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Anwar G, Mamut R, Wang J. Characterization of Complete Mitochondrial Genomes of the Five Peltigera and Comparative Analysis with Relative Species. J Fungi (Basel) 2023; 9:969. [PMID: 37888225 PMCID: PMC10607270 DOI: 10.3390/jof9100969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/15/2023] [Accepted: 09/16/2023] [Indexed: 10/28/2023] Open
Abstract
In the present study, the complete mitochondrial genomes of five Peltigera species (Peltigera elisabethae, Peltigera neocanina, Peltigera canina, Peltigera ponojensis, Peltigera neckeri) were sequenced, assembled and compared with relative species. The five mitogenomes were all composed of circular DNA molecules, and their ranged from 58,132 bp to 69,325 bp. The mitochondrial genomes of the five Peltigera species contain 15 protein-coding genes (PCGs), 2 rRNAs, 26-27 tRNAs and an unidentified open reading frame (ORF). The PCG length, AT skew and GC skew varied among the 15 PCGs in the five mitogenomes. Among the 15 PCGs, cox2 had the least K2P genetic distance, indicating that the gene was highly conserved. The synteny analysis revealed that the coding regions were highly conserved in the Peltigera mitochondrial genomes, but gene rearrangement occurred in the intergenic regions. The phylogenetic analysis based on the 14 PCGs showed that the 11 Peltigera species formed well-supported topologies, indicating that the protein-coding genes in the mitochondrial genome may be used as a reliable molecular tool in the study of the phylogenetic relationship of Peltigera.
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Affiliation(s)
| | - Reyim Mamut
- College of Life Sciences and Technology, Xinjiang University, Urumchi 830017, China; (G.A.); (J.W.)
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Lyu T, Zhou S, Fang J, Wang L, Shi L, Dong Y, Zhang H. Convergent Genomic Signatures of High-Altitude Adaptation among Six Independently Evolved Mammals. Animals (Basel) 2022; 12:ani12243572. [PMID: 36552492 PMCID: PMC9774524 DOI: 10.3390/ani12243572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/08/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
The species living in the Qinghai-Tibet Plateau provide an excellent model system for studying the relationship between molecular convergent evolution and adaptation. Distant species experiencing the same selection pressure (i.e., hypoxia, low temperature and strong ultraviolet radiation) are likely to evolve similar genetic adaptations independently. Here, we performed comparative genomics studies on six independently evolved high-altitude species. The results also showed that the convergent evolution of the six species was mainly reflected at the level of rapidly evolving genes, and the functions of these rapidly evolving genes were mainly related to hypoxia response and DNA damage repair. In addition, we found that high-altitude species had more gene family changes than their low-altitude relatives, except for the order Lagomorpha. The results also show that the convergence of the gene family contraction of high-altitude species is much greater than that of expansion, revealing a possible pattern of species in adapting to high-altitude. Furthermore, we detected a positive selection signature in four genes related to hypoxia response and ultraviolet radiation damage in these six species (FYCO1, ERBIN, SCAMP1 and CXCL10). Our study reveals that hypoxia response might play an important role in the adaptation of independently evolved species to a high-altitude environment, providing a basic perspective for further exploring the high-altitude adaptation mechanism of different related species in the future.
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Affiliation(s)
- Tianshu Lyu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150000, China
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Shengyang Zhou
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Jiaohui Fang
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Lidong Wang
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Lupeng Shi
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Yuehuan Dong
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Honghai Zhang
- College of Life Science, Qufu Normal University, Qufu 273165, China
- Correspondence:
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Korec E, Ungrová L, Hejnar J, Grieblová A, Zelená K. Three new genes associated with longevity in the European Bison. Vet Anim Sci 2022; 17:100266. [PMID: 35957660 PMCID: PMC9361326 DOI: 10.1016/j.vas.2022.100266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Evžen Korec
- Zoologická zahrada Tábor a.s., Dukelských Hrdinů 19, 170 00, Prague 7, Czech Republic
- Corresponding author.
