied almost entirely on concatenation methods, which do not accommodate gene tree heterogeneity, a property that simulations and theory have identified as a likely cause of incongruent phylogenies. However, this incongruence has not yet been demonstrated in empirical studies. Several key relationships among eutherian mammals remain controversial and conflicting among previous studies, including the root of eutherian tree and the relationships within Euarchontoglires and Laurasiatheria. Both bayesian and maximum-likelihood analysis of genome-wide data of 447 nuclear genes from 37 species show that concatenation methods indeed yield strong incongruence in the phylogeny of eutherian mammals, as revealed by subsampling analyses of loci and taxa, which produced strongly conflicting topologies. In contrast, the coalescent methods, which accommodate gene tree heterogeneity, yield a phylogeny that is robust to variable gene and taxon sampling and is congruent with geographic data. The data also demonstrate that incomplete lineage sorting, a major source of gene tree heterogeneity, is relevant to deep-level phylogenies, such as those among eutherian mammals. Our results firmly place the eutherian root between Atlantogenata and Boreoeutheria and support ungulate polyphyly and a sister-group relationship between Scandentia and Primates. This study demonstrates that the incongruence introduced by concatenation methods is a major cause of long-standing uncertainty in the phylogeny of eutherian mammals, and the same may apply to other clades. Our analyses suggest that such incongruence can be resolved using phylogenomic data and coalescent methods that deal explicitly with gene tree heterogeneity.
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Svartman M, Stanyon R. The chromosomes of Afrotheria and their bearing on mammalian genome evolution. Cytogenet Genome Res 2012; 137:144-53. [PMID: 22868637 DOI: 10.1159/000341387] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Afrotheria is the clade of placental mammals that, together with Xenarthra, Euarchontoglires and Laurasiatheria, represents 1 of the 4 main recognized supraordinal eutherian clades. It reunites 6 orders of African origin: Proboscidea, Sirenia, Hyracoidea, Macroscelidea, Afrosoricida and Tubulidentata. The apparently unlikely relationship among such disparate morphological taxa and their possible basal position at the base of the eutherian phylogenetic tree led to a great deal of attention and research on the group. The use of biomolecular data was pivotal in Afrotheria studies, as they were the basis for the recognition of this clade. Although morphological evidence is still scarce, a plethora of molecular data firmly attests to the phylogenetic relationship among these mammals of African origin. Modern cytogenetic techniques also gave a significant contribution to the study of Afrotheria, revealing chromosome signatures for the group as a whole, as well as for some of its internal relationships. The associations of human chromosomes HSA1/19 and 5/21 were found to be chromosome signatures for the group and provided further support for Afrotheria. Additional chromosome synapomorphies were also identified linking elephants and manatees in Tethytheria (the associations HSA2/3, 3/13, 8/22, 18/19 and the lack of HSA4/8) and elephant shrews with the aardvark (HSA2/8, 3/20 and 10/17). Herein, we review the current knowledge on Afrotheria chromosomes and genome evolution. The already available data on the group suggests that further work on this apparently bizarre assemblage of mammals will provide important data to a better understanding on mammalian genome evolution.
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Affiliation(s)
- M Svartman
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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Svartman M. Chromosome evolution in Xenarthra: new insights from an ancient group. Cytogenet Genome Res 2012; 137:130-43. [PMID: 22678153 DOI: 10.1159/000339115] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The Magnaorder Xenarthra is one of the four main supraordinal eutherian clades, together with Afrotheria, Euarchontoglires and Laurasiatheria. Xenarthra is an eminently Central and South American group of special interest in phylogenetic studies due to its possible position at the base of the eutherian tree. The use of modern cytogenetic techniques in some species of Xenarthra has provided important insights into the karyotypic evolution of mammals. Nevertheless, chromosome analyses in the group are still restricted, with only a few individuals of each species studied and karyotype descriptions mostly without banding patterns. In addition, it is likely that still unknown species exist and that the chromosome variability in the group is underestimated. We present a review of the currently available data on Xenarthra chromosomes and genomes and on the impact that their study has had in the understanding of mammalian genome evolution. It is clear that further cytogenetic analyses in Xenarthra, including banding patterns and molecular approaches, are likely to help in the identification of new species, reveal still undetected chromosome variations, provide information to support conservation strategies planning, and greatly contribute to a better understanding of mammalian genome evolution.
