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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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Tejada JV, Antoine PO, Münch P, Billet G, Hautier L, Delsuc F, Condamine FL. Bayesian Total-Evidence Dating Revisits Sloth Phylogeny and Biogeography: A Cautionary Tale on Morphological Clock Analyses. Syst Biol 2024; 73:125-139. [PMID: 38041854 PMCID: PMC11129595 DOI: 10.1093/sysbio/syad069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 11/06/2023] [Accepted: 11/14/2023] [Indexed: 12/04/2023] Open
Abstract
Combining morphological and molecular characters through Bayesian total-evidence dating allows inferring the phylogenetic and timescale framework of both extant and fossil taxa, while accounting for the stochasticity and incompleteness of the fossil record. Such an integrative approach is particularly needed when dealing with clades such as sloths (Mammalia: Folivora), for which developmental and biomechanical studies have shown high levels of morphological convergence whereas molecular data can only account for a limited percentage of their total species richness. Here, we propose an alternative hypothesis of sloth evolution that emphasizes the pervasiveness of morphological convergence and the importance of considering the fossil record and an adequate taxon sampling in both phylogenetic and biogeographic inferences. Regardless of different clock models and morphological datasets, the extant sloth Bradypus is consistently recovered as a megatherioid, and Choloepus as a mylodontoid, in agreement with molecular-only analyses. The recently extinct Caribbean sloths (Megalocnoidea) are found to be a monophyletic sister-clade of Megatherioidea, in contrast to previous phylogenetic hypotheses. Our results contradict previous morphological analyses and further support the polyphyly of "Megalonychidae," whose members were found in five different clades. Regardless of taxon sampling and clock models, the Caribbean colonization of sloths is compatible with the exhumation of islands along Aves Ridge and its geological time frame. Overall, our total-evidence analysis illustrates the difficulty of positioning highly incomplete fossils, although a robust phylogenetic framework was recovered by an a posteriori removal of taxa with high percentages of missing characters. Elimination of these taxa improved topological resolution by reducing polytomies and increasing node support. However, it introduced a systematic and geographic bias because most of these incomplete specimens are from northern South America. This is evident in biogeographic reconstructions, which suggest Patagonia as the area of origin of many clades when taxa are underrepresented, but Amazonia and/or Central and Southern Andes when all taxa are included. More generally, our analyses demonstrate the instability of topology and divergence time estimates when using different morphological datasets and clock models and thus caution against making macroevolutionary inferences when node support is weak or when uncertainties in the fossil record are not considered.
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Affiliation(s)
- Julia V Tejada
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
- Institut des Sciences de l’Évolution de Montpellier, UMR 5554, Université de Montpellier, CNRS, IRD, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Pierre-Olivier Antoine
- Institut des Sciences de l’Évolution de Montpellier, UMR 5554, Université de Montpellier, CNRS, IRD, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Philippe Münch
- Géosciences Montpellier, UMR 5243, Université de Montpellier, CNRS, Université des Antilles, Place Eugène Bataillon, 34095 Montpellier, France
| | - Guillaume Billet
- Centre de Recherche en Paléontologie—Paris, CR2P—UMR 7207, Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, 8 rue Buffon 75005, Paris
| | - Lionel Hautier
- Institut des Sciences de l’Évolution de Montpellier, UMR 5554, Université de Montpellier, CNRS, IRD, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Frédéric Delsuc
- Institut des Sciences de l’Évolution de Montpellier, UMR 5554, Université de Montpellier, CNRS, IRD, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Fabien L Condamine
- Institut des Sciences de l’Évolution de Montpellier, UMR 5554, Université de Montpellier, CNRS, IRD, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
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Dabala E, Guédon A, Ficheux G, Béal L, Moxham B, Plaisant O. Homologies of spinal ascending nociceptive pathways between rats and macaques: can we transpose to human? A review and analysis of the literature. Surg Radiol Anat 2023; 45:1443-1460. [PMID: 37507602 DOI: 10.1007/s00276-023-03212-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 07/18/2023] [Indexed: 07/30/2023]
Abstract
PURPOSE Due to the difficulty of using neural tracers in humans, knowledge of the nociceptive system's anatomy is mainly derived from studies in animals and mainly in rats. The aim of this study was to investigate the morphological differences of the ascending spinal nociceptive pathways between the rat and the macaque monkey; in order to evaluate the variability of this anatomy during phylogenesis, and thus to know if the anatomical description of these pathways can be transposed from the rat to the human. METHODS A review and analysis of the literature were performed. The criteria used for comparison were: origins, pathways, their terminations in target structures, and projections from target structures of ascending spinal nociceptive pathways. The monkey was used as an intermediate species for comparison because of the lack of data in humans. The hypothesis of transposition of anatomy between rat and human was considered rejected if differences were found between rat and monkey. RESULTS An anatomical difference in termination was found for the spino-annular or spino-periaqueductal grey (spino-PAG) pathway and transposition of its anatomy from rat to human was rejected. No difference was found in other pathways and the transposition of their anatomy from rat to human was therefore, not rejected. CONCLUSION This work highlights the conservation of most of the ascending spinal nociceptive pathways' anatomy between rat and monkey. Thus, the possibility for a transposition of their anatomy between rat and human is not rejected.
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Affiliation(s)
- Eric Dabala
- Department of Anatomy, Université Catholique de Lille, Lille, France.
- Université Paris Cité, Paris, France.
| | - Alexis Guédon
- Université Paris Cité, Paris, France
- Department of Interventional Neuroradiology, INSERM UMR_S 1140, Lariboisière Hospital, AP-HP Nord, Paris, France
| | - Guillaume Ficheux
- Department of Anatomy, Université Catholique de Lille, Lille, France
| | - Louis Béal
- Department of Anatomy, Université Catholique de Lille, Lille, France
| | - Bernard Moxham
- Cardiff School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
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Castro ANC, Illia MC, Lendez PA, Illia MPC, Zimmermann B, Torres GJM, Carril J, Burgos BM, Ghezzi MD, Diez JJB, Barbeito CG. Hepatic hematopoiesis in the alpaca (Vicugna pacos), a species with development in hypoxic environments. Tissue Cell 2023; 82:102079. [PMID: 37058813 DOI: 10.1016/j.tice.2023.102079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/11/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023]
Abstract
Hematopoiesis occurs in different anatomical niches throughout the life of the individual. The first hematopoietic extra-embryonic stage is replaced by a intra-embryonic stage that occurs in a region that is adjacent to the dorsal aorta. Then, the prenatal hematopoietic function is continued by the liver and spleen, and later by the bone marrow. The objective of the present work was to describe the morphological characteristics of hepatic hematopoiesis in the alpaca and to analyze the proportion of the hematopoietic compartment of the organ and the cell types, at different times of ontogeny. Sixty-two alpaca samples were collected from the municipal slaughterhouse of Huancavelica, Perú. They were processed by routine histological techniques. Hematoxylin-eosin staining, special dyes, immunohistochemical techniques and supplementary analyses by lectinhistochemistry, were performed. The prenatal liver is an important structure in the expansion and differentiation of hematopoietic stem cells. Their hematopoietic activity was characterized by four stages: initiation, expansion, peak, and involution. The liver started its hematopoietic function at 21 days EGA and it was maintained until shortly before birth. Differences were found in the proportion and morphology of the hematopoietic tissue in the different groups corresponding to each gestational stage.
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Tavares FDS, Oliveira da Silva W, Ferguson-Smith MA, Klautau AGCDM, Oliveira JM, Rodrigues ALF, Melo-Santos G, Pieczarka JC, Nagamachi CY, Noronha RCR. Ancestral chromosomal signatures of Paenungulata (Afroteria) reveal the karyotype of Amazonian manatee (Trichechus inunguis, Sirenia: Trichechidae) as the oldest among American manatees. BMC Genomics 2023; 24:38. [PMID: 36694120 PMCID: PMC9872332 DOI: 10.1186/s12864-023-09129-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 01/11/2023] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Chromosomal painting in manatees has clarified questions about the rapid evolution of sirenians within the Paenungulata clade. Further cytogenetic studies in Afrotherian species may provide information about their evolutionary dynamics, revealing important insights into the ancestral karyotype in the clade representatives. The karyotype of Trichechus inunguis (TIN, Amazonian manatee) was investigated by chromosome painting, using probes from Trichechus manatus latirostris (TML, Florida manatee) to analyze the homeologies between these sirenians. RESULTS A high similarity was found between these species, with 31 homologous segments in TIN, nineteen of which are whole autosomes, besides the X and Y sex chromosomes. Four chromosomes from TML (4, 6, 8, and 9) resulted in two hybridization signals, totaling eight acrocentrics in the TIN karyotype. This study confirmed in TIN the chromosomal associations of Homo sapiens (HSA) shared in Afrotheria, such as the 5/21 synteny, and in the Paenungulata clade with the syntenies HSA 2/3, 8/22, and 18/19, in addition to the absence of HSA 4/8 common in eutherian ancestral karyotype (EAK). CONCLUSIONS TIN shares more conserved chromosomal signals with the Paenungulata Ancestral Karyotype (APK, 2n = 58) than Procavia capensis (Hyracoidea), Loxodonta africana (Proboscidea) and TML (Sirenia), where TML presents less conserved signals with APK, demonstrating that its karyotype is the most derived among the representatives of Paenungulata. The chromosomal changes that evolved from APK to the T. manatus and T. inunguis karyotypes (7 and 4 changes, respectively) are more substantial within the Trichechus genus compared to other paenungulates. Among these species, T. inunguis presents conserved traits of APK in the American manatee genus. Consequently, the karyotype of T. manatus is more derived than that of T. inunguis.