| | - Lenka Ungrová
- Zoologická zahrada Tábor a.s., Dukelských Hrdinů 19, 170 00, Prague 7, Czech Republic
- Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Jiří Hejnar
- Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Adéla Grieblová
- Zoologická zahrada Tábor a.s., Dukelských Hrdinů 19, 170 00, Prague 7, Czech Republic
| | - Kateřina Zelená
- Zoologická zahrada Tábor a.s., Dukelských Hrdinů 19, 170 00, Prague 7, Czech Republic
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Kamani J, Irene S, Qasim AMMM, Olubade TA, Abasiama MS, Gajibo A, Balami PU, Shands M, Harrus S. Nucleotide sequence types (ntSTs) of Anaplasma marginale in cattle in Nigeria based on the major surface protein 5 (msp5) gene. Acta Trop 2022; 233:106544. [PMID: 35636526 DOI: 10.1016/j.actatropica.2022.106544] [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: 04/27/2022] [Revised: 05/23/2022] [Accepted: 05/25/2022] [Indexed: 11/15/2022]
Abstract
Bovine anaplasmosis caused by Anaplasma marginale is an important endemic disease that exerts negative impact on livestock production with huge socioeconomic consequences in most developing countries. Genetic studies have reported the existence of diverse ntSTs of A. marginale with varying pathogenicity in different countries. Continuous studies to obtain accurate information on disease etiologies is desirable for the formulation of cost-effective control measures. To this end, 582 blood samples from cattle were collected from 10 out of the 36 States of Nigeria from April 2021 to March 2022 and analyzed based on the major surface protein 5 (msp5) gene to determine the ntSTs of A. marginale in Nigeria. In all, 38 out of the 582 samples (6.5%) from cattle in the different Agro-ecological Zones (AEZs) of Nigeria were positive. The Nigerian A. marginale nucleotide sequences were 96.7 to 100% identical to sequences from other countries and were placed in distinct clusters with other A. marginale sequences deposited in GenBank. Network analysis revealed three ntSTs (#2, #4 & #8) of A. marginale from Nigeria with a nucleotide sequence type diversity (Hd) of 0.8, nucleotide diversity (Pi) of 0.015 and average number of nucleotide differences (k) of 7.09. Two different amino acid substitution sites were found in Nigerian and worldwide sequences at positions 148 and 160. This is the first nationwide report on the ntST diversity and genetic characterization of A. marginale in cattle in Nigeria based on the msp5 gene. Bovine anaplasmosis is widespread in Nigeria and deserves further attention.
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Affiliation(s)
- Joshua Kamani
- National Veterinary Research Institute (NVRI), PMB 01 Vom, Plateau State, Nigeria.
| | - Sacristán Irene
- Animal Health Research Centre, National Institute for Agricultural and Food Research and Technology (INIA), Centro Superior de Investigaciones Científicas (CSIC), Valdeolmos, Madrid, Spain
| | | | - Toyin A Olubade
- National Veterinary Research Institute (NVRI), PMB 01 Vom, Plateau State, Nigeria
| | | | - Ali Gajibo
- National Veterinary Research Institute (NVRI), PMB 01 Vom, Plateau State, Nigeria
| | - Peter Umar Balami
- National Veterinary Research Institute (NVRI), PMB 01 Vom, Plateau State, Nigeria
| | - Mike Shands
- School of Geographical and Earth Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Shimon Harrus
- Koret School of Veterinary Medicine, The Hebrew University of Jerusalem, Rehovot, Israel
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Karyotypical Confirmation of Natural Hybridization between Two Manatee Species, Trichechus manatus and Trichechus inunguis. Life (Basel) 2022; 12:life12050616. [PMID: 35629284 PMCID: PMC9145575 DOI: 10.3390/life12050616] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/17/2022] [Accepted: 04/18/2022] [Indexed: 01/20/2023] Open
Abstract
Two species of manatees are found in Northern Brazil—the Antillean manatee (Trichechus manatus), which is found along the coast from Florida to Northeastern Brazil, and the Amazonian manatee (Trichechus inunguis), endemic to the Amazon drainage basin. These species show a sympatric distribution in the region of the Marajó Archipelago, an estuarine area surrounding the Amazon River mouth. There is evidence of the occurrence of interspecific hybrids in this area, based on mitochondrial DNA analyses, although the use of nuclear markers has not corroborated this proposal. Considering that these species show very distinct karyotypes, despite being closely related (2n = 48 in T. manatus and 2n = 56 in T. inunguis), hybrids would present distinct chromosome numbers. Based on this, we conducted cytogenetic analyses using classic and molecular techniques in three calves found stranded in the Marajó Island and Amapá coast. The results showed that one of them, morphologically classified as T. inunguis, presented the correspondent karyotype, with 2n = 56. However, the other two, which were phenotypically similar to T. manatus, showed 2n = 49. Despite the same diploid number, their G-banding patterns revealed some differences. The results of the distribution of some microsatellite sequences have also confirmed the heterozygosity of some chromosomal pairs in these two individuals. These results are the first indubitable confirmation of the occurrence of natural hybrids between T. manatus and T. inunguis, and also brings about some issues concerning the viability of hybrids, considering that these two individuals do not correspond to an F1 hybrid, but instead, both presented a possible F2 karyotype.
