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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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2
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Gu T, Hu J, Yu L. Evolution and conservation genetics of pangolins. Integr Zool 2024; 19:426-441. [PMID: 38146613 DOI: 10.1111/1749-4877.12796] [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] [Indexed: 12/27/2023]
Abstract
Pangolins (Pholidota, Manidae) are classified as an evolutionarily distinct and globally endangered mammal due to their unique morphology (nail-like scales and a myrmecophagous diet) and being the victim of heavy poaching and worldwide trafficking. As such, pangolins serve as a textbook example for studying the special phenotypic evolutionary adaptations and conservation genetics of an endangered species. Recent years have demonstrated significant advancements in the fields of molecular genetics and genomics, which have translated to a series of important research achievements and breakthroughs concerning the evolution and conservation genetics of pangolins. This review comprehensively presents the hitherto advances in phylogeny, adaptive evolution, conservation genetics, and conservation genomics that are related to pangolins, which will provide an ample understanding of their diversity, molecular adaptation mechanisms, and evolutionary potentials. In addition, we highlight the priority of investigating species/population diversity among pangolins and suggest several avenues of research that are highly relevant for future pangolin conservation.
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Affiliation(s)
- Tongtong Gu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Jingyang Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
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3
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Lavrov DV, Diaz MC, Maldonado M, Morrow CC, Perez T, Pomponi SA, Thacker RW. Phylomitogenomics bolsters the high-level classification of Demospongiae (phylum Porifera). PLoS One 2023; 18:e0287281. [PMID: 38048310 PMCID: PMC10695373 DOI: 10.1371/journal.pone.0287281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/15/2023] [Indexed: 12/06/2023] Open
Abstract
Class Demospongiae is the largest in the phylum Porifera (Sponges) and encompasses nearly 8,000 accepted species in three subclasses: Keratosa, Verongimorpha, and Heteroscleromorpha. Subclass Heteroscleromorpha contains ∼90% of demosponge species and is subdivided into 17 orders. The higher level classification of demosponges underwent major revision as the result of nearly three decades of molecular studies. However, because most of the previous molecular work only utilized partial data from a small number of nuclear and mitochondrial (mt) genes, this classification scheme needs to be tested by larger datasets. Here we compiled a mt dataset for 136 demosponge species-including 64 complete or nearly complete and six partial mt-genome sequences determined or assembled for this study-and used it to test phylogenetic relationships among Demospongiae in general and Heteroscleromorpha in particular. We also investigated the phylogenetic position of Myceliospongia araneosa, a highly unusual demosponge without spicules and spongin fibers, currently classified as Demospongiae incertae sedis, for which molecular data were not available. Our results support the previously inferred sister-group relationship between Heteroscleromorpha and Keratosa + Verongimorpha and suggest five main clades within Heteroscleromorpha: Clade C0 composed of order Haplosclerida; Clade C1 composed of Scopalinida, Sphaerocladina, and Spongillida; Clade C2 composed of Axinellida, Biemnida, Bubarida; Clade C3 composed of Tetractinellida; and Clade C4 composed of Agelasida, Clionaida, Desmacellida, Merliida, Suberitida, Poecilosclerida, Polymastiida, and Tethyida. The inferred relationships among these clades were (C0(C1(C2(C3+C4)))). Analysis of molecular data from M. araneosa placed it in the C3 clade as a sister taxon to the highly skeletonized tetractinellids Microscleroderma sp. and Leiodermatium sp. Molecular clock analysis dated divergences among the major clades in Heteroscleromorpha from the Cambrian to the Early Silurian, the origins of most heteroscleromorph orders in the middle Paleozoic, and the most basal splits within these orders around the Paleozoic to Mesozoic transition. Overall, the results of this study are mostly congruent with the accepted classification of Heteroscleromorpha, but add temporal perspective and new resolution to phylogenetic relationships within this subclass.
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Affiliation(s)
- Dennis V. Lavrov
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, United States of America
| | - Maria C. Diaz
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, Florida, United States of America
- Museo Marino de Margarita, Boca de Río, Nueva Esparta, Venezuela
| | - Manuel Maldonado
- Department of Marine Ecology, Centro de Estudios Avanzados de Blanes (CEAB-CSIC), Girona, Spain
| | - Christine C. Morrow
- Zoology Department, School of Natural Sciences & Ryan Institute, NUI Galway, University Road, Galway, Ireland
- Ireland and Queen’s University Marine Laboratory, Portaferry, Northern Ireland
| | - Thierry Perez
- Institut Méditerranéen de la Biodiversité et d’Ecologie marine et continentale (IMBE), CNRS, Aix-Marseille Université, IRD, Avignon Université City, Provence, France
| | - Shirley A. Pomponi
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, Florida, United States of America
| | - Robert W. Thacker
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, United States of America
- Smithsonian Tropical Research Institute, Balboa, Panama City, Republic of Panama
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Mora JM, Ruedas LA. Updated list of the mammals of Costa Rica, with notes on recent taxonomic changes. Zootaxa 2023; 5357:451-501. [PMID: 38220635 DOI: 10.11646/zootaxa.5357.4.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Indexed: 01/16/2024]
Abstract
Although Costa Rica occupies a mere 0.03% of the Earths land area, it nevertheless has recorded within its borders approximately 5% of the global diversity of mammals, thus making it one of the worlds megadiverse countries. Over the past ten years, 22 species have been added to the countrys inventory, bringing the total number known as here documented to 271; Chiroptera account for ten of these, having grown to 124 from 114; rodents have increased by eight species, from 47 to 55, with the caveat that we include three invasive species of Muridae that have gone feral. In contrast, the number of orders has decreased by one, by Artiodactyla incorporating the former Cetacea. Notes are provided for all taxonomic novelties since the last update. Since the first taxonomic compendium of the mammals of Costa Rica in 1869, the number of known species has grown by approximately 1.22 species year-1 (R2 = 0.96). Since 1983 however, this growth rate has been 1.64 species year-1 (R2 = 0.98). Despite this strong growth, an asymptote in the number of known species has not been reached. Conservation remains a primary need: over 60% of the countrys mammal species show population trends that are decreasing (13%), unknown (37%), or not assessed (11%), based on IUCN criteria. These analyses suggest that much remains to be known regarding the number of mammal species living in Costa Rica, but also that much more remains to be done to safeguard Costa Ricas exceptional biodiversity heritage.
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Affiliation(s)
- Jos Manuel Mora
- Department of Biology and Museum of Vertebrate Biology; Portland State University; Portland; Oregon 97207-0751; USA; Carrera de Gestin Ecoturstica; Sede Central; Universidad Tcnica Nacional; Alajuela; Costa Rica.
| | - Luis A Ruedas
- Department of Biology and Museum of Vertebrate Biology; Portland State University; Portland; Oregon 97207-0751; USA.
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Setiaji A, Lestari DA, Pandupuspitasari NS, Agusetyaningsih I, Khan FA. Genetic characteristics of complete mtDNA genome sequence of Indonesian local rabbit (Oryctolagus cuniculus). J Genet Eng Biotechnol 2023; 21:96. [PMID: 37812313 PMCID: PMC10562326 DOI: 10.1186/s43141-023-00546-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/20/2023] [Indexed: 10/10/2023]
Abstract
BACKGROUND Indonesian local rabbit (Oryctolagus cuniculus) is a local breed in Indonesia. We reveal the mitochondrial genome sequence of the Indonesian local Rabbit for the first time. A better understanding of the mechanisms underlying these beneficial aspects of local breeds over imported ones requires detailed genetic investigations, of which mtDNA genome sequencing is of particular importance. Such an investigation will solve the major issues of misidentification with Javanese hares (Lepus nigricollis) and maternal lineage. In addition, this information will guide better statistics on the Indonesian local rabbit breed population and strategies for its conservation and breeding plans. This study aimed to identify and explore the characteristics of the mtDNA genomes of Indonesian local rabbits. RESULT This study observed that the length of the mtDNA genome is 17,469 bp, consisting of two ribosomal RNA (12S rRNA, 16S rRNA), 22 transfer RNA genes (trnR, trnG, trnK, trnD, trnS, trnY, trnC, trnN, trnA, trnW, trnM, trnQ, trnl, trnL, trnV, trnF, trnP, trnT, trnE, trnL, trnS, trnH), 13 protein-coding genes (PCGs) (ND4l, ND3, COX3, ATP6, ATP8, COX2, COX1, ND2, ND1, CYTB, ND6, ND5, ND4), a replication origin, and a noncoding control region (D-loop). CONCLUSIONS mtDNA genome of Indonesian local rabbit was the longest and had the most extended D-loop sequence among the other references of Oryctolagus cuniculus. Other specific differences were also found in the percentage of nucleotides and variation in most of the PCGs when they were aligned with Oryctolagus cuniculus references from GenBank. Indonesian local Rabbits strongly suspected brought from Europe during the colonial period in Indonesia.
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Affiliation(s)
- Asep Setiaji
- Department of Animal Science, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, 50275, Indonesia
| | - Dela Ayu Lestari
- Department of Animal Science, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, 50275, Indonesia.
| | | | - Ikania Agusetyaningsih
- Department of Animal Science, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, 50275, Indonesia
| | - Faheem Ahmed Khan
- Research Center for Animal Husbandry, National Research and Innovation Agency (BRIN), South Tangerang, 15314, Indonesia
- Faculty of Science and Technology, University of Central Punjab, Lahore, 54000, Pakistan
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Gu TT, Wu H, Yang F, Gaubert P, Heighton SP, Fu Y, Liu K, Luo SJ, Zhang HR, Hu JY, Yu L. Genomic analysis reveals a cryptic pangolin species. Proc Natl Acad Sci U S A 2023; 120:e2304096120. [PMID: 37748052 PMCID: PMC10556634 DOI: 10.1073/pnas.2304096120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 07/26/2023] [Indexed: 09/27/2023] Open
Abstract
Eight extant species of pangolins are currently recognized. Recent studies found that two mitochondrial haplotypes identified in confiscations in Hong Kong could not be assigned to any known pangolin species, implying the existence of a species. Here, we report that two additional mitochondrial haplotypes identified in independent confiscations from Yunnan align with the putative species haplotypes supporting the existence of this mysterious species/population. To verify the new species scenario we performed a comprehensive analysis of scale characteristics and 138 whole genomes representing all recognized pangolin species and the cryptic new species, 98 of which were generated here. Our morphometric results clearly attributed this cryptic species to Asian pangolins (Manis sp.) and the genomic data provide robust and compelling evidence that it is a pangolin species distinct from those recognized previously, which separated from the Philippine pangolin and Malayan pangolin over 5 Mya. Our study provides a solid genomic basis for its formal recognition as the ninth pangolin species or the fifth Asian one, supporting a new taxonomic classification of pangolins. The effects of glacial climate changes and recent anthropogenic activities driven by illegal trade are inferred to have caused its population decline with the genomic signatures showing low genetic diversity, a high level of inbreeding, and high genetic load. Our finding greatly expands current knowledge of pangolin diversity and evolution and has vital implications for conservation efforts to prevent the extinction of this enigmatic and endangered species from the wild.
