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Stejskalova K, Janova E, Splichalova P, Futas J, Oppelt J, Vodicka R, Horin P. Twelve toll-like receptor (TLR) genes in the family Equidae - comparative genomics, selection and evolution. Vet Res Commun 2024; 48:725-741. [PMID: 37874499 PMCID: PMC10998774 DOI: 10.1007/s11259-023-10245-4] [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: 07/18/2023] [Accepted: 10/18/2023] [Indexed: 10/25/2023]
Abstract
Toll-like receptors (TLRs) represent an important part of the innate immune system. While human and murine TLRs have been intensively studied, little is known about TLRs in non-model species. The order Perissodactyla comprises a variety of free-living and domesticated species exposed to different pathogens in different habitats and is therefore suitable for analyzing the diversity and evolution of immunity-related genes. We analyzed TLR genes in the order Perissodactyla with a focus on the family Equidae. Twelve TLRs were identified by bioinformatic analyses of online genomic resources; their sequences were confirmed in equids by genomic DNA re-sequencing of a panel of nine species. The expression of TLR11 and TLR12 was confirmed in the domestic horse by cDNA sequencing. Phylogenetic reconstruction of the TLR gene family in Perissodactyla identified six sub-families. TLR4 clustered together with TLR5; the TLR1-6-10 subfamily showed a high degree of sequence identity. The average estimated evolutionary divergence of all twelve TLRs studied was 0.3% among the Equidae; the most divergent CDS were those of Equus caballus and Equus hemionus kulan (1.34%) in the TLR3, and Equus africanus somaliensis and Equus quagga antiquorum (2.1%) in the TLR1 protein. In each TLR gene, there were haplotypes shared between equid species, most extensively in TLR3 and TLR9 CDS, and TLR6 amino acid sequence. All twelve TLR genes were under strong negative overall selection. Signatures of diversifying selection in specific codon sites were detected in all TLRs except TLR8. Differences in the selection patterns between virus-sensing and non-viral TLRs were observed.
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Affiliation(s)
- K Stejskalova
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, 61242, Czech Republic
| | - E Janova
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, 61242, Czech Republic
- RG Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - P Splichalova
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, 61242, Czech Republic
| | - J Futas
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, 61242, Czech Republic
- RG Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - J Oppelt
- RG Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czech Republic
| | | | - P Horin
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, 61242, Czech Republic.
- RG Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czech Republic.
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Brannan EO, Hartley GA, O’Neill RJ. Mechanisms of Rapid Karyotype Evolution in Mammals. Genes (Basel) 2023; 15:62. [PMID: 38254952 PMCID: PMC10815390 DOI: 10.3390/genes15010062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
Chromosome reshuffling events are often a foundational mechanism by which speciation can occur, giving rise to highly derivative karyotypes even amongst closely related species. Yet, the features that distinguish lineages prone to such rapid chromosome evolution from those that maintain stable karyotypes across evolutionary time are still to be defined. In this review, we summarize lineages prone to rapid karyotypic evolution in the context of Simpson's rates of evolution-tachytelic, horotelic, and bradytelic-and outline the mechanisms proposed to contribute to chromosome rearrangements, their fixation, and their potential impact on speciation events. Furthermore, we discuss relevant genomic features that underpin chromosome variation, including patterns of fusions/fissions, centromere positioning, and epigenetic marks such as DNA methylation. Finally, in the era of telomere-to-telomere genomics, we discuss the value of gapless genome resources to the future of research focused on the plasticity of highly rearranged karyotypes.
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Affiliation(s)
- Emry O. Brannan
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; (E.O.B.); (G.A.H.)
| | - Gabrielle A. Hartley
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; (E.O.B.); (G.A.H.)
| | - Rachel J. O’Neill
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; (E.O.B.); (G.A.H.)
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
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Appeltant R, Hermes R, Holtze S, Modina SC, Galli C, Bjarkadottir BD, Adeniran BV, Wei X, Swegen A, Hildebrandt TB, Williams SA. The neonatal southern white rhinoceros ovary contains oogonia in germ cell nests. Commun Biol 2023; 6:1049. [PMID: 37848538 PMCID: PMC10582104 DOI: 10.1038/s42003-023-05256-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 08/18/2023] [Indexed: 10/19/2023] Open
Abstract
The northern white rhinoceros is functionally extinct with only two females left. Establishing methods to culture ovarian tissues, follicles, and oocytes to generate eggs will support conservation efforts using in vitro embryo production. To the best of our knowledge, this is the first description of the structure and molecular signature of any rhinoceros, more specifically, we describe the neonatal and adult southern white rhinoceros (Ceratotherium simum simum) ovary; the closest relation of the northern white rhinoceros. Interestingly, all ovaries contain follicles despite advanced age. Analysis of the neonate reveals a population of cells molecularly characterised as mitotically active, pluripotent with germ cell properties. These results indicate that unusually, the neonatal ovary still contains oogonia in germ cell nests at birth, providing an opportunity for fertility preservation. Therefore, utilising ovaries from stillborn and adult rhinoceros can provide cells for advanced assisted reproductive technologies and investigating the neonatal ovaries of other endangered species is crucial for conservation.
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Affiliation(s)
- Ruth Appeltant
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Women's Centre, Level 3, John Radcliffe Hospital, Oxford, UK
- Gamete Research Centre, Veterinary Physiology and Biochemistry, Department of Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - Robert Hermes
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str 17, D-10315, Berlin, Germany
| | - Susanne Holtze
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str 17, D-10315, Berlin, Germany
| | - Silvia Clotilde Modina
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Via dell'Università 6, 26900, Lodi, Italy
| | - Cesare Galli
- Avantea srl, Laboratory of Reproductive Technologies, Via Porcellasco 7/F, 26100, Cremona, Italy
- Fondazione Avantea, 26100, Cremona, Italy
| | - Briet D Bjarkadottir
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Women's Centre, Level 3, John Radcliffe Hospital, Oxford, UK
| | - Babatomisin V Adeniran
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Women's Centre, Level 3, John Radcliffe Hospital, Oxford, UK
| | - Xi Wei
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Women's Centre, Level 3, John Radcliffe Hospital, Oxford, UK
| | - Aleona Swegen
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Women's Centre, Level 3, John Radcliffe Hospital, Oxford, UK
- Priority Research Centre for Reproductive Science, University of Newcastle, Callaghan, 2308, NSW, Australia
| | - Thomas Bernd Hildebrandt
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Via dell'Università 6, 26900, Lodi, Italy
- Freie Universität Berlin, D-14195, Berlin, Germany
| | - Suzannah A Williams
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Women's Centre, Level 3, John Radcliffe Hospital, Oxford, UK.
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Klećkowska-Nawrot J, Goździewska-Harłajczuk K, Kupczyńska M, Kaleta-Kuratewicz K, Kuropka P, Barszcz K. Anatomical, Histological and Histochemical Observations of the Eyelids and Orbital Glands in the Lowland Tapir ( Tapirus terrestris Linnaeus, 1785) (Perissodactyla: Ceratomorpha). Animals (Basel) 2023; 13:2081. [PMID: 37443879 DOI: 10.3390/ani13132081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/18/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
The lowland tapir is one of four species belonging to the Tapiridae family of the Ceratomorpha suborder, similar to Rhinocerotidae. This study describes anatomy with morphometry, histology (hematoxylin and eosin, Masson-Goldner trichrome, Movat pentachrome, mucicarmine, picro-Mallory trichrome) and histochemistry (PAS, AB pH 1.0, AB pH 2.5; AB pH2.5/PAS and HDI) of the upper and lower eyelids, and superficial gland of the third eyelid with the third eyelid, deep gland of the third eyelid, and lacrimal gland. The aim of the work is to show the features of the above-mentioned structures typical only for Tapiridae, as well as to show the presence of similarities and differences between the families forming the order Perissodactyla. The eyelashes on the upper eyelid were long, while those of the lower eyelid were short and much less prominent. In the upper and lower eyelid sebaceous glands, a characteristic simple alveolar gland producing a mucus-like secretion and poorly developed tarsal glands were observed. The marginal zone of the posterior surface of the eyelids was covered by stratified columnar epithelium with 18-21 layers of nucleated cells, while the bulbar zone of these surfaces was covered by cubic multilayer epithelium with 6-11 non-keratinized layers of cells and with sparse goblet cells. In only lower eyelids, numerous lymphoid nodules, diffuse lymphocytes and high endothelial venules were observed. The superficial gland was an acinar complex which secreted mucous and contained plasma cells within the interlobular and interlobular connective tissue. The upper and lower branches of the third eyelid were the shape of a bent "caudal fin" and were composed of hyaline cartilage, and they contained conjunctiva associated lymphoid tissue (CALT). The deep gland was also an acinar complex producing a serous character and having numerous diffuse lymphocytes. The lacrimal gland was an acinar complex producing seromucous secretions and had numerous plasma cells located in the glandular interstitium. The results of our research indicate that the features of the anatomy of the eyelids and orbital region in the lowland tapir are also typical of the family Tapiridae, but also have features common to the families Equidae and Rhinocerotidae. We confirm the presence of poorly developed tarsal glands in both eyelids as well as presence of a palpebral part of the lacrimal gland in the upper eyelid, which is typical only to Tapirus terrestris.
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Affiliation(s)
- Joanna Klećkowska-Nawrot
- Division of Animal Anatomy, Department of Biostructure and Animal Physiology, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Kożuchowska 1, 51-631 Wroclaw, Poland
| | - Karolina Goździewska-Harłajczuk
- Division of Animal Anatomy, Department of Biostructure and Animal Physiology, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Kożuchowska 1, 51-631 Wroclaw, Poland
| | - Marta Kupczyńska
- Department of Morphological Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Nowoursynowska 159, 02-787 Warsaw, Poland
| | - Katarzyna Kaleta-Kuratewicz
- Division of Animal Histology, Department of Biostructure and Animal Physiology, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Norwida 25, 50-375 Wroclaw, Poland
| | - Piotr Kuropka
- Division of Animal Histology, Department of Biostructure and Animal Physiology, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Norwida 25, 50-375 Wroclaw, Poland
| | - Karolina Barszcz
- Department of Morphological Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Nowoursynowska 159, 02-787 Warsaw, Poland
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Tsangaras K, Mayer J, Mirza O, Dayaram A, Higgins DP, Bryant B, Campbell-Ward M, Sangster C, Casteriano A, Höper D, Beer M, Greenwood AD. Evolutionarily Young African Rhinoceros Gammaretroviruses. J Virol 2023; 97:e0193222. [PMID: 37022231 PMCID: PMC10134878 DOI: 10.1128/jvi.01932-22] [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: 12/16/2022] [Accepted: 03/17/2023] [Indexed: 04/07/2023] Open
Abstract
High-throughput sequences were generated from DNA and cDNA from four Southern white rhinoceros (Ceratotherium simum simum) located in the Taronga Western Plain Zoo in Australia. Virome analysis identified reads that were similar to Mus caroli endogenous gammaretrovirus (McERV). Previous analysis of perissodactyl genomes did not recover gammaretroviruses. Our analysis, including the screening of the updated white rhinoceros (Ceratotherium simum) and black rhinoceros (Diceros bicornis) draft genomes identified high-copy orthologous gammaretroviral ERVs. Screening of Asian rhinoceros, extinct rhinoceros, domestic horse, and tapir genomes did not identify related gammaretroviral sequences in these species. The newly identified proviral sequences were designated SimumERV and DicerosERV for the white and black rhinoceros retroviruses, respectively. Two long terminal repeat (LTR) variants (LTR-A and LTR-B) were identified in the black rhinoceros, with different copy numbers associated with each (n = 101 and 373, respectively). Only the LTR-A lineage (n = 467) was found in the white rhinoceros. The African and Asian rhinoceros lineages diverged approximately 16 million years ago. Divergence age estimation of the identified proviruses suggests that the exogenous retroviral ancestor of the African rhinoceros ERVs colonized their genomes within the last 8 million years, a result consistent with the absence of these gammaretroviruses from Asian rhinoceros and other perissodactyls. The black rhinoceros germ line was colonized by two lineages of closely related retroviruses and white rhinoceros by one. Phylogenetic analysis indicates a close evolutionary relationship with ERVs of rodents including sympatric African rats, suggesting a possible African origin of the identified rhinoceros gammaretroviruses. IMPORTANCE Rhinoceros genomes were thought to be devoid of gammaretroviruses, as has been determined for other perissodactyls (horses, tapirs, and rhinoceros). While this may be true of most rhinoceros, the African white and black rhinoceros genomes have been colonized by evolutionarily young gammaretroviruses (SimumERV and DicerosERV for the white and black rhinoceros, respectively). These high-copy endogenous retroviruses (ERVs) may have expanded in multiple waves. The closest relative of SimumERV and DicerosERV is found in rodents, including African endemic species. Restriction of the ERVs to African rhinoceros suggests an African origin for the rhinoceros gammaretroviruses.
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Affiliation(s)
- Kyriakos Tsangaras
- Department of Life and Health Sciences, University of Nicosia, Nicosia, Cyprus
| | - Jens Mayer
- Institute of Human Genetics, Medical Faculty, University of Saarland, Homburg, Germany
| | - Omar Mirza
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | - Anisha Dayaram
- Institute of Neurophysiology, Charité—Universitätsmedizin Berlin, Berlin, Germany
| | - Damien P. Higgins
- Sydney School of Veterinary Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Benn Bryant
- Taronga Western Plains Zoo, Dubbo, New South Wales, Australia
| | | | - Cheryl Sangster
- Taronga Conservation Society Australia, Mosman, New South Wales, Australia
| | - Andrea Casteriano
- Sydney School of Veterinary Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Alex D. Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
- School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
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Ghosh T, Kumar S, Sharma K, Kakati P, Sharma A, Mondol S. Consideration of genetic variation and evolutionary history in future conservation of Indian one-horned rhinoceros (Rhinoceros unicornis). BMC Ecol Evol 2022; 22:92. [PMID: 35858827 PMCID: PMC9301832 DOI: 10.1186/s12862-022-02045-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 07/14/2022] [Indexed: 11/11/2022] Open
Abstract
Background The extant members of the Asian rhinos have experienced severe population and range declines since Pleistocene through a combination of natural and anthropogenic factors. The one-horned rhino is the only Asian species recovered from such conditions but most of the extant populations are reaching carrying capacity. India currently harbours ~ 83% of the global wild one-horned rhino populations distributed across seven protected areas. Recent assessments recommend reintroduction-based conservation approaches for the species, and implementation of such efforts would greatly benefit from detailed genetic assessments and evolutionary history of these populations. Using mitochondrial data, we investigated the phylogeography, divergence and demographic history of one-horned rhinos across its Indian range. Results We report the first complete mitogenome from all the extant Indian wild one-horned rhino populations (n = 16 individuals). Further, we identified all polymorphic sites and assessed rhino phylogeography (2531 bp mtDNA, n = 111 individuals) across India. Results showed 30 haplotypes distributed as three distinct genetic clades (Fst value 0.68–1) corresponding to the states of Assam (n = 28 haplotypes), West Bengal and Uttar Pradesh (both monomorphic). The reintroduced population of Uttar Pradesh showed maternal signatures of Chitwan National Park, Nepal. Mitochondrial phylogenomics suggests one-horned rhino diverged from its recent common ancestors ~ 950 Kya and different populations (Assam, West Bengal and Uttar Pradesh/Nepal) coalesce at ~ 190–50 Kya, corroborating with the paleobiogeography history of the Indian subcontinent. Further, the demography analyses indicated historical decline in female effective population size ~ 300–200 Kya followed by increasing trends during ~ 110–60 Kya. Conclusion The phylogeography and phylogenomic outcomes suggest recognition of three ‘Evolutionary Significant Units (ESUs)’ in Indian rhino. With ongoing genetic isolation of the current populations, future management efforts should focus on identifying genetically variable founder animals and consider periodic supplementation events while planning future rhino reintroduction programs in India. Such well-informed, multidisciplinary approach will be the only way to ensure evolutionary, ecological and demographic stability of the species across its range. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-02045-2.