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Gaite PL, Aala, Jr. W, Bacus M, Labrador C, Numeron AM, Gamalo LE, Murao LA. The first complete mitochondrial genome sequence of Cynopterus brachyotis (Chiroptera, Pteropodidae) from the Philippines. Biodivers Data J 2022; 10:e72768. [PMID: 35210914 PMCID: PMC8860972 DOI: 10.3897/bdj.10.e72768] [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: 08/09/2021] [Accepted: 09/28/2021] [Indexed: 11/16/2022] Open
Abstract
The technical limitations of capillary sequencing in providing insights on phylogeny have been greatly aided in recent years by the implementation of next generation sequencing platforms which can generate whole mitochondrial genome (mitogenome) sequences. In this study, enriched mitochondrial DNA of Cynopterusbrachyotis from Mindanao, Philippines was sequenced using the Illumina MiSeq platform. A total of 653,967 clean paired-end reads was assembled using a MIRA-MITObim pipeline, resulting in a consensus mitogenome sequence length of 17,382 bases and a GC content of 41.48%, which is consistent with other published mitogenomes in fruit bats. The assembled C.brachyotis mitogenome was annotated using the MITOS online server and was able to resolve all mitochondrial genes, except for one transfer RNA gene (trnT) which may be further resolved by additional capillary sequencing of the region. Sequence analysis showed that the Philippine C.brachyotis is only 90%-91% homologous with other Cynopterus spp., based on its full mitogenome sequence. Phylogenetic analysis of fruit bat mitogenomes, deposited in online repositories, revealed that the Philippine C.brachyotis in this study has diverged from Asian Cynopterus, namely Cynopterusbrachyotis and Cynopterussphinx from other parts of Asia (100% bootstrap support) with the latter two forming a separate clade. This divergence at the species level was consistent with phylogentic inference using cytochrome oxidase 1 (CO1) and cytochrome B (cytb) gene markers. Our results strengthen the previously reported hypothesis that the Cynopteruscf.brachyotis in the Philippines is distinct from its Asian counterparts and should be, therefore, treated as a new species.