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Affiliation(s)
- Tong-Tong Gu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming650500, China
| | - Hong Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming650500, China
| | - Feng Yang
- Kadoorie Farm and Botanic Garden, Tai Po, Hong Kong Special Administrative Region999077, China
| | - Philippe Gaubert
- Laboratoire Evolution et Diversité Biologique, Université Toulouse III–Paul Sabatier, 31062Toulouse Cedex 9, France
- Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Porto4450-208, Portugal
| | - Sean P. Heighton
- Laboratoire Evolution et Diversité Biologique, Université Toulouse III–Paul Sabatier, 31062Toulouse Cedex 9, France
| | - Yeyizhou Fu
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing100871, China
| | - Ke Liu
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing100871, China
| | - Shu-Jin Luo
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing100871, China
| | - Hua-Rong Zhang
- Kadoorie Farm and Botanic Garden, Tai Po, Hong Kong Special Administrative Region999077, China
| | - Jing-Yang Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming650500, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming650500, China
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Ruiz-Puerta EJ, Keighley X, Desjardins SPA, Gotfredsen AB, Pan SE, Star B, Boessenkool S, Barrett JH, McCarthy ML, Andersen LW, Born EW, Howse LR, Szpak P, Pálsson S, Malmquist HJ, Rufolo S, Jordan PD, Olsen MT. Holocene deglaciation drove rapid genetic diversification of Atlantic walrus. Proc Biol Sci 2023; 290:20231349. [PMID: 37752842 PMCID: PMC10523089 DOI: 10.1098/rspb.2023.1349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 08/27/2023] [Indexed: 09/28/2023] Open
Abstract
Rapid global warming is severely impacting Arctic ecosystems and is predicted to transform the abundance, distribution and genetic diversity of Arctic species, though these linkages are poorly understood. We address this gap in knowledge using palaeogenomics to examine how earlier periods of global warming influenced the genetic diversity of Atlantic walrus (Odobenus rosmarus rosmarus), a species closely associated with sea ice and shallow-water habitats. We analysed 82 ancient and historical Atlantic walrus mitochondrial genomes (mitogenomes), including now-extinct populations in Iceland and the Canadian Maritimes, to reconstruct the Atlantic walrus' response to Arctic deglaciation. Our results demonstrate that the phylogeography and genetic diversity of Atlantic walrus populations was initially shaped by the last glacial maximum (LGM), surviving in distinct glacial refugia, and subsequently expanding rapidly in multiple migration waves during the late Pleistocene and early Holocene. The timing of diversification and establishment of distinct populations corresponds closely with the chronology of the glacial retreat, pointing to a strong link between walrus phylogeography and sea ice. Our results indicate that accelerated ice loss in the modern Arctic may trigger further dispersal events, likely increasing the connectivity of northern stocks while isolating more southerly stocks putatively caught in small pockets of suitable habitat.
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Affiliation(s)
- Emily J. Ruiz-Puerta
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5-7, 1353 Copenhagen Kobenhavn, Denmark
- Arctic Centre & Groningen Institute of Archaeology, Faculty of Arts, University of Groningen, PO Box 716, 9700 AS Groningen, The Netherlands
| | - Xénia Keighley
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5-7, 1353 Copenhagen Kobenhavn, Denmark
- The Bureau of Meteorology, The Treasury Building, Parkes Place West, Parkes, Australian Capital Territory 2600, Australia
| | - Sean P. A. Desjardins
- Arctic Centre & Groningen Institute of Archaeology, Faculty of Arts, University of Groningen, PO Box 716, 9700 AS Groningen, The Netherlands
- Palaeobiology Section, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, Ontario, Canada K1P 6P4
| | - Anne Birgitte Gotfredsen
- Section for GeoGenetics, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen Kobenhavn, Denmark
| | - Shyong En Pan
- Palaeobiology Section, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, Ontario, Canada K1P 6P4
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Blindernveien 31, 0371 Oslo, Norway
| | - Sanne Boessenkool
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Blindernveien 31, 0371 Oslo, Norway
| | - James H. Barrett
- Department of Archaeology and Cultural History, NTNU University Museum, 7491 Trondheim, Norway
- McDonald Institute for Archaeological Research, Department of Archaeology, University of Cambridge, Downing Street, Cambridge CB2 3ER, UK
| | - Morgan L. McCarthy
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5-7, 1353 Copenhagen Kobenhavn, Denmark
| | - Liselotte W. Andersen
- Department of Ecoscience, Aarhus University, CF Møllers Allé 4-8, build. 1110, 8000 Aarhus C, Denmark
| | - Erik W. Born
- Greenland Institute of Natural Resources, PO Box 570, 3900 Nuuk, Greenland
| | - Lesley R. Howse
- Archaeology Centre, University of Toronto, 19 Ursula Franklin Street, Toronto, Ontario Canada M5S 2S2
| | - Paul Szpak
- Department of Anthropology, Trent University, 1600 West Bank Drive, Peterborough, Ontario, Canada K9L 0G2
| | - Snæbjörn Pálsson
- Faculty of Life and Environmental Sciences, University of Iceland, Askja, Sturlugata 7, 101 Reykjavik, Iceland
| | - Hilmar J. Malmquist
- Icelandic Museum of Natural History, Suðurlandsbraut 24, 108 Reykjavík, Iceland
| | - Scott Rufolo
- Palaeobiology Section, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, Ontario, Canada K1P 6P4
| | - Peter D. Jordan
- Department of Archaeology and Ancient History, Lund University, Helgonavägen 3, 223 62 Lund, Sweden
- Global Station for Indigenous Studies and Cultural Diversity (GSI), GI-CoRE, HokkaidoUniversity, Japan
| | - Morten Tange Olsen
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5-7, 1353 Copenhagen Kobenhavn, Denmark
- Natural History Museum of Denmark, University of Copenhagen, Denmark
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8
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Falcon F, Tanaka EM, Rodriguez-Terrones D. Transposon waves at the water-to-land transition. Curr Opin Genet Dev 2023; 81:102059. [PMID: 37343338 DOI: 10.1016/j.gde.2023.102059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/02/2023] [Accepted: 05/15/2023] [Indexed: 06/23/2023]
Abstract
The major transitions in vertebrate evolution are associated with significant genomic reorganizations. In contrast to the evolutionary processes that occurred at the origin of vertebrates or prior to the radiation of teleost fishes, no whole-genome duplication events occurred during the water-to-land transition, and it remains an open question how did genome dynamics contribute to this prominent evolutionary event. Indeed, the recent sequencing of sarcopterygian and amphibian genomes has revealed that the extant lineages immediately preceding and succeeding this transition harbor an exceptional number of transposable elements and it is tempting to speculate that these sequences might have catalyzed the adaptations that enabled vertebrates to venture into land. Here, we review the genome dynamics associated with the major transitions in vertebrate evolution and discuss how the highly repetitive genomic landscapes revealed by recent efforts to characterize the genomes of amphibians and sarcopterygians argue for turbulent genome dynamics occurring before the water-to-land transition and possibly enabling it.
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Affiliation(s)
- Francisco Falcon
- Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter, 1030, Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria. https://twitter.com/@FcoJFalcon
| | - Elly M Tanaka
- Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter, 1030, Vienna, Austria.
| | - Diego Rodriguez-Terrones
- Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter, 1030, Vienna, Austria.
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9
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Wilson D, Rogers JD. Evaluating Compression-Based Phylogeny Estimation in the Presence of Incomplete Lineage Sorting. J Comput Biol 2023; 30:250-260. [PMID: 36848254 DOI: 10.1089/cmb.2022.0197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
This study assesses characteristics of the normalized compression distance (NCD) technique for building phylogenetic trees from molecular data. We examined results from a mammalian biological data set as well as a collection of simulated data with varying levels of incomplete lineage sorting. The implementation of NCD we analyze is a concatenation-based, distance-based, alignment-free, and model-free phylogeny estimation method, which takes concatenated unaligned sequence data as input and outputs a matrix of distances. We compare the NCD phylogeny estimation method with various other methods, including coalescent- and concatenation-based methods.
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Affiliation(s)
- Deangelo Wilson
- School of Computing, DePaul University, Chicago, Illinois, USA
| | - John D Rogers
- School of Computing, DePaul University, Chicago, Illinois, USA
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10
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Janiak MC, Silva FE, Beck RMD, de Vries D, Kuderna LFK, Torosin NS, Melin AD, Marquès-Bonet T, Goodhead IB, Messias M, da Silva MNF, Sampaio I, Farias IP, Rossi R, de Melo FR, Valsecchi J, Hrbek T, Boubli JP. 205 newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates. Mol Ecol 2022; 31:3888-3902. [PMID: 35638312 PMCID: PMC9546496 DOI: 10.1111/mec.16554] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/06/2022] [Accepted: 05/20/2022] [Indexed: 12/02/2022]
Abstract
Mitochondrial DNA remains a cornerstone for molecular ecology, especially for study species from which high‐quality tissue samples cannot be easily obtained. Methods using mitochondrial markers are usually reliant on reference databases, but these are often incomplete. Furthermore, available mitochondrial genomes often lack crucial metadata, such as sampling location, limiting their utility for many analyses. Here, we assembled 205 new mitochondrial genomes for platyrrhine primates, most from the Amazon and with known sampling locations. We present a dated mitogenomic phylogeny based on these samples along with additional published platyrrhine mitogenomes, and use this to assess support for the long‐standing riverine barrier hypothesis (RBH), which proposes that river formation was a major driver of speciation in Amazonian primates. Along the Amazon, Negro, and Madeira rivers, we found mixed support for the RBH. While we identified divergences that coincide with a river barrier, only some occur synchronously and also overlap with the proposed dates of river formation. The most compelling evidence is for the Amazon river potentially driving speciation within bearded saki monkeys (Chiropotes spp.) and within the smallest extant platyrrhines, the marmosets and tamarins. However, we also found that even large rivers do not appear to be barriers for some primates, including howler monkeys (Alouatta spp.), uakaris (Cacajao spp.), sakis (Pithecia spp.), and robust capuchins (Sapajus spp.). Our results support a more nuanced, clade‐specific effect of riverine barriers and suggest that other evolutionary mechanisms, besides the RBH and allopatric speciation, may have played an important role in the diversification of platyrrhines.