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Affiliation(s)
- M Svartman
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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Azevedo NF, Svartman M, Manchester A, de Moraes-Barros N, Stanyon R, Vianna-Morgante AM. Chromosome painting in three-toed sloths: a cytogenetic signature and ancestral karyotype for Xenarthra. BMC Evol Biol 2012; 12:36. [PMID: 22429690 PMCID: PMC3383463 DOI: 10.1186/1471-2148-12-36] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2011] [Accepted: 03/19/2012] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Xenarthra (sloths, armadillos and anteaters) represent one of four currently recognized Eutherian mammal supraorders. Some phylogenomic studies point to the possibility of Xenarthra being at the base of the Eutherian tree, together or not with the supraorder Afrotheria. We performed painting with human autosomes and X-chromosome specific probes on metaphases of two three-toed sloths: Bradypus torquatus and B. variegatus. These species represent the fourth of the five extant Xenarthra families to be studied with this approach. RESULTS Eleven human chromosomes were conserved as one block in both B. torquatus and B. variegatus: (HSA 5, 6, 9, 11, 13, 14, 15, 17, 18, 20, 21 and the X chromosome). B. torquatus, three additional human chromosomes were conserved intact (HSA 1, 3 and 4). The remaining human chromosomes were represented by two or three segments on each sloth. Seven associations between human chromosomes were detected in the karyotypes of both B. torquatus and B. variegatus: HSA 3/21, 4/8, 7/10, 7/16, 12/22, 14/15 and 17/19. The ancestral Eutherian association 16/19 was not detected in the Bradypus species. CONCLUSIONS Our results together with previous reports enabled us to propose a hypothetical ancestral Xenarthran karyotype with 48 chromosomes that would differ from the proposed ancestral Eutherian karyotype by the presence of the association HSA 7/10 and by the split of HSA 8 into three blocks, instead of the two found in the Eutherian ancestor. These same chromosome features point to the monophyly of Xenarthra, making this the second supraorder of placental mammals to have a chromosome signature supporting its monophyly.
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Affiliation(s)
- Nathália F Azevedo
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, Cidade Universitária, São Paulo, Brazil
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Delsuc F, Superina M, Tilak MK, Douzery EJ, Hassanin A. Molecular phylogenetics unveils the ancient evolutionary origins of the enigmatic fairy armadillos. Mol Phylogenet Evol 2012; 62:673-80. [DOI: 10.1016/j.ympev.2011.11.008] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 11/03/2011] [Accepted: 11/14/2011] [Indexed: 11/17/2022]
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Lin Y, Rajan V, Moret BME. Fast and accurate phylogenetic reconstruction from high-resolution whole-genome data and a novel robustness estimator. J Comput Biol 2012; 18:1131-9. [PMID: 21899420 DOI: 10.1089/cmb.2011.0114] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The rapid accumulation of whole-genome data has renewed interest in the study of genomic rearrangements. Comparative genomics, evolutionary biology, and cancer research all require models and algorithms to elucidate the mechanisms, history, and consequences of these rearrangements. However, even simple models lead to NP-hard problems, particularly in the area of phylogenetic analysis. Current approaches are limited to small collections of genomes and low-resolution data (typically a few hundred syntenic blocks). Moreover, whereas phylogenetic analyses from sequence data are deemed incomplete unless bootstrapping scores (a measure of confidence) are given for each tree edge, no equivalent to bootstrapping exists for rearrangement-based phylogenetic analysis. We describe a fast and accurate algorithm for rearrangement analysis that scales up, in both time and accuracy, to modern high-resolution genomic data. We also describe a novel approach to estimate the robustness of results-an equivalent to the bootstrapping analysis used in sequence-based phylogenetic reconstruction. We present the results of extensive testing on both simulated and real data showing that our algorithm returns very accurate results, while scaling linearly with the size of the genomes and cubically with their number. We also present extensive experimental results showing that our approach to robustness testing provides excellent estimates of confidence, which, moreover, can be tuned to trade off thresholds between false positives and false negatives. Together, these two novel approaches enable us to attack heretofore intractable problems, such as phylogenetic inference for high-resolution vertebrate genomes, as we demonstrate on a set of six vertebrate genomes with 8,380 syntenic blocks. A copy of the software is available on demand.