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Not just for males: flehmen as a tool for detection of reproductive status and individual recognition across sexes in four African equid species. Behav Processes 2022; 203:104773. [DOI: 10.1016/j.beproc.2022.104773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 11/20/2022]
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Evolution of the Family Equidae, Subfamily Equinae, in North, Central and South America, Eurasia and Africa during the Plio-Pleistocene. BIOLOGY 2022; 11:biology11091258. [PMID: 36138737 PMCID: PMC9495906 DOI: 10.3390/biology11091258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/17/2022] [Accepted: 08/19/2022] [Indexed: 11/17/2022]
Abstract
Studies of horse evolution arose during the middle of the 19th century, and several hypotheses have been proposed for their taxonomy, paleobiogeography, paleoecology and evolution. The present contribution represents a collaboration of 19 multinational experts with the goal of providing an updated summary of Pliocene and Pleistocene North, Central and South American, Eurasian and African horses. At the present time, we recognize 114 valid species across these continents, plus 4 North African species in need of further investigation. Our biochronology and biogeography sections integrate Equinae taxonomic records with their chronologic and geographic ranges recognizing regional biochronologic frameworks. The paleoecology section provides insights into paleobotany and diet utilizing both the mesowear and light microscopic methods, along with calculation of body masses. We provide a temporal sequence of maps that render paleoclimatic conditions across these continents integrated with Equinae occurrences. These records reveal a succession of extinctions of primitive lineages and the rise and diversification of more modern taxa. Two recent morphological-based cladistic analyses are presented here as competing hypotheses, with reference to molecular-based phylogenies. Our contribution represents a state-of-the art understanding of Plio-Pleistocene Equus evolution, their biochronologic and biogeographic background and paleoecological and paleoclimatic contexts.
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Roberts EK, Tardif S, Wright EA, Platt RN, Bradley RD, Hardy DM. Rapid divergence of a gamete recognition gene promoted macroevolution of Eutheria. Genome Biol 2022; 23:155. [PMID: 35821049 PMCID: PMC9275260 DOI: 10.1186/s13059-022-02721-y] [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: 11/18/2021] [Accepted: 06/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Speciation genes contribute disproportionately to species divergence, but few examples exist, especially in vertebrates. Here we test whether Zan, which encodes the sperm acrosomal protein zonadhesin that mediates species-specific adhesion to the egg's zona pellucida, is a speciation gene in placental mammals. RESULTS Genomic ontogeny reveals that Zan arose by repurposing of a stem vertebrate gene that was lost in multiple lineages but retained in Eutheria on acquiring a function in egg recognition. A 112-species Zan sequence phylogeny, representing 17 of 19 placental Orders, resolves all species into monophyletic groups corresponding to recognized Orders and Suborders, with <5% unsupported nodes. Three other rapidly evolving germ cell genes (Adam2, Zp2, and Prm1), a paralogous somatic cell gene (TectA), and a mitochondrial gene commonly used for phylogenetic analyses (Cytb) all yield trees with poorer resolution than the Zan tree and inferior topologies relative to a widely accepted mammalian supertree. Zan divergence by intense positive selection produces dramatic species differences in the protein's properties, with ordinal divergence rates generally reflecting species richness of placental Orders consistent with expectations for a speciation gene that acts across a wide range of taxa. Furthermore, Zan's combined phylogenetic utility and divergence exceeds those of all other genes known to have evolved in Eutheria by positive selection, including the only other mammalian speciation gene, Prdm9. CONCLUSIONS Species-specific egg recognition conferred by Zan's functional divergence served as a mode of prezygotic reproductive isolation that promoted the extraordinary adaptive radiation and success of Eutheria.
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Affiliation(s)
- Emma K. Roberts
- Department of Biological Sciences, Texas Tech University, Lubbock, TX USA
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX USA
| | - Steve Tardif
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX USA
- Reproductive Biology Division, JangoBio, Fitchburg, WI USA
| | - Emily A. Wright
- Department of Biological Sciences, Texas Tech University, Lubbock, TX USA
| | - Roy N. Platt
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX USA
| | - Robert D. Bradley
- Department of Biological Sciences, Texas Tech University, Lubbock, TX USA
- Natural Science Research Laboratory, Museum of Texas Tech University, Lubbock, TX USA
| | - Daniel M. Hardy
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX USA
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Pluháček J, Tučková V, Šárová R, King SRB. Why wait to mark? Possible reasons behind latency from olfactory exploration to overmarking in four African equid species. Anim Cogn 2022; 25:1443-1452. [PMID: 35554766 DOI: 10.1007/s10071-022-01625-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 03/30/2022] [Accepted: 04/02/2022] [Indexed: 11/30/2022]
Abstract
Whereas most studies on overmarking in mammals analysed the rate of overmarking, that those investigate time between exploration of an olfactory stimulus and the response to it remain less common, with inconsistent results. We examined the latency in time between elimination by the sender and sniffing by the receiver, and from sniffing and overmarking, in four captive African equid species to explore differences among species, and among age and sex classes. We investigated these latency time periods in light of three potential hypotheses explaining overmarking behaviour in equids: social bonds, group cohesion, and intrasexual competition. Analysing 1684 events of sniffing and 719 of overmarking among 130 individuals, we found that (i) the time from elimination to overmarking was shorter among female friends and in parent-offspring dyads, proving support to the social bond hypothesis; (ii) intraspecific differences in time periods do not reflect the social organisation of species, thus not supporting the group cohesion hypothesis; (iii) males were more attracted to elimination of conspecifics than females, and female's eliminations were inspected longer, in line with the sexual competition hypothesis and/or reproductive behaviour. In addition, we found that the younger foals came to sniff eliminations faster than older ones, and in larger groups foals devoted longer time to sniffing the elimination before overmarking. We concluded that examination of the elimination could be driven by motivations other than the decision to overmark. Whereas overmarking serves to express bonds to a familiar individual, the latency of overmarking reflects more reproductive interests.
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Affiliation(s)
- Jan Pluháček
- Department of Ethology, Institute of Animal Science, Přátelství 815, Uhříněves, 10400, Prague, Czech Republic.
- Ostrava Zoo, Michálkovická 2081/197, 71000, Ostrava, Czech Republic.
- Departement of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 71000, Ostrava, Czech Republic.
| | - Vladimíra Tučková
- Department of Zoology, Faculty of Science, University of South Bohemia, Branišovská 1760, 37005, České Budějovice, Czech Republic
| | - Radka Šárová
- Department of Ethology, Institute of Animal Science, Přátelství 815, Uhříněves, 10400, Prague, Czech Republic
| | - Sarah R B King
- Natural Resource Ecology Laboratory, Warner College of Natural Resources, Colorado State University, Campus Delivery 1499, Fort Collins, USA
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Gregor R, Probst M, Eyal S, Aksenov A, Sasson G, Horovitz I, Dorrestein PC, Meijler MM, Mizrahi I. Mammalian gut metabolomes mirror microbiome composition and host phylogeny. THE ISME JOURNAL 2022; 16:1262-1274. [PMID: 34903850 PMCID: PMC9038745 DOI: 10.1038/s41396-021-01152-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 10/18/2021] [Accepted: 11/09/2021] [Indexed: 12/19/2022]
Abstract
In the past decade, studies on the mammalian gut microbiome have revealed that different animal species have distinct gut microbial compositions. The functional ramifications of this variation in microbial composition remain unclear: do these taxonomic differences indicate microbial adaptations to host-specific functionality, or are these diverse microbial communities essentially functionally redundant, as has been indicated by previous metagenomics studies? Here, we examine the metabolic content of mammalian gut microbiomes as a direct window into ecosystem function, using an untargeted metabolomics platform to analyze 101 fecal samples from a range of 25 exotic mammalian species in collaboration with a zoological center. We find that mammalian metabolomes are chemically diverse and strongly linked to microbiome composition, and that metabolome composition is further correlated to the phylogeny of the mammalian host. Specific metabolites enriched in different animal species included modified and degraded host and dietary compounds such as bile acids and triterpenoids, as well as fermentation products such as lactate and short-chain fatty acids. Our results suggest that differences in microbial taxonomic composition are indeed translated to host-specific metabolism, indicating that taxonomically distant microbiomes are more functionally diverse than redundant.
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Affiliation(s)
- Rachel Gregor
- Department of Chemistry, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Maraike Probst
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Stav Eyal
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Alexander Aksenov
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Goor Sasson
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Igal Horovitz
- The Zoological Center Tel Aviv-Ramat Gan, Ramat Gan, Israel
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Michael M Meijler
- Department of Chemistry, Ben-Gurion University of the Negev, Be'er Sheva, Israel.
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel.
| | - Itzhak Mizrahi
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel.
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel.
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12
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13
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Houssaye A, de Perthuis A, Houée G. Sesamoid bones also show functional adaptation in their microanatomy-The example of the patella in Perissodactyla. J Anat 2022; 240:50-65. [PMID: 34402049 PMCID: PMC8655183 DOI: 10.1111/joa.13530] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 07/21/2021] [Accepted: 07/21/2021] [Indexed: 11/27/2022] Open
Abstract
The patella is the largest sesamoid bone of the skeleton. It is strongly involved in the knee, improving output force and velocity of the knee extensors, and thus plays a major role in locomotion and limb stability. However, the relationships between its structure and functional constraints, that would enable a better understanding of limb bone functional adaptations, are poorly known. This contribution proposes a comparative analysis, both qualitative and quantitative, of the microanatomy of the whole patella in perissodactyls, which show a wide range of morphologies, masses, and locomotor abilities, in order to investigate how the microanatomy of the patella adapts to evolutionary constraints. The inner structure of the patella consists of a spongiosa surrounded by a compact cortex. Contrary to our expectations, there is no increase in compactness with bone size, and thus body size and weight, but only an increase in the tightness of the spongiosa. No particular thickening of the cortex associated with muscle insertions is noticed but a strong thickening is observed anteriorly at about mid-length, where the strong intermediate patellar ligament inserts. The trabeculae are mainly oriented perpendicularly to the posterior articular surface, which highlights that the main stress is anteroposteriorly directed, maintaining the patella against the femoral trochlea. Conversely, anteriorly, trabeculae are rather circumferentially oriented, following the insertion of the patellar ligament and, possibly also, of the quadriceps tendon. A strong variation is observed among perissodactyl families but also intraspecifically, which is in accordance with previous studies suggesting a higher variability in sesamoid bones. Clear trends are nevertheless observed between the three families. Equids have a much thinner cortex than ceratomorphs. Rhinos and equids, both characterized by a development of the medial border, show an increase in trabecular density laterally suggesting stronger stresses laterally. The inner structure in tapirs is more homogeneous despite the absence of medial development of the medial border with no "compensation" of the inner structure, which suggests different stresses on their knees associated with a different morphology of their patellofemoral joint.
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Affiliation(s)
- Alexandra Houssaye
- Département Adaptations du vivantUMR 7179 CNRS/Muséum National d'Histoire NaturelleParisFrance
| | - Adrien de Perthuis
- Département Adaptations du vivantUMR 7179 CNRS/Muséum National d'Histoire NaturelleParisFrance
| | - Guillaume Houée
- Département Adaptations du vivantUMR 7179 CNRS/Muséum National d'Histoire NaturelleParisFrance
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14
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Mallet C, Houssaye A, Cornette R, Billet G. Long bone shape variation in the forelimb of Rhinocerotoidea: relation with size, body mass and body proportions. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
In quadrupeds, limb bones are strongly affected by functional constraints linked to weight support, but few studies have addressed the complementary effects of mass, size and body proportions on limb bone shape. During their history, Rhinocerotoidea have displayed a great diversity of body masses and relative size and proportions of limb bones, from small tapir-like forms to giant species. Here, we explore the evolutionary variation of shapes in forelimb bones and its relationship with body mass in Rhinocerotoidea. Our results indicate a general increase in robustness and greater development of muscular insertions in heavier species, counteracting the higher weight loadings induced by an increased body mass. The shape of the humerus changes allometrically and exhibits a strong phylogenetic signal. Shapes of the radius and ulna display a stronger link with body mass repartition than with the absolute mass itself. Congruent shape variation between the humerus and the proximal part of the ulna suggests that the elbow joint is comprised of two strongly covariant structures. In addition, our work confirms the uniqueness of giant Paraceratheriidae among Rhinocerotoidea, whose shape variation is related to both a high body mass and a cursorial forelimb construction.