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Affiliation(s)
- Mareike C Janiak
- School of Science, Engineering & Environment, University of Salford, Salford, United Kingdom
| | - Felipe E Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Brazil.,Department of Evolutionary Biology and Ecology, Université Libre de Bruxelles, Belgium
| | - Robin M D Beck
- School of Science, Engineering & Environment, University of Salford, Salford, United Kingdom
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford, Salford, United Kingdom
| | - Lukas F K Kuderna
- Ilumina Inc., Hayward, CA, USA.,Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain
| | - Nicole S Torosin
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Amanda D Melin
- Department of Anthropology & Archaeology and Department of Medical Genetics, University of Calgary, Calgary, AB, Canada.,Alberta Children's Hospital Research Institute, Calgary, AB, Canada
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, Cerdanyola del Vallès, Barcelona, Spain
| | - Ian B Goodhead
- School of Science, Engineering & Environment, University of Salford, Salford, United Kingdom
| | - Mariluce Messias
- Department of Biology, Universidade Federal de Rondônia, Porto Velho, Brazil
| | - Maria N F da Silva
- Coleção de Mamíferos, Instituto Nacional de Pesquisas da Amazônia, Brazil
| | | | - Izeni P Farias
- Laboratory of Evolution and Animal Genetics, Universidade Federal do Amazonas, Brazil
| | - Rogerio Rossi
- Instituto de Biociências, Universidade Federal do Mato Grosso, Brazil
| | - Fabiano R de Melo
- Department of Forestry Engineering, Universidade Federal de Viçosa, Brazil
| | - João Valsecchi
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Brazil
| | - Tomas Hrbek
- Department of Biology, Trinity University, San Antonio, TX, USA
| | - Jean P Boubli
- School of Science, Engineering & Environment, University of Salford, Salford, United Kingdom.,Coleção de Mamíferos, Instituto Nacional de Pesquisas da Amazônia, Brazil
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11
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Seasonal Pattern in Serum Estradiol, Progesterone, and Prolactin Concentrations in Rescued Wild Female Taiwanese Pangolin (Manis pentadactyla pentadactyla). JOURNAL OF ZOOLOGICAL AND BOTANICAL GARDENS 2022. [DOI: 10.3390/jzbg3020019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Pangolins are under severe threat of surging poaching rates globally; therefore, there is a demand to ascertain reproductive measures to ensure captive breeding and management strategies. Due to the absence of substantial information on the pangolin, endocrinology and reproductive physiology studies around the globe are merely based on captive observations that have failed to report the chronographs and hormonal cyclicity of the reproductive events. This study attempts to evaluate the annual pattern of reproductive steroids (estradiol-17β and progesterone) and prolactin in 16 wild female Taiwanese pangolins rehabilitated by Pingtung Rescue Center of Endangered Wild Animals, Taiwan. Novel immunoassays, i.e., chemiluminometric assays, have been used to quantify the serum reproductive steroids and contribute to a better understanding of the endocrine correlates of function in the Taiwanese pangolin. The hematological findings were characterized by monthly median concentration. The circulating reproductive hormones demonstrated seasonal reproductive activity by confirming a peak in serum estradiol concentrations in December and considerably higher progesterone concentrations in November/December, and March/April. The rise in prolactin in December and peak values in April suggest participation in the ovulatory process and mating. Collectively, these findings can help maximize the reproductive efficiency of pangolin species in captivity, i.e., by timely pairing and prioritizing the care of the breeding pairs to optimize breeding efforts and, therefore, effectively support conservation breeding programs and restore the natural population in the ecosystems.
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12
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Barrett JH, Khamaiko N, Ferrari G, Cuevas A, Kneale C, Hufthammer AK, Pálsdóttir AH, Star B. Walruses on the Dnieper: new evidence for the intercontinental trade of Greenlandic ivory in the Middle Ages. Proc Biol Sci 2022; 289:20212773. [PMID: 35382600 PMCID: PMC8984804 DOI: 10.1098/rspb.2021.2773] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Mediaeval walrus hunting in Iceland and Greenland-driven by Western European demand for ivory and walrus hide ropes-has been identified as an important pre-modern example of ecological globalization. By contrast, the main origin of walrus ivory destined for eastern European markets, and then onward trade to Asia, is assumed to have been Arctic Russia. Here, we investigate the geographical origin of nine twelfth-century CE walrus specimens discovered in Kyiv, Ukraine-combining archaeological typology (based on chaîne opératoire assessment), ancient DNA (aDNA) and stable isotope analysis. We show that five of seven specimens tested using aDNA can be genetically assigned to a western Greenland origin. Moreover, six of the Kyiv rostra had been sculpted in a way typical of Greenlandic imports to Western Europe, and seven are tentatively consistent with a Greenland origin based on stable isotope analysis. Our results suggest that demand for the products of Norse Greenland's walrus hunt stretched not only to Western Europe but included Ukraine and, by implication given linked trade routes, also Russia, Byzantium and Asia. These observations illuminate the surprising scale of mediaeval ecological globalization and help explain the pressure this process exerted on distant wildlife populations and those who harvested them.
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Affiliation(s)
- James H. Barrett
- Department of Archaeology and Cultural History, NTNU Vitenskapsmuseet, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Natalia Khamaiko
- Institute of Archaeology, National Academy of Sciences of Ukraine, 12 Heroiv Stalingrada Ave., 04210 Kyiv, Ukraine
| | - Giada Ferrari
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
| | - Angélica Cuevas
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
| | - Catherine Kneale
- McDonald Institute for Archaeological Research, Department of Archaeology, University of Cambridge, Downing Street, Cambridge CB2 3ER, UK
| | - Anne Karin Hufthammer
- Department of Natural History, The University Museum, University of Bergen, PO Box 7800, 5020 Bergen, Norway
| | - Albína Hulda Pálsdóttir
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
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13
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Kundu S, Pakrashi A, Kamalakannan M, Singha D, Tyagi K, Banerjee D, Venkatraman C, Kumar V. Complete mitogenome of the endangered and endemic Nicobar treeshrew (Tupaia nicobarica) and comparison with other Scandentians. Sci Rep 2022; 12:877. [PMID: 35042947 PMCID: PMC8766473 DOI: 10.1038/s41598-022-04907-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/29/2021] [Indexed: 11/09/2022] Open
Abstract
The Nicobar treeshrew (Tupaia nicobarica) is an endangered small mammal endemic to the Nicobar Island of the Andaman Sea, India regarded as an alternative experimental animal model in biomedical research. The present study aimed to assemble the first mitochondrial genome of T. nicobarica to elucidate its phylogenetic position with respect to other Scandentians. The structure and variation of the novel mitochondrial genome were analyzed and compared with other Scandentians. The complete mitogenome (17,164 bp) encodes 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNAs), two ribosomal RNA (rRNAs), and one control region (CR). Most of the genes were encoded on majority strand, except nad6 and eight tRNAs. The nonsynonymous/synonymous ratio in all PCGs indicates strong negative selection among all Tupaiidae species. The comparative study of CRs revealed the occurrence of tandem repeats (CGTACA) found in T. nicobarica. The phylogenetic analyses (Maximum Likelihood and Bayesian Inference) showed distinct clustering of T. nicobarica with high branch supports and depict a substantial divergence time (12-19 MYA) from the ancestor lineage of Tupaiidae. The 16S rRNA dataset corroborates the taxonomic rank of two subspecies of T. nicobarica from the Great and Little Nicobar Islands. In the future, whole nuclear genome sequencing is necessary to further improve our understanding of evolutionary relationships among treeshrews, and will have implications for biomedical research.
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Affiliation(s)
- Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Calcutta, 700053, India
| | - Avas Pakrashi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Calcutta, 700053, India
| | | | - Devkant Singha
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Calcutta, 700053, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Calcutta, 700053, India
| | - Dhriti Banerjee
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Calcutta, 700053, India
- Mammal and Osteology Section, Zoological Survey of India, Calcutta, 700053, India
| | | | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Calcutta, 700053, India.
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14
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Kundu S, Kamalakannan M, Tyagi K, Kumar V. Complete mitochondrial genome of critically endangered Crocidura nicobarica (Soricidae: Eulipotyphla) from the Great Nicobar Island, India. Mitochondrial DNA B Resour 2021; 6:3418-3422. [PMID: 34869866 PMCID: PMC8638613 DOI: 10.1080/23802359.2021.1999188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/23/2021] [Indexed: 11/30/2022] Open
Abstract
The mitogenome (17,388 bp) of the Nicobar shrew, Crocidura nicobarica was determined in the present study. The mitogenome comprises 13 PCGs (11,427 bp), 22 tRNAs (1507 bp), two rRNAs (2538 bp), and a major non-coding control region (1932 bp). The Maximum Likelihood phylogeny clearly discriminates all the studied Crocidura species with high bootstrap support by concatenated PCGs. The studied species, C. nicobarica shows a close relationship with Crocidura orientalis, distributed in Java, Indonesia. The lineage diversification and zoogeographic patterns are congruent in the present analyses and encouraged further sampling and more molecular data to elucidate their in-depth evolutionary relationship.
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Affiliation(s)
- Shantanu Kundu
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, India
| | | | - Kaomud Tyagi
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, India
| | - Vikas Kumar
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, India
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15
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Prothero DR, Domning D, Fordyce RE, Foss S, Janis C, Lucas S, Marriott KL, Metais G, Naish D, Padian K, Rössner G, Solounias N, Spaulding M, Stucky RM, Theodor J, Uhen M. On the Unnecessary and Misleading Taxon “Cetartiodactyla”. J MAMM EVOL 2021. [DOI: 10.1007/s10914-021-09572-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Tian J, Du J, Han J, Li D, Song X. Complete Mitochondrial Genome of the South American Fur Seal Arctocephalus australis (Carnivora: Otariidae) and Its Phylogenetic Implications. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421050124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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17
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Houssaye A, Martin F, Boisserie JR, Lihoreau F. Paleoecological Inferences from Long Bone Microanatomical Specializations in Hippopotamoidea (Mammalia, Artiodactyla). J MAMM EVOL 2021. [DOI: 10.1007/s10914-021-09536-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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18
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Hu J, Roos C, Lv X, Kuang W, Yu L. Molecular Genetics Supports a Potential Fifth Asian Pangolin Species (Mammalia, Pholidota, Manis). Zoolog Sci 2021; 37:538-543. [PMID: 33269869 DOI: 10.2108/zs200084] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 08/17/2020] [Indexed: 11/17/2022]
Abstract
Recently, two mitochondrial haplotypes, H4 and H8, of Manis sp. were found in two seizures in Hong Kong that do not correspond to Manis javanica, Manis pentadactyla or Manis crassicaudata of Asian pangolin species or any African pangolin species. It was proposed that both haplotypes derived from Manis culionensis, an unknown lineage of M. javanica, or a thus far unidentified Asian pangolin species (Manis sp.). To further investigate these three hypotheses, we used two mitochondrial genes of all eight known extant pangolin species and conducted phylogenetic tree reconstructions, divergence time estimation, and species delimitation analyses. All analyses consistently confirmed that these two haplotypes of Manis sp. constitute a distinct lineage, potentially representing a fifth Asian pangolin species, which originated around the Late Miocene to Early Pliocene (6.95 [4.64-9.85] million years ago). Our study provides genetic support for a potential fifth Asian pangolin species and helps to better understand species diversity of Asian pangolins, which is urgently needed for effective conservation work.