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Affiliation(s)
- Y Lin
- Laboratory for Computational Biology and Bioinformatics, EPFL, Lausanne, Switzerland
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Yu HT, Ma GC, Lee DJ, Chin SC, Chen TL, Tsao HS, Lin WH, Wu SH, Lin CC, Chen M. Use of a cytogenetic whole-genome comparison to resolve phylogenetic relationships among three species: implications for mammalian systematics and conservation biology. Theriogenology 2011; 77:1615-23. [PMID: 22192390 DOI: 10.1016/j.theriogenology.2011.12.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 12/06/2011] [Accepted: 12/06/2011] [Indexed: 10/14/2022]
Abstract
The objective was to apply a novel modification of a genome-wide, comparative cytogenetic technique (comparative genomic hybridization, comparative genomic hybridization (CGH)), to study species belonging to the myrmecophagous (ant/termite eating) mammalian orders/superorders (Pholidota, Tubulidentata, Carnivora, and Xenarthra), as a model for other applications in mammalian systematics and conservation biology. In this study, CGH was applied to high-quality metaphase spreads of pangolin (Pholidota), using probes of sloth and canine (Xenarthra and Carnivora, respectively) genomic DNA labeled with different fluorophores, thereby facilitating analysis of the visible color spectrum on pangolin karyotypes. Our results posited that pholidotes are closer to carnivores than to xenarthrans, which confirmed the current consensus that myrmecophagy in these mammalian lineages was more likely because of homoplasy (convergent evolution) than being an ancestral character. Since the modified CGH technique used is genome-wide, has chromosome-level resolution, and does not need full genome sequencing, it has considerable potential in systematics and other fields.
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Affiliation(s)
- Hon-Tsen Yu
- Institute of Zoology and Department of Life Science, National Taiwan University, Taipei, Taiwan
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Koyabu D, Endo H, Mitgutsch C, Suwa G, Catania KC, Zollikofer CPE, Oda SI, Koyasu K, Ando M, Sánchez-Villagra MR. Heterochrony and developmental modularity of cranial osteogenesis in lipotyphlan mammals. EvoDevo 2011; 2:21. [PMID: 22040374 PMCID: PMC3247175 DOI: 10.1186/2041-9139-2-21] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 11/01/2011] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Here we provide the most comprehensive study to date on the cranial ossification sequence in Lipotyphla, the group which includes shrews, moles and hedgehogs. This unique group, which encapsulates diverse ecological modes, such as terrestrial, subterranean, and aquatic lifestyles, is used to examine the evolutionary lability of cranial osteogenesis and to investigate the modularity of development. RESULTS An acceleration of developmental timing of the vomeronasal complex has occurred in the common ancestor of moles. However, ossification of the nasal bone has shifted late in the more terrestrial shrew mole. Among the lipotyphlans, sequence heterochrony shows no significant association with modules derived from developmental origins (that is, neural crest cells vs. mesoderm derived parts) or with those derived from ossification modes (that is, dermal vs. endochondral ossification). CONCLUSIONS The drastic acceleration of vomeronasal development in moles is most likely coupled with the increased importance of the rostrum for digging and its use as a specialized tactile surface, both fossorial adaptations. The late development of the nasal in shrew moles, a condition also displayed by hedgehogs and shrews, is suggested to be the result of an ecological reversal to terrestrial lifestyle and reduced functional importance of the rostrum. As an overall pattern in lipotyphlans, our results reject the hypothesis that ossification sequence heterochrony occurs in modular fashion when considering the developmental patterns of the skull. We suggest that shifts in the cranial ossification sequence are not evolutionarily constrained by developmental origins or mode of ossification.