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Affiliation(s)
- Christophe Mallet
- Mécanismes adaptatifs et évolution (MECADEV), UMR 7179, Muséum National d’Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), 55 rue Buffon, CP 55, 75005 Paris, France
| | - Alexandra Houssaye
- Mécanismes adaptatifs et évolution (MECADEV), UMR 7179, Muséum National d’Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), 55 rue Buffon, CP 55, 75005 Paris, France
| | - Raphaël Cornette
- Institut de Systématique, Evolution, Biodiversité (ISYEB), UMR 7205, MNHN, CNRS, Sorbonne Université (SU), École Pratique des Hautes Études, Université des Antilles, 57 rue Cuvier, CP 50, 75005 Paris, France
| | - Guillaume Billet
- Centre de Recherche en Paléontologie – Paris (CR2P), UMR 7207, MNHN, CNRS, SU, 8 rue Buffon, CP 38, 75005 Paris, France
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15
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Dalton DL, Prost S. Rhinoceros genomes uncover family secrets. Nature 2021; 599:209-210. [PMID: 34667298 DOI: 10.1038/d41586-021-02777-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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16
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Liu S, Westbury MV, Dussex N, Mitchell KJ, Sinding MHS, Heintzman PD, Duchêne DA, Kapp JD, von Seth J, Heiniger H, Sánchez-Barreiro F, Margaryan A, André-Olsen R, De Cahsan B, Meng G, Yang C, Chen L, van der Valk T, Moodley Y, Rookmaaker K, Bruford MW, Ryder O, Steiner C, Bruins-van Sonsbeek LGR, Vartanyan S, Guo C, Cooper A, Kosintsev P, Kirillova I, Lister AM, Marques-Bonet T, Gopalakrishnan S, Dunn RR, Lorenzen ED, Shapiro B, Zhang G, Antoine PO, Dalén L, Gilbert MTP. Ancient and modern genomes unravel the evolutionary history of the rhinoceros family. Cell 2021; 184:4874-4885.e16. [PMID: 34433011 DOI: 10.1016/j.cell.2021.07.032] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 06/16/2021] [Accepted: 07/23/2021] [Indexed: 12/27/2022]
Abstract
Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early divergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses. This early Miocene (∼16 million years ago [mya]) split post-dates the land bridge formation between the Afro-Arabian and Eurasian landmasses. Our analyses also show that while rhinoceros genomes in general exhibit low levels of genome-wide diversity, heterozygosity is lowest and inbreeding is highest in the modern species. These results suggest that while low genetic diversity is a long-term feature of the family, it has been particularly exacerbated recently, likely reflecting recent anthropogenic-driven population declines.
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Affiliation(s)
- Shanlin Liu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark.
| | - Michael V Westbury
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Nicolas Dussex
- Centre for Palaeogenetics, Svante Arrhenius vag 20C, Stockholm 10691, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm 10405, Sweden; Department of Zoology, Stockholm University, Stockholm 10691, Sweden
| | - Kieren J Mitchell
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia
| | - Mikkel-Holger S Sinding
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Peter D Heintzman
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø 9037, Norway
| | - David A Duchêne
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Joshua D Kapp
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Johanna von Seth
- Centre for Palaeogenetics, Svante Arrhenius vag 20C, Stockholm 10691, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm 10405, Sweden; Department of Zoology, Stockholm University, Stockholm 10691, Sweden
| | - Holly Heiniger
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia
| | - Fátima Sánchez-Barreiro
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Ashot Margaryan
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Remi André-Olsen
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17121 Solna, Sweden
| | - Binia De Cahsan
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Guanliang Meng
- China National Genebank, BGI Shenzhen, Shenzhen 518083, China
| | - Chentao Yang
- China National Genebank, BGI Shenzhen, Shenzhen 518083, China
| | - Lei Chen
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Tom van der Valk
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Yoshan Moodley
- Department of Zoology, University of Venda, Thohoyandou 0950, Republic of South Africa
| | - Kees Rookmaaker
- Editor of the Rhino Resource Center, Utrecht, the Netherlands
| | - Michael W Bruford
- School of Biosciences, Sir Martin Evans Building, Cardiff University, Cardiff CF10 3AX, UK; Sustainable Places Research Institute, Cardiff University, Cardiff CF10 3BA, UK
| | - Oliver Ryder
- San Diego Zoo Wildlife Alliance, Beckman Center for Conservation Research, San Diego, CA 92027, USA
| | - Cynthia Steiner
- San Diego Zoo Wildlife Alliance, Beckman Center for Conservation Research, San Diego, CA 92027, USA
| | | | - Sergey Vartanyan
- N.A. Shilo North-East Interdisciplinary Scientific Research Institute, Far East Branch, Russian Academy of Sciences (NEISRI FEB RAS), Magadan 685000, Russia
| | - Chunxue Guo
- China National Genebank, BGI Shenzhen, Shenzhen 518083, China
| | - Alan Cooper
- South Australian Museum, Adelaide, SA 5000, Australia
| | - Pavel Kosintsev
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia; Ural Federal University, Yekaterinburg, Russia
| | - Irina Kirillova
- Institute of Geography, Russian Academy of Sciences, Moscow 119017, Russia
| | - Adrian M Lister
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain; Centre Nacional d'Anàlisi Genòmica, Centre for Genomic Regulation (CNAG-CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Shyam Gopalakrishnan
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Robert R Dunn
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark; Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Eline D Lorenzen
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 96050, USA
| | - Guojie Zhang
- China National Genebank, BGI Shenzhen, Shenzhen 518083, China; Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Pierre-Olivier Antoine
- Institut des Sciences de l'Évolution, Université Montpellier, CNRS, IRD, EPHE, Montpellier 34095, France
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius vag 20C, Stockholm 10691, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm 10405, Sweden; Department of Zoology, Stockholm University, Stockholm 10691, Sweden.
| | - M Thomas P Gilbert
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark; Norwegian University of Science and Technology (NTNU) University Museum, Trondheim 7012, Norway.
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17
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Osthoff G, Beukes B, Steyn AC, Hugo A, Deacon F, Butler HJB, O'Neill FH, Grobler JP. Milk composition of white rhinoceros over lactation and comparison with other Perissodactyla. Zoo Biol 2021; 40:417-428. [PMID: 34010488 DOI: 10.1002/zoo.21618] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 03/17/2021] [Accepted: 04/23/2021] [Indexed: 11/10/2022]
Abstract
The proximate composition of milk from fifteen free-ranging white rhinoceroses at different lactation stages is reported with detailed analysis of fatty acid composition and minerals. Lactose is the main component at 7.93 ± 0.53%, followed by 0.93 ± 0.19% protein, 1.76 ± 0.39% fat, 0.40 ± 0.18% ash, 0.05 ± 0.01% glucose, and 0.04 ± 0.02% non protein nitrogen The interindividual variation of all the components is high, showing no trend of change over lactation. The K and P content decreased over lactation. The fatty acid composition of rhinoceros milk is characteristic with a high saturated fatty acids content of 62%-84%, of which the medium chain fatty acids form the major portion. The C10:0, C12:0, C16:0, and C18:1c9 are the major fatty acids in the milk fat. The results are compared with the two other Perissodactylae families, the Equidae and Tapiridae. Differences in gross composition are small, but the milk of the Rhinocerotidae have the lowest gross energy, while the milk fats consist of the highest amounts of saturated fatty acids, while the low levels of C16:1c9 and C18:1c9 indicate the lowest mammary Δ9-desaturase activity.
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Affiliation(s)
- Gernot Osthoff
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
| | - Blake Beukes
- Department of Animal Wildlife and Grassland Sciences, University of the Free State, Bloemfontein, South Africa
| | - Aletta C Steyn
- Department of Animal Wildlife and Grassland Sciences, University of the Free State, Bloemfontein, South Africa
| | - Arnold Hugo
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
| | - Francois Deacon
- Department of Animal Wildlife and Grassland Sciences, University of the Free State, Bloemfontein, South Africa
| | - Hendrik J B Butler
- Department of Zoology and Entomology, University of the Free State, Bloemfontein, South Africa
| | - Frans H O'Neill
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
| | - J Paul Grobler
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
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18
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Bai B, Meng J, Zhang C, Gong YX, Wang YQ. The origin of Rhinocerotoidea and phylogeny of Ceratomorpha (Mammalia, Perissodactyla). Commun Biol 2020; 3:509. [PMID: 32929169 PMCID: PMC7490376 DOI: 10.1038/s42003-020-01205-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 08/04/2020] [Indexed: 11/09/2022] Open
Abstract
Rhinoceroses have been considered to have originated from tapiroids in the middle Eocene; however, the transition remains controversial, and the first unequivocal rhinocerotoids appeared about 4 Ma later than the earliest tapiroids of the Early Eocene. Here we describe 5 genera and 6 new species of rhinoceroses recently discovered from the early Eocene to the early middle Eocene deposits of the Erlian Basin of Inner Mongolia, China. These new materials represent the earliest members of rhinocerotoids, forstercooperiids, and/or hyrachyids, and bridge the evolutionary gap between the early Eocene ceratomorphs and middle Eocene rhinocerotoids. The phylogenetic analyses using parsimony and Bayesian inference methods support their affinities with rhinocerotoids, and also illuminate the phylogenetic relationships and biogeography of Ceratomorpha, although some discrepancies are present between the two criteria. The nearly contemporary occurrence of various rhinocerotoids indicates that the divergence of different rhinocerotoid groups occurred no later than the late early Eocene, which is soon after the split between the rhinocerotoids and the tapiroids in the early early Eocene. However, the Bayesian tip-dating estimate suggests that the divergence of different ceratomorph groups occurred in the middle Paleocene.
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Affiliation(s)
- Bin Bai
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China. .,CAS Center for Excellence in Life and Paleoenvironment, Beijing, 100044, China.
| | - Jin Meng
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China.,Division of Paleontology, American Museum of Natural History, New York, NY, 10024, USA.,Earth and Environmental Sciences, Graduate Center, City University of New York, New York, NY, 10016, USA
| | - Chi Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing, 100044, China
| | - Yan-Xin Gong
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing, 100044, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuan-Qing Wang
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China. .,CAS Center for Excellence in Life and Paleoenvironment, Beijing, 100044, China. .,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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19
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Noonan MJ, Fleming CH, Tucker MA, Kays R, Harrison A, Crofoot MC, Abrahms B, Alberts SC, Ali AH, Altmann J, Antunes PC, Attias N, Belant JL, Beyer DE, Bidner LR, Blaum N, Boone RB, Caillaud D, de Paula RC, de la Torre JA, Dekker J, DePerno CS, Farhadinia M, Fennessy J, Fichtel C, Fischer C, Ford A, Goheen JR, Havmøller RW, Hirsch BT, Hurtado C, Isbell LA, Janssen R, Jeltsch F, Kaczensky P, Kaneko Y, Kappeler P, Katna A, Kauffman M, Koch F, Kulkarni A, LaPoint S, Leimgruber P, Macdonald DW, Markham AC, McMahon L, Mertes K, Moorman CE, Morato RG, Moßbrucker AM, Mourão G, O'Connor D, Oliveira‐Santos LGR, Pastorini J, Patterson BD, Rachlow J, Ranglack DH, Reid N, Scantlebury DM, Scott DM, Selva N, Sergiel A, Songer M, Songsasen N, Stabach JA, Stacy‐Dawes J, Swingen MB, Thompson JJ, Ullmann W, Vanak AT, Thaker M, Wilson JW, Yamazaki K, Yarnell RW, Zieba F, Zwijacz‐Kozica T, Fagan WF, Mueller T, Calabrese JM. Effects of body size on estimation of mammalian area requirements. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2020; 34:1017-1028. [PMID: 32362060 PMCID: PMC7496598 DOI: 10.1111/cobi.13495] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/27/2019] [Accepted: 12/24/2019] [Indexed: 06/08/2023]
Abstract
Accurately quantifying species' area requirements is a prerequisite for effective area-based conservation. This typically involves collecting tracking data on species of interest and then conducting home-range analyses. Problematically, autocorrelation in tracking data can result in space needs being severely underestimated. Based on the previous work, we hypothesized the magnitude of underestimation varies with body mass, a relationship that could have serious conservation implications. To evaluate this hypothesis for terrestrial mammals, we estimated home-range areas with global positioning system (GPS) locations from 757 individuals across 61 globally distributed mammalian species with body masses ranging from 0.4 to 4000 kg. We then applied block cross-validation to quantify bias in empirical home-range estimates. Area requirements of mammals <10 kg were underestimated by a mean approximately15%, and species weighing approximately100 kg were underestimated by approximately50% on average. Thus, we found area estimation was subject to autocorrelation-induced bias that was worse for large species. Combined with the fact that extinction risk increases as body mass increases, the allometric scaling of bias we observed suggests the most threatened species are also likely to be those with the least accurate home-range estimates. As a correction, we tested whether data thinning or autocorrelation-informed home-range estimation minimized the scaling effect of autocorrelation on area estimates. Data thinning required an approximately93% data loss to achieve statistical independence with 95% confidence and was, therefore, not a viable solution. In contrast, autocorrelation-informed home-range estimation resulted in consistently accurate estimates irrespective of mass. When relating body mass to home range size, we detected that correcting for autocorrelation resulted in a scaling exponent significantly >1, meaning the scaling of the relationship changed substantially at the upper end of the mass spectrum.
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Affiliation(s)
- Michael J. Noonan
- Smithsonian Conservation Biology InstituteNational Zoological Park1500 Remount RoadFront RoyalVA22630U.S.A.
- Department of BiologyUniversity of MarylandCollege ParkMD20742U.S.A.
| | - Christen H. Fleming
- Smithsonian Conservation Biology InstituteNational Zoological Park1500 Remount RoadFront RoyalVA22630U.S.A.
- Department of BiologyUniversity of MarylandCollege ParkMD20742U.S.A.
| | - Marlee A. Tucker
- Senckenberg Biodiversity and Climate Research CentreSenckenberg Gesellschaft für NaturforschungSenckenberganlage 25Frankfurt (Main)60325Germany
- Department of Biological SciencesGoethe UniversityMax‐von‐Laue‐Straße 9Frankfurt (Main)60438Germany
- Department of Environmental ScienceInstitute for Wetland and Water ResearchRadboud UniversityP.O. Box 9010NijmegenGLNL‐6500The Netherlands
| | - Roland Kays
- North Carolina Museum of Natural SciencesBiodiversity LabRaleighNC27601U.S.A.
- Fisheries, Wildlife, and Conservation Biology Program, College of Natural Resources Campus Box 8001North Carolina State UniversityRaleighNC27695U.S.A.
| | - Autumn‐Lynn Harrison
- Migratory Bird CenterSmithsonian Conservation Biology InstituteWashingtonD.C.20013U.S.A.
| | - Margaret C. Crofoot
- Department of AnthropologyUniversity of California, DavisDavisCA95616U.S.A.