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Affiliation(s)
- Jingyang Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, 650091, Kunming, China
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, D-37077, Göttingen, Germany
| | - Xue Lv
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, 650091, Kunming, China
| | - Weimin Kuang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, 650091, Kunming, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, 650091, Kunming, China,
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19
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Phillips MJ, Shazwani Zakaria S. Enhancing mitogenomic phylogeny and resolving the relationships of extinct megafaunal placental mammals. Mol Phylogenet Evol 2021; 158:107082. [PMID: 33482383 DOI: 10.1016/j.ympev.2021.107082] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 12/21/2020] [Accepted: 01/11/2021] [Indexed: 10/22/2022]
Abstract
Mitochondrial genomes provided the first widely used sequences that were sufficiently informative to resolve relationships among animals across a wide taxonomic domain, from within species to between phyla. However, mitogenome studies supported several anomalous relationships and fell partly out of favour as sequencing multiple, independent nuclear loci proved to be highly effective. A tendency to blame mitochondrial DNA (mtDNA) has overshadowed efforts to understand and ameliorate underlying model misspecification. Here we find that influential assessments of the infidelity of mitogenome phylogenies have often been overstated, but nevertheless, substitution saturation and compositional non-stationarity substantially mislead reconstruction. We show that RY coding the mtDNA, excluding protein-coding 3rd codon sites, partitioning models based on amino acid hydrophobicity and enhanced taxon sampling improve the accuracy of mitogenomic phylogeny reconstruction for placental mammals, almost to the level of multi-gene nuclear datasets. Indeed, combined analysis of mtDNA with 3-fold longer nuclear sequence data either maintained or improved upon the nuclear support for all generally accepted clades, even those that mtDNA alone did not favour, thus indicating "hidden support". Confident mtDNA phylogeny reconstruction is especially important for understanding the evolutionary dynamics of mitochondria themselves, and for merging extinct taxa into the tree of life, with ancient DNA often only accessible as mtDNA. Our ancient mtDNA analyses lend confidence to the relationships of three extinct megafaunal taxa: glyptodonts are nested within armadillos, the South American ungulate, Macrauchenia is sister to horses and rhinoceroses, and sabre-toothed and scimitar cats are the monophyletic sister-group of modern cats.
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Affiliation(s)
- Matthew J Phillips
- School of Biology and Environmental Science, Queensland University of Technology, 2 George Street, Brisbane 4000, QLD, Australia.
| | - Sarah Shazwani Zakaria
- School of Biology and Environmental Science, Queensland University of Technology, 2 George Street, Brisbane 4000, QLD, Australia; School of Biology, Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM) Caw. Negeri Sembilan, Kuala Pilah 72000, Malaysia
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20
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Lv X, Hu J, Hu Y, Li Y, Xu D, Ryder OA, Irwin DM, Yu L. Diverse phylogenomic datasets uncover a concordant scenario of laurasiatherian interordinal relationships. Mol Phylogenet Evol 2020; 157:107065. [PMID: 33387649 DOI: 10.1016/j.ympev.2020.107065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 12/22/2020] [Accepted: 12/24/2020] [Indexed: 10/22/2022]
Abstract
Resolving the interordinal relationships in the mammalian superorder Laurasiatheria has been among the most intractable problems in higher-level mammalian systematics, with many conflicting hypotheses having been proposed. The present study collected three different sources of genome-scale data with comprehensive taxon sampling of laurasiatherian species, including two protein-coding datasets (4,186 protein-coding genes for an amino acid dataset comprising 2,761,247 amino acid residues and a nucleotide dataset comprising 5,516,340 nucleotides from 1st and 2nd codon positions), an intronic dataset (1,210 introns comprising 1,162,723 nucleotides) and an ultraconserved elements (UCEs) dataset (1,246 UCEs comprising 1,946,472 nucleotides) from 40 species representing all six laurasiatherian orders and 7 non-laurasiatherian outgroups. Remarkably, phylogenetic trees reconstructed with the four datasets using different tree-building methods (RAxML, FastTree, ASTRAL and MP-EST) all supported the relationship (Eulipotyphla, (Chiroptera, ((Carnivora, Pholidota), (Cetartiodactyla, Perissodactyla)))). We find a resolution of interordinal relationships of Laurasiatheria among all types of markers used in the present study, and the likelihood ratio tests for tree comparisons confirmed that the present tree topology is the optimal hypothesis compared to other examined hypotheses. Jackknifing subsampling analyses demonstrate that the results of laurasiatherian tree reconstruction varied with the number of loci and ordinal representatives used, which are likely the two main contributors to phylogenetic disagreements of Laurasiatheria seen in previous studies. Our study provides significant insight into laurasiatherian evolution, and moreover, an important methodological strategy and reference for resolving phylogenies of adaptive radiation, which have been a long-standing challenge in the field of phylogenetics.
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Affiliation(s)
- Xue Lv
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China; School of Life Sciences, Yunnan University, Kunming, China
| | - Jingyang Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China; School of Life Sciences, Yunnan University, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Yiwen Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China; School of Life Sciences, Yunnan University, Kunming, China
| | - Yitian Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China; School of Life Sciences, Yunnan University, Kunming, China
| | - Dongming Xu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming, China
| | - Oliver A Ryder
- Institute for Conservation Research, San Diego Zoo Global, Escondido, CA, USA
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.
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21
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Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression. PLoS Biol 2020; 18:e3000954. [PMID: 33270638 PMCID: PMC7738166 DOI: 10.1371/journal.pbio.3000954] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 12/15/2020] [Accepted: 11/02/2020] [Indexed: 12/17/2022] Open
Abstract
Our understanding of the evolutionary history of primates is undergoing continual revision due to ongoing genome sequencing efforts. Bolstered by growing fossil evidence, these data have led to increased acceptance of once controversial hypotheses regarding phylogenetic relationships, hybridization and introgression, and the biogeographical history of primate groups. Among these findings is a pattern of recent introgression between species within all major primate groups examined to date, though little is known about introgression deeper in time. To address this and other phylogenetic questions, here, we present new reference genome assemblies for 3 Old World monkey (OWM) species: Colobus angolensis ssp. palliatus (the black and white colobus), Macaca nemestrina (southern pig-tailed macaque), and Mandrillus leucophaeus (the drill). We combine these data with 23 additional primate genomes to estimate both the species tree and individual gene trees using thousands of loci. While our species tree is largely consistent with previous phylogenetic hypotheses, the gene trees reveal high levels of genealogical discordance associated with multiple primate radiations. We use strongly asymmetric patterns of gene tree discordance around specific branches to identify multiple instances of introgression between ancestral primate lineages. In addition, we exploit recent fossil evidence to perform fossil-calibrated molecular dating analyses across the tree. Taken together, our genome-wide data help to resolve multiple contentious sets of relationships among primates, while also providing insight into the biological processes and technical artifacts that led to the disagreements in the first place. Combining three newly sequenced primate genomes with other published genomes, this study adapts a little-known method for detecting ancient introgression to genome-scale data, revealing multiple previously unknown examples of hybridization between primate species.
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22
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Arora B, Jai-Chyi Pei K, Feng Weng C, Ching-Min Sun N. Measuring fecal metabolites of endogenous steroids using ESI-MS/MS spectra in Taiwanese pangolin, (order Pholidota, family Manidae, Genus: Manis): A non-invasive method for endangered species. Gen Comp Endocrinol 2020; 299:113607. [PMID: 32882210 DOI: 10.1016/j.ygcen.2020.113607] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 08/19/2020] [Accepted: 08/24/2020] [Indexed: 11/22/2022]
Abstract
Pangolins are 'keystone species' driven towards extinction due to a lack of profound awareness and illegal trade. The drivers urge for immediate development in the understanding of demographics and reproductive dynamics of this species. In this study, we developed and validated a quantitative method to measure pangolin fecal extracts using the electrospray (ESI-MS/MS) interface in positive ionization mode. The method aids in the measurement of hormones from the hypothalamic-pituitary-adrenal (HPA) and hypothalamic-pituitary-gonadal (HPG) axis, making it a possibly appropriate technique to understand the cross-talk between the axes. The study aims to measure the relative abundance of adrenal and gonadal hormones such as corticosterone, cortisol, estrone, estradiol-17β, progesterone, testosterone, and a number of its metabolites. From the dried fecal extract, the principal metabolite identified from the estrogen family was estradiol-17β, whereas the gestagen family revealed that the pregnane series is predominated in 5α-configuration. On the other hand, epiandrosterone was seen as the dominant form in the male fecal extracts. Additionally, the glucocorticoids are excreted majorly as corticosterone, but traces of cortisol are also present in both the male and female fecal samples. The physiological validation confirmed that the ESI-MS/MS technique is suitable to determine physiologically caused differences in the fecal steroid concentrations. Physiologically, the age structure in pangolin is not responsible for causing differences within gender. However, the results revealed that glucocorticoids might vary between the sexes, i.e., males have a higher relative abundance of glucocorticoids over females. Therefore, our studies show that some of the main adrenal and gonadal metabolites can be predicted by exploiting MS/MS, which can steer research to potentially assess the reproductive status of captive and free-ranging pangolin species.
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Affiliation(s)
- Bharti Arora
- Department of Natural Resources and Environmental Studies, National Dong Hwa University, Taiwan.
| | - Kurtis Jai-Chyi Pei
- Institute of Wildlife Conservation, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Ching Feng Weng
- Department of Life Sciences, National Dong Hwa University, Taiwan
| | - Nick Ching-Min Sun
- Graduate Institute of Bioresources, National Pingtung University of Science and Technology, Pingtung, Taiwan
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23
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Bhagwandin A, Debipersadh U, Kaswera-Kyamakya C, Gilissen E, Rockland KS, Molnár Z, Manger PR. Distribution, number, and certain neurochemical identities of infracortical white matter neurons in the brains of three megachiropteran bat species. J Comp Neurol 2020; 528:3023-3038. [PMID: 32103488 DOI: 10.1002/cne.24894] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/06/2020] [Accepted: 02/24/2020] [Indexed: 12/13/2022]
Abstract
A large population of infracortical white matter neurons, or white matter interstitial cells (WMICs), are found within the subcortical white matter of the mammalian telencephalon. We examined WMICs in three species of megachiropterans, Megaloglossus woermanni, Casinycteris argynnis, and Rousettus aegyptiacus, using immunohistochemical and stereological techniques. Immunostaining for neuronal nuclear marker (NeuN) revealed substantial numbers of WMICs in each species-M. woermanni 124,496 WMICs, C. argynnis 138,458 WMICs, and the larger brained R. aegyptiacus having an estimated WMIC population of 360,503. To examine the range of inhibitory neurochemical types we used antibodies against parvalbumin, calbindin, calretinin, and neural nitric oxide synthase (nNOS). The calbindin and nNOS immunostained neurons were the most commonly observed, while those immunoreactive for calretinin and parvalbumin were sparse. The proportion of WMICs exhibiting inhibitory neurochemical profiles was ~26%, similar to that observed in previously studied primates. While for the most part the WMIC population in the megachiropterans studied was similar to that observed in other mammals, the one feature that differed was the high proportion of WMICs immunoreactive to calbindin, whereas in primates (macaque monkey, lar gibbon and human) the highest proportion of inhibitory WMICs contain calretinin. Interestingly, there appears to be an allometric scaling of WMIC numbers with brain mass. Further quantitative comparative work across more mammalian species will reveal the developmental and evolutionary trends associated with this infrequently studied neuronal population.