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How can mating systems inform future biobanking strategies? An illustration using two Indonesian bovids, banteng (Bos javanicus) and lowland anoa (Bubalus depressicornis). Anim Reprod Sci 2022; 238:106943. [DOI: 10.1016/j.anireprosci.2022.106943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 01/21/2022] [Accepted: 02/06/2022] [Indexed: 11/17/2022]
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Boonmar S, Saengsawang P, Mitsuwan W, Panjai D, Kidsin K, Sansamur C, Wichianrat I. The first report of the seroprevalence of antibodies against Bartonella spp. in water buffaloes (Bubalus bubalis) from South Thailand. Vet World 2021; 14:3144-3148. [PMID: 35153405 PMCID: PMC8829419 DOI: 10.14202/vetworld.2021.3144-3148] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/08/2021] [Indexed: 11/19/2022] Open
Abstract
Background and Aim: Bartonellosis is an emerging worldwide zoonosis caused by bacteria belonging to the genus Bartonella. Several studies have been conducted on the prevalence of Bartonella infections from animals and humans, including reports from wild and domestic ruminants. However, there has been only one report of Bartonella infection in water buffaloes from the northeastern part of Thailand. Moreover, the seroprevalence of Bartonella spp. in water buffaloes still remains unknown. This study was conducted to explore the prevalence of Bartonella spp. among water buffaloes from South Thailand using molecular and serological techniques. Materials and Methods: A total of 312 samples (156 blood and 156 sera) of 156 water buffaloes from 29 farms in Phatthalung Province, South Thailand, were collected from January to March 2021. All samples were screened for Bartonella spp. using polymerase chain reaction and indirect immunofluorescence assay. Results: The seroprevalence of antibodies against three Bartonella spp. was 16.03% (25/156, 95% confidence interval: 10.65-22.74%), and among 25 water buffaloes with seroprevalence, 56%, 20%, and 24% were positive for antibodies against Bartonellahenselae, Bartonellavinsonii subspp. berkhoffii, and Bartonellatamiae, respectively. No significant difference was detected among seroprevalence, gender, age, and ectoparasite infestation. Conclusion: This is the first report of the seroprevalence of antibodies against B. henselae, B. vinsonii subspp. berkhoffii, and B. tamiae in water buffaloes from South Thailand. Further studies are required on the epidemiology of Bartonella infection among water buffaloes, related personnel, and ectoparasites.
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Affiliation(s)
- Sumalee Boonmar
- Akkhraratchakumari Veterinary College, Walailak University, Thasala, Nakhon Si Thammarat, 80160, Thailand
| | - Phirabhat Saengsawang
- Akkhraratchakumari Veterinary College, Walailak University, Thasala, Nakhon Si Thammarat, 80160, Thailand
| | - Watcharapong Mitsuwan
- Akkhraratchakumari Veterinary College, Walailak University, Thasala, Nakhon Si Thammarat, 80160, Thailand; Research Center of Excellence in Innovation of Essential Oil, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Decha Panjai
- Department of Medical Sciences, National Institute of Health, Ministry of Public Health, Nonthaburi, 11000, Thailand
| | - Kamchai Kidsin
- Animal Health Section, The Eight Regional Livestock Development, Surat Thani 84000, Thailand
| | - Chalutwan Sansamur
- Akkhraratchakumari Veterinary College, Walailak University, Thasala, Nakhon Si Thammarat, 80160, Thailand
| | - Ittidet Wichianrat
- Akkhraratchakumari Veterinary College, Walailak University, Thasala, Nakhon Si Thammarat, 80160, Thailand
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Calamari ZT. Total Evidence Phylogenetic Analysis Supports New Morphological Synapomorphies for Bovidae (Mammalia, Artiodactyla). AMERICAN MUSEUM NOVITATES 2021. [DOI: 10.1206/3970.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Tu VT, Görföl T, Csorba G, Arai S, Kikuchi F, Fukui D, Koyabu D, Furey NM, Bawm S, Lin KS, Alviola P, Hang CT, Son NT, Tuan TA, Hassanin A. Integrative taxonomy and biogeography of Asian yellow house bats (Vespertilionidae:
Scotophilus
) in the Indomalayan Region. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vuong Tan Tu
- Institute of Ecology and Biological Resources Vietnam Academy of Science and Technology Hanoi Vietnam
- Graduate University of Science and TechnologyVietnam Academy of Science and Technology Hanoi Vietnam
- Institut de Systématique, Évolution, Biodiversité (ISYEB) Sorbonne UniversitéMNHNCNRSEPHE, UA ‐ Muséum National d’Histoire Naturelle Paris France
- Service de Systématique Moléculaire UMS 2700 Muséum national d’Histoire naturelle Paris France
| | - Tamás Görföl
- Department of Zoology Hungarian Natural History Museum Budapest Hungary
- National Laboratory of Virology Szentágothai Research