- Smithsonian Tropical Research InstituteBalboa Ancon0843‐03092Republic of Panama
| | - Briana Abrahms
- Environmental Research DivisionNOAA Southwest Fisheries Science CenterMontereyCA93940U.S.A.
| | - Susan C. Alberts
- Departments of Biology and Evolutionary AnthropologyDuke UniversityDurhamNC27708U.S.A.
| | | | - Jeanne Altmann
- Department of Ecology and EvolutionPrinceton University106A Guyot HallPrincetonNJ08544U.S.A.
| | - Pamela Castro Antunes
- Department of EcologyFederal University of Mato Grosso do SulCampo GrandeMS79070–900Brazil
| | - Nina Attias
- Programa de Pós‐Graduaçao em Biologia Animal, Universidade Federal do Mato Grosso do SulCidade UniversitáriaAv. Costa e SilvaCampo GrandeMato Grosso do Sul79070‐900Brazil
| | - Jerrold L. Belant
- Camp Fire Program in Wildlife Conservation, State University of New YorkCollege of Environmental Science and ForestrySyracuseNY13210U.S.A.
| | - Dean E. Beyer
- Michigan Department of Natural Resources1990 U.S. 41 SouthMarquetteMI49855U.S.A.
| | - Laura R. Bidner
- Department of AnthropologyUniversity of California, DavisDavisCA95616U.S.A.
- Mpala Research CentreNanyuki555–104000Kenya
| | - Niels Blaum
- University of Potsdam, Plant Ecology and Nature ConservationAm Mühlenberg 3Potsdam14476Germany
| | - Randall B. Boone
- Natural Resource Ecology LaboratoryColorado State UniversityFort CollinsCO80523U.S.A.
- Department of Ecosystem Science and SustainabilityColorado State UniversityFort CollinsCO80523U.S.A.
| | - Damien Caillaud
- Department of AnthropologyUniversity of California, DavisDavisCA95616U.S.A.
| | - Rogerio Cunha de Paula
- National Research Center for Carnivores ConservationChico Mendes Institute for the Conservation of BiodiversityEstrada Municipal Hisaichi Takebayashi 8600AtibaiaSP12952‐011Brazil
| | - J. Antonio de la Torre
- Instituto de Ecología, Universidad Nacional Autónoma de Mexico and CONACyTCiudad UniversitariaMexicoD.F.04318Mexico
| | - Jasja Dekker
- Jasja Dekker DierecologieEnkhuizenstraat 26ArnhemWZ6843The Netherlands
| | - Christopher S. DePerno
- Fisheries, Wildlife, and Conservation Biology Program, College of Natural Resources Campus Box 8001North Carolina State UniversityRaleighNC27695U.S.A.
| | - Mohammad Farhadinia
- Wildlife Conservation Research Unit, Department of ZoologyUniversity of OxfordTubney House, OxfordshireOxfordOX13 5QLU.K.
- Future4Leopards FoundationTehranIran
| | | | - Claudia Fichtel
- German Primate CenterBehavioral Ecology & Sociobiology UnitKellnerweg 4Göttingen37077Germany
| | - Christina Fischer
- Restoration Ecology, Department of Ecology and Ecosystem ManagementTechnische Universität MünchenEmil‐Ramann‐Straße 6Freising85354Germany
| | - Adam Ford
- The Irving K. Barber School of Arts and Sciences, Unit 2: BiologyThe University of British ColumbiaOkanagan Campus, SCI 109, 1177 Research RoadKelownaBCV1V 1V7Canada
| | - Jacob R. Goheen
- Department of Zoology and PhysiologyUniversity of WyomingLaramieWY82071U.S.A.
| | | | - Ben T. Hirsch
- Zoology and Ecology, College of Science and EngineeringJames Cook UniversityTownsvilleQLD4811Australia
| | - Cindy Hurtado
- Museo de Historia NaturalUniversidad Nacional Mayor de San MarcosLima15072Peru
- Department of Forest Resources ManagementThe University of British ColumbiaVancouverBCV6T 1Z4Canada
| | - Lynne A. Isbell
- Department of AnthropologyUniversity of California, DavisDavisCA95616U.S.A.
- Mpala Research CentreNanyuki555–104000Kenya
| | - René Janssen
- Bionet NatuuronderzoekValderstraat 39Stein6171ELThe Netherlands
| | - Florian Jeltsch
- University of Potsdam, Plant Ecology and Nature ConservationAm Mühlenberg 3Potsdam14476Germany
| | - Petra Kaczensky
- Norwegian Institute for Nature Research — NINASluppenTrondheimNO‐7485Norway
- Research Institute of Wildlife Ecology, University of Veterinary MedicineSavoyenstraße 1ViennaA‐1160Austria
| | - Yayoi Kaneko
- Tokyo University of Agriculture and TechnologyTokyo183–8509Japan
| | - Peter Kappeler
- German Primate CenterBehavioral Ecology & Sociobiology UnitKellnerweg 4Göttingen37077Germany
| | - Anjan Katna
- Ashoka Trust for Research in Ecology and the Environment (ATREE)BangaloreKarnataka560064India
- Manipal Academy of Higher EducationManipalKarnataka576104India
| | - Matthew Kauffman
- U.S. Geological Survey, Wyoming Cooperative Fish and Wildlife Research Unit, Department of Zoology and PhysiologyUniversity of WyomingLaramieWY82071U.S.A.
| | - Flavia Koch
- German Primate CenterBehavioral Ecology & Sociobiology UnitKellnerweg 4Göttingen37077Germany
| | - Abhijeet Kulkarni
- Ashoka Trust for Research in Ecology and the Environment (ATREE)BangaloreKarnataka560064India
| | - Scott LaPoint
- Max Planck Institute for OrnithologyVogelwarte RadolfzellAm Obstberg 1RadolfzellD‐78315Germany
- Black Rock Forest65 Reservoir RoadCornwallNY12518U.S.A.
| | - Peter Leimgruber
- Smithsonian Conservation Biology InstituteNational Zoological Park1500 Remount RoadFront RoyalVA22630U.S.A.
| | - David W. Macdonald
- Wildlife Conservation Research Unit, Department of ZoologyUniversity of OxfordTubney House, OxfordshireOxfordOX13 5QLU.K.
| | | | - Laura McMahon
- Office of Applied ScienceDepartment of Natural ResourcesRhinelanderWI54501U.S.A.
| | - Katherine Mertes
- Smithsonian Conservation Biology InstituteNational Zoological Park1500 Remount RoadFront RoyalVA22630U.S.A.
| | - Christopher E. Moorman
- Fisheries, Wildlife, and Conservation Biology Program, College of Natural Resources Campus Box 8001North Carolina State UniversityRaleighNC27695U.S.A.
| | - Ronaldo G. Morato
- National Research Center for Carnivores ConservationChico Mendes Institute for the Conservation of BiodiversityEstrada Municipal Hisaichi Takebayashi 8600AtibaiaSP12952‐011Brazil
- Institute for the Conservation of Neotropical Carnivores – Pró‐CarnívorosAtibaiaSao Paulo12945‐010Brazil
| | | | - Guilherme Mourão
- Embrapa PantanalRua 21 de setembro 1880Corumb´aMS79320–900Brazil
| | - David O'Connor
- Department of Biological SciencesGoethe UniversityMax‐von‐Laue‐Straße 9Frankfurt (Main)60438Germany
- San Diego Zoo Institute of Conservation Research15600 San Pasqual Valley RoadEscondidoCA92027U.S.A.
- National Geographic Partners1145 17th Street NWWashingtonD.C.20036U.S.A.
| | | | - Jennifer Pastorini
- Centre for Conservation and Research26/7 C2 Road, KodigahawewaJulpallamaTissamaharama82600Sri Lanka
- Anthropologisches InstitutUniversität ZürichWinterthurerstrasse 190Zurich8057Switzerland
| | - Bruce D. Patterson
- Integrative Research CenterField Museum of Natural HistoryChicagoIL60605U.S.A.
| | - Janet Rachlow
- Department of Fish and Wildlife SciencesUniversity of Idaho875 Perimeter Drive MS 1136MoscowID83844‐1136U.S.A.
| | - Dustin H. Ranglack
- Department of BiologyUniversity of Nebraska at KearneyKearneyNE68849U.S.A.
| | - Neil Reid
- Institute for Global Food Security (IGFS), School of Biological SciencesQueen's University BelfastBelfastBT9 5DLU.K.
| | - David M. Scantlebury
- School of Biological SciencesQueen's University Belfast19 Chlorine GardensBelfastNorthern IrelandBT9 5DLU.K.
| | - Dawn M. Scott
- School of Life SciencesKeele UniversityKeeleStaffordshireST5 5BGU.K.
| | - Nuria Selva
- Institute of Nature ConservationPolish Academy of SciencesMickiewicza 33Krakow31–120Poland
| | - Agnieszka Sergiel
- Institute of Nature ConservationPolish Academy of SciencesMickiewicza 33Krakow31–120Poland
| | - Melissa Songer
- Smithsonian Conservation Biology InstituteNational Zoological Park1500 Remount RoadFront RoyalVA22630U.S.A.
| | - Nucharin Songsasen
- Smithsonian Conservation Biology InstituteNational Zoological Park1500 Remount RoadFront RoyalVA22630U.S.A.
| | - Jared A. Stabach
- Smithsonian Conservation Biology InstituteNational Zoological Park1500 Remount RoadFront RoyalVA22630U.S.A.
| | - Jenna Stacy‐Dawes
- San Diego Zoo Institute of Conservation Research15600 San Pasqual Valley RoadEscondidoCA92027U.S.A.
| | - Morgan B. Swingen
- Fisheries, Wildlife, and Conservation Biology Program, College of Natural Resources Campus Box 8001North Carolina State UniversityRaleighNC27695U.S.A.
- 1854 Treaty Authority4428 Haines RoadDuluthMN55811U.S.A.
| | - Jeffrey J. Thompson
- Asociación Guyra Paraguay – CONACYTParque Ecológico Asunción VerdeAsuncion1101Paraguay
- Instituto SaiteCoronel Felix Cabrera 166Asuncion1101Paraguay
| | - Wiebke Ullmann
- University of Potsdam, Plant Ecology and Nature ConservationAm Mühlenberg 3Potsdam14476Germany
| | - Abi Tamim Vanak
- Ashoka Trust for Research in Ecology and the Environment (ATREE)BangaloreKarnataka560064India
- Wellcome Trust/DBT India AllianceHyderabad500034India
- School of Life SciencesUniversity of KwaZulu‐NatalWestvilleDurban4041South Africa
| | - Maria Thaker
- Centre for Ecological SciencesIndian Institute of ScienceBangalore560012India
| | - John W. Wilson
- Department of Zoology & EntomologyUniversity of PretoriaPretoria0002South Africa
| | - Koji Yamazaki
- Ibaraki Nature MuseumZoological Laboratory700 OsakiBando‐cityIbaraki306–0622Japan
- Forest Ecology LaboratoryDepartment of Forest ScienceTokyo University of Agriculture1‐1‐1 SakuragaokaSetagaya‐KuTokyo156–8502Japan
| | - Richard W. Yarnell
- School of Animal, Rural and Environmental SciencesNottingham Trent UniversityBrackenhurst CampusSouthwellNG25 0QFU.K.
| | - Filip Zieba
- Tatra National ParkKúznice 1Zakopane34–500Poland
| | | | - William F. Fagan
- Department of BiologyUniversity of MarylandCollege ParkMD20742U.S.A.
| | - Thomas Mueller
- Senckenberg Biodiversity and Climate Research CentreSenckenberg Gesellschaft für NaturforschungSenckenberganlage 25Frankfurt (Main)60325Germany
- Department of Biological SciencesGoethe UniversityMax‐von‐Laue‐Straße 9Frankfurt (Main)60438Germany
| | - Justin M. Calabrese
- Smithsonian Conservation Biology InstituteNational Zoological Park1500 Remount RoadFront RoyalVA22630U.S.A.
- Department of BiologyUniversity of MarylandCollege ParkMD20742U.S.A.
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Santagostino M, Piras FM, Cappelletti E, Del Giudice S, Semino O, Nergadze SG, Giulotto E. Insertion of Telomeric Repeats in the Human and Horse Genomes: An Evolutionary Perspective. Int J Mol Sci 2020; 21:E2838. [PMID: 32325780 PMCID: PMC7215372 DOI: 10.3390/ijms21082838] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 01/06/2023] Open
Abstract
Interstitial telomeric sequences (ITSs) are short stretches of telomeric-like repeats (TTAGGG)n at nonterminal chromosomal sites. We previously demonstrated that, in the genomes of primates and rodents, ITSs were inserted during the repair of DNA double-strand breaks. These conclusions were derived from sequence comparisons of ITS-containing loci and ITS-less orthologous loci in different species. To our knowledge, insertion polymorphism of ITSs, i.e., the presence of an ITS-containing allele and an ITS-less allele in the same species, has not been described. In this work, we carried out a genome-wide analysis of 2504 human genomic sequences retrieved from the 1000 Genomes Project and a PCR-based analysis of 209 human DNA samples. In spite of the large number of individual genomes analyzed we did not find any evidence of insertion polymorphism in the human population. On the contrary, the analysis of ITS loci in the genome of a single horse individual, the reference genome, allowed us to identify five heterozygous ITS loci, suggesting that insertion polymorphism of ITSs is an important source of genetic variability in this species. Finally, following a comparative sequence analysis of horse ITSs and of their orthologous empty loci in other Perissodactyla, we propose models for the mechanism of ITS insertion during the evolution of this order.
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Affiliation(s)
| | | | | | | | | | | | - Elena Giulotto
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy; (M.S.); (F.M.P.); (E.C.); (S.D.G.); (O.S.); (S.G.N.)
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21
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Margaryan A, Sinding MHS, Liu S, Vieira FG, Chan YL, Nathan SKSS, Moodley Y, Bruford MW, Gilbert MTP. Recent mitochondrial lineage extinction in the critically endangered Javan rhinoceros. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Abstract
The Javan rhinoceros (Rhinoceros sondaicus) is one of five extant rhinoceros species and among the rarest large mammals on Earth. Once widespread across Southeast Asia, it is now on the verge of extinction, with only one wild population remaining (estimated at ~60 individuals) on the island of Java, Indonesia. To assess the past genetic diversity of the female lineage of R. sondaicus, we generated mitochondrial genome data from eight museum specimens dating back to the 19th century, before the range of the Javan rhinoceros was dramatically reduced, for comparison against mitochondrial DNA (mtDNA) sequences of current R. sondaicus and other rhinoceros species. We succeeded in reconstructing five full and three partial ancient mitogenomes from the eight samples. We used BEAST to assess the phylogenetic relationship of the five extant rhinoceros species and the historical samples. The results show that the oldest and most diverse mtDNA lineages of R. sondaicus are found in historical samples, indicating a significant reduction of mtDNA diversity in modern Javan rhinos. We anticipate that the newly sequenced data will represent a useful resource for improving our understanding of evolutionary history of this species, should future studies be able to increase the available dataset. We hope this information may help in conservation efforts for this species.