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Affiliation(s)
- Adhil Bhagwandin
- School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, Parktown, Johannesburg, South Africa
- Division of Clinical Anatomy and Biological Anthropology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
| | - Ulsana Debipersadh
- School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, Parktown, Johannesburg, South Africa
| | | | - Emmanuel Gilissen
- Department of African Zoology, Royal Museum for Central Africa, Tervuren, Belgium
- Laboratory of Histology and Neuropathology, Université Libre de Bruxelles, Brussels, Belgium
- Department of Anthropology, University of Arkansas, Fayetteville, Arkansas, USA
| | - Kathleen S Rockland
- Department of Anatomy and Neurobiology, Boston University, School of Medicine, Boston, Massachusetts, USA
| | - Zoltán Molnár
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Paul R Manger
- School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, Parktown, Johannesburg, South Africa
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Kundu S, Kumar V, Tyagi K, Chandra K. The complete mitochondrial genome of the endangered Assam Roofed Turtle, Pangshura sylhetensis (Testudines: Geoemydidae): Genomic features and phylogeny. PLoS One 2020; 15:e0225233. [PMID: 32324729 PMCID: PMC7179895 DOI: 10.1371/journal.pone.0225233] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 04/08/2020] [Indexed: 12/02/2022] Open
Abstract
The Assam Roofed Turtle, Pangshura sylhetensis is an endangered and least studied species endemic to India and Bangladesh. The present study decodes the first complete mitochondrial genome of P. sylhetensis (16,568 bp) by using next-generation sequencing. The assembly encodes 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control region (CR). Most of the genes were encoded on the majority strand, except NADH dehydrogenase subunit 6 (nad6) and eight tRNAs. All PCGs start with an ATG initiation codon, except for Cytochrome oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 5 (nad5), which both start with GTG codon. The study also found the typical cloverleaf secondary structures in most of the predicted tRNA structures, except for serine (trnS1) which lacks of conventional DHU arm and loop. Both Bayesian and maximum-likelihood phylogenetic inference using 13 concatenated PCGs demonstrated strong support for the monophyly of all 52 Testudines species within their respective families and revealed Batagur trivittata as the nearest neighbor of P. sylhetensis. The mitogenomic phylogeny with other amniotes is congruent with previous research, supporting the sister relationship of Testudines and Archosaurians (birds and crocodilians). Additionally, the mitochondrial Gene Order (GO) analysis indicated plesiomorphy with the typical vertebrate GO in most of the Testudines species.
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Affiliation(s)
- Shantanu Kundu
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, India
| | - Vikas Kumar
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, India
| | - Kaomud Tyagi
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, India
| | - Kailash Chandra
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, India
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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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Trevisan B, Alcantara DM, Machado DJ, Marques FP, Lahr DJ. Genome skimming is a low-cost and robust strategy to assemble complete mitochondrial genomes from ethanol preserved specimens in biodiversity studies. PeerJ 2019; 7:e7543. [PMID: 31565556 PMCID: PMC6746217 DOI: 10.7717/peerj.7543] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 07/24/2019] [Indexed: 12/17/2022] Open
Abstract
Global loss of biodiversity is an ongoing process that concerns both local and global authorities. Studies of biodiversity mainly involve traditional methods using morphological characters and molecular protocols. However, conventional methods are a time consuming and resource demanding task. The development of high-throughput sequencing (HTS) techniques has reshaped the way we explore biodiversity and opened a path to new questions and novel empirical approaches. With the emergence of HTS, sequencing the complete mitochondrial genome became more accessible, and the number of genome sequences published has increased exponentially during the last decades. Despite the current state of knowledge about the potential of mitogenomics in phylogenetics, this is still a relatively under-explored area for a multitude of taxonomic groups, especially for those without commercial relevance, non-models organisms and with preserved DNA. Here we take the first step to assemble and annotate the genomes from HTS data using a new protocol of genome skimming which will offer an opportunity to extend the field of mitogenomics to under-studied organisms. We extracted genomic DNA from specimens preserved in ethanol. We used Nextera XT DNA to prepare indexed paired-end libraries since it is a powerful tool for working with diverse samples, requiring a low amount of input DNA. We sequenced the samples in two different Illumina platform (MiSeq or NextSeq 550). We trimmed raw reads, filtered and had their quality tested accordingly. We performed the assembly using a baiting and iterative mapping strategy, and the annotated the putative mitochondrion through a semi-automatic procedure. We applied the contiguity index to access the completeness of each new mitogenome. Our results reveal the efficiency of the proposed method to recover the whole mitogenomes of preserved DNA from non-model organisms even if there are gene rearrangement in the specimens. Our findings suggest the potential of combining the adequate platform and library to the genome skimming as an innovative approach, which opens a new range of possibilities of its use to obtain molecular data from organisms with different levels of preservation.
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Affiliation(s)
- Bruna Trevisan
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Daniel M.C. Alcantara
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Denis Jacob Machado
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
- Department of Bioinformatics and Genomics / College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, NC, United States of America
| | - Fernando P.L. Marques
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Daniel J.G. Lahr
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
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Kornienko IV, Faleeva TG, Oreshkova NV, Grigoriev SE, Grigorieva LV, Putintseva YA, Krutovsky KV. Structural and Functional Organization of the Mitochondrial DNA Control Region in the Woolly Mammoth (Mammuthus primigenius). Mol Biol 2019. [DOI: 10.1134/s002689331904006x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Nyakatura JA. Early primate evolution: insights into the functional significance of grasping from motion analyses of extant mammals. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz057] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- John A Nyakatura
- AG Morphologie und Formengeschichte, Institut für Biologie, Humboldt Universität, Philippstraße, Berlin, Germany
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Comparison of mitochondrial DNA enrichment and sequencing methods from fish tissue. Food Chem 2019; 294:333-338. [PMID: 31126471 DOI: 10.1016/j.foodchem.2019.05.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 05/02/2019] [Accepted: 05/06/2019] [Indexed: 01/06/2023]
Abstract
Sparid fish species have different commercial values related to their organoleptic features. Mitochondrial (mt) DNA provides a potential tool to distinguish species, but the enrichment of high-quality mtDNA from total genomic DNA is critical to obtain entire mtDNA sequences. Conventional mtDNA isolation is relatively low-cost and proficient. However, high numbers of PCR cycles can lead to artefacts (10-6 mutations/bp). We describe a rapid protocol for mtDNA extraction and enrichment from fish tissues, based on conventional miniprep columns and paramagnetic bead-based purification, without the need to employ PCR amplification. This newly described method generates a substrate for next-generation sequencing (NGS) analysis and is likely to have wider applications for mitochondrial studies in other fish families to help ensure traceability and differentiation of fish with high commercial values.
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Silva SM, Ruedas LA, Santos LH, e Silva JDS, Aleixo A. Illuminating the obscured phylogenetic radiation of South American SylvilagusGray, 1867 (Lagomorpha: Leporidae). J Mammal 2019. [DOI: 10.1093/jmammal/gyy186] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Sofia Marques Silva
- Coordenação de Zoologia, Museu Paraense Emílio Goeldi, Campus de Pesquisa, Avenida Perimetral, CEP, Belém, Pará, Brazil
| | - Luis A Ruedas
- Coordenação de Zoologia, Museu Paraense Emílio Goeldi, Campus de Pesquisa, Avenida Perimetral, CEP, Belém, Pará, Brazil
| | - Larissa Hasnah Santos
- Portland State University, Department of Biology and Museum of Natural History, SRTC-246, Portland, OR, USA
| | - José de Sousa e Silva
- Coordenação de Zoologia, Museu Paraense Emílio Goeldi, Campus de Pesquisa, Avenida Perimetral, CEP, Belém, Pará, Brazil
| | - Alexandre Aleixo
- Coordenação de Zoologia, Museu Paraense Emílio Goeldi, Campus de Pesquisa, Avenida Perimetral, CEP, Belém, Pará, Brazil
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Star B, Barrett JH, Gondek AT, Boessenkool S. Ancient DNA reveals the chronology of walrus ivory trade from Norse Greenland. Proc Biol Sci 2018; 285:rspb.2018.0978. [PMID: 30089624 PMCID: PMC6111184 DOI: 10.1098/rspb.2018.0978] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/12/2018] [Indexed: 01/27/2023] Open
Abstract
The importance of the Atlantic walrus ivory trade for the colonization, peak, and collapse of the medieval Norse colonies on Greenland has been extensively debated. Nevertheless, no studies have directly traced medieval European ivory back to distinct Arctic populations of walrus. Analysing the entire mitogenomes of 37 archaeological specimens from Europe, Svalbard, and Greenland, we here discover that Atlantic walrus comprises two monophyletic mitochondrial (MT) clades, which diverged between 23 400 and 251 120 years ago. Our improved genomic resolution allows us to reinterpret the geographical distribution of partial MT data from 306 modern and nineteenth-century specimens, finding that one of these clades was exclusively accessible to Greenlanders. With this discovery, we ascertain the biological origin of 23 archaeological specimens from Europe (most dated between 900 and 1400 CE). These results reveal a significant shift in trade from an early, predominantly eastern source towards a near exclusive representation of Greenland ivory. Our study provides empirical evidence for how this remote Arctic resource was progressively integrated into a medieval pan-European trade network, contributing to both the resilience and vulnerability of Norse Greenland society.