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Affiliation(s)
- Daisuke Koyabu
- Paläontologisches Institut und Museum, Universität Zürich, Karl Schmid-Strasse 4, CH-8006 Zürich, Switzerland
- The University Museum, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, 113-0033 Tokyo, Japan
| | - Hideki Endo
- The University Museum, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, 113-0033 Tokyo, Japan
| | - Christian Mitgutsch
- Paläontologisches Institut und Museum, Universität Zürich, Karl Schmid-Strasse 4, CH-8006 Zürich, Switzerland
| | - Gen Suwa
- The University Museum, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, 113-0033 Tokyo, Japan
| | - Kenneth C Catania
- Department of Biological Sciences, Vanderbilt University, VU Station B, Box 35-1634, Nashville, USA
| | - Christoph PE Zollikofer
- Anthropologisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Sen-ichi Oda
- Department of Zoology, Okayama University of Science, Ridaichou, Kita-ku, 700-0005 Okayama, Japan
| | - Kazuhiko Koyasu
- The Second Department of Anatomy, School of Dentistry, Aichi-Gakuin University, Kusumotochou 1-100, 464-8650 Nagoya, Japan
| | - Motokazu Ando
- Faculty of Agriculture, Tokyo University of Agriculture, Funako 1737, 243-0034 Atsugi, Japan
| | - Marcelo R Sánchez-Villagra
- Paläontologisches Institut und Museum, Universität Zürich, Karl Schmid-Strasse 4, CH-8006 Zürich, Switzerland
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Finckbeiner S, Ko PJ, Carrington B, Sood R, Gross K, Dolnick B, Sufrin J, Liu P. Transient knockdown and overexpression reveal a developmental role for the zebrafish enosf1b gene. Cell Biosci 2011; 1:32. [PMID: 21943404 PMCID: PMC3197473 DOI: 10.1186/2045-3701-1-32] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Accepted: 09/26/2011] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Despite detailed in vivo knowledge of glycolytic enolases and many bacterial non-enolase members of the superfamily, little is known about the in vivo function of vertebrate non-enolase enolase superfamily members (ENOSF1s). Results of previous studies suggest involvement of the β splice form of ENOSF1 in breast and colon cancers. This study used the zebrafish (Danio rerio) as a vertebrate model of ENOSF1β function. RESULTS Whole mount in situ hybridization (WISH) showed that zebrafish ENOSF1β (enosf1b) is zygotic and expressed ubiquitously through the first 24 hours post fertilization (hpf). After 24 hpf, enosf1b expression is restricted to the notochord. Embryos injected with enosf1b-EGFP mRNA grew slower than EGFP mRNA-injected embryos but caught up to the EGFP-injected embryos by 48 hpf. Embryos injected with ATG or exon 10 enosf1b mRNA-targeting morpholinos had kinked notochords, shortened anterior-posterior axes, and circulatory edema. WISH for ntl or pax2a expression showed that embryos injected with either morpholino have deformed notochord and pronephros. TUNEL staining revealed increased apoptosis in the peri-notochord region. CONCLUSIONS This study is the first report of ENOSF1 function in a vertebrate and shows that ENOSF1 is required for embryonic development. Increased apoptosis following enosf1b knockdown suggests a potential survival advantage for increased ENOSF1β expression in human cancers.
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Affiliation(s)
- Steve Finckbeiner
- Oncogenesis and Development Section, National Human Genome Research Institute, 49 Convent Drive, Bethesda MD, 20892, USA
- Program of Molecular Pharmacology and Cancer Therapeutics, Roswell Park Graduate Division, State University of New York at Buffalo, Elm and Carlton Streets, Buffalo NY, 14263, USA
| | - Pin-Joe Ko
- Oncogenesis and Development Section, National Human Genome Research Institute, 49 Convent Drive, Bethesda MD, 20892, USA
| | - Blake Carrington
- Zebrafish Core, National Human Genome Research Institute, 49 Convent Drive, Bethesda MD, 20892, USA
| | - Raman Sood
- Oncogenesis and Development Section, National Human Genome Research Institute, 49 Convent Drive, Bethesda MD, 20892, USA
- Zebrafish Core, National Human Genome Research Institute, 49 Convent Drive, Bethesda MD, 20892, USA
| | - Kenneth Gross
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo NY, 14263, USA
| | - Bruce Dolnick
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo NY, 14263, USA
| | - Janice Sufrin
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo NY, 14263, USA
| | - Paul Liu
- Oncogenesis and Development Section, National Human Genome Research Institute, 49 Convent Drive, Bethesda MD, 20892, USA
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Scalici M, Panchetti F. Morphological cranial diversity contributes to phylogeny in soft-furred sengis (Afrotheria, Macroscelidea). ZOOLOGY 2011; 114:85-94. [PMID: 21333512 DOI: 10.1016/j.zool.2010.09.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Revised: 08/30/2010] [Accepted: 09/19/2010] [Indexed: 11/28/2022]
Abstract
Despite the well-supported Macroscelidea phylogeny proposed at the end of the 1960s, several systematic arrangements have been suggested in the last 20 years, raising doubts about the phylogeny of the Macroscelidinae; sengi inter-specific relationships are still debated to this day. The main issue of concern involves the supposed Elephantulus diphyly. To solve this persisting debate about sengi phylogeny, we examined the cranium ventral surface of 13 species using geometric morphometric techniques and neighbour-joining algorithms. This study supported the idea that the ventral side of the sengi cranium has the potential to provide important signals for reconstructing the Macroscelidea phylogeny. The phylogenetic signals seemed to differentiate between two major clades in the sengi radiation. In the first clade, the two monospecific genera (Petrodromus and Macroscelides), the two African Horn species (Elephantulus revoilii and E. rufescens), and the only North African species (E. rozeti) were clustered together. The second clade includes the remnant south-central African Elephantulus species. Our results were in agreement with both mitochondrial and nuclear data, confirmed that there is no Elephantulus monophyly and highlighted the close relationship between Petrodromus and E. rozeti. It appears that all the soft-furred sengi species are organised in two evolutionary lines: an old monophyletic clade, comprising only Elephantulus species, and a new polyphyletic clade, including P. tetradactylus, M. proboscideus, and E. rozeti. This requires a taxonomic and nomenclatural rearrangement within Macroscelidinae, where the phylogenetic position of the remnant 4 (of 12) Elephantulus species has yet to be fully defined.