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Affiliation(s)
- Ashot Margaryan
- Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia
| | - Mikkel-Holger S Sinding
- Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Shanlin Liu
- Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- BGI-Shenzhen, Shenzhen, China
| | - Filipe Garrett Vieira
- Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Yvonne L Chan
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE, Sweden
| | | | - Yoshan Moodley
- Department of Zoology, University of Venda, Thohoyandou, Republic of South Africa
| | - Michael W Bruford
- School of Biosciences and Sustainable Places Institute, Cardiff University, Cardiff, UK
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Norwegian University of Science and Technology, University Museum, Norway
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Li J, Shang S, Fang N, Zhu Y, Zhang J, Irwin DM, Zhang S, Wang Z. Accelerated Evolution of Limb-Related Gene Hoxd11 in the Common Ancestor of Cetaceans and Ruminants (Cetruminantia). G3 (BETHESDA, MD.) 2020; 10:515-524. [PMID: 31792005 PMCID: PMC7003097 DOI: 10.1534/g3.119.400512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 11/24/2019] [Indexed: 11/18/2022]
Abstract
Reduced numbers of carpal and tarsal bones (wrist and ankle joints) are extensively observed in the clade of Cetacea and Ruminantia (Cetruminantia). Homebox D11 (Hoxd11) is one of the important genes required for limb development in mammals. Mutations in Hoxd11 can lead to defects in particular bones of limbs, including carpus and tarsus. To test whether evolutionary changes in Hoxd11 underlie the loss of these bones in Cetruminantia, we sequenced and analyzed Hoxd11 coding sequences and compared them with other 5' HoxA and HoxD genes in a taxonomic coverage of Cetacea, Ruminantia and other mammalian relatives. Statistical tests on the Hoxd11 sequences found an accelerated evolution in the common ancestor of cetaceans and ruminants, which coincided with the reduction of carpal and tarsal bones in this clade. Five amino acid substitutions (G222S, G227A, G229S, A240T and G261V) and one amino acid deletion (G254Del) occurred in this lineage. In contrast, other 5' HoxA and HoxD genes do not show this same evolutionary pattern, but instead display a highly conserved pattern of evolution in this lineage. Accelerated evolution of Hoxd11, but not other 5' HoxA and HoxD genes, is probably related to the reduction of the carpal and tarsal bones in Cetruminantia. Moreover, we found two amino acid substitutions (G110S and D223N) in Hoxd11 that are unique to the lineage of Cetacea, which coincided with hindlimb loss in the common ancestor of cetaceans. Our results give molecular evidence of Hoxd11 adaptive evolution in cetaceans and ruminants, which could be correlated with limb morphological adaptation.
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Affiliation(s)
- Jun Li
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Songyang Shang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Na Fang
- State Key Laboratory of Estuarine and Coastal Research, Institute of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China, and
| | - Yubo Zhu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Junpeng Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Shuyi Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhe Wang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China,
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Etienne C, Mallet C, Cornette R, Houssaye A. Influence of mass on tarsus shape variation: a morphometrical investigation among Rhinocerotidae (Mammalia: Perissodactyla). Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Abstract
Many tetrapod lineages show extreme increases in body mass in their evolutionary history, associated with important osteological changes. The ankle joint, essential for foot movement, is assumed to be particularly affected in this regard. We investigated the morphological adaptations of the astragalus and the calcaneus in Rhinocerotidae, and analysed them in light of a comparative analysis with other Perissodactyla. We performed 3D geometric morphometrics and correlated shape with centroid size of the bone and body mass of the species. Our results show that mass has an influence on bone shape in Rhinocerotidae and in Perissodactyla, but this is not as strong as expected. In heavy animals the astragalus has a flatter trochlea, orientated more proximally, associated with a more upright posture of the limb. The calcaneus is more robust, possibly to sustain the greater tension force exerted by the muscles during plantarflexion. Both bones show wider articular facets, providing greater cohesion and better dissipation of the loading forces. The body plan of the animals also has an influence. Short-legged Teleoceratina have a flatter astragalus than the other rhinocerotids. Paraceratherium has a thinner calcaneus than expected. This study clarifies adaptations to high body weight among Rhinocerotidae and calls for similar investigations in other groups with massive forms.
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Affiliation(s)
- Cyril Etienne
- UMR 7179, Mécanismes Adaptatifs et Evolution, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Christophe Mallet
- UMR 7179, Mécanismes Adaptatifs et Evolution, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Raphaël Cornette
- UMR 7205, Institut de Systématique, Evolution, Biodiversité, Centre National de la Recherche Scientifique, Muséum National d’Histoire Naturelle, Sorbonne Université, Ecole Publique des Hautes Etudes, Paris, France
| | - Alexandra Houssaye
- UMR 7179, Mécanismes Adaptatifs et Evolution, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
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Jiao H, Zhang L, Xie HW, Simmons NB, Liu H, Zhao H. Trehalase Gene as a Molecular Signature of Dietary Diversification in Mammals. Mol Biol Evol 2020; 36:2171-2183. [PMID: 31311032 PMCID: PMC6759077 DOI: 10.1093/molbev/msz127] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Diet is a key factor in determining and structuring animal diversity and adaptive radiations. The mammalian fossil record preserves phenotypic evidence of many dietary shifts, whereas genetic changes followed by dietary diversification in mammals remain largely unknown. To test whether living mammals preserve molecular evidence of dietary shifts, we examined the trehalase gene (Treh), which encodes an enzyme capable of digesting trehalose from insect blood, in bats and other mammals with diverse diets. Bats represent the largest dietary radiation among all mammalian orders, with independent origins of frugivory, nectarivory, carnivory, omnivory, and even sanguivory in an otherwise insectivorous clade. We found that Treh has been inactivated in unrelated bat lineages that independently radiated into noninsectivorous niches. Consistently, purifying selection has been markedly relaxed in noninsectivorous bats compared with their insectivorous relatives. Enzymatic assays of intestinal trehalase in bats suggest that trehalase activity tends to be lost or markedly reduced in noninsectivorous bats compared with their insectivorous relatives. Furthermore, our survey of Treh in 119 mammal species, which represent a deeper evolutionary timeframe, additionally identified a number of other independent losses of Treh in noninsectivorous species, recapitulating the evolutionary pattern that we found in bats. These results document a molecular record of dietary diversification in mammals, and suggest that such molecular signatures of dietary shifts would help us understand both historical and modern changes of animal diets.
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Affiliation(s)
- Hengwu Jiao
- Department of Ecology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Libiao Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Huan-Wang Xie
- Department of Ecology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Nancy B Simmons
- Department of Mammalogy, American Museum of Natural History, New York, NY
| | - Hui Liu
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Huabin Zhao
- Department of Ecology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
- Corresponding author: E-mail:
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Pluháček J, Tučková V, Šárová R, King SRB. Effect of social organisation on interspecific differences in overmarking behaviour of foals in African equids. Anim Cogn 2019; 23:131-140. [DOI: 10.1007/s10071-019-01323-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 10/01/2019] [Accepted: 10/22/2019] [Indexed: 11/28/2022]
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26
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Pérez SD, Grummer JA, Fernandes-Santos RC, José CT, Medici EP, Marcili A. Phylogenetics, patterns of genetic variation and population dynamics of Trypanosoma terrestris support both coevolution and ecological host-fitting as processes driving trypanosome evolution. Parasit Vectors 2019; 12:473. [PMID: 31604471 PMCID: PMC6790053 DOI: 10.1186/s13071-019-3726-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/16/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A considerable amount of evidence has favored ecological host-fitting, rather than coevolution, as the main mechanism responsible for trypanosome divergence. Nevertheless, beyond the study of human pathogenic trypanosomes, the genetic basis of host specificity among trypanosomes isolated from forest-inhabiting hosts remains largely unknown. METHODS To test possible scenarios on ecological host-fitting and coevolution, we combined a host capture recapture strategy with parasite genetic data and studied the genetic variation, population dynamics and phylogenetic relationships of Trypanosoma terrestris, a recently described trypanosome species isolated from lowland tapirs in the Brazilian Pantanal and Atlantic Forest biomes. RESULTS We made inferences of T. terrestris population structure at three possible sources of genetic variation: geography, tapir hosts and 'putative' vectors. We found evidence of a bottleneck affecting the contemporary patterns of parasite genetic structure, resulting in little genetic diversity and no evidence of genetic structure among hosts or biomes. Despite this, a strongly divergent haplotype was recorded at a microgeographical scale in the landscape of Nhecolândia in the Pantanal. However, although tapirs are promoting the dispersion of the parasites through the landscape, neither geographical barriers nor tapir hosts were involved in the isolation of this haplotype. Taken together, these findings suggest that either host-switching promoted by putative vectors or declining tapir population densities are influencing the current parasite population dynamics and genetic structure. Similarly, phylogenetic analyses revealed that T. terrestris is strongly linked to the evolutionary history of its perissodactyl hosts, suggesting a coevolving scenario between Perissodactyla and their trypanosomes. Additionally, T. terrestris and T. grayi are closely related, further indicating that host-switching is a common feature promoting trypanosome evolution. CONCLUSIONS This study provides two lines of evidence, both micro- and macroevolutionary, suggesting that both host-switching by ecological fitting and coevolution are two important and non-mutually-exclusive processes driving the evolution of trypanosomes. In line with other parasite systems, our results support that even in the face of host specialization and coevolution, host-switching may be common and is an important determinant of parasite diversification.
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Affiliation(s)
- Sergio D Pérez
- Department of Preventive Veterinary Medicine and Animal Science, Faculty of Veterinary Medicine, University of São Paulo, São Paulo, Brazil.,Departamento de Biología, Facultad de Ciencias, Universidad del Tolima, Ibagué, Colombia
| | - Jared A Grummer
- Department of Zoology and Biodiversity Research Center, University of British Columbia, Vancouver, Canada
| | - Renata C Fernandes-Santos
- Lowland Tapir Conservation Initiative (LTCI), Institute for Ecological Research (IPÊ), Campo Grande, Brazil.,Tapir Specialist Group (TSG), Species Survival Commission (SSC), International Union for Conservation of Nature (IUCN), Houston, USA.,Brazilian Institute for Conservation Medicine (TRÍADE), Campo Grande, Brazil
| | - Caroline Testa José
- Lowland Tapir Conservation Initiative (LTCI), Institute for Ecological Research (IPÊ), Campo Grande, Brazil
| | - Emília Patrícia Medici
- Lowland Tapir Conservation Initiative (LTCI), Institute for Ecological Research (IPÊ), Campo Grande, Brazil.,Tapir Specialist Group (TSG), Species Survival Commission (SSC), International Union for Conservation of Nature (IUCN), Houston, USA.,Escola Superior de Conservação Ambiental e Sustentabilidade (ESCAS/IPÊ), Nazaré Paulista, Brazil
| | - Arlei Marcili
- Department of Preventive Veterinary Medicine and Animal Science, Faculty of Veterinary Medicine, University of São Paulo, São Paulo, Brazil. .,Masters program in Medicine and Animal Welfare, Santo Amaro University, São Paulo, Brazil.
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27
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MacLaren JA, McHorse BK. Comparative forelimb myology and muscular architecture of a juvenile Malayan tapir (Tapirus indicus). J Anat 2019; 236:85-97. [PMID: 31515803 DOI: 10.1111/joa.13087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2019] [Indexed: 12/21/2022] Open
Abstract
The absence of preserved soft tissues in the fossil record is frequently a hindrance for palaeontologists wishing to investigate morphological shifts in key skeletal systems, such as the limbs. Understanding the soft tissue composition of modern species can aid in understanding changes in musculoskeletal features through evolution, including those pertaining to locomotion. Establishing anatomical differences in soft tissues utilising an extant phylogenetic bracket can, in turn, assist in interpreting morphological changes in hard tissues and modelling musculoskeletal movements during evolutionary transitions (e.g. digit reduction in perissodactyls). Perissodactyls (horses, rhinoceroses, tapirs and their relatives) are known to have originated with a four-toed (tetradactyl) forelimb condition. Equids proceeded to reduce all but their central digit, resulting in monodactyly, whereas tapirs retained the ancestral tetradactyl state. The modern Malayan tapir (Tapirus indicus) has been shown to exhibit fully functional tetradactyly in its forelimb, more so than any other tapir, and represents an ideal case-study for muscular arrangement and architectural comparison with the highly derived monodactyl Equus. Here, we present the first quantification of muscular architecture of a tetradactyl perissodactyl (T. indicus), and compare it to measurements from modern monodactyl caballine horse (Equus ferus caballus). Each muscle of the tapir forelimb was dissected out from a cadaver and measured for architectural properties: muscle-tendon unit (MTU) length, MTU mass, muscle mass, pennation angle, and resting fibre length. Comparative parameters [physiological cross-sectional area (PCSA), muscle volume, and % muscle mass] were then calculated from the raw measurements. In the shoulder region, the infraspinatus of T. indicus exhibits dual origination sites on either side of the deflected scapular spine. Within ungulates, this condition has only been previously reported in suids. Differences in relative contribution to limb muscle mass between T. indicus and Equus highlight forelimb muscles that affect mobility in the lateral and medial digits (e.g. extensor digitorum lateralis). These muscles were likely reduced in equids during their evolutionary transition from tetradactyl forest-dwellers to monodactyl, open-habitat specialists. Patterns of PCSA across the forelimb were similar between T. indicus and Equus, with the notable exceptions of the biceps brachii and flexor carpi ulnaris, which were much larger in Equus. The differences observed in PCSA between the tapir and horse forelimb muscles highlight muscles that are essential for maintaining stability in the monodactyl limb while moving at high speeds. This quantitative dataset of muscle architecture in a functionally tetradactyl perissodactyl is a pivotal first step towards reconstructing the locomotor capabilities of extinct, four-toed ancestors of modern perissodactyls, and providing further insights into the equid locomotor transition.