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Affiliation(s)
- Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
| | - James H Barrett
- McDonald Institute for Archaeological Research, Department of Archaeology, University of Cambridge, Downing Street, Cambridge CB2 3ER, UK
| | - Agata T Gondek
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
| | - Sanne Boessenkool
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
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Ben Slimen H, Awadi A, Tolesa ZG, Knauer F, Alves PC, Makni M, Suchentrunk F. Positive selection on the mitochondrial ATP synthase 6and the NADH dehydrogenase 2genes across 22 hare species (genus Lepus). J ZOOL SYST EVOL RES 2018. [DOI: 10.1111/jzs.12204] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hichem Ben Slimen
- Unité de recherche Génomique des Insectes ravageurs des Cultures d'intérêt agronomique; Faculty of Sciences of Tunis; University of Tunis El Manar; Tunis Tunisia
- Institut Supérieur de Biotechnologie de Béja; University of Jendouba; Béja Tunisia
| | - Asma Awadi
- Unité de recherche Génomique des Insectes ravageurs des Cultures d'intérêt agronomique; Faculty of Sciences of Tunis; University of Tunis El Manar; Tunis Tunisia
| | | | - Felix Knauer
- Research Institute of Wildlife Ecology; University of Veterinary Medicine Vienna; Vienna Austria
| | - Paulo Célio Alves
- CIBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; Universidade do Porto; Vairão Portugal
| | - Mohamed Makni
- Unité de recherche Génomique des Insectes ravageurs des Cultures d'intérêt agronomique; Faculty of Sciences of Tunis; University of Tunis El Manar; Tunis Tunisia
| | - Franz Suchentrunk
- Research Institute of Wildlife Ecology; University of Veterinary Medicine Vienna; Vienna Austria
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Lei R, Frasier CL, Hawkins MTR, Engberg SE, Bailey CA, Johnson SE, McLain AT, Groves CP, Perry GH, Nash SD, Mittermeier RA, Louis EE. Phylogenomic Reconstruction of Sportive Lemurs (genus Lepilemur) Recovered from Mitogenomes with Inferences for Madagascar Biogeography. J Hered 2018; 108:107-119. [PMID: 28173059 DOI: 10.1093/jhered/esw072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 09/30/2016] [Indexed: 11/12/2022] Open
Abstract
The family Lepilemuridae includes 26 species of sportive lemurs, most of which were recently described. The cryptic morphological differences confounded taxonomy until recent molecular studies; however, some species’ boundaries remain uncertain. To better understand the genus Lepilemur, we analyzed 35 complete mitochondrial genomes representing all recognized 26 sportive lemur taxa and estimated divergence dates. With our dataset we recovered 25 reciprocally monophyletic lineages, as well as an admixed clade containing Lepilemur mittermeieri and Lepilemur dorsalis. Using modern distribution data, an ancestral area reconstruction and an ecological vicariance analysis were performed to trace the history of diversification and to test biogeographic hypotheses. We estimated the initial split between the eastern and western Lepilemur clades to have occurred in the Miocene. Divergence of most species occurred from the Pliocene to the Pleistocene. The biogeographic patterns recovered in this study were better addressed with a combinatorial approach including climate, watersheds, and rivers. Generally, current climate and watershed hypotheses performed better for western and eastern clades, while speciation of northern clades was not adequately supported using the ecological factors incorporated in this study. Thus, multiple mechanisms likely contributed to the speciation and distribution patterns in Lepilemur.
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Affiliation(s)
- Runhua Lei
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
| | - Cynthia L Frasier
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
| | - Melissa T R Hawkins
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
| | - Shannon E Engberg
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
| | - Carolyn A Bailey
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
| | - Steig E Johnson
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB, Canada
| | - Adam T McLain
- Department of Mathematics and Sciences, State University of New York Polytechnic Institute, Utica, NY, USA
| | - Colin P Groves
- School of Archaeology and Anthropology, Australian National University, Canberra, ACT, Australia
| | - George H Perry
- Departments of Anthropology and Biology, Pennsylvania State University, University Park, PA, USA
| | | | | | - Edward E Louis
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
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Prakash Kumar V, Rajpoot A, Srivastav A, Nigam P, Kumar V, A. M, Prakash Goyal S. Phylogenetic relationship and molecular dating of Indian pangolin (Manis crassicaudata) with other extant pangolin species based on complete cytochrome b mitochondrial gene. Mitochondrial DNA A DNA Mapp Seq Anal 2018. [DOI: 10.1080/24701394.2018.1445241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
| | - Ankita Rajpoot
- Molecular Systematics Laboratory, Zoological Survey of India NRC, Dehradun, Uttarakhand, India
| | | | - Parag Nigam
- Wildlife Institute of India, Dehradun, Uttarakhand, India
| | - Vinay Kumar
- Wildlife Institute of India, Dehradun, Uttarakhand, India
| | - Madhanraj A.
- Wildlife Institute of India, Dehradun, Uttarakhand, India
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Abdoli R, Zamani P, Ghasemi M. Genetic similarities and phylogenetic analysis of human and farm animal species based on mitogenomic nucleotide sequences. Meta Gene 2018. [DOI: 10.1016/j.mgene.2017.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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38
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Steyn C, Soley JT, Crole MR. Osteology and Radiological Anatomy of the Thoracic Limbs of Temminck's Ground Pangolin (Smutsia temminckii
). Anat Rec (Hoboken) 2017; 301:624-635. [DOI: 10.1002/ar.23733] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/14/2017] [Accepted: 08/27/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Christine Steyn
- Department of Anatomy and Physiology, Faculty of Veterinary Science; University of Pretoria; Onderstepoort South Africa
| | - John T. Soley
- Department of Anatomy and Physiology, Faculty of Veterinary Science; University of Pretoria; Onderstepoort South Africa
| | - Martina R. Crole
- Department of Anatomy and Physiology, Faculty of Veterinary Science; University of Pretoria; Onderstepoort South Africa
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Jacobs B, Garcia ME, Shea-Shumsky NB, Tennison ME, Schall M, Saviano MS, Tummino TA, Bull AJ, Driscoll LL, Raghanti MA, Lewandowski AH, Wicinski B, Ki Chui H, Bertelsen MF, Walsh T, Bhagwandin A, Spocter MA, Hof PR, Sherwood CC, Manger PR. Comparative morphology of gigantopyramidal neurons in primary motor cortex across mammals. J Comp Neurol 2017; 526:496-536. [PMID: 29088505 DOI: 10.1002/cne.24349] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/19/2017] [Accepted: 10/24/2017] [Indexed: 12/11/2022]
Abstract
Gigantopyramidal neurons, referred to as Betz cells in primates, are characterized by large somata and extensive basilar dendrites. Although there have been morphological descriptions and drawings of gigantopyramidal neurons in a limited number of species, quantitative investigations have typically been limited to measures of soma size. The current study thus employed two separate analytical approaches: a morphological investigation using the Golgi technique to provide qualitative and quantitative somatodendritic measures of gigantopyramidal neurons across 19 mammalian species from 7 orders; and unbiased stereology to compare the soma volume of layer V pyramidal and gigantopyramidal neurons in primary motor cortex between 11 carnivore and 9 primate species. Of the 617 neurons traced in the morphological analysis, 181 were gigantopyramidal neurons, with deep (primarily layer V) pyramidal (n = 203) and superficial (primarily layer III) pyramidal (n = 233) neurons quantified for comparative purposes. Qualitatively, dendritic morphology varied considerably across species, with some (sub)orders (e.g., artiodactyls, perissodactyls, feliforms) exhibiting bifurcating, V-shaped apical dendrites. Basilar dendrites exhibited idiosyncratic geometry across and within taxonomic groups. Quantitatively, most dendritic measures were significantly greater in gigantopyramidal neurons than in superficial and deep pyramidal neurons. Cluster analyses revealed that most taxonomic groups could be discriminated based on somatodendritic morphology for both superficial and gigantopyramidal neurons. Finally, in agreement with Brodmann, gigantopyramidal neurons in both the morphological and stereological analyses were larger in feliforms (especially in the Panthera species) than in other (sub)orders, possibly due to specializations in muscle fiber composition and musculoskeletal systems.
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Affiliation(s)
- Bob Jacobs
- Laboratory of Quantitative Neuromorphology, Neuroscience Program, Colorado College, Colorado Springs, Colorado
| | - Madeleine E Garcia
- Laboratory of Quantitative Neuromorphology, Neuroscience Program, Colorado College, Colorado Springs, Colorado
| | - Noah B Shea-Shumsky
- Laboratory of Quantitative Neuromorphology, Neuroscience Program, Colorado College, Colorado Springs, Colorado
| | - Mackenzie E Tennison
- Laboratory of Quantitative Neuromorphology, Neuroscience Program, Colorado College, Colorado Springs, Colorado
| | - Matthew Schall
- Laboratory of Quantitative Neuromorphology, Neuroscience Program, Colorado College, Colorado Springs, Colorado
| | - Mark S Saviano
- Laboratory of Quantitative Neuromorphology, Neuroscience Program, Colorado College, Colorado Springs, Colorado
| | - Tia A Tummino
- Laboratory of Quantitative Neuromorphology, Neuroscience Program, Colorado College, Colorado Springs, Colorado
| | - Anthony J Bull
- Human Biology and Kinesiology, Colorado College, Colorado Springs, Colorado
| | - Lori L Driscoll
- Laboratory of Quantitative Neuromorphology, Neuroscience Program, Colorado College, Colorado Springs, Colorado
| | - Mary Ann Raghanti
- Department of Anthropology and School of Biomedical Sciences, Kent State University, Kent, Ohio
| | | | - Bridget Wicinski
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Hong Ki Chui
- Laboratory of Quantitative Neuromorphology, Neuroscience Program, Colorado College, Colorado Springs, Colorado
| | - Mads F Bertelsen
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, Fredericksberg, Denmark
| | - Timothy Walsh
- Smithsonian National Zoological Park, Washington, District of Columbia
| | - Adhil Bhagwandin
- School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Muhammad A Spocter
- School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Anatomy, Des Moines University, Des Moines, Iowa.,Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, Iowa
| | - Patrick R Hof
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Chet C Sherwood
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, District of Columbia
| | - Paul R Manger
- School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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du Toit Z, du Plessis M, Dalton DL, Jansen R, Paul Grobler J, Kotzé A. Mitochondrial genomes of African pangolins and insights into evolutionary patterns and phylogeny of the family Manidae. BMC Genomics 2017; 18:746. [PMID: 28934931 PMCID: PMC5609056 DOI: 10.1186/s12864-017-4140-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 09/14/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND This study used next generation sequencing to generate the mitogenomes of four African pangolin species; Temminck's ground pangolin (Smutsia temminckii), giant ground pangolin (S. gigantea), white-bellied pangolin (Phataginus tricuspis) and black-bellied pangolin (P. tetradactyla). RESULTS The results indicate that the mitogenomes of the African pangolins are 16,558 bp for S. temminckii, 16,540 bp for S. gigantea, 16,649 bp for P. tetradactyla and 16,565 bp for P. tricuspis. Phylogenetic comparisons of the African pangolins indicated two lineages with high posterior probabilities providing evidence to support the classification of two genera; Smutsia and Phataginus. The total GC content between African pangolins was observed to be similar between species (36.5% - 37.3%). The most frequent codon was found to be A or C at the 3rd codon position. Significant variations in GC-content and codon usage were observed for several regions between African and Asian pangolin species which may be attributed to mutation pressure and/or natural selection. Lastly, a total of two insertions of 80 bp and 28 bp in size respectively was observed in the control region of the black-bellied pangolin which were absent in the other African pangolin species. CONCLUSIONS The current study presents reference mitogenomes of all four African pangolin species and thus expands on the current set of reference genomes available for six of the eight extant pangolin species globally and represents the first phylogenetic analysis with six pangolin species using full mitochondrial genomes. Knowledge of full mitochondrial DNA genomes will assist in providing a better understanding on the evolution of pangolins which will be essential for conservation genetic studies.