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Affiliation(s)
- Massimiliano Scalici
- Department of Biology, Roma Tre University, viale Guglielmo Marconi 446, 00146 Rome, Italy.
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Goremykin VV, Nikiforova SV, Bininda-Emonds ORP. Automated Removal of Noisy Data in Phylogenomic Analyses. J Mol Evol 2010; 71:319-31. [DOI: 10.1007/s00239-010-9398-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Accepted: 10/06/2010] [Indexed: 10/18/2022]
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Roehrs ZP, Lack JB, Van Den Bussche RA. Tribal phylogenetic relationships within Vespertilioninae (Chiroptera: Vespertilionidae) based on mitochondrial and nuclear sequence data. J Mammal 2010. [DOI: 10.1644/09-mamm-a-325.1] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Kuntner M, May-Collado LJ, Agnarsson I. Phylogeny and conservation priorities of afrotherian mammals (Afrotheria, Mammalia). ZOOL SCR 2010. [DOI: 10.1111/j.1463-6409.2010.00452.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Poulakakis N, Stamatakis A. Recapitulating the evolution of Afrotheria: 57 genes and rare genomic changes (RGCs) consolidate their history. SYST BIODIVERS 2010. [DOI: 10.1080/14772000.2010.484436] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Yu HT, Ma GC, Lee DJ, Chin SC, Tsao HS, Wu SH, Shih SY, Chen M. Molecular delineation of the Y-borne Sry gene in the Formosan pangolin (Manis pentadactyla pentadactyla) and its phylogenetic implications for Pholidota in extant mammals. Theriogenology 2010; 75:55-64. [PMID: 20739052 DOI: 10.1016/j.theriogenology.2010.07.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Revised: 07/16/2010] [Accepted: 07/18/2010] [Indexed: 01/29/2023]
Abstract
The systematic status of Pholidota has been a matter of debate, particularly regarding the apparent inconsistency between morphological and molecular studies. The Sry gene, a master regulator of male sex determination in eutherian mammals, has not yet been used for phylogenetic analyses of extant mammals. The objective of the present study was to clone and characterize the complete gene (1300 base pairs; bp) and amino acid sequences (229 residues) of Sry from the Formosan pangolin (Manis pentadactyla pentadactyla), a member of Pholidota. The Sry amino acid identity between pangolin and other reported species ranged from 42.5% (mouse, Mus musculus) to 84.1% (European hare, Lepus europaeus). Sequence conservation was primarily in the high motility group (HMG) box (234 bp), whereas homology outside the HMG box was low. The cloned Sry was mapped to the pangolin Y chromosome by fluorescence in situ hybridization (FISH); this was confirmed to be the first Y-borne molecular marker identified in Pholidota. Based on Bayesian phylogenetic analysis for Sry HMG sequences from 36 representative taxa, including the Formosan pangolin, Pholidota was more closely related to Carnivora than to Xenarthra, consistent with the emerging molecular tree inferred from markers not located on the Y chromosome. In conclusion, this study characterized the gene structure of Sry of the Formosan pangolin and provided insights into the phylogenetic position of Pholidota.
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Affiliation(s)
- Hon-Tsen Yu
- Institute of Zoology, Department of Life Science, National Taiwan University, Taipei, Taiwan
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Stößel A, Junold A, Fischer MS. The morphology of the eutherian ethmoidal region and its implications for higher-order phylogeny. J ZOOL SYST EVOL RES 2010. [DOI: 10.1111/j.1439-0469.2009.00560.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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