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Affiliation(s)
- Flávia Dos Santos Tavares
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal Do Pará (UFPA), Pará, Belém, Brazil
| | - Willam Oliveira da Silva
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal Do Pará (UFPA), Pará, Belém, Brazil
| | - Malcolm Andrew Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Jairo Moura Oliveira
- Zoological Park of Santarém - Universidade da Amazônia (ZOOUNAMA), Pará, Santarém, Brazil
| | - Angélica Lúcia Figueiredo Rodrigues
- Instituto de Biologia e Conservação de Mamíferos Aquáticos da Amazônia, Universidade Federal Rural da Amazônia (UFRA), Pará, Belém, Brazil
- Secretaria de Educação Do Estado Do Pará (SEDUC-PA), Belém, Brazil
| | - Gabriel Melo-Santos
- Instituto de Biologia e Conservação de Mamíferos Aquáticos da Amazônia, Universidade Federal Rural da Amazônia (UFRA), Pará, Belém, Brazil
- Laboratório de Ecologia Marinha e Conservação, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratório de Ecologia de Aves e Comportamento Animal, Universidade Estadual do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Julio Cesar Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal Do Pará (UFPA), Pará, Belém, Brazil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal Do Pará (UFPA), Pará, Belém, Brazil
| | - Renata Coelho Rodrigues Noronha
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal Do Pará (UFPA), Pará, Belém, Brazil.
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O’Brien SJ, Luo SJ. Taxonomic species recognition should be consistent. Natl Sci Rev 2022; 9:nwad022. [PMID: 36788967 PMCID: PMC9923365 DOI: 10.1093/nsr/nwad022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/23/2023] [Indexed: 01/26/2023] Open
Affiliation(s)
- Stephen J O’Brien
- Guy Harvey Oceanographic Center, Halmos College of Arts and Sciences, Nova Southeastern University, USA
| | - Shu-Jin Luo
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, China
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Brady PL, Springer MS. The effects of fossil taxa, hypothetical predicted ancestors, and a molecular scaffold on pseudoextinction analyses of extant placental orders. PLoS One 2021; 16:e0257338. [PMID: 34534236 PMCID: PMC8448315 DOI: 10.1371/journal.pone.0257338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/30/2021] [Indexed: 12/02/2022] Open
Abstract
Pseudoextinction analyses, which simulate extinction in extant taxa, use molecular phylogenetics to assess the accuracy of morphological phylogenetics. Previous pseudoextinction analyses have shown a failure of morphological phylogenetics to place some individual placental orders in the correct superordinal clade. Recent work suggests that the inclusion of hypothetical ancestors of extant placental clades, estimated by ancestral state reconstructions of morphological characters, may increase the accuracy of morphological phylogenetic analyses. However, these studies reconstructed direct hypothetical ancestors for each extant taxon based on a well-corroborated molecular phylogeny, which is not possible for extinct taxa that lack molecular data. It remains to be determined if pseudoextinct taxa, and by proxy extinct taxa, can be accurately placed when their immediate hypothetical ancestors are unknown. To investigate this, we employed molecular scaffolds with the largest available morphological data set for placental mammals. Each placental order was sequentially treated as pseudoextinct by exempting it from the molecular scaffold and recoding soft morphological characters as missing for all its constituent species. For each pseudoextinct data set, we omitted the pseudoextinct taxon and performed a parsimony ancestral state reconstruction to obtain hypothetical predicted ancestors. Each pseudoextinct order was then evaluated in seven parsimony analyses that employed combinations of fossil taxa, hypothetical predicted ancestors, and a molecular scaffold. In treatments that included fossils, hypothetical predicted ancestors, and a molecular scaffold, only 8 of 19 pseudoextinct placental orders (42%) retained the same interordinal placement as on the molecular scaffold. In treatments that included hypothetical predicted ancestors but not fossils or a scaffold, only four placental orders (21%) were recovered in positions that are congruent with the scaffold. These results indicate that hypothetical predicted ancestors do not increase the accuracy of pseudoextinct taxon placement when the immediate hypothetical ancestor of the taxon is unknown. Hypothetical predicted ancestors are not a panacea for morphological phylogenetics.
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Affiliation(s)
- Peggy L. Brady
- Department of Evolution, Ecology, and Evolutionary Biology, University of California, Riverside, Riverside, CA, United States of America
| | - Mark S. Springer
- Department of Evolution, Ecology, and Evolutionary Biology, University of California, Riverside, Riverside, CA, United States of America
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Asher RJ, Smith MR. Phylogenetic Signal and Bias in Paleontology. Syst Biol 2021; 71:986-1008. [PMID: 34469583 PMCID: PMC9248965 DOI: 10.1093/sysbio/syab072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 08/24/2021] [Accepted: 08/27/2021] [Indexed: 11/12/2022] Open
Abstract
An unprecedented amount of evidence now illuminates the phylogeny of living mammals and birds on the Tree of Life. We use this tree to measure phylogenetic value of data typically used in paleontology (bones and teeth) from six datasets derived from five published studies. We ask three interrelated questions: 1) Can these data adequately reconstruct known parts of the Tree of Life? 2) Is accuracy generally similar for studies using morphology, or do some morphological datasets perform better than others? 3) Does the loss of non-fossilizable data cause taxa to occur in misleadingly basal positions? Adding morphology to DNA datasets usually increases congruence of resulting topologies to the well corroborated tree, but this varies among morphological datasets. Extant taxa with a high proportion of missing morphological characters can greatly reduce phylogenetic resolution when analyzed together with fossils. Attempts to ameliorate this by deleting extant taxa missing morphology are prone to decreased accuracy due to long-branch artefacts. We find no evidence that fossilization causes extinct taxa to incorrectly appear at or near topologically basal branches. Morphology comprises the evidence held in common by living taxa and fossils, and phylogenetic analysis of fossils greatly benefits from inclusion of molecular and morphological data sampled for living taxa, whatever methods are used for phylogeny estimation.
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Affiliation(s)
- Robert J Asher
- Department of Zoology, Downing St., University of Cambridge CB2 3EJ, UK
| | - Martin R Smith
- Department of Earth Sciences, Lower Mount Joy, Durham University, Durham DH1 3LE, UK
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Ospina-Garcés SM, León-Paniagua L. Sexual dimorphism and geographic variation of the skull of the fishing bat Noctilio leporinus (Chiroptera: Noctilionidae) in Mexico. REV MEX BIODIVERS 2021. [DOI: 10.22201/ib.20078706e.2021.92.3518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Murphy WJ, Foley NM, Bredemeyer KR, Gatesy J, Springer MS. Phylogenomics and the Genetic Architecture of the Placental Mammal Radiation. Annu Rev Anim Biosci 2020; 9:29-53. [PMID: 33228377 DOI: 10.1146/annurev-animal-061220-023149] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The genomes of placental mammals are being sequenced at an unprecedented rate. Alignments of hundreds, and one day thousands, of genomes spanning the rich living and extinct diversity of species offer unparalleled power to resolve phylogenetic controversies, identify genomic innovations of adaptation, and dissect the genetic architecture of reproductive isolation. We highlight outstanding questions about the earliest phases of placental mammal diversification and the promise of newer methods, as well as remaining challenges, toward using whole genome data to resolve placental mammal phylogeny. The next phase of mammalian comparative genomics will see the completion and application of finished-quality, gapless genome assemblies from many ordinal lineages and closely related species. Interspecific comparisons between the most hypervariable genomic loci will likely reveal large, but heretofore mostly underappreciated, effects on population divergence, morphological innovation, and the origin of new species.
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Affiliation(s)
- William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA;
| | - Nicole M Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA;
| | - Kevin R Bredemeyer
- Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA;
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
| | - Mark S Springer
- Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, California 92521, USA
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Koch NM, Parry LA. Death is on Our Side: Paleontological Data Drastically Modify Phylogenetic Hypotheses. Syst Biol 2020; 69:1052-1067. [DOI: 10.1093/sysbio/syaa023] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/02/2020] [Accepted: 03/17/2020] [Indexed: 12/11/2022] Open
Abstract
Abstract
Fossils are the only remaining evidence of the majority of species that have ever existed, providing a direct window into events in evolutionary history that shaped the diversification of life on Earth. Phylogenies underpin our ability to make sense of evolution but are routinely inferred using only data available from living organisms. Although extinct taxa have been shown to add crucial information for inferring macroevolutionary patterns and processes (such as ancestral states, paleobiogeography and diversification dynamics), the role fossils play in reconstructing phylogeny is controversial. Since the early years of phylogenetic systematics, different studies have dismissed the impact of fossils due to their incompleteness, championed their ability to overturn phylogenetic hypotheses or concluded that their behavior is indistinguishable from that of extant taxa. Based on taxon addition experiments on empirical data matrices, we show that the inclusion of paleontological data has a remarkable effect in phylogenetic inference. Incorporating fossils often (yet not always) induces stronger topological changes than increasing sampling of extant taxa. Fossils also produce unique topological rearrangements, allowing the exploration of regions of treespace that are never visited by analyses of only extant taxa. Previous studies have proposed a suite of explanations for the topological behavior of fossils, such as their retention of unique morphologies or their ability to break long branches. We develop predictive models that demonstrate that the possession of distinctive character state combinations is the primary predictor of the degree of induced topological change, and that the relative impact of taxa (fossil and extant) can be predicted to some extent before any phylogenetic analysis. Our results bolster the consensus of recent empirical studies by showing the unique role of paleontological data in phylogenetic inference, and provide the first quantitative assessment of its determinants, with broad consequences for the design of taxon sampling in both morphological and total-evidence analyses. [phylogeny, morphology, fossils, parsimony, Bayesian inference.]
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Affiliation(s)
- Nicolás Mongiardino Koch
- Department of Geology & Geophysics, Yale University, 210 Whitney Avenue, New Haven, CT 06510, USA
| | - Luke A Parry
- Department of Geology & Geophysics, Yale University, 210 Whitney Avenue, New Haven, CT 06510, USA
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Springer MS, Foley NM, Brady PL, Gatesy J, Murphy WJ. Evolutionary Models for the Diversification of Placental Mammals Across the KPg Boundary. Front Genet 2019; 10:1241. [PMID: 31850081 PMCID: PMC6896846 DOI: 10.3389/fgene.2019.01241] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 11/08/2019] [Indexed: 01/29/2023] Open
Abstract
Deciphering the timing of the placental mammal radiation is a longstanding problem in evolutionary biology, but consensus on the tempo and mode of placental diversification remains elusive. Nevertheless, an accurate timetree is essential for understanding the role of important events in Earth history (e.g., Cretaceous Terrestrial Revolution, KPg mass extinction) in promoting the taxonomic and ecomorphological diversification of Placentalia. Archibald and Deutschman described three competing models for the diversification of placental mammals, which are the Explosive, Long Fuse, and Short Fuse Models. More recently, the Soft Explosive Model and Trans-KPg Model have emerged as additional hypotheses for the placental radiation. Here, we review molecular and paleontological evidence for each of these five models including the identification of general problems that can negatively impact divergence time estimates. The Long Fuse Model has received more support from relaxed clock studies than any of the other models, but this model is not supported by morphological cladistic studies that position Cretaceous eutherians outside of crown Placentalia. At the same time, morphological cladistics has a poor track record of reconstructing higher-level relationships among the orders of placental mammals including the results of new pseudoextinction analyses that we performed on the largest available morphological data set for mammals (4,541 characters). We also examine the strengths and weaknesses of different timetree methods (node dating, tip dating, and fossilized birth-death dating) that may now be applied to estimate the timing of the placental radiation. While new methods such as tip dating are promising, they also have problems that must be addressed if these methods are to effectively discriminate among competing hypotheses for placental diversification. Finally, we discuss the complexities of timetree estimation when the signal of speciation times is impacted by incomplete lineage sorting (ILS) and hybridization. Not accounting for ILS results in dates that are older than speciation events. Hybridization, in turn, can result in dates than are younger or older than speciation dates. Disregarding this potential variation in "gene" history across the genome can distort phylogenetic branch lengths and divergence estimates when multiple unlinked genomic loci are combined together in a timetree analysis.
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Affiliation(s)
- Mark S. Springer
- Department of Evolution, Ecology, and Evolutionary Biology, University of California, Riverside, Riverside, CA, United States
| | - Nicole M. Foley
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| | - Peggy L. Brady
- Department of Evolution, Ecology, and Evolutionary Biology, University of California, Riverside, Riverside, CA, United States
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, United States
| | - William J. Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
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Asher RJ, Smith MR, Rankin A, Emry RJ. Congruence, fossils and the evolutionary tree of rodents and lagomorphs. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190387. [PMID: 31417738 PMCID: PMC6689570 DOI: 10.1098/rsos.190387] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 06/19/2019] [Indexed: 05/10/2023]
Abstract
Given an evolutionary process, we expect distinct categories of heritable data, sampled in ever larger amounts, to converge on a single tree of historical relationships. We tested this assertion by undertaking phylogenetic analyses of a new morphology-DNA dataset for mammals, focusing on Glires and including the oldest known skeletons of geomyoid and Ischyromys rodents. Our results support geomyoids in the mouse-related clade (Myomorpha) and a ricochetal locomotor pattern for the common ancestor of geomyoid rodents. They also support Ischyromys in the squirrel-related clade (Sciuromorpha) and the evolution of sciurids and Aplodontia from extinct, 'protrogomorph'-grade rodents. Moreover, ever larger samples of characters from our dataset increased congruence with an independent, well-corroborated tree. Addition of morphology from fossils increased congruence to a greater extent than addition of morphology from extant taxa, consistent with fossils' temporal proximity to the common ancestors of living species, reflecting the historical, phylogenetic signal present in our data, particularly in morphological characters from fossils. Our results support the widely held but poorly tested intuition that fossils resemble the common ancestors shared by living species, and that fossilizable hard tissues (i.e. bones and teeth) help to reconstruct the evolutionary tree of life.
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Affiliation(s)
- Robert J. Asher
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Martin R. Smith
- Department of Earth Sciences, University of Durham, Durham, UK
| | - Aime Rankin
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Robert J. Emry
- Department of Paleobiology, Smithsonian Institution, Washington, DC, USA
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14
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Beck RMD, Baillie C. Improvements in the fossil record may largely resolve current conflicts between morphological and molecular estimates of mammal phylogeny. Proc Biol Sci 2018; 285:20181632. [PMID: 30963896 PMCID: PMC6304057 DOI: 10.1098/rspb.2018.1632] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/23/2018] [Indexed: 01/16/2023] Open
Abstract
Phylogenies of mammals based on morphological data continue to show several major areas of conflict with the current consensus view of their relationships, which is based largely on molecular data. This raises doubts as to whether current morphological character sets are able to accurately resolve mammal relationships. We tested this under a hypothetical 'best case scenario' by using ancestral state reconstruction (under both maximum parsimony and maximum likelihood) to infer the morphologies of fossil ancestors for all clades present in a recent comprehensive DNA sequence-based phylogeny of mammals, and then seeing what effect the subsequent inclusion of these predicted ancestors had on unconstrained phylogenetic analyses of morphological data. We found that this resulted in topologies that are highly congruent with the current consensus phylogeny, at least when the predicted ancestors are assumed to be well preserved and densely sampled. Most strikingly, several analyses recovered the monophyly of clades that have never been found in previous morphology-only studies, such as Afrotheria and Laurasiatheria. Our results suggest that, at least in principle, improvements in the fossil record-specifically the discovery of fossil taxa that preserve the ancestral or near-ancestral morphologies of the nodes in the current consensus-may be sufficient to largely reconcile morphological and molecular estimates of mammal phylogeny, even using current morphological character sets.
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Affiliation(s)
- Robin M. D. Beck
- School of Environment and Life Sciences, University of Salford, Manchester M5 4WT, UK
| | - Charles Baillie
- School of Environment and Life Sciences, University of Salford, Manchester M5 4WT, UK
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15
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Cascini M, Mitchell KJ, Cooper A, Phillips MJ. Reconstructing the Evolution of Giant Extinct Kangaroos: Comparing the Utility of DNA, Morphology, and Total Evidence. Syst Biol 2018; 68:520-537. [DOI: 10.1093/sysbio/syy080] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 11/20/2018] [Accepted: 11/20/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- Manuela Cascini
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, 2, George Street, Brisbane, QLD 4000, Australia
| | - Kieren J Mitchell
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, North Terrace Campus, South Australia 5005, Australia
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, North Terrace Campus, South Australia 5005, Australia
| | - Matthew J Phillips
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, 2, George Street, Brisbane, QLD 4000, Australia
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16
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Genome-Wide Evolutionary Analysis of Natural History and Adaptation in the World's Tigers. Curr Biol 2018; 28:3840-3849.e6. [PMID: 30482605 DOI: 10.1016/j.cub.2018.09.019] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 07/01/2018] [Accepted: 09/10/2018] [Indexed: 12/25/2022]
Abstract
No other species attracts more international resources, public attention, and protracted controversies over its intraspecific taxonomy than the tiger (Panthera tigris) [1, 2]. Today, fewer than 4,000 free-ranging tigers survive, covering only 7% of their historical range, and debates persist over whether they comprise six, five, or two subspecies [3-6]. The lack of consensus over the number of tiger subspecies has partially hindered the global effort to recover the species from the brink of extinction, as both captive breeding and landscape intervention of wild populations increasingly require an explicit delineation of the conservation management units [7]. The recent coalescence to a late Pleistocene bottleneck (circa 110 kya) [5, 8, 9] poses challenges for detecting tiger subspecific morphological traits, suggesting that elucidating intraspecific evolution in the tiger requires analyses at the genomic scale. Here, we present whole-genome sequencing analyses from 32 voucher specimens that resolve six statistically robust monophyletic clades corresponding to extant subspecies, including the recently recognized Malayan tiger (P. tigris jacksoni). The intersubspecies gene flow is very low, corroborating the recognized phylogeographic units. We identified multiple genomic regions that are candidates for identifying the adaptive divergence of subspecies. The body-size-related gene ADH7 appears to have been strongly selected in the Sumatran tiger, perhaps in association with adaptation to the tropical Sunda Islands. The identified genomic signatures provide a solid basis for recognizing appropriate conservation management units in the tiger and can benefit global conservation strategic planning for this charismatic megafauna icon.
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17
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Phillips MJ, Fruciano C. The soft explosive model of placental mammal evolution. BMC Evol Biol 2018; 18:104. [PMID: 29969980 PMCID: PMC6029115 DOI: 10.1186/s12862-018-1218-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 06/19/2018] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Recent molecular dating estimates for placental mammals echo fossil inferences for an explosive interordinal diversification, but typically place this event some 10-20 million years earlier than the Paleocene fossils, among apparently more "primitive" mammal faunas. RESULTS However, current models of molecular evolution do not adequately account for parallel rate changes, and result in dramatic divergence underestimates for large, long-lived mammals such as whales and hominids. Calibrating among these taxa shifts the rate model errors deeper in the tree, inflating interordinal divergence estimates. We employ simulations based on empirical rate variation, which show that this "error-shift inflation" can explain previous molecular dating overestimates relative to fossil inferences. Molecular dating accuracy is substantially improved in the simulations by focusing on calibrations for taxa that retain plesiomorphic life-history characteristics. Applying this strategy to the empirical data favours the soft explosive model of placental evolution, in line with traditional palaeontological interpretations - a few Cretaceous placental lineages give rise to a rapid interordinal diversification following the 66 Ma Cretaceous-Paleogene boundary mass extinction. CONCLUSIONS Our soft explosive model for the diversification of placental mammals brings into agreement previously incongruous molecular, fossil, and ancestral life history estimates, and closely aligns with a growing consensus for a similar model for bird evolution. We show that recent criticism of the soft explosive model relies on ignoring both experimental controls and statistical confidence, as well as misrepresentation, and inconsistent interpretations of morphological phylogeny. More generally, we suggest that the evolutionary properties of adaptive radiations may leave current molecular dating methods susceptible to overestimating the timing of major diversification events.
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Affiliation(s)
- Matthew J. Phillips
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Australia
| | - Carmelo Fruciano
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Australia
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18
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Springer MS, Murphy WJ, Roca AL. Appropriate fossil calibrations and tree constraints uphold the Mesozoic divergence of solenodons from other extant mammals. Mol Phylogenet Evol 2018; 121:158-165. [PMID: 29331683 DOI: 10.1016/j.ympev.2018.01.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 12/27/2017] [Accepted: 01/09/2018] [Indexed: 11/30/2022]
Abstract
The mammalian order Eulipotyphla includes four extant families of insectivorans: Solenodontidae (solenodons); Talpidae (moles); Soricidae (shrews); and Erinaceidae (hedgehogs). Of these, Solenodontidae includes only two extant species, which are endemic to the largest islands of the Greater Antilles: Cuba and Hispaniola. Most molecular studies suggest that eulipotyphlan families diverged from each other across several million years, with the basal split between Solenodontidae and other families occurring in the Late Cretaceous. By contrast, Sato et al. (2016) suggest that eulipotyphlan families diverged from each other in a polytomy ∼58.6 million years ago (Mya). This more recent divergence estimate for Solenodontidae versus other extant eulipotyphlans suggests that solenodons must have arrived in the Greater Antilles via overwater dispersal rather than vicariance. Here, we show that the young timetree estimates for eulipotyphlan families and the polytomy are due to an inverted ingroup-outgroup arrangement of the tree, the result of using Tracer rather than TreeAnnotator to compile interfamilial divergence times, and of not enforcing the monophly of well-established clades such as Laurasiatheria and Eulipotyphla. Finally, Sato et al.'s (2016) timetree includes several zombie lineages where estimated divergence times are much younger than minimum ages that are implied by the fossil record. We reanalyzed Sato et al.'s (2016) original data with enforced monophyly for well-established clades and updated fossil calibrations that eliminate the inference of zombie lineages. Our resulting timetrees, which were compiled with TreeAnnotator rather than Tracer, produce dates that are in good agreement with other recent studies and place the basal split between Solenodontidae and other eulipotyphlans in the Late Cretaceous.
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Affiliation(s)
- Mark S Springer
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA 92521, USA.
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Alfred L Roca
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA
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19
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Kealy S, Beck R. Total evidence phylogeny and evolutionary timescale for Australian faunivorous marsupials (Dasyuromorphia). BMC Evol Biol 2017; 17:240. [PMID: 29202687 PMCID: PMC5715987 DOI: 10.1186/s12862-017-1090-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/22/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The order Dasyuromorphia is a diverse radiation of faunivorous marsupials, comprising >80 modern species in Australia and New Guinea. It includes dasyurids, the numbat (the myrmecobiid Myrmecobius fasciatus) and the recently extinct thylacine (the thylacinid Thylacinus cyncocephalus). There is also a diverse fossil record of dasyuromorphians and "dasyuromorphian-like" taxa known from Australia. We present the first total evidence phylogenetic analyses of the order, based on combined morphological and molecular data (including a novel set of 115 postcranial characters), to resolve relationships and calculate divergence dates. We use this information to analyse the diversification dynamics of modern dasyuromorphians. RESULTS Our morphology-only analyses are poorly resolved, but our molecular and total evidence analyses confidently resolve most relationships within the order, and are strongly congruent with recent molecular studies. Thylacinidae is the first family to diverge within the order, and there is strong support for four tribes within Dasyuridae (Dasyurini, Phascogalini, Planigalini and Sminthopsini). Among fossil taxa, Ankotarinja and Keeuna do not appear to be members of Dasyuromorphia, whilst Barinya and Mutpuracinus are of uncertain relationships within the order. Divergence dates calculated using total evidence tip-and-node dating are younger than both molecular node-dating and total evidence tip-dating, but appear more congruent with the fossil record and are relatively insensitive to calibration strategy. The tip-and-node divergence dates indicate that Dasyurini, Phascogalini and Sminthopsini began to radiate almost simultaneously during the middle-to-late Miocene (11.5-13.1 MYA; composite 95% HPD: 9.5-15.9 MYA); the median estimates for these divergences are shortly after a drop in global temperatures (the middle Miocene Climatic Transition), and coincide with a faunal turnover event in the mammalian fossil record of Australia. Planigalini radiated much later, during the latest Miocene to earliest Pliocene (6.5 MYA; composite 95% HPD: 4.4-8.9 MYA); the median estimates for these divergences coincide with an increase in grass pollen in the Australian palynological record that suggests the development of more open habitats, which are preferred by modern planigale species. CONCLUSIONS Our results provide a phylogenetic and temporal framework for interpreting the evolution of modern and fossil dasyuromorphians, but future progress will require a much improved fossil record.
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Affiliation(s)
- Shimona Kealy
- Archaeology and Natural History, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Acton, ACT Australia
| | - Robin Beck
- School of Environment and Life Sciences, University of Salford, Salford, M5 4WT UK
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20
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Sansom RS, Wills MA, Williams T. Dental Data Perform Relatively Poorly in Reconstructing Mammal Phylogenies: Morphological Partitions Evaluated with Molecular Benchmarks. Syst Biol 2017; 66:813-822. [PMID: 28003534 PMCID: PMC5790133 DOI: 10.1093/sysbio/syw116] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 11/30/2016] [Accepted: 12/20/2016] [Indexed: 01/27/2023] Open
Abstract
Phylogenetic trees underpin reconstructions of evolutionary history and tests of evolutionary hypotheses. They are inferred from both molecular and morphological data, yet the relative value of morphology has been questioned in this context due to perceived homoplasy, developmental linkage, and nonindependence of characters. Nevertheless, fossil data are limited to incomplete subsets of preserved morphology, and different regions are treated as equivalent. Through meta-analysis of 40 data sets, we show here that the dental and osteological characters of mammals convey significantly different phylogenetic signals, and that osteological characters are significantly more compatible with molecular trees. Furthermore, the application of simplified paleontological filters (retaining only dental data) results in significantly greater loss of phylogenetic signal than random character ablation. Although the mammal fossil record is largely comprised of teeth, dental data alone are generally found to be less reliable for phylogenetic reconstruction given their incongruence with osteological and molecular data. These findings highlight the need for rigorous meta-analyses of distributions of homoplasy in morphological data. These tests, and consequent refinements to phylogenetic analyses that they permit, promise to improve the quality of all macroevolutionary studies that hinge on accurate trees. [Homoplasy; Mammalia; morphology; osteology; phylogeny; teeth.
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Affiliation(s)
- Robert S. Sansom
- School of Earth and Environmental Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Matthew Albion Wills
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Tamara Williams
- School of Earth and Environmental Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
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21
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Breaux B, Deiss TC, Chen PL, Cruz-Schneider MP, Sena L, Hunter ME, Bonde RK, Criscitiello MF. The Florida manatee (Trichechus manatus latirostris) immunoglobulin heavy chain suggests the importance of clan III variable segments in repertoire diversity. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 72:57-68. [PMID: 28131767 DOI: 10.1016/j.dci.2017.01.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 01/23/2017] [Accepted: 01/23/2017] [Indexed: 06/06/2023]
Abstract
Manatees are a vulnerable, charismatic sentinel species from the evolutionarily divergent Afrotheria. Manatee health and resistance to infectious disease is of great concern to conservation groups, but little is known about their immune system. To develop manatee-specific tools for monitoring health, we first must have a general knowledge of how the immunoglobulin heavy (IgH) chain locus is organized and transcriptionally expressed. Using the genomic scaffolds of the Florida manatee (Trichechus manatus latirostris), we characterized the potential IgH segmental diversity and constant region isotypic diversity and performed the first Afrotherian repertoire analysis. The Florida manatee has low V(D)J combinatorial diversity (3744 potential combinations) and few constant region isotypes. They also lack clan III V segments, which may have caused reduced VH segment numbers. However, we found productive somatic hypermutation concentrated in the complementarity determining regions. In conclusion, manatees have limited IGHV clan and combinatorial diversity. This suggests that clan III V segments are essential for maintaining IgH locus diversity.
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Affiliation(s)
- Breanna Breaux
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
| | - Thaddeus C Deiss
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
| | - Patricia L Chen
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
| | | | - Leonardo Sena
- Laboratory of Medical and Human Genetics, Federal University of Pará, Belém, Pará, Brazil.
| | - Margaret E Hunter
- Wetland and Aquatic Research Center, U.S. Geological Survey, 7920 NW 71st Street, Gainesville, FL 32653, USA.
| | - Robert K Bonde
- Wetland and Aquatic Research Center, U.S. Geological Survey, 7920 NW 71st Street, Gainesville, FL 32653, USA.
| | - Michael F Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA; Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, College Station, TX 77843, USA.
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22
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Grealy A, Phillips M, Miller G, Gilbert MTP, Rouillard JM, Lambert D, Bunce M, Haile J. Eggshell palaeogenomics: Palaeognath evolutionary history revealed through ancient nuclear and mitochondrial DNA from Madagascan elephant bird (Aepyornis sp.) eggshell. Mol Phylogenet Evol 2017; 109:151-163. [DOI: 10.1016/j.ympev.2017.01.005] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 12/20/2016] [Accepted: 01/07/2017] [Indexed: 01/12/2023]
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23
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Samuels ME, Regnault S, Hutchinson JR. Evolution of the patellar sesamoid bone in mammals. PeerJ 2017; 5:e3103. [PMID: 28344905 PMCID: PMC5363259 DOI: 10.7717/peerj.3103] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 02/17/2017] [Indexed: 12/22/2022] Open
Abstract
The patella is a sesamoid bone located in the major extensor tendon of the knee joint, in the hindlimb of many tetrapods. Although numerous aspects of knee morphology are ancient and conserved among most tetrapods, the evolutionary occurrence of an ossified patella is highly variable. Among extant (crown clade) groups it is found in most birds, most lizards, the monotreme mammals and almost all placental mammals, but it is absent in most marsupial mammals as well as many reptiles. Here, we integrate data from the literature and first-hand studies of fossil and recent skeletal remains to reconstruct the evolution of the mammalian patella. We infer that bony patellae most likely evolved between four and six times in crown group Mammalia: in monotremes, in the extinct multituberculates, in one or more stem-mammal genera outside of therian or eutherian mammals and up to three times in therian mammals. Furthermore, an ossified patella was lost several times in mammals, not including those with absent hindlimbs: once or more in marsupials (with some re-acquisition) and at least once in bats. Our inferences about patellar evolution in mammals are reciprocally informed by the existence of several human genetic conditions in which the patella is either absent or severely reduced. Clearly, development of the patella is under close genomic control, although its responsiveness to its mechanical environment is also important (and perhaps variable among taxa). Where a bony patella is present it plays an important role in hindlimb function, especially in resisting gravity by providing an enhanced lever system for the knee joint. Yet the evolutionary origins, persistence and modifications of a patella in diverse groups with widely varying habits and habitats-from digging to running to aquatic, small or large body sizes, bipeds or quadrupeds-remain complex and perplexing, impeding a conclusive synthesis of form, function, development and genetics across mammalian evolution. This meta-analysis takes an initial step toward such a synthesis by collating available data and elucidating areas of promising future inquiry.
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Affiliation(s)
- Mark E. Samuels
- Department of Medicine, University of Montreal, Montreal, QC, Canada
- Centre de Recherche du CHU Ste-Justine, Montreal, QC, Canada
| | - Sophie Regnault
- Department of Comparative Biomedical Sciences, Structure and Motion Laboratory, The Royal Veterinary College, London Hertfordshire, UK
| | - John R. Hutchinson
- Department of Comparative Biomedical Sciences, Structure and Motion Laboratory, The Royal Veterinary College, London Hertfordshire, UK
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24
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Kear BP, Aplin KP, Westerman M. Bandicoot fossils and DNA elucidate lineage antiquity amongst xeric-adapted Australasian marsupials. Sci Rep 2016; 6:37537. [PMID: 27881865 PMCID: PMC5121598 DOI: 10.1038/srep37537] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 10/31/2016] [Indexed: 11/09/2022] Open
Abstract
Bandicoots (Peramelemorphia) are a unique order of Australasian marsupials whose sparse fossil record has been used as prima facie evidence for climate change coincident faunal turnover. In particular, the hypothesized replacement of ancient rainforest-dwelling extinct lineages by antecedents of xeric-tolerant extant taxa during the late Miocene (~10 Ma) has been advocated as a broader pattern evident amongst other marsupial clades. Problematically, however, this is in persistent conflict with DNA phylogenies. We therefore determine the pattern and timing of bandicoot evolution using the first combined morphological + DNA sequence dataset of Peramelemorphia. In addition, we document a remarkably archaic new fossil peramelemorphian taxon that inhabited a latest Quaternary mosaic savannah-riparian forest ecosystem on the Aru Islands of Eastern Indonesia. Our phylogenetic analyses reveal that unsuspected dental homoplasy and the detrimental effects of missing data collectively obscure stem bandicoot relationships. Nevertheless, recalibrated molecular clocks and multiple ancestral area optimizations unanimously infer an early diversification of modern xeric-adapted forms. These probably originated during the late Palaeogene (30-40 Ma) alongside progenitors of other desert marsupials, and thus occupied seasonally dry heterogenous habitats long before the onset of late Neogene aridity.
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Affiliation(s)
- Benjamin P Kear
- Museum of Evolution, Uppsala University, Norbyvägen 16, SE-752 36 Uppsala, Sweden.,Department of Earth Sciences, Uppsala University, Villavägen 16, SE-752 36 Uppsala, Sweden
| | - Ken P Aplin
- Division of Mammals, National Museum of Natural History, Smithsonian Institution, P.O. Box. 37012, Washington, DC, 20013-7012, USA
| | - Michael Westerman
- Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Victoria 3086, Australia
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25
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Springer MS, Emerling CA, Meredith RW, Janečka JE, Eizirik E, Murphy WJ. Waking the undead: Implications of a soft explosive model for the timing of placental mammal diversification. Mol Phylogenet Evol 2016; 106:86-102. [PMID: 27659724 DOI: 10.1016/j.ympev.2016.09.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 09/15/2016] [Accepted: 09/18/2016] [Indexed: 02/06/2023]
Abstract
The explosive, long fuse, and short fuse models represent competing hypotheses for the timing of placental mammal diversification. Support for the explosive model, which posits both interordinal and intraordinal diversification after the KPg mass extinction, derives from morphological cladistic studies that place Cretaceous eutherians outside of crown Placentalia. By contrast, most molecular studies favor the long fuse model wherein interordinal cladogenesis occurred in the Cretaceous followed by intraordinal cladogenesis after the KPg boundary. Phillips (2016) proposed a soft explosive model that allows for the emergence of a few lineages (Xenarthra, Afrotheria, Euarchontoglires, Laurasiatheria) in the Cretaceous, but otherwise agrees with the explosive model in positing the majority of interordinal diversification after the KPg mass extinction. Phillips (2016) argues that rate transference errors associated with large body size and long lifespan have inflated previous estimates of interordinal divergence times, and further suggests that most interordinal divergences are positioned after the KPg boundary when rate transference errors are avoided through the elimination of calibrations in large-bodied and/or long lifespan clades. Here, we show that rate transference errors can also occur in the opposite direction and drag forward estimated divergence dates when calibrations in large-bodied/long lifespan clades are omitted. This dragging forward effect results in the occurrence of more than half a billion years of 'zombie lineages' on Phillips' preferred timetree. By contrast with ghost lineages, which are a logical byproduct of an incomplete fossil record, zombie lineages occur when estimated divergence dates are younger than the minimum age of the oldest crown fossils. We also present the results of new timetree analyses that address the rate transference problem highlighted by Phillips (2016) by deleting taxa that exceed thresholds for body size and lifespan. These analyses recover all interordinal divergence times in the Cretaceous and are consistent with the long fuse model of placental diversification. Finally, we outline potential problems with morphological cladistic analyses of higher-level relationships among placental mammals that may account for the perceived discrepancies between molecular and paleontological estimates of placental divergence times.
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Affiliation(s)
- Mark S Springer
- Department of Biology, University of California, Riverside, CA 92521, USA.
| | | | - Robert W Meredith
- Department of Biology and Molecular Biology, Montclair State University, Montclair, NJ 07043, USA
| | - Jan E Janečka
- Department of Biological Sciences, Duquesne University, Pittsburgh, PA 15282, USA
| | - Eduardo Eizirik
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS 90619-900, Brazil
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
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26
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Gatesy J, Meredith RW, Janecka JE, Simmons MP, Murphy WJ, Springer MS. Resolution of a concatenation/coalescence kerfuffle: partitioned coalescence support and a robust family‐level tree for Mammalia. Cladistics 2016; 33:295-332. [DOI: 10.1111/cla.12170] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2016] [Indexed: 12/14/2022] Open
Affiliation(s)
- John Gatesy
- Department of Biology University of California Riverside CA 92521 USA
| | - Robert W. Meredith
- Department of Biology and Molecular Biology Montclair State University Montclair NJ 07043 USA
| | - Jan E. Janecka
- Department of Biological Sciences Duquesne University Pittsburgh PA 15282 USA
| | - Mark P. Simmons
- Department of Biology Colorado State University Fort Collins CO 80523 USA
| | - William J. Murphy
- Department of Veterinary Integrative Biosciences Texas A&M University College Station TX 77843 USA
| | - Mark S. Springer
- Department of Biology University of California Riverside CA 92521 USA
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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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28
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Response to Comment by Faurby, Werdelin and Svenning. Genome Biol 2016; 17:90. [PMID: 27150130 PMCID: PMC4858819 DOI: 10.1186/s13059-016-0942-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 04/11/2016] [Indexed: 11/10/2022] Open
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29
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Buckley M. Ancient collagen reveals evolutionary history of the endemic South American 'ungulates'. Proc Biol Sci 2016; 282:20142671. [PMID: 25833851 PMCID: PMC4426609 DOI: 10.1098/rspb.2014.2671] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Since the late eighteenth century, fossils of bizarre extinct creatures have been described from the Americas, revealing a previously unimagined chapter in the history of mammals. The most bizarre of these are the ‘native’ South American ungulates thought to represent a group of mammals that evolved in relative isolation on South America, but with an uncertain affinity to any particular placental lineage. Many authors have considered them descended from Laurasian ‘condylarths’, which also includes the probable ancestors of perissodactyls and artiodactyls, whereas others have placed them either closer to the uniquely South American xenarthrans (anteaters, armadillos and sloths) or the basal afrotherians (e.g. elephants and hyraxes). These hypotheses have been debated owing to conflicting morphological characteristics and the hitherto inability to retrieve molecular information. Of the ‘native’ South American mammals, only the toxodonts and litopterns persisted until the Late Pleistocene–Early Holocene. Owing to known difficulties in retrieving ancient DNA (aDNA) from specimens from warm climates, this research presents a molecular phylogeny for both Macrauchenia patachonica (Litopterna) and Toxodon platensis (Notoungulata) recovered using proteomics-based (liquid chromatography–tandem mass spectrometry) sequencing analyses of bone collagen. The results place both taxa in a clade that is monophyletic with the perissodactyls, which today are represented by horses, rhinoceroses and tapirs.
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Affiliation(s)
- Michael Buckley
- Faculty of Life Sciences, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK
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30
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Leaché AD, Banbury BL, Linkem CW, de Oca ANM. Phylogenomics of a rapid radiation: is chromosomal evolution linked to increased diversification in north american spiny lizards (Genus Sceloporus)? BMC Evol Biol 2016; 16:63. [PMID: 27000803 PMCID: PMC4802581 DOI: 10.1186/s12862-016-0628-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 02/29/2016] [Indexed: 01/25/2023] Open
Abstract
Background Resolving the short phylogenetic branches that result from rapid evolutionary diversification often requires large numbers of loci. We collected targeted sequence capture data from 585 nuclear loci (541 ultraconserved elements and 44 protein-coding genes) to estimate the phylogenetic relationships among iguanian lizards in the North American genus Sceloporus. We tested for diversification rate shifts to determine if rapid radiation in the genus is correlated with chromosomal evolution. Results The phylogenomic trees that we obtained for Sceloporus using concatenation and coalescent-based species tree inference provide strong support for the monophyly and interrelationships among nearly all major groups. The diversification analysis supported one rate shift on the Sceloporus phylogeny approximately 20–25 million years ago that is associated with the doubling of the speciation rate from 0.06 species/million years (Ma) to 0.15 species/Ma. The posterior probability for this rate shift occurring on the branch leading to the Sceloporus species groups exhibiting increased chromosomal diversity is high (posterior probability = 0.997). Conclusions Despite high levels of gene tree discordance, we were able to estimate a phylogenomic tree for Sceloporus that solves some of the taxonomic problems caused by previous analyses of fewer loci. The taxonomic changes that we propose using this new phylogenomic tree help clarify the number and composition of the major species groups in the genus. Our study provides new evidence for a putative link between chromosomal evolution and the rapid divergence and radiation of Sceloporus across North America. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0628-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adam D Leaché
- Department of Biology, University of Washington, Seattle, Washington, 98195, USA. .,Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, 98195, USA.
| | - Barbara L Banbury
- Department of Biology, University of Washington, Seattle, Washington, 98195, USA.,Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Mail Stop M4-B402, Seattle, 98109, Washington, USA
| | - Charles W Linkem
- Department of Biology, University of Washington, Seattle, Washington, 98195, USA
| | - Adrián Nieto-Montes de Oca
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, México
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31
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Mounce RCP, Sansom R, Wills MA. Sampling diverse characters improves phylogenies: Craniodental and postcranial characters of vertebrates often imply different trees. Evolution 2016; 70:666-86. [PMID: 26899622 DOI: 10.1111/evo.12884] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 12/23/2015] [Accepted: 01/15/2016] [Indexed: 12/30/2022]
Abstract
Morphological cladograms of vertebrates are often inferred from greater numbers of characters describing the skull and teeth than from postcranial characters. This is either because the skull is believed to yield characters with a stronger phylogenetic signal (i.e., contain less homoplasy), because morphological variation therein is more readily atomized, or because craniodental material is more widely available (particularly in the palaeontological case). An analysis of 85 vertebrate datasets published between 2000 and 2013 confirms that craniodental characters are significantly more numerous than postcranial characters, but finds no evidence that levels of homoplasy differ in the two partitions. However, a new partition test, based on tree-to-tree distances (as measured by the Robinson Foulds metric) rather than tree length, reveals that relationships inferred from the partitions are significantly different about one time in three, much more often than expected. Such differences may reflect divergent selective pressures in different body regions, resulting in different localized patterns of homoplasy. Most systematists attempt to sample characters broadly across body regions, but this is not always possible. We conclude that trees inferred largely from either craniodental or postcranial characters in isolation may differ significantly from those that would result from a more holistic approach. We urge the latter.
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Affiliation(s)
- Ross C P Mounce
- The Milner Centre for Evolution, Department of Biology and Biochemistry, The University of Bath, The Avenue, Claverton Down, Bath, BA2 7AY, United Kingdom
| | - Robert Sansom
- Department of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, United Kingdom
| | - Matthew A Wills
- The Milner Centre for Evolution, Department of Biology and Biochemistry, The University of Bath, The Avenue, Claverton Down, Bath, BA2 7AY, United Kingdom.
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32
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Phillips MJ. Geomolecular Dating and the Origin of Placental Mammals. Syst Biol 2015; 65:546-57. [PMID: 26658702 DOI: 10.1093/sysbio/syv115] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 12/03/2015] [Indexed: 11/13/2022] Open
Abstract
In modern evolutionary divergence analysis the role of geological information extends beyond providing a timescale, to informing molecular rate variation across the tree. Here I consider the implications of this development. I use fossil calibrations to test the accuracy of models of molecular rate evolution for placental mammals, and reveal substantial misspecification associated with life history rate correlates. Adding further calibrations to reduce dating errors at specific nodes unfortunately tends to transfer underlying rate errors to adjacent branches. Thus, tight calibration across the tree is vital to buffer against rate model errors. I argue that this must include allowing maximum bounds to be tight when good fossil records permit, otherwise divergences deep in the tree will tend to be inflated by the interaction of rate errors and asymmetric confidence in minimum and maximum bounds. In the case of placental mammals I sought to reduce the potential for transferring calibration and rate model errors across the tree by focusing on well-supported calibrations with appropriately conservative maximum bounds. The resulting divergence estimates are younger than others published recently, and provide the long-anticipated molecular signature for the placental mammal radiation observed in the fossil record near the 66 Ma Cretaceous-Paleogene extinction event.
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Affiliation(s)
- Matthew J Phillips
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, QLD 4000, Australia
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33
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Manz CL, Chester SGB, Bloch JI, Silcox MT, Sargis EJ. New partial skeletons of Palaeocene Nyctitheriidae and evaluation of proposed euarchontan affinities. Biol Lett 2015; 11:20140911. [PMID: 25589486 DOI: 10.1098/rsbl.2014.0911] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Small-bodied, insectivorous Nyctitheriidae are known in the Palaeogene fossil record almost exclusively from teeth and fragmentary jaws and have been referred to Eulipotyphla (shrews, moles and hedgehogs) based on dental similarities. By contrast, isolated postcrania attributed to the group suggest arboreality and a relationship to Euarchonta (primates, treeshrews and colugos). Cretaceous-Palaeocene adapisoriculid insectivores have also been proposed as early euarchontans based on postcranial similarities. We describe the first known dentally associated nyctitheriid auditory regions and postcrania, and use them to test the proposed relationship to Euarchonta with cladistic analyses of 415 dental, cranial and postcranial characteristics scored for 92 fossil and extant mammalian taxa. Although nyctitheriid postcrania share similarities with euarchontans likely related to arboreality, results of cladistic analyses suggest that nyctitheriids are closely related to Eulipotyphla. Adapisoriculidae is found to be outside of crown Placentalia. These results suggest that similarities in postcranial morphology among nyctitheriids, adapisoriculids and euarchontans represent separate instances of convergence or primitive retention of climbing capabilities.
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Affiliation(s)
- Carly L Manz
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA Department of Geological Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Stephen G B Chester
- Department of Anthropology and Archaeology, City University of New York, Brooklyn College, Brooklyn, NY 11210, USA New York Consortium in Evolutionary Primatology (NYCEP), New York, NY 10024, USA
| | - Jonathan I Bloch
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Mary T Silcox
- Department of Anthropology, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, Canada M1C 1A4
| | - Eric J Sargis
- Department of Anthropology, Yale University, New Haven, CT 06520, USA Division of Vertebrate Paleontology, Yale Peabody Museum of Natural History, New Haven, CT 06520, USA
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34
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Springer MS, Signore AV, Paijmans JLA, Vélez-Juarbe J, Domning DP, Bauer CE, He K, Crerar L, Campos PF, Murphy WJ, Meredith RW, Gatesy J, Willerslev E, MacPhee RDE, Hofreiter M, Campbell KL. Interordinal gene capture, the phylogenetic position of Steller's sea cow based on molecular and morphological data, and the macroevolutionary history of Sirenia. Mol Phylogenet Evol 2015; 91:178-93. [PMID: 26050523 DOI: 10.1016/j.ympev.2015.05.022] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 05/22/2015] [Accepted: 05/28/2015] [Indexed: 01/02/2023]
Abstract
The recently extinct (ca. 1768) Steller's sea cow (Hydrodamalis gigas) was a large, edentulous North Pacific sirenian. The phylogenetic affinities of this taxon to other members of this clade, living and extinct, are uncertain based on previous morphological and molecular studies. We employed hybridization capture methods and second generation sequencing technology to obtain >30kb of exon sequences from 26 nuclear genes for both H. gigas and Dugong dugon. We also obtained complete coding sequences for the tooth-related enamelin (ENAM) gene. Hybridization probes designed using dugong and manatee sequences were both highly effective in retrieving sequences from H. gigas (mean=98.8% coverage), as were more divergent probes for regions of ENAM (99.0% coverage) that were designed exclusively from a proboscidean (African elephant) and a hyracoid (Cape hyrax). New sequences were combined with available sequences for representatives of all other afrotherian orders. We also expanded a previously published morphological matrix for living and fossil Sirenia by adding both new taxa and nine new postcranial characters. Maximum likelihood and parsimony analyses of the molecular data provide robust support for an association of H. gigas and D. dugon to the exclusion of living trichechids (manatees). Parsimony analyses of the morphological data also support the inclusion of H. gigas in Dugongidae with D. dugon and fossil dugongids. Timetree analyses based on calibration density approaches with hard- and soft-bounded constraints suggest that H. gigas and D. dugon diverged in the Oligocene and that crown sirenians last shared a common ancestor in the Eocene. The coding sequence for the ENAM gene in H. gigas does not contain frameshift mutations or stop codons, but there is a transversion mutation (AG to CG) in the acceptor splice site of intron 2. This disruption in the edentulous Steller's sea cow is consistent with previous studies that have documented inactivating mutations in tooth-specific loci of a variety of edentulous and enamelless vertebrates including birds, turtles, aardvarks, pangolins, xenarthrans, and baleen whales. Further, branch-site dN/dS analyses provide evidence for positive selection in ENAM on the stem dugongid branch where extensive tooth reduction occurred, followed by neutral evolution on the Hydrodamalis branch. Finally, we present a synthetic evolutionary tree for living and fossil sirenians showing several key innovations in the history of this clade including character state changes that parallel those that occurred in the evolutionary history of cetaceans.
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Affiliation(s)
- Mark S Springer
- Department of Biology, University of California, Riverside, CA 92521, USA.
| | - Anthony V Signore
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Johanna L A Paijmans
- Department of Biology, The University of York, Wentworth Way, Heslington, York YO10 5DD, UK
| | - Jorge Vélez-Juarbe
- Department of Mammalogy, Natural History Museum of Los Angeles County, Los Angeles, CA 90007, USA
| | - Daryl P Domning
- Laboratory of Evolutionary Biology, Department of Anatomy, Howard University, Washington, DC 20059, USA; Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Cameron E Bauer
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Kai He
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Lorelei Crerar
- Department of Biology, George Mason University, Fairfax, VA 22030, USA
| | - Paula F Campos
- Center for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark; CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Robert W Meredith
- Department of Biology and Molecular Biology, Montclair State University, Montclair, NJ 07043, USA
| | - John Gatesy
- Department of Biology, University of California, Riverside, CA 92521, USA
| | - Eske Willerslev
- Center for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Ross D E MacPhee
- Department of Mammalogy, American Museum of Natural History, New York, NY 10024, USA
| | - Michael Hofreiter
- Department of Biology, The University of York, Wentworth Way, Heslington, York YO10 5DD, UK; Adaptive and Evolutionary Genomics, Institute for Biochemistry and Biology, Faculty of Mathematics and Natural Sciences, University of Potsdam, Karl-Liebknecht-Strasse 24-24, 14476 Potsdam, Germany
| | - Kevin L Campbell
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
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Scotland RW, Steel M. Circumstances in which parsimony but not compatibility will be provably misleading. Syst Biol 2015; 64:492-504. [PMID: 25634097 PMCID: PMC4395848 DOI: 10.1093/sysbio/syv008] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Accepted: 01/23/2015] [Indexed: 11/12/2022] Open
Abstract
Phylogenetic methods typically rely on an appropriate model of how data evolved in order to infer an accurate phylogenetic tree. For molecular data, standard statistical methods have provided an effective strategy for extracting phylogenetic information from aligned sequence data when each site (character) is subject to a common process. However, for other types of data (e.g., morphological data), characters can be too ambiguous, homoplastic, or saturated to develop models that are effective at capturing the underlying process of change. To address this, we examine the properties of a classic but neglected method for inferring splits in an underlying tree, namely, maximum compatibility. By adopting a simple and extreme model in which each character either fits perfectly on some tree, or is entirely random (but it is not known which class any character belongs to) we are able to derive exact and explicit formulae regarding the performance of maximum compatibility. We show that this method is able to identify a set of non-trivial homoplasy-free characters, when the number [Formula: see text] of taxa is large, even when the number of random characters is large. In contrast, we show that a method that makes more uniform use of all the data-maximum parsimony-can provably estimate trees in which none of the original homoplasy-free characters support splits.
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Affiliation(s)
| | - Mike Steel
- Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand
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36
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Buenaventura E, Pape T. Phylogeny of the Peckia-genus group: evolution of male genitalia in the major necrophagous guild of Neotropical flesh flies (Diptera: Sarcophagidae). ORG DIVERS EVOL 2015. [DOI: 10.1007/s13127-015-0203-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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37
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Lanier HC, Knowles LL. Applying species-tree analyses to deep phylogenetic histories: Challenges and potential suggested from a survey of empirical phylogenetic studies. Mol Phylogenet Evol 2015; 83:191-9. [DOI: 10.1016/j.ympev.2014.10.022] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 08/30/2014] [Accepted: 10/29/2014] [Indexed: 10/24/2022]
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38
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Llamas B, Brotherton P, Mitchell KJ, Templeton JEL, Thomson VA, Metcalf JL, Armstrong KN, Kasper M, Richards SM, Camens AB, Lee MSY, Cooper A. Late pleistocene Australian marsupial DNA clarifies the affinities of extinct megafaunal kangaroos and wallabies. Mol Biol Evol 2014; 32:574-84. [PMID: 25526902 DOI: 10.1093/molbev/msu338] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Understanding the evolution of Australia's extinct marsupial megafauna has been hindered by a relatively incomplete fossil record and convergent or highly specialized morphology, which confound phylogenetic analyses. Further, the harsh Australian climate and early date of most megafaunal extinctions (39-52 ka) means that the vast majority of fossil remains are unsuitable for ancient DNA analyses. Here, we apply cross-species DNA capture to fossils from relatively high latitude, high altitude caves in Tasmania. Using low-stringency hybridization and high-throughput sequencing, we were able to retrieve mitochondrial sequences from two extinct megafaunal macropodid species. The two specimens, Simosthenurus occidentalis (giant short-faced kangaroo) and Protemnodon anak (giant wallaby), have been radiocarbon dated to 46-50 and 40-45 ka, respectively. This is significantly older than any Australian fossil that has previously yielded DNA sequence information. Processing the raw sequence data from these samples posed a bioinformatic challenge due to the poor preservation of DNA. We explored several approaches in order to maximize the signal-to-noise ratio in retained sequencing reads. Our findings demonstrate the critical importance of adopting stringent processing criteria when distant outgroups are used as references for mapping highly fragmented DNA. Based on the most stringent nucleotide data sets (879 bp for S. occidentalis and 2,383 bp for P. anak), total-evidence phylogenetic analyses confirm that macropodids consist of three primary lineages: Sthenurines such as Simosthenurus (extinct short-faced kangaroos), the macropodines (all other wallabies and kangaroos), and the enigmatic living banded hare-wallaby Lagostrophus fasciatus (Lagostrophinae). Protemnodon emerges as a close relative of Macropus (large living kangaroos), a position not supported by recent morphological phylogenetic analyses.
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Affiliation(s)
- Bastien Llamas
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, SA, Australia
| | - Paul Brotherton
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, SA, Australia
| | - Kieren J Mitchell
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, SA, Australia
| | - Jennifer E L Templeton
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, SA, Australia School of Biological Sciences, Flinders University, SA, Australia
| | - Vicki A Thomson
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, SA, Australia
| | - Jessica L Metcalf
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, SA, Australia
| | - Kyle N Armstrong
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, SA, Australia
| | - Marta Kasper
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, SA, Australia
| | - Stephen M Richards
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, SA, Australia
| | - Aaron B Camens
- School of Biological Sciences, Flinders University, SA, Australia School of Earth and Environmental Sciences, University of Adelaide, SA, Australia
| | - Michael S Y Lee
- School of Earth and Environmental Sciences, University of Adelaide, SA, Australia Earth Sciences Section, The South Australian Museum, SA, Australia
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, SA, Australia
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39
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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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40
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Pattinson DJ, Thompson RS, Piotrowski AK, Asher RJ. Phylogeny, Paleontology, and Primates: Do Incomplete Fossils Bias the Tree of Life? Syst Biol 2014; 64:169-86. [DOI: 10.1093/sysbio/syu077] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- David J. Pattinson
- Department of Zoology, Downing Street, Cambridge, CB2 3EJ; 2Division of Ecology and Evolution, Imperial College London, South Kensington Campus, London, SW7 2AZ; 3Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD; and 4Department of Physics, Cavendish Laboratory, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
- Department of Zoology, Downing Street, Cambridge, CB2 3EJ; 2Division of Ecology and Evolution, Imperial College London, South Kensington Campus, London, SW7 2AZ; 3Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD; and 4Department of Physics, Cavendish Laboratory, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
- Department of Zoology, Downing Street, Cambridge, CB2 3EJ; 2Division of Ecology and Evolution, Imperial College London, South Kensington Campus, London, SW7 2AZ; 3Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD; and 4Department of Physics, Cavendish Laboratory, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Richard S. Thompson
- Department of Zoology, Downing Street, Cambridge, CB2 3EJ; 2Division of Ecology and Evolution, Imperial College London, South Kensington Campus, London, SW7 2AZ; 3Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD; and 4Department of Physics, Cavendish Laboratory, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Aleks K. Piotrowski
- Department of Zoology, Downing Street, Cambridge, CB2 3EJ; 2Division of Ecology and Evolution, Imperial College London, South Kensington Campus, London, SW7 2AZ; 3Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD; and 4Department of Physics, Cavendish Laboratory, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Robert J. Asher
- Department of Zoology, Downing Street, Cambridge, CB2 3EJ; 2Division of Ecology and Evolution, Imperial College London, South Kensington Campus, London, SW7 2AZ; 3Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD; and 4Department of Physics, Cavendish Laboratory, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
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41
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The common marmoset genome provides insight into primate biology and evolution. Nat Genet 2014; 46:850-7. [PMID: 25038751 PMCID: PMC4138798 DOI: 10.1038/ng.3042] [Citation(s) in RCA: 162] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 06/27/2014] [Indexed: 02/06/2023]
Abstract
A first analysis of the genome sequence of the common marmoset (Callithrix jacchus), assembled using traditional Sanger methods and Ensembl annotation, has permitted genomic comparison with apes and that old world monkeys and the identification of specific molecular features a rapid reproductive capacity partly due to may contribute to the unique biology of diminutive The common marmoset has prevalence of this dizygotic primate. twins. Remarkably, these twins share placental circulation and exchange hematopoietic stem cells in utero, resulting in adults that are hematopoietic chimeras. We observed positive selection or non-synonymous substitutions for genes encoding growth hormone / insulin-like growth factor (growth pathways), respiratory complex I (metabolic pathways), immunobiology, and proteases (reproductive and immunity pathways). In addition, both protein-coding and microRNA genes related to reproduction exhibit rapid sequence evolution. This New World monkey genome sequence enables significantly increased power for comparative analyses among available primate genomes and facilitates biomedical research application.
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Dávalos LM, Velazco PM, Warsi OM, Smits PD, Simmons NB. Integrating Incomplete Fossils by Isolating Conflicting Signal in Saturated and Non-Independent Morphological Characters. Syst Biol 2014; 63:582-600. [DOI: 10.1093/sysbio/syu022] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Korrodi-Gregório L, Margarida Lopes A, Esteves SLC, Afonso S, Lemos de Matos A, Lissovsky AA, da Cruz e Silva OAB, da Cruz e Silva EF, Esteves PJ, Fardilha M. An intriguing shift occurs in the novel protein phosphatase 1 binding partner, TCTEX1D4: evidence of positive selection in a pika model. PLoS One 2013; 8:e77236. [PMID: 24130861 PMCID: PMC3795061 DOI: 10.1371/journal.pone.0077236] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 09/01/2013] [Indexed: 12/21/2022] Open
Abstract
T-complex testis expressed protein 1 domain containing 4 (TCTEX1D4) contains the canonical phosphoprotein phosphatase 1 (PPP1) binding motif, composed by the amino acid sequence RVSF. We identified and validated the binding of TCTEX1D4 to PPP1 and demonstrated that indeed this protein is a novel PPP1 interacting protein. Analyses of twenty-one mammalian species available in public databases and seven Lagomorpha sequences obtained in this work showed that the PPP1 binding motif 90RVSF93 is present in all of them and is flanked by a palindromic sequence, PLGS, except in three species of pikas (Ochotona princeps, O. dauurica and O. pusilla). Furthermore, for the Ochotona species an extra glycosylation site, motif 96NLS98, and the loss of the palindromic sequence were observed. Comparison with other lagomorphs suggests that this event happened before the Ochotona radiation. The dN/dS for the sequence region comprising the PPP1 binding motif and the flanking palindrome highly supports the hypothesis that for Ochotona species this region has been evolving under positive selection. In addition, mutational screening shows that the ability of pikas TCTEX1D4 to bind to PPP1 is maintained, although the PPP1 binding motif is disrupted, and the N- and C-terminal surrounding residues are also abrogated. These observations suggest pika as an ideal model to study novel PPP1 complexes regulatory mechanisms.