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Affiliation(s)
- Zelda du Toit
- Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
- Centre for Conservation Science, National Zoological Gardens of South Africa, P.O. Box 754, Pretoria, 0001, South Africa
| | - Morné du Plessis
- Centre for Conservation Science, National Zoological Gardens of South Africa, P.O. Box 754, Pretoria, 0001, South Africa
| | - Desiré L Dalton
- Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa.
- Centre for Conservation Science, National Zoological Gardens of South Africa, P.O. Box 754, Pretoria, 0001, South Africa.
- Department of Zoology, University of Venda, Thohoyandou, South Africa.
| | - Raymond Jansen
- Department of Environmental, Water and Earth Sciences, Tshwane University of Technology, Private Bag X680, Pretoria, 0001, South Africa
| | - J Paul Grobler
- Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - Antoinette Kotzé
- Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
- Centre for Conservation Science, National Zoological Gardens of South Africa, P.O. Box 754, Pretoria, 0001, South Africa
- Department of Environmental, Water and Earth Sciences, Tshwane University of Technology, Private Bag X680, Pretoria, 0001, South Africa
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Horreo JL. Revisiting the mitogenomic phylogeny of Salmoninae: new insights thanks to recent sequencing advances. PeerJ 2017; 5:e3828. [PMID: 28948107 PMCID: PMC5609519 DOI: 10.7717/peerj.3828] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 08/29/2017] [Indexed: 12/24/2022] Open
Abstract
The phylogeny of the Salmonidae family, the only living one of the Order Salmoniformes, remains still unclear because of several reasons. Such reasons include insufficient taxon sampling and/or DNA information. The use of complete mitochondrial genomes (mitogenomics) could provide some light on it, but despite the high number of mitogenomes of species belonging to this family published during last years, an integrative work containing all this information has not been done. In this work, the phylogeny of 46 Salmonidae species was inferred from their mitogenomic sequences. Results include a Bayesian molecular-dated phylogenetic tree with very high statistical support showing Coregoninae and Salmoninae as sister subfamilies, as well as several new phylogenetic relationships among species and genus of the family. All these findings contribute to improve our understanding of the Salmonidae systematics and could have consequences on related evolutionary studies, as well as highlight the importance of revisiting phylogenies with integrative studies.
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Affiliation(s)
- Jose L. Horreo
- Department of Biodiversity and Evolutionary Biology, National Museum of Natural Sciences (CSIC), Madrid, Spain
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Two mitochondrial genomes in Alcedinidae (Ceryle rudis/Halcyon pileata) and the phylogenetic placement of Coraciiformes. Genetica 2017; 145:431-440. [PMID: 28791584 DOI: 10.1007/s10709-017-9978-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 08/03/2017] [Indexed: 10/19/2022]
Abstract
Coraciiformes comprises 209 species belonging to ten families with significant divergence on external morphologies and life styles. The phylogenetic placement of Coraciiformes was still in debate. Here, we determined the complete mitochondrial genomes (mitogenomes) of Crested Kingfisher (Ceryle rudis) and Black-capped Kingfisher (Halcyon pileata). The mitogenomes were 17,355 bp (C. rudis) and 17,612 bp (H. pileata) in length, and both of them contained 37 genes (two rRNA genes, 22 tRNA genes and 13 protein-coding genes) and one control region. The gene organizations and characters of two mitogenomes were similar with those of other mitogenomes in Coraciiformes, however the sizes and nucleotide composition of control regions in different mitogenomes were significantly different. Phylogenetic trees were constructed with both Bayesian and Maximum Likelihood methods based on mitogenome sequences from 11 families of six orders. The trees based on two different data sets supported the basal position of Psittacidae (Psittaciformes), the closest relationship between Cuculiformes (Cuculidae) and Trogoniformes (Trogonidae), and the close relationship between Coraciiformes and Piciformes. The phylogenetic placement of the clade including Cuculiformes and Trogoniformes has not been resolved in present study, which need further investigations with more molecular markers and species. The mitogenome sequences presented here provided valuable data for further taxonomic studies on Coraciiformes and other related groups.
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Tolesa Z, Bekele E, Tesfaye K, Ben Slimen H, Valqui J, Getahun A, Hartl GB, Suchentrunk F. Mitochondrial and nuclear DNA reveals reticulate evolution in hares (Lepus spp., Lagomorpha, Mammalia) from Ethiopia. PLoS One 2017; 12:e0180137. [PMID: 28767659 PMCID: PMC5540492 DOI: 10.1371/journal.pone.0180137] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 06/10/2017] [Indexed: 11/28/2022] Open
Abstract
For hares (Lepus spp., Leporidae, Lagomorpha, Mammalia) from Ethiopia no conclusive molecular phylogenetic data are available. To provide a first molecular phylogenetic model for the Abyssinian Hare (Lepus habessinicus), the Ethiopian Hare (L. fagani), and the Ethiopian Highland Hare (L. starcki) and their evolutionary relationships to hares from Africa, Eurasia, and North America, we phylogenetically analysed mitochondrial ATPase subunit 6 (ATP6; n = 153 / 416bp) and nuclear transferrin (TF; n = 155 / 434bp) sequences of phenotypically determined individuals. For the hares from Ethiopia, genotype composition at twelve microsatellite loci (n = 107) was used to explore both interspecific gene pool separation and levels of current hybridization, as has been observed in some other Lepus species. For phylogenetic analyses ATP6 and TF sequences of Lepus species from South and North Africa (L. capensis, L. saxatilis), the Anatolian peninsula and Europe (L. europaeus, L. timidus) were also produced and additional TF sequences of 18 Lepus species retrieved from GenBank were included as well. Median joining networks, neighbour joining, maximum likelihood analyses, as well as Bayesian inference resulted in similar models of evolution of the three species from Ethiopia for the ATP6 and TF sequences, respectively. The Ethiopian species are, however, not monophyletic, with signatures of contemporary uni- and bidirectional mitochondrial introgression and/ or shared ancestral polymorphism. Lepus habessinicus carries mtDNA distinct from South African L. capensis and North African L. capensis sensu lato; that finding is not in line with earlier suggestions of its conspecificity with L. capensis. Lepus starcki has mtDNA distinct from L. capensis and L. europaeus, which is not in line with earlier suggestions to include it either in L. capensis or L. europaeus. Lepus fagani shares mitochondrial haplotypes with the other two species from Ethiopia, despite its distinct phenotypic and microsatellite differences; moreover, it is not represented by a species-specific mitochondrial haplogroup, suggesting considerable mitochondrial capture by the other species from Ethiopia or species from other parts of Africa. Both mitochondrial and nuclear sequences indicate close phylogenetic relationships among all three Lepus species from Ethiopia, with L. fagani being surprisingly tightly connected to L. habessinicus. TF sequences suggest close evolutionary relationships between the three Ethiopian species and Cape hares from South and North Africa; they further suggest that hares from Ethiopia hold a position ancestral to many Eurasian and North American species.
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Affiliation(s)
- Zelalem Tolesa
- Department of Biology, Hawassa University, Hawassa, Ethiopia
- Zoologisches Institut, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Endashaw Bekele
- Department of Microbial, Cellular, and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Kassahun Tesfaye
- Department of Microbial, Cellular, and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
- Centre of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Hichem Ben Slimen
- Institut Supérieur de Biotechnologie de Béja, Avenue Habib Bourguiba, Béja, Tunisia
| | - Juan Valqui
- Zoologisches Institut, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Abebe Getahun
- Department of Zoological Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Günther B. Hartl
- Zoologisches Institut, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Franz Suchentrunk
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
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Doronina L, Churakov G, Kuritzin A, Shi J, Baertsch R, Clawson H, Schmitz J. Speciation network in Laurasiatheria: retrophylogenomic signals. Genome Res 2017; 27:997-1003. [PMID: 28298429 PMCID: PMC5453332 DOI: 10.1101/gr.210948.116] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 02/23/2017] [Indexed: 11/24/2022]
Abstract
Rapid species radiation due to adaptive changes or occupation of new ecospaces challenges our understanding of ancestral speciation and the relationships of modern species. At the molecular level, rapid radiation with successive speciations over short time periods-too short to fix polymorphic alleles-is described as incomplete lineage sorting. Incomplete lineage sorting leads to random fixation of genetic markers and hence, random signals of relationships in phylogenetic reconstructions. The situation is further complicated when you consider that the genome is a mosaic of ancestral and modern incompletely sorted sequence blocks that leads to reconstructed affiliations to one or the other relative, depending on the fixation of their shared ancestral polymorphic alleles. The laurasiatherian relationships among Chiroptera, Perissodactyla, Cetartiodactyla, and Carnivora present a prime example for such enigmatic affiliations. We performed whole-genome screenings for phylogenetically diagnostic retrotransposon insertions involving the representatives bat (Chiroptera), horse (Perissodactyla), cow (Cetartiodactyla), and dog (Carnivora), and extracted among 162,000 preselected cases 102 virtually homoplasy-free, phylogenetically informative retroelements to draw a complete picture of the highly complex evolutionary relations within Laurasiatheria. All possible evolutionary scenarios received considerable retrotransposon support, leaving us with a network of affiliations. However, the Cetartiodactyla-Carnivora relationship as well as the basal position of Chiroptera and an ancestral laurasiatherian hybridization process did exhibit some very clear, distinct signals. The significant accordance of retrotransposon presence/absence patterns and flanking nucleotide changes suggest an important influence of mosaic genome structures in the reconstruction of species histories.
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Affiliation(s)
- Liliya Doronina
- Institute of Experimental Pathology, ZMBE, University of Münster, 48149 Münster, Germany
| | - Gennady Churakov
- Institute of Experimental Pathology, ZMBE, University of Münster, 48149 Münster, Germany
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
| | - Andrej Kuritzin
- Department of System Analysis, Saint Petersburg State Institute of Technology, 190013 St. Petersburg, Russia
| | - Jingjing Shi
- Institute of Experimental Pathology, ZMBE, University of Münster, 48149 Münster, Germany
| | - Robert Baertsch
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
| | - Hiram Clawson
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
| | - Jürgen Schmitz
- Institute of Experimental Pathology, ZMBE, University of Münster, 48149 Münster, Germany
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Feijoo M, Parada A. Macrosystematics of eutherian mammals combining HTS data to expand taxon coverage. Mol Phylogenet Evol 2017; 113:76-83. [PMID: 28487261 DOI: 10.1016/j.ympev.2017.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 05/04/2017] [Accepted: 05/04/2017] [Indexed: 02/04/2023]
Abstract
In the last few years high-throughput sequencing technologies have permitted significant advances in mammalian phylogenetic studies from a genomic perspective. However, these studies have been restricted to a sparse number of species with available reference genomes. Thus, several issues inside the eutherian mammals phylogeny remain unresolved. This may be due in part to limited taxon sampling, as taxonomic density is known to affect phylogenetic resolution. In this context, we present a protocol to increase taxon coverage using high-throughput sequencing data (RNA or DNA) generated for other biological studies and available in public databases. Following this procedure we addressed pending or controversial issues concerning the phylogenetic position of Dermoptera, Pholidota and Chiroptera, considering multiple and independent loci. Also for Chiroptera and Arctoidea we evaluated the relationships of the lineages that compose it. Although the maximum number of genes used is moderate (95), in some cases taxon coverage doubles that of previous related studies. Globally, all coalescent-based (STAR, MP-EST and ASTRAL) and concatenated (IQ-TREE and BEAST2) methods used for species tree reconstruction were consistent to each other and most of interrogated nodes received high statistical support.