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Affiliation(s)
- Jamie A MacLaren
- Functional Morphology Lab, Department of Biology, Universiteit Antwerpen, Antwerp, Belgium.,Evolution and Diversity Dynamics Lab, Department of Geology, Université Liège, Liège, Belgium
| | - Brianna K McHorse
- Museum of Comparative Zoology, Cambridge, MA, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.,Concord Field Station, Department of Organismic and Evolutionary Biology, Harvard University, Bedford, MA, USA
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Cappellini E, Welker F, Pandolfi L, Ramos-Madrigal J, Samodova D, Rüther PL, Fotakis AK, Lyon D, Moreno-Mayar JV, Bukhsianidze M, Rakownikow Jersie-Christensen R, Mackie M, Ginolhac A, Ferring R, Tappen M, Palkopoulou E, Dickinson MR, Stafford TW, Chan YL, Götherström A, Nathan SKSS, Heintzman PD, Kapp JD, Kirillova I, Moodley Y, Agusti J, Kahlke RD, Kiladze G, Martínez-Navarro B, Liu S, Sandoval Velasco M, Sinding MHS, Kelstrup CD, Allentoft ME, Orlando L, Penkman K, Shapiro B, Rook L, Dalén L, Gilbert MTP, Olsen JV, Lordkipanidze D, Willerslev E. Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny. Nature 2019; 574:103-107. [PMID: 31511700 PMCID: PMC6894936 DOI: 10.1038/s41586-019-1555-y] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 08/12/2019] [Indexed: 11/10/2022]
Abstract
Ancient DNA (aDNA) sequencing has enabled reconstruction of speciation, migration, and admixture events for extinct taxa1. Outside the permafrost, however, irreversible aDNA post-mortem degradation2 has so far limited aDNA recovery to the past ~0.5 million years (Ma)3. Contrarily, tandem mass spectrometry (MS) allowed sequencing ~1.5 million year (Ma) old collagen type I (COL1)4 and suggested the presence of protein residues in Cretaceous fossil remains5, although with limited phylogenetic use6. In the absence of molecular evidence, the speciation of several Early and Middle Pleistocene extinct species remain contentious. In this study, we address the phylogenetic relationships of the Eurasian Pleistocene Rhinocerotidae7–9 using a ~1.77 Ma old dental enamel proteome of a Stephanorhinus specimen from the Dmanisi archaeological site in Georgia (South Caucasus)10. Molecular phylogenetic analyses place the Dmanisi Stephanorhinus as a sister group to the woolly (Coelodonta antiquitatis) and Merck’s rhinoceros (S. kirchbergensis) clade. We show that Coelodonta evolved from an early Stephanorhinus lineage and that the latter includes at least two distinct evolutionary lines. As such, the genus Stephanorhinus is currently paraphyletic and its systematic revision is therefore needed. We demonstrate that Early Pleistocene dental enamel proteome sequencing overcomes the limits of ancient collagen- and aDNA-based phylogenetic inference. It also provides additional information about the sex and taxonomic assignment of the specimens analysed. Dental enamel, the hardest tissue in vertebrates11, is highly abundant in the fossil record. Our findings reveal that palaeoproteomic investigation of this material can push biomolecular investigation further back into the Early Pleistocene.
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Affiliation(s)
- Enrico Cappellini
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. .,Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Frido Welker
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Luca Pandolfi
- Dipartimento di Scienze della Terra, Università degli Studi di Firenze, Florence, Italy
| | - Jazmín Ramos-Madrigal
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Diana Samodova
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Patrick L Rüther
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Anna K Fotakis
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - David Lyon
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - J Víctor Moreno-Mayar
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Meaghan Mackie
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Aurélien Ginolhac
- Life Sciences Research Unit, University of Luxembourg, Belvaux, Luxembourg
| | - Reid Ferring
- Department of Geography and Environment, University of North Texas, Denton, TX, USA
| | - Martha Tappen
- Department of Anthropology, University of Minnesota, Minneapolis, MN, USA
| | | | | | | | - Yvonne L Chan
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | | | - Peter D Heintzman
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.,Tromsø University Museum, The Arctic University of Norway (UiT), Tromsø, Norway
| | - Joshua D Kapp
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Irina Kirillova
- Ice Age Museum, National Alliance of Shidlovskiy 'Ice Age', Moscow, Russia
| | - Yoshan Moodley
- Department of Zoology, University of Venda, Thohoyandou, South Africa
| | - Jordi Agusti
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.,Institut Català de Paleoecologia Humana i Evolució Social, Universitat Rovira i Virgili, Tarragona, Spain
| | | | - Gocha Kiladze
- Geology Department, Tbilisi State University, Tbilisi, Georgia
| | - Bienvenido Martínez-Navarro
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.,Institut Català de Paleoecologia Humana i Evolució Social, Universitat Rovira i Virgili, Tarragona, Spain.,Departament d'Història i Geografia, Universitat Rovira i Virgili, Tarragona, Spain
| | - Shanlin Liu
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,BGI Shenzhen, Shenzen, China
| | | | - Mikkel-Holger S Sinding
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Christian D Kelstrup
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ludovic Orlando
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, Université Paul Sabatier, Toulouse, France
| | | | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Lorenzo Rook
- Dipartimento di Scienze della Terra, Università degli Studi di Firenze, Florence, Italy
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - M Thomas P Gilbert
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
| | | | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. .,Department of Zoology, University of Cambridge, Cambridge, UK. .,Wellcome Trust Sanger Institute, Hinxton, UK. .,Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark.
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An interferon-gamma release assay for the diagnosis of the Mycobacterium bovis infection in white rhinoceros (Ceratotherium simum). Vet Immunol Immunopathol 2019; 217:109931. [PMID: 31522092 DOI: 10.1016/j.vetimm.2019.109931] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 08/07/2019] [Accepted: 08/14/2019] [Indexed: 11/20/2022]
Abstract
Mycobacterium bovis (M. bovis), the cause of bovine tuberculosis, is endemic in Kruger National Park (KNP), South Africa. The risk of spread of M. bovis infection currently prevents translocation of white rhinoceros (Ceratotherium simum) from this population. Therefore, accurate assays are necessary for screening this threatened species. Interferon gamma (IFN-γ) release assays (IGRA) are commonly used for tuberculosis diagnosis in humans and other wildlife species. Hence, the aim of this study was to develop an IGRA for M. bovis detection in white rhinoceros. Heparinized whole blood was collected from immobilized white rhinoceros in KNP (n = 131) and incubated overnight in QuantiFERON®-TB Gold (QFT) blood collection tubes, after which the plasma was harvested following centrifugation. Tissue samples for mycobacterial culture were available from a subset of 21 rhinoceros. The concentration of IFN-γ in plasma samples was measured using the Mabtech equine IFN-γ ELISAPRO kit. An IGRA result was calculated as the difference in IFN-γ concentrations in the QFT Nil and TB antigen tubes. Using test results for the white rhinoceros with known infection status, a diagnostic cut-off value was calculated as 21 pg/ml. Additionally, cut-off values for IFN-γ concentrations for plasma from QFT Nil and QFT Mitogen tubes were calculated to increase confidence in IGRA result interpretation. The combination of the QFT stimulation platform and Mabtech equine IFN-γ ELISA is a promising diagnostic test to distinguish between of M. bovis-infected and -uninfected white rhinoceros.
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Monteiro FA, Weirauch C, Felix M, Lazoski C, Abad-Franch F. Evolution, Systematics, and Biogeography of the Triatominae, Vectors of Chagas Disease. ADVANCES IN PARASITOLOGY 2019. [PMID: 29530308 DOI: 10.1016/bs.apar.2017.12.002] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
In this chapter, we review and update current knowledge about the evolution, systematics, and biogeography of the Triatominae (Hemiptera: Reduviidae)-true bugs that feed primarily on vertebrate blood. In the Americas, triatomines are the vectors of Trypanosoma cruzi, the etiological agent of Chagas disease. Despite declining incidence and prevalence, Chagas disease is still a major public health concern in Latin America. Triatomines occur also in the Old World, where vector-borne T. cruzi transmission has not been recorded. Triatomines evolved from predatory reduviid bugs, most likely in the New World, and diversified extensively across the Americas (including the Caribbean) and in parts of Asia and Oceania. Here, we first discuss our current understanding of how, how many times, and when the blood-feeding habit might have evolved among the Reduviidae. Then we present a summary of recent advances in the systematics of this diverse group of insects, with an emphasis on the contribution of molecular tools to the clarification of taxonomic controversies. Finally, and in the light of both up-to-date phylogenetic hypotheses and a thorough review of distribution records, we propose a global synthesis of the biogeography of the Triatominae. Over 130 triatomine species contribute to maintaining T. cruzi transmission among mammals (sometimes including humans) in almost every terrestrial ecoregion of the Americas. This means that Chagas disease will never be eradicated and underscores the fact that effective disease prevention will perforce require stronger, long-term vector control-surveillance systems.
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Affiliation(s)
- Fernando Araujo Monteiro
- Laboratório de Epidemiologia e Sistemática Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil.
| | | | - Márcio Felix
- Laboratório de Biodiversidade Entomológica, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Cristiano Lazoski
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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May-Davis S, Vermeulen Z, Brown WY. A Primitive Trait in Two Breeds of Equus Caballus Revealed by Comparative Anatomy of the Distal Limb. Animals (Basel) 2019; 9:ani9060355. [PMID: 31197123 PMCID: PMC6617308 DOI: 10.3390/ani9060355] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 05/31/2019] [Accepted: 06/04/2019] [Indexed: 11/25/2022] Open
Abstract
Simple Summary Understanding the complexities and evolutionary links between extinct and extant equids has been vital to genetic conservation and preservation of primitive traits. As domestication of the equid expanded, the loss of primitive traits that ensured survival in a wild environment has not been documented. In this study, the presence of functional interosseous muscle II and IV in the distal limb has been reported, and yet its existence could only be confirmed in relatives and two closely bred descendants of the extinct Tarpan. The morphology described was ligamentous in structure displaying clear longitudinal fibres with a skeletal origin and soft tissue insertion into the medial and lateral branches of the interosseous muscle III (suspensory ligament) dorsal to the sesamoids, similar in orientation to the flexor digitorum profundus ligamentum accessorium (inferior check ligament). Hence, providing a functional medial and lateral stability to the metacarpophalangeal joint (fetlock joint), which equates to one of the functions of the medial and lateral digits in the Mesohippus and Merychippus. The comparable anatomic links between species of the same family that experienced geographical isolation yet display structural conformity appears to be in response to a specific environment. Surmising this potential remnant of functional evolution is a primitive trait and not a breed anomaly. Abstract The 55-million-year history of equine phylogeny has been well-documented from the skeletal record; however, this is less true for the soft tissue structures that are now vestigial in modern horse. A recent study reported that two ligamentous structures resembling functional interosseous muscle II and IV were evident in Dutch Konik horses. The current study investigates this finding and compares it to members of the genus Equus to identify either a breed anomaly or functional primitive trait. Distal limbs (n = 574) were dissected from four species of Equus; E. caballus, E. asinus, E. przewalskii and E. quagga boehmi. E. caballus is represented by 18 breeds of horse, including the primitive Dutch Konik’. The interosseous muscle II and IV were evident in all four species, but only two breeds of E. caballus expressed this trait-the Dutch Konik and Bosnian Mountain Horse. These two breeds were the only close descendants of the extinct Equus ferus ferus (Tarpan) represented in this study. In conclusion, the interosseous muscle II and IV originated from the distal nodule of metacarpal II and IV, respectively, and inserted into the corresponding branches of interosseous muscle III proximal to the sesamoids. This suggests a functional role in medial and lateral joint stability and a primitive trait in modern equids.
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Affiliation(s)
- Sharon May-Davis
- Canine and Equine Research Group, University of New England, Armidale, NSW 2351, Australia.
| | | | - Wendy Y Brown
- Canine and Equine Research Group, University of New England, Armidale, NSW 2351, Australia.
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32
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Chileshe J, Goosen WJ, Buss PE, van Helden PD, Warren R, Parsons SDC, Miller MA. A commercial ELISA for detection of interferon gamma in white rhinoceros. J Vet Diagn Invest 2019; 31:531-536. [PMID: 30973098 DOI: 10.1177/1040638719843955] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Bovine tuberculosis (bTB), caused by Mycobacterium bovis, is endemic in Kruger National Park, South Africa, home to the largest population of white rhinoceros (Ceratotherium simum) in the world. In 2016, the first cases of naturally occurring bTB were reported in white rhinoceros; however, there is a lack of understanding of infection and disease process in this species. Prevention and control of transmission depends on the availability of accurate tools to detect M. bovis infection. Interferon gamma (IFN-γ) assays are a reliable detection method for TB in other animal species, and studies have indicated that these tests can be used in white rhinoceros. We sought to screen and optimize a commercial IFN-γ enzyme-linked immunosorbent assay (ELISA) to detect endogenous white rhinoceros IFN-γ in mitogen-stimulated whole blood as a basis for developing a test for M. bovis infection. Optimizations included identifying ELISA antibodies and determining the effect of sample matrix, ELISA plate incubation temperature, ELISA linearity, assay reproducibility, and the assay's limit of quantification. The optimized assay employed an equine IFN-γ antibody pair that was used to create a commercial ELISA kit. This ELISA had a linear response to recombinant equine and endogenous rhinoceros IFN-γ (range: 7.8-125 pg/mL). When incubated at 37°C, the ELISA was highly reproducible, with an optimal recovery and a low limit of quantification, indicating that the Mabtech equine IFN-γ ELISAPRO kit is a robust assay for measuring white rhinoceros IFN-γ.
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Affiliation(s)
- Josephine Chileshe
- Department of Science and Technology-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa (Chileshe, Goosen, van Helden, Warren, Parsons, Miller).,Veterinary Wildlife Services, South African National Parks, Kruger National Park, Skukuza, South Africa (Buss)
| | - Wynand J Goosen
- Department of Science and Technology-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa (Chileshe, Goosen, van Helden, Warren, Parsons, Miller).,Veterinary Wildlife Services, South African National Parks, Kruger National Park, Skukuza, South Africa (Buss)
| | - Peter E Buss
- Department of Science and Technology-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa (Chileshe, Goosen, van Helden, Warren, Parsons, Miller).,Veterinary Wildlife Services, South African National Parks, Kruger National Park, Skukuza, South Africa (Buss)
| | - Paul D van Helden
- Department of Science and Technology-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa (Chileshe, Goosen, van Helden, Warren, Parsons, Miller).,Veterinary Wildlife Services, South African National Parks, Kruger National Park, Skukuza, South Africa (Buss)
| | - Robin Warren
- Department of Science and Technology-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa (Chileshe, Goosen, van Helden, Warren, Parsons, Miller).,Veterinary Wildlife Services, South African National Parks, Kruger National Park, Skukuza, South Africa (Buss)
| | - Sven D C Parsons
- Department of Science and Technology-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa (Chileshe, Goosen, van Helden, Warren, Parsons, Miller).,Veterinary Wildlife Services, South African National Parks, Kruger National Park, Skukuza, South Africa (Buss)
| | - Michele A Miller
- Department of Science and Technology-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa (Chileshe, Goosen, van Helden, Warren, Parsons, Miller).,Veterinary Wildlife Services, South African National Parks, Kruger National Park, Skukuza, South Africa (Buss)
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MacLaren JA, Nauwelaerts S. Modern Tapirs as Morphofunctional Analogues for Locomotion in Endemic Eocene European Perissodactyls. J MAMM EVOL 2019. [DOI: 10.1007/s10914-019-09460-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Zhu H, Gifford RJ, Murcia PR. Distribution, Diversity, and Evolution of Endogenous Retroviruses in Perissodactyl Genomes. J Virol 2018; 92:e00927-18. [PMID: 30209175 PMCID: PMC6232481 DOI: 10.1128/jvi.00927-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/01/2018] [Indexed: 01/01/2023] Open
Abstract
The evolution of mammalian genomes has been shaped by interactions with endogenous retroviruses (ERVs). In this study, we investigated the distribution and diversity of ERVs in the mammalian order Perissodactyla, with a view to understanding their impact on the evolution of modern equids (family Equidae). We characterize the major ERV lineages in the horse genome in terms of their genomic distribution, ancestral genome organization, and time of activity. Our results show that subsequent to their ancestral divergence from rhinoceroses and tapirs, equids acquired four novel ERV lineages. We show that two of these ERV lineages proliferated extensively in the lineage leading to modern horses, and one contains loci that are actively transcribed in specific tissues. In addition, we show that the white rhinoceros has resisted germ line colonization by retroviruses for more than 54 million years-longer than any other extant mammalian species. The map of equine ERVs that we provide here will be of great utility to future studies aiming to investigate the potential functional roles of equine ERVs and their impact on equine evolution.IMPORTANCE ERVs in the host genome are highly informative about the long-term interactions of retroviruses and hosts. They are also interesting because they have influenced the evolution of mammalian genomes in various ways. In this study, we derive a calibrated timeline describing the process through which ERV diversity has been generated in the equine germ line. We determined the distribution and diversity of perissodactyl ERV lineages and inferred their retrotranspositional activity during evolution, thereby gaining insight into the long-term coevolutionary history of retroviruses and mammals. Our study provides a platform for future investigations to identify equine ERV loci involved in physiological processes and/or pathological conditions.
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Affiliation(s)
- Henan Zhu
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | | | - Pablo Ramiro Murcia
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
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Evolution and extinction of the giant rhinoceros Elasmotherium sibiricum sheds light on late Quaternary megafaunal extinctions. Nat Ecol Evol 2018; 3:31-38. [PMID: 30478308 DOI: 10.1038/s41559-018-0722-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 10/16/2018] [Indexed: 11/08/2022]
Abstract
Understanding extinction events requires an unbiased record of the chronology and ecology of victims and survivors. The rhinoceros Elasmotherium sibiricum, known as the 'Siberian unicorn', was believed to have gone extinct around 200,000 years ago-well before the late Quaternary megafaunal extinction event. However, no absolute dating, genetic analysis or quantitative ecological assessment of this species has been undertaken. Here, we show, by accelerator mass spectrometry radiocarbon dating of 23 individuals, including cross-validation by compound-specific analysis, that E. sibiricum survived in Eastern Europe and Central Asia until at least 39,000 years ago, corroborating a wave of megafaunal turnover before the Last Glacial Maximum in Eurasia, in addition to the better-known late-glacial event. Stable isotope data indicate a dry steppe niche for E. sibiricum and, together with morphology, a highly specialized diet that probably contributed to its extinction. We further demonstrate, with DNA sequencing data, a very deep phylogenetic split between the subfamilies Elasmotheriinae and Rhinocerotinae that includes all the living rhinoceroses, settling a debate based on fossil evidence and confirming that the two lineages had diverged by the Eocene. As the last surviving member of the Elasmotheriinae, the demise of the 'Siberian unicorn' marked the extinction of this subfamily.
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36
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Janečka JE, Davis BW, Ghosh S, Paria N, Das PJ, Orlando L, Schubert M, Nielsen MK, Stout TAE, Brashear W, Li G, Johnson CD, Metz RP, Zadjali AMA, Love CC, Varner DD, Bellott DW, Murphy WJ, Chowdhary BP, Raudsepp T. Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes. Nat Commun 2018; 9:2945. [PMID: 30054462 PMCID: PMC6063916 DOI: 10.1038/s41467-018-05290-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 05/23/2018] [Indexed: 01/08/2023] Open
Abstract
Dynamic evolutionary processes and complex structure make the Y chromosome among the most diverse and least understood regions in mammalian genomes. Here, we present an annotated assembly of the male specific region of the horse Y chromosome (eMSY), representing the first comprehensive Y assembly in odd-toed ungulates. The eMSY comprises single-copy, equine specific multi-copy, PAR transposed, and novel ampliconic sequence classes. The eMSY gene density approaches that of autosomes with the highest number of retained X-Y gametologs recorded in eutherians, in addition to novel Y-born and transposed genes. Horse, donkey and mule testis RNAseq reveals several candidate genes for stallion fertility. A novel testis-expressed XY ampliconic sequence class, ETSTY7, is shared with the parasite Parascaris genome, providing evidence for eukaryotic horizontal transfer and inter-chromosomal mobility. Our study highlights the dynamic nature of the Y and provides a reference sequence for improved understanding of equine male development and fertility.
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Affiliation(s)
| | - Brian W Davis
- Texas A&M University, College Station, TX, 77843, USA
| | | | - Nandina Paria
- Texas Scottish Rite Hospital for Children, Dallas, TX, 75219, USA
| | - Pranab J Das
- ICAR-National Research Centre on Pig, Guwahati, Assam, 781131, India
| | - Ludovic Orlando
- Natural History Museum of Denmark, 1350K, Copenhagen, Denmark.,Université de Toulouse, Université Paul Sabatier, 31000, Toulouse, France
| | - Mikkel Schubert
- Natural History Museum of Denmark, 1350K, Copenhagen, Denmark
| | | | | | | | - Gang Li
- Texas A&M University, College Station, TX, 77843, USA
| | | | - Richard P Metz
- Texas A&M AgriLife Research, College Station, TX, 77843, USA
| | | | | | | | | | | | - Bhanu P Chowdhary
- Texas A&M University, College Station, TX, 77843, USA. .,United Arab Emirates University, Al Ain, 15551, UAE.
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Vďačný P. Evolutionary Associations of Endosymbiotic Ciliates Shed Light on the Timing of the Marsupial-Placental Split. Mol Biol Evol 2018; 35:1757-1769. [PMID: 29659942 PMCID: PMC5995207 DOI: 10.1093/molbev/msy071] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Trichostome ciliates are among the most conspicuous protists in the gastrointestinal tract of a large variety of vertebrates. However, little is still known about phylogeny of the trichostome/vertebrate symbiotic systems, evolutionary correlations between trichostome extrinsic traits, and character-dependent diversification of trichostomes. These issues were investigated here, using the relaxed molecular clock technique along with stochastic mapping of character evolution, and binary-state speciation and extinction models. Clock analyses revealed that trichostomes colonized the vertebrate gastrointestinal tract ∼135 Ma, that is, near the paleontological minimum for the split of therian mammals into marsupials and placentals. According to stochastic mapping, the last common ancestor of trichostomes most likely invaded the hindgut of a mammal. Although multiple shifts to fish/amphibian or avian hosts and to the foregut compartments took place during the trichostome phylogeny, only transition to the foregut was recognized as a key innovation responsible for the explosive radiation of ophryoscolecid trichostomes after the Cretaceous/Tertiary boundary, when ungulates began their diversification. Since crown radiations of main trichostome lineages follow those of their mammalian hosts and are in agreement with their historic dispersal routes, the present time-calibrated phylogeny might help to elucidate controversies in the geological and molecular timing of the split between marsupials and placental mammals.
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Affiliation(s)
- Peter Vďačný
- Department of Zoology, Comenius University in Bratislava, Bratislava, Slovakia
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38
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Maclaren JA, Hulbert RC, Wallace SC, Nauwelaerts S. A morphometric analysis of the forelimb in the genus Tapirus (Perissodactyla: Tapiridae) reveals influences of habitat, phylogeny and size through time and across geographical space. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Jamie A Maclaren
- Department of Biology, Universiteit Antwerpen, Campus Drie Eiken, Universiteitsplein, Wilrijk, Antwerp,, Belgium
| | - Richard C Hulbert
- Florida Museum of Natural History, University of Florida, Dickinson Hall, Gainesville, Florida, FL, USA
| | - Steven C Wallace
- Don Sundquist Center of Excellence in Paleontology, Department of Geosciences, East Tennessee State University, Johnson City TN, USA
| | - Sandra Nauwelaerts
- Department of Biology, Universiteit Antwerpen, Campus Drie Eiken, Universiteitsplein, Wilrijk, Antwerp,, Belgium
- Centre for Research and Conservation, Koninklijke Maatschappij voor Dierkunde (KMDA), Koningin Astridplein, Antwerp, Belgium
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39
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May-Davis S, Brown W, Vermeulen Z. The Disappearing Lamellae: Implications of New Findings in the Family Equidae Suggest the Loss of Nuchal Ligament Lamellae on C6 and C7 Occurred After Domestication. J Equine Vet Sci 2018; 68:108-114. [PMID: 31256881 DOI: 10.1016/j.jevs.2018.03.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 03/14/2018] [Accepted: 03/14/2018] [Indexed: 10/17/2022]
Abstract
Conflicting data predominantly describes the equine nuchal ligament lamellae (NLL) attachments as C2-C6 or C2-C7; however, preliminary evidence suggests C2-C5. This study aimed to identify morphological variations in the attachments of the NLL in four species of the family equidae and determine if the variations were species or breed linked. Cadaveric examination evaluated 98 equids; Equusasinus (n = 2), Equus ferus caballus (n = 93), Equus przewalskii (n = 2), and Equus quagga boehmi (n = 1). Twenty breeds of E. f. caballus were included according to breed type-modern horse (n = 81), ancient type (n = 10), primitive (n = 4). Of the 98 equids, observations were divided into three categories according to the NLL attachments: C2-C5, C2-C6, and C2-C7; in category C2-C7, E. f. caballus (n = 3/93), modern horse 0 of 81, ancient 1 of 8, primitive 2 of 4; in category C2-C6, modern horse 2 of 81; in category C2-C5, modern horse 79 of 81, ancient type 7 of 8, primitive 2 of 4. Equus asinus, E. przewalskii, and E. q. boehmi all expressed category C2-C7. In total, 88 of 98 expressed category C2-C5; 2 of 98 category C2-C6; and 8 of 98 category C2-C7. These findings suggest that category C2-C5 provides sufficient evidence to suggest a normal occurrence. The high incidence of an absent NLL on C6 and C7 may be considered a contributing factor in caudal cervical osteoarthritis. Furthermore, category C2-C7 still exists in an ancient and primitive breed closely related to the tarpan, implying the NLL may have been attached from C2 to C7 in prehistoric horse before domestication. This hypothesis is supported by the findings of E. asinus, E. przewalskii, and E. q. boehmi, displaying attachments from C2 to C7.
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Affiliation(s)
- Sharon May-Davis
- The University of New England, Canine and Equine Research Group, Armidale, New South Wales, Australia.
| | - Wendy Brown
- The University of New England, Canine and Equine Research Group, Armidale, New South Wales, Australia
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40
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Sookdeo A, Hepp CM, Boissinot S. Contrasted patterns of evolution of the LINE-1 retrotransposon in perissodactyls: the history of a LINE-1 extinction. Mob DNA 2018; 9:12. [PMID: 29610583 PMCID: PMC5872511 DOI: 10.1186/s13100-018-0117-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 03/22/2018] [Indexed: 12/30/2022] Open
Abstract
Background LINE-1 (L1) is the dominant autonomously replicating non-LTR retrotransposon in mammals. Although our knowledge of L1 evolution across the tree of life has considerably improved in recent years, what we know of L1 evolution in mammals is biased and comes mostly from studies in primates (mostly human) and rodents (mostly mouse). It is unclear if patterns of evolution that are shared between those two groups apply to other mammalian orders. Here we performed a detailed study on the evolution of L1 in perissodactyls by making use of the complete genome of the domestic horse and of the white rhinoceros. This mammalian order offers an excellent model to study the extinction of L1 since the rhinoceros is one of the few mammalian species to have lost active L1. Results We found that multiple L1 lineages, carrying different 5’UTRs, have been simultaneously active during the evolution of perissodactyls. We also found that L1 has continuously amplified and diversified in horse. In rhinoceros, L1 was very prolific early on. Two successful families were simultaneously active until ~20my ago but became extinct suddenly at exactly the same time. Conclusions The general pattern of L1 evolution in perissodactyls is very similar to what was previously described in mouse and human, suggesting some commonalities in the way mammalian genomes interact with L1. We confirmed the extinction of L1 in rhinoceros and we discuss several possible mechanisms. Electronic supplementary material The online version of this article (10.1186/s13100-018-0117-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Akash Sookdeo
- 1Department of Biology, New York University, New York, NY USA
| | - Crystal M Hepp
- 2School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ USA
| | - Stéphane Boissinot
- 3New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
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41
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Stoops MA, Winget GD, DeChant CJ, Ball RL, Roth TL. Early fetal sexing in the rhinoceros by detection of male-specific genes in maternal serum. Mol Reprod Dev 2018; 85:197-204. [PMID: 29437259 DOI: 10.1002/mrd.22953] [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: 08/29/2017] [Accepted: 12/31/2017] [Indexed: 01/26/2023]
Abstract
Genetic sexing of animals with long gestation time benefits the management of captive populations. Here, X and Y chromosome-specific primers, based on equine gene sequencing data, were developed and tested on captive rhinoceroses (10 males, 20 females) representing four species (Diceros bicornis, Certaotherium simum simum, Rhinoceros unicornis, and Dicerorhinus sumatrensis). The Y chromosome-specific primer set targeted SRY (Sex-determining region Y), and amplified a 177-bp product following PCR of DNA extracted from males, but not females, of all species. A primer set based on the equine AMEL (Amelogenin) gene resulted in a 232-bp product following PCR of all rhinoceros species. These gene-specific primer sets were then evaluated for their ability to determine gender in cell-free DNA from rhinoceros serum. Modifications to the original extraction and PCR protocols were required to obtain sufficient DNA quantities from serum, and both DNA yield and PCR amplification were substantially reduced or absent following multiple freeze-thaw cycles of serum. When fresh serum from 14 pregnant rhinoceroses (ultimately bearing seven male and seven female calves), representing four species at different stages of gestation (Days 61-490), were probed in a PCR-based assay, an accuracy of 71% was achieved for male-specific gene detection of SRY, which improved to 100% by including a reamplification step into the protocol. Such early sex determination should be a valuable tool for current management practices as well as future assisted reproduction of rhinoceroses.
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Affiliation(s)
- Monica A Stoops
- Center for Conservation and Research of Endangered Wildlife, Cincinnati Zoo and Botanical Garden, Cincinnati, Ohio
| | - G Douglas Winget
- Center for Conservation and Research of Endangered Wildlife, Cincinnati Zoo and Botanical Garden, Cincinnati, Ohio
| | - Christopher J DeChant
- Center for Conservation and Research of Endangered Wildlife, Cincinnati Zoo and Botanical Garden, Cincinnati, Ohio
| | | | - Terri L Roth
- Center for Conservation and Research of Endangered Wildlife, Cincinnati Zoo and Botanical Garden, Cincinnati, Ohio
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42
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Matsui K. How can we reliably identify a taxon based on humeral morphology? Comparative morphology of desmostylian humeri. PeerJ 2017; 5:e4011. [PMID: 29134151 PMCID: PMC5683048 DOI: 10.7717/peerj.4011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/19/2017] [Indexed: 11/20/2022] Open
Abstract
Desmostylia is a clade of marine mammals belonging to either Tethytheria or Perissodactyla. Rich fossil records of Desmostylia were found in the Oligocene to Miocene strata of the Northern Pacific Rim, especially in the northwestern region, which includes the Japanese archipelago. Fossils in many shapes and forms, including whole or partial skeletons, skulls, teeth, and fragmentary bones have been discovered from this region. Despite the prevalent availability of fossil records, detailed taxonomic identification based on fragmentary postcranial materials has been difficult owing to to our limited knowledge of the postcranial diagnostic features of many desmostylian taxa. In this study, I propose the utilization of diagnostic characters found in the humerus to identify desmostylian genus. These characters can be used to identify isolated desmostylian humeri at the genus level, contributing to a better understanding of the stratigraphic and geographic distributions of each genus.
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Affiliation(s)
- Kumiko Matsui
- Department of Geology and Paleontology, National Museum of Nature and Science, Tsukuba, Japan
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43
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Gaubert P, Antunes A, Meng H, Miao L, Peigné S, Justy F, Njiokou F, Dufour S, Danquah E, Alahakoon J, Verheyen E, Stanley WT, O’Brien SJ, Johnson WE, Luo SJ. The Complete Phylogeny of Pangolins: Scaling Up Resources for the Molecular Tracing of the Most Trafficked Mammals on Earth. J Hered 2017; 109:347-359. [DOI: 10.1093/jhered/esx097] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/02/2017] [Indexed: 01/08/2023] Open
Affiliation(s)
- Philippe Gaubert
- Institut des Sciences de l’Evolution de Montpellier (ISEM)—UM-CNRS-IRD-EPHE, Université, France
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Portugal
| | - Agostinho Antunes
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Portugal
| | - Hao Meng
- School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, China
| | - Lin Miao
- School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, China
| | - Stéphane Peigné
- Centre de recherche sur la paléobiodiversité et les paléoenvironnements (CR2P)—UMR 7207 MNHN/CNRS/UPMC, Muséum national d’Histoire naturelle—CP38, France
| | - Fabienne Justy
- Institut des Sciences de l’Evolution de Montpellier (ISEM)—UM-CNRS-IRD-EPHE, Université, France
| | - Flobert Njiokou
- Laboratoire de Parasitologie et Ecologie, Université de Yaoundé I, Faculté des Sciences, Cameroon
| | | | - Emmanuel Danquah
- Department of Wildlife and Range Management, Faculty of Renewable Natural Resources, Kwame Nkrumah University of Science and Technology, Ghana
| | | | - Erik Verheyen
- OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Belgium
- Evolutionary Ecology Group, University of Antwerp, Belgium
| | | | - Stephen J O’Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Russia
- Oceanographic Center, Dania Beach, FL
- Nova Southeastern University, Ft Lauderdale, FL
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA
| | - Shu-Jin Luo
- School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, China
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44
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Lopes-Marques M, Ruivo R, Fonseca E, Teixeira A, Castro LFC. Unusual loss of chymosin in mammalian lineages parallels neo-natal immune transfer strategies. Mol Phylogenet Evol 2017; 116:78-86. [DOI: 10.1016/j.ympev.2017.08.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 08/07/2017] [Accepted: 08/25/2017] [Indexed: 12/20/2022]
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45
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Genetic variation of complete mitochondrial genome sequences of the Sumatran rhinoceros (Dicerorhinus sumatrensis). CONSERV GENET 2017. [DOI: 10.1007/s10592-017-1011-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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46
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MacLaren JA, Nauwelaerts S. Interspecific variation in the tetradactyl manus of modern tapirs (Perissodactyla: Tapirus
) exposed using geometric morphometrics. J Morphol 2017; 278:1517-1535. [DOI: 10.1002/jmor.20728] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 05/26/2017] [Accepted: 06/23/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Jamie A. MacLaren
- Department of Biology; Universiteit Antwerpen, Building D, Campus Drie Eiken, Universiteitsplein; Wilrijk, Antwerp 2610 Belgium
| | - Sandra Nauwelaerts
- Department of Biology; Universiteit Antwerpen, Building D, Campus Drie Eiken, Universiteitsplein; Wilrijk, Antwerp 2610 Belgium
- Centre for Research and Conservation, Koninklijke Maatschappij voor Dierkunde (KMDA), Koningin Astridplein 26; Antwerp 2018 Belgium
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47
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Kowalczyk K, Frąckowiak H. Arterial Patterns of the Face in Perissodactyla. Anat Rec (Hoboken) 2017; 300:1529-1534. [PMID: 28681434 DOI: 10.1002/ar.23638] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 02/07/2017] [Accepted: 02/08/2017] [Indexed: 11/08/2022]
Abstract
Considerable consistency in the arterial pattern of the head has been observed in species of Artiodactyla, but few studies have examined the order Perissodactyla. Here, we describe arteries supplying the intermandibular, mental, masseteric, buccal, labial, and nasal regions in eight perissodactylans, including representing of all families comprising this order. Observations were made on a total of 45 preparations of head arteries, obtained by injection of arteries with acetone-dissolved stained vinyl superchloride or stained latex LBS3060. In the Equidae species alone it was found that the facial artery descends from the linguofacial trunk. In tapirs and rhinos the facial artery branches off directly from the main arteries of the head. In tapirs alone it was found that the inferior alveolar artery gives off the buccal and sublingual arteries, and then extends into the mental artery. In the rhino a specific feature of the arterial pattern of the head was the exit of the occipital artery from the superficial temporal artery. In all equines studied, the transverse facial artery gave off a larger blood vessel to the masseter muscle and ran along the facial crest, while in tapirs and rhinos the transverse facial artery fanned out branches in the masseteric fossa. The variations observed can be considered in future studies on the origin of Perissodactyla. In this context, we note that the most similar patterns of exit and course of the facial, mental, transverse facial and infraorbital arteries exist in tapirs and rhinos (Ceratomorpha suborder), at least among the perissodactylans studied here. Anat Rec, 300:1529-1534, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Karolina Kowalczyk
- Department of Anatomy of Animals, Poznan University of Life Sciences, PL-60-625, Poznań, Poland
| | - Hieronim Frąckowiak
- Department of Anatomy of Animals, Poznan University of Life Sciences, PL-60-625, Poznań, Poland
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48
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Bai B, Meng J, Wang YQ, Wang HB, Holbrook L. Osteology of The Middle Eocene Ceratomorph Hyrachyus modestus (Mammalia, Perissodactyla). BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2017. [DOI: 10.1206/0003-0090-413.1.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Bin Bai
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing; and State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, CAS, Nanjing
| | - Jin Meng
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing; and Division of Paleontology, American Museum of Natural History, New York
| | - Yuan-Qing Wang
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing; and College of Earth Science, UCAS, Beijing
| | - Hai-Bing Wang
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing; and UCAS, Beijing
| | - Luke Holbrook
- Department of Biological Sciences, Rowan University, Glassboro, NJ; Division of Paleontology, American Museum of Natural History; and Department of Vertebrate Zoology, Academy of Natural Sciences of Drexel University, Philadelphia
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49
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Welker F, Smith GM, Hutson JM, Kindler L, Garcia-Moreno A, Villaluenga A, Turner E, Gaudzinski-Windheuser S. Middle Pleistocene protein sequences from the rhinoceros genus Stephanorhinus and the phylogeny of extant and extinct Middle/Late Pleistocene Rhinocerotidae. PeerJ 2017; 5:e3033. [PMID: 28316883 PMCID: PMC5354071 DOI: 10.7717/peerj.3033] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 01/26/2017] [Indexed: 11/20/2022] Open
Abstract
Background Ancient protein sequences are increasingly used to elucidate the phylogenetic relationships between extinct and extant mammalian taxa. Here, we apply these recent developments to Middle Pleistocene bone specimens of the rhinoceros genus Stephanorhinus. No biomolecular sequence data is currently available for this genus, leaving phylogenetic hypotheses on its evolutionary relationships to extant and extinct rhinoceroses untested. Furthermore, recent phylogenies based on Rhinocerotidae (partial or complete) mitochondrial DNA sequences differ in the placement of the Sumatran rhinoceros (Dicerorhinus sumatrensis). Therefore, studies utilising ancient protein sequences from Middle Pleistocene contexts have the potential to provide further insights into the phylogenetic relationships between extant and extinct species, including Stephanorhinus and Dicerorhinus. Methods ZooMS screening (zooarchaeology by mass spectrometry) was performed on several Late and Middle Pleistocene specimens from the genus Stephanorhinus, subsequently followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) to obtain ancient protein sequences from a Middle Pleistocene Stephanorhinus specimen. We performed parallel analysis on a Late Pleistocene woolly rhinoceros specimen and extant species of rhinoceroses, resulting in the availability of protein sequence data for five extant species and two extinct genera. Phylogenetic analysis additionally included all extant Perissodactyla genera (Equus, Tapirus), and was conducted using Bayesian (MrBayes) and maximum-likelihood (RAxML) methods. Results Various ancient proteins were identified in both the Middle and Late Pleistocene rhinoceros samples. Protein degradation and proteome complexity are consistent with an endogenous origin of the identified proteins. Phylogenetic analysis of informative proteins resolved the Perissodactyla phylogeny in agreement with previous studies in regards to the placement of the families Equidae, Tapiridae, and Rhinocerotidae. Stephanorhinus is shown to be most closely related to the genera Coelodonta and Dicerorhinus. The protein sequence data further places the Sumatran rhino in a clade together with the genus Rhinoceros, opposed to forming a clade with the black and white rhinoceros species. Discussion The first biomolecular dataset available for Stephanorhinus places this genus together with the extinct genus Coelodonta and the extant genus Dicerorhinus. This is in agreement with morphological studies, although we are unable to resolve the order of divergence between these genera based on the protein sequences available. Our data supports the placement of the genus Dicerorhinus in a clade together with extant Rhinoceros species. Finally, the availability of protein sequence data for both extinct European rhinoceros genera allows future investigations into their geographic distribution and extinction chronologies.
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Affiliation(s)
- Frido Welker
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany; BioArCh, Department of Archaeology, University of York, York, UK
| | - Geoff M Smith
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM, Neuwied, Germany; Department of Anthropology, University of California Davis, Davis, CA, USA
| | - Jarod M Hutson
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM, Neuwied, Germany; Current affiliation: Department of Paleobiology, Smithsonian Institution, Washington, D.C., USA
| | - Lutz Kindler
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM, Neuwied, Germany; Department of Pre- and Protohistoric Archaeology, Institute of Ancient Studies, Johannes-Gutenberg Universität Mainz, Mainz, Germany
| | - Alejandro Garcia-Moreno
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM , Neuwied , Germany
| | - Aritza Villaluenga
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM , Neuwied , Germany
| | - Elaine Turner
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM , Neuwied , Germany
| | - Sabine Gaudzinski-Windheuser
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM, Neuwied, Germany; Department of Pre- and Protohistoric Archaeology, Institute of Ancient Studies, Johannes-Gutenberg Universität Mainz, Mainz, Germany
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50
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Muangkram Y, Wajjwalku W, Amano A, Sukmak M. The novel primers for mammal species identification-based mitochondrial cytochrome b sequence: implication for reserved wild animals in Thailand and endangered mammal species in Southeast Asia. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 29:62-72. [PMID: 27758125 DOI: 10.1080/24701394.2016.1238902] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We presented the powerful techniques for species identification using the short amplicon of mitochondrial cytochrome b gene sequence. Two faecal samples and one single hair sample of the Asian tapir were tested using the new cytochrome b primers. The results showed a high sequence similarity with the mainland Asian tapir group. The comparative sequence analysis of the reserved wild mammals in Thailand and the other endangered mammal species from Southeast Asia comprehensibly verified the potential of our novel primers. The forward and reverse primers were 94.2 and 93.2%, respectively, by the average value of the sequence identity among 77 species sequences, and the overall mean distance was 35.9%. This development technique could provide rapid, simple, and reliable tools for species confirmation. Especially, it could recognize the problematic biological specimens contained less DNA material from illegal products and assist with wildlife crime investigation of threatened species and related forensic casework.
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Affiliation(s)
- Yuttamol Muangkram
- a Graduate School of Life Sciences , Ritsumeikan University , Kusatsu , Shiga , Japan.,b Faculty of Veterinary Medicine , Kasetsart University , Kamphaeng Saen , Nakhon Pathom , Thailand
| | - Worawidh Wajjwalku
- b Faculty of Veterinary Medicine , Kasetsart University , Kamphaeng Saen , Nakhon Pathom , Thailand
| | - Akira Amano
- a Graduate School of Life Sciences , Ritsumeikan University , Kusatsu , Shiga , Japan
| | - Manakorn Sukmak
- b Faculty of Veterinary Medicine , Kasetsart University , Kamphaeng Saen , Nakhon Pathom , Thailand
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