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Affiliation(s)
- Luís Korrodi-Gregório
- Laboratory of Signal Transduction, Centre for Cell Biology, Health Sciences Department and Biology Department, University of Aveiro, Aveiro, Portugal
| | - Ana Margarida Lopes
- CIBIO/UP, Centro de Investigação em Biodiversidade e Recursos Genéticos/Universidade do Porto, InBio, Laboratório Associado, Vairão, Portugal
- Departamento de Zoologia e Antropologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- INSERM, Institut National de la Santé et de la Recherche Médicale, Unit 892, Université de Nantes, Nantes, France
| | - Sara L. C. Esteves
- Laboratory of Signal Transduction, Centre for Cell Biology, Health Sciences Department and Biology Department, University of Aveiro, Aveiro, Portugal
| | - Sandra Afonso
- CIBIO/UP, Centro de Investigação em Biodiversidade e Recursos Genéticos/Universidade do Porto, InBio, Laboratório Associado, Vairão, Portugal
| | - Ana Lemos de Matos
- CIBIO/UP, Centro de Investigação em Biodiversidade e Recursos Genéticos/Universidade do Porto, InBio, Laboratório Associado, Vairão, Portugal
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States of America
| | | | - Odete A. B. da Cruz e Silva
- Laboratory of Neurosciences, Centre for Cell Biology, Health Sciences Department and Biology Department, University of Aveiro, Aveiro, Portugal
| | - Edgar F. da Cruz e Silva
- Laboratory of Signal Transduction, Centre for Cell Biology, Health Sciences Department and Biology Department, University of Aveiro, Aveiro, Portugal
| | - Pedro José Esteves
- CIBIO/UP, Centro de Investigação em Biodiversidade e Recursos Genéticos/Universidade do Porto, InBio, Laboratório Associado, Vairão, Portugal
- CESPU, Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde, Gandra PRD, Portugal
- * E-mail: (MF); (PJE)
| | - Margarida Fardilha
- Laboratory of Signal Transduction, Centre for Cell Biology, Health Sciences Department and Biology Department, University of Aveiro, Aveiro, Portugal
- * E-mail: (MF); (PJE)
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Springer MS, Meredith RW, Teeling EC, Murphy WJ. Technical comment on "The placental mammal ancestor and the post-K-Pg radiation of placentals". Science 2013; 341:613. [PMID: 23929967 DOI: 10.1126/science.1238025] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
O'Leary et al. (Research Article, 8 February 2013, p. 662) examined mammalian relationships and divergence times and concluded that a single placental ancestor crossed the Cretaceous-Paleogene (K-Pg) boundary. This conclusion relies on phylogenetic analyses that fail to discriminate between homology and homoplasy and further implies virus-like rates of nucleotide substitution in early Paleocene placentals.
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Affiliation(s)
- Mark S Springer
- Department of Biology, University of California, Riverside, CA 92521, USA.
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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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Romiguier J, Ranwez V, Delsuc F, Galtier N, Douzery EJP. Less is more in mammalian phylogenomics: AT-rich genes minimize tree conflicts and unravel the root of placental mammals. Mol Biol Evol 2013; 30:2134-44. [PMID: 23813978 DOI: 10.1093/molbev/mst116] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Despite the rapid increase of size in phylogenomic data sets, a number of important nodes on animal phylogeny are still unresolved. Among these, the rooting of the placental mammal tree is still a controversial issue. One difficulty lies in the pervasive phylogenetic conflicts among genes, with each one telling its own story, which may be reliable or not. Here, we identified a simple criterion, that is, the GC content, which substantially helps in determining which gene trees best reflect the species tree. We assessed the ability of 13,111 coding sequence alignments to correctly reconstruct the placental phylogeny. We found that GC-rich genes induced a higher amount of conflict among gene trees and performed worse than AT-rich genes in retrieving well-supported, consensual nodes on the placental tree. We interpret this GC effect mainly as a consequence of genome-wide variations in recombination rate. Indeed, recombination is known to drive GC-content evolution through GC-biased gene conversion and might be problematic for phylogenetic reconstruction, for instance, in an incomplete lineage sorting context. When we focused on the AT-richest fraction of the data set, the resolution level of the placental phylogeny was greatly increased, and a strong support was obtained in favor of an Afrotheria rooting, that is, Afrotheria as the sister group of all other placentals. We show that in mammals most conflicts among gene trees, which have so far hampered the resolution of the placental tree, are concentrated in the GC-rich regions of the genome. We argue that the GC content-because it is a reliable indicator of the long-term recombination rate-is an informative criterion that could help in identifying the most reliable molecular markers for species tree inference.
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Affiliation(s)
- Jonathan Romiguier
- CNRS, Université Montpellier, Institut des Sciences de l'Evolution, Montpellier, France.
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Janies DA, Studer J, Handelman SK, Linchangco G. A comparison of supermatrix and supertree methods for multilocus phylogenetics using organismal datasets. Cladistics 2013; 29:560-566. [DOI: 10.1111/cla.12014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/31/2012] [Indexed: 11/28/2022] Open
Affiliation(s)
- Daniel A. Janies
- Department of Bioinformatics and Genomics; College of Computing and Informatics; University of North Carolina at Charlotte; 9201 University City Blvd; Charlotte; NC; 28223; USA
| | - Jonathon Studer
- Case Western Reserve University School of Law; 11075 East Boulevard; Cleveland; OH; 44106; USA
| | - Samuel K. Handelman
- Department of Pharmacology; College of Medicine; The Ohio State University; 333 W. 10th Ave.; Columbus; OH; 43210; USA
| | - Gregorio Linchangco
- Department of Bioinformatics and Genomics; College of Computing and Informatics; University of North Carolina at Charlotte; 9201 University City Blvd; Charlotte; NC; 28223; USA
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Sansom RS, Wills MA. Fossilization causes organisms to appear erroneously primitive by distorting evolutionary trees. Sci Rep 2013; 3:2545. [PMID: 23985991 PMCID: PMC3756334 DOI: 10.1038/srep02545] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 08/12/2013] [Indexed: 11/29/2022] Open
Abstract
Fossils are vital for calibrating rates of molecular and morphological change through geological time, and are the only direct source of data documenting macroevolutionary transitions. Many evolutionary studies therefore require the robust phylogenetic placement of extinct organisms. Here, we demonstrate that the inevitable bias of the fossil record to preserve just hard, skeletal morphology systemically distorts phylogeny. Removal of soft part characters from 78 modern vertebrate and invertebrate morphological datasets resulted in significant changes to phylogenetic signal; it caused individual taxa to drift from their original position, predominately downward toward the root of their respective trees. This last bias could systematically inflate evolutionary rates inferred from molecular data because first fossil occurrences will not be recognised as such. Stem-ward slippage, whereby fundamental taphonomic biases cause fossils to be interpreted as erroneously primitive, is therefore a ubiquitous problem for all biologists attempting to infer macroevolutionary rates or sequences.
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Affiliation(s)
- Robert S. Sansom
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Matthew A. Wills
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
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Lebedev VS, Bannikova AA, Pagès M, Pisano J, Michaux JR, Shenbrot GI. Molecular phylogeny and systematics of Dipodoidea: a test of morphology-based hypotheses. ZOOL SCR 2012. [DOI: 10.1111/zsc.12002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Dávalos LM, Cirranello AL, Geisler JH, Simmons NB. Understanding phylogenetic incongruence: lessons from phyllostomid bats. Biol Rev Camb Philos Soc 2012; 87:991-1024. [PMID: 22891620 PMCID: PMC3573643 DOI: 10.1111/j.1469-185x.2012.00240.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 07/04/2012] [Accepted: 07/18/2012] [Indexed: 12/25/2022]
Abstract
All characters and trait systems in an organism share a common evolutionary history that can be estimated using phylogenetic methods. However, differential rates of change and the evolutionary mechanisms driving those rates result in pervasive phylogenetic conflict. These drivers need to be uncovered because mismatches between evolutionary processes and phylogenetic models can lead to high confidence in incorrect hypotheses. Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species. For more than a decade, evolutionary relationships among members of the New World bat family Phyllostomidae inferred from morphological and molecular data have been in conflict. Here, we develop and apply methods to minimize systematic biases, uncover the biological mechanisms underlying phylogenetic conflict, and outline data requirements for future phylogenomic and morphological data collection. We introduce new morphological data for phyllostomids and outgroups and expand previous molecular analyses to eliminate methodological sources of phylogenetic conflict such as taxonomic sampling, sparse character sampling, or use of different algorithms to estimate the phylogeny. We also evaluate the impact of biological sources of conflict: saturation in morphological changes and molecular substitutions, and other processes that result in incongruent trees, including convergent morphological and molecular evolution. Methodological sources of incongruence play some role in generating phylogenetic conflict, and are relatively easy to eliminate by matching taxa, collecting more characters, and applying the same algorithms to optimize phylogeny. The evolutionary patterns uncovered are consistent with multiple biological sources of conflict, including saturation in morphological and molecular changes, adaptive morphological convergence among nectar-feeding lineages, and incongruent gene trees. Applying methods to account for nucleotide sequence saturation reduces, but does not completely eliminate, phylogenetic conflict. We ruled out paralogy, lateral gene transfer, and poor taxon sampling and outgroup choices among the processes leading to incongruent gene trees in phyllostomid bats. Uncovering and countering the possible effects of introgression and lineage sorting of ancestral polymorphism on gene trees will require great leaps in genomic and allelic sequencing in this species-rich mammalian family. We also found evidence for adaptive molecular evolution leading to convergence in mitochondrial proteins among nectar-feeding lineages. In conclusion, the biological processes that generate phylogenetic conflict are ubiquitous, and overcoming incongruence requires better models and more data than have been collected even in well-studied organisms such as phyllostomid bats.
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Affiliation(s)
- Liliana M Dávalos
- Department of Ecology and Evolution, and Consortium for Inter-Disciplinary Environmental Research, State University of New York at Stony BrookStony Brook, NY 11794, USA
| | - Andrea L Cirranello
- Division of Vertebrate Zoology (Mammalogy), American Museum of Natural HistoryNew York, NY 10024, USA
- Department of Anatomical Sciences, State University of New York at Stony BrookStony Brook, NY 11794, USA
| | - Jonathan H Geisler
- Department of Anatomy, New York College of Osteopathic MedicineOld Westbury, NY 11568, USA
| | - Nancy B Simmons
- Division of Vertebrate Zoology (Mammalogy), American Museum of Natural HistoryNew York, NY 10024, USA
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