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Affiliation(s)
- M Feijoo
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo CP 11400, Uruguay.
| | - A Parada
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia CP 5090000, Chile.
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Ben Slimen H, Schaschl H, Knauer F, Suchentrunk F. Selection on the mitochondrial ATP synthase 6 and the NADH dehydrogenase 2 genes in hares (Lepus capensis L., 1758) from a steep ecological gradient in North Africa. BMC Evol Biol 2017; 17:46. [PMID: 28173765 PMCID: PMC5297179 DOI: 10.1186/s12862-017-0896-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 01/26/2017] [Indexed: 11/30/2022] Open
Abstract
Background Recent studies of selection on mitochondrial (mt) OXPHOS genes suggest adaptation due mainly to environmental variation. In this context, Tunisian hares that display several external phenotypes with phylogenetically rather homogenous gene pool and shallow population structure provide a good precondition to detect positive selection on mt genes related to environmental/climatic variation, specifically ambient temperature and precipitation. Results We used codon-based methods along with population genetic data to test for positive selection on ATPase synthase 6 (ATP6) and NADH dehydrogenase 2 (ND2) of cape hares (Lepus capensis) collected along a steep ecological gradient in Tunisia. We found significantly higher differentiation at the ATP6 locus across Tunisia, with sub-humid Mediterranean, semi-arid, and arid Sahara climate than for fourteen unlinked supposedly neutrally evolving nuclear microsatellites and mt control region sequences. This suggested positive selection on ATP6 sequences, which was confirmed by several codon-based tests for one sequence site that together with a second site translated into four different amino acids. Positive selection on ND2 sequences was also confirmed by several codon-based tests. The corresponding frequencies of the two most prevalent variants at each locus varied significantly across climate regions, and our logistic general linear models of occurrence of those proteins indicated significant effects of mean annual temperature for ATP6 and mean minimum temperature of the coldest month of the year for ND2, independent of geographical location, annual precipitation, and the respective co-occurring protein at the second locus. Moreover, presence of the ancestral ATP6 protein, as inferred from phylogenetic networks, was positively affected by the simultaneous presence of the derived ND2 protein and vice versa, independent of temperature, precipitation, or geographic location. Finally, we obtained a significant coevolution signal for the ancestral ATP6 and derived ND2 sequences and vice versa. Conclusions positive selection was strongly suggested by the population genetic approach and the codon-based tests in both mtDNA genes. Moreover, the two most prevalent proteins at the ATP6 locus were distributed at significantly varying frequencies across the study area with a significant effect of mean annual temperature on the occurrence of the ATP6 proteins independent of geographical coordinates and the co-occuring ND2 protein variant. For ND2, occurrence of the two most frequent protein variants was significantly influenced by the mean minimum temperature of the coldest month, independent of the co-occurring ATP6 protein variant and geographical coordinates. This strongly suggests direct involvement of ambient temperature in the adaptation of the studied mtOXPHOS genes. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0896-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hichem Ben Slimen
- UR Génomique des Insectes Ravageurs des Cultures d'Intérêt Agronomique (GIRC), Université de Tunis El-Manar, 2092, El Manar, Tunisia. .,Institut Supérieur de Biotechnologie de Béja, Beja, 9000, Tunisia.
| | - Helmut Schaschl
- Department of Anthropology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Felix Knauer
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstrasse 1, 1160, Vienna, Austria
| | - Franz Suchentrunk
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstrasse 1, 1160, Vienna, Austria
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Ruiz-García M, Chacón D, Plese T, Schuler I, Shostell JM. Mitogenomics phylogenetic relationships of the current sloth's genera and species (Bradypodidae and Megalonychidae). Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:281-299. [PMID: 28129732 DOI: 10.1080/24701394.2016.1275602] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We sequenced the complete mitogenome of 39 sloths (19 Bradypus variegatus, 4 B. tridactylus, 1 B. pygmaeus, 1 B. torquatus, 4 Choloepus didactylus, and 10 C. hoffmanni). A Bayesian tree (BI) indicated a temporal split between Bradypus and Choloepus around 31 million years ago (MYA, Oligocene) and the other major splits within each genera during the Miocene and Pliocene. A haplotype network (MJN) estimated a lower temporal split between the sloth genera (around 23.5 MYA). Both methods detected the ancestor of B. torquatus as the first to diverge within Bradypus (21 for BI and 19 MJN), followed by that of the ancestor of B. tridactylus. The split of B. pygmaeus from the common ancestor with B. variegatus was around 12 MYA (BI) or 4.3 MYA (MJN). The splits among the previous populations of B. variegatus began around 8 MYA (BI) or 3.6 MYA (MJN). The trans-Andean population was the first to diverge from the remaining cis-Andean populations of B. variegatus. The genetic differentiation of the trans-Andean B. variegatus population relative to the cis-Andean B. variegatus is similar to that found for different species of sloths. The mitogenomic analysis resolved the differentiation of C. hoffmanni from the C. didactylus individuals of the Guiana Shield. However, one C. didactylus from the Colombian Amazon specimen was inside the C. hoffmanni clade. This could be the first example of possible natural hybridization in the Amazon of both Choloepus taxa or the existence of un-differentiable phenotypes of these two species in some Amazonian areas.
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Affiliation(s)
- Manuel Ruiz-García
- a Departamento de Biología, Facultad de Ciencias , Pontificia Universidad Javeriana , Bogotá , DC , Colombia
| | - Diego Chacón
- a Departamento de Biología, Facultad de Ciencias , Pontificia Universidad Javeriana , Bogotá , DC , Colombia
| | | | - Ingrid Schuler
- a Departamento de Biología, Facultad de Ciencias , Pontificia Universidad Javeriana , Bogotá , DC , Colombia
| | - Joseph Mark Shostell
- c Math, Science and Technology Department , University of Minnesota Crookston , Crookston , MN , USA
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Hung CM, Drovetski SV, Zink RM. Matching loci surveyed to questions asked in phylogeography. Proc Biol Sci 2016; 283:20152340. [PMID: 26962145 DOI: 10.1098/rspb.2015.2340] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Although mitochondrial DNA (mtDNA) has long been used for assessing genetic variation within and between populations, its workhorse role in phylogeography has been criticized owing to its single-locus nature. The only choice for testing mtDNA results is to survey nuclear loci, which brings into contrast the difference in locus effective size and coalescence times. Thus, it remains unclear how erroneous mtDNA-based estimates of species history might be, especially for evolutionary events in the recent past. To test the robustness of mtDNA and nuclear sequences in phylogeography, we provide one of the largest paired comparisons of summary statistics and demographic parameters estimated from mitochondrial, five Z-linked and 10 autosomal genes of 30 avian species co-distributed in the Caucasus and Europe. The results suggest that mtDNA is robust in estimating inter-population divergence but not in intra-population diversity, which is sensitive to population size change. Here, we provide empirical evidence showing that mtDNA was more likely to detect population divergence than any other single locus owing to its smaller Ne and thus faster coalescent time. Therefore, at least in birds, numerous studies that have based their inferences of phylogeographic patterns solely on mtDNA should not be readily dismissed.
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Affiliation(s)
- Chih-Ming Hung
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Sergei V Drovetski
- Division of Birds, National Museum of Natural History, Smithsonian Institution, Washington, DC 20004, USA
| | - Robert M Zink
- Bell Museum and Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, MN, USA
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49
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Kumar VP, Thakur M, Rajpoot A, Joshi BD, Nigam P, Ahmad K, Kumar D, Goyal SP. Resolving the phylogenetic status and taxonomic relationships of the Hangul (Cervus elaphus hanglu) in the family Cervidae. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:835-842. [PMID: 27937071 DOI: 10.1080/24701394.2016.1197217] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The Hangul (Cervus elaphus hanglu) is a "Least Concern" deer species, and it is the only survivor of the Red Deer group in the Indian subcontinent. The phylogenetic status of the Hangul relative to the other members of the family Cervidae is not known because sequence data are not available in public databases. Therefore, this study was carried out to determine the phylogenetic status and delineate the genetic boundaries of the Hangul with respect to the other Red Deer subspecies on the basis of cytochrome b gene sequence data (ca 421 bp). There are three major monophyletic groups of the Red Deer in the phylogenetic tree, which are referred to as the western (Hap-01 to Hap-10), eastern (Hap-11 to Hap-20) and tarim (Hap-21 to Hap-25) groups. The overall haplotype diversity and per-site nucleotide diversity were 0.9771 (±0.0523) and 0.0388 (±0.00261), respectively. In the phylogenetic tree, the Hangul clustered with the tarim group (Yarkand and Bactrian Red Deer) with a strong bootstrap support (92%) and was found to be genetically closer to the Bactrian Red Deer than to the Yarkand Red Deer. Our molecular analysis supported the idea that the Hangul diverged from the Bactrian Red Deer and migrated to India from Tajikistan approximately 1.2 MYA.
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Affiliation(s)
- Ved P Kumar
- a Wildlife Institute of India , Chandrabani , Dehradun , Uttarakhand , India.,b Department of Zoology, Veer Kunwar Singh University , Arrah , Bihar , India
| | - Mukesh Thakur
- c Amity Institute of Wildlife Sciences, Amity University , Noida , Uttar Pradesh , India
| | - Ankita Rajpoot
- d Zoological Survey of India, NRC , Dehradun , Uttarakhand , India
| | - Bhim Dutt Joshi
- a Wildlife Institute of India , Chandrabani , Dehradun , Uttarakhand , India
| | - Parag Nigam
- a Wildlife Institute of India , Chandrabani , Dehradun , Uttarakhand , India
| | - Khursheed Ahmad
- e Centre for Mountain Wildlife Sciences, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology , Srinagar , Jammu & Kashmir , India
| | - Dhyanendra Kumar
- b Department of Zoology, Veer Kunwar Singh University , Arrah , Bihar , India
| | - Surendra P Goyal
- a Wildlife Institute of India , Chandrabani , Dehradun , Uttarakhand , India
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50
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A new complete mitogenome of the critically endangered Chinese pangolin Manis pentadactyla. CONSERV GENET RESOUR 2016. [DOI: 10.1007/s12686-016-0586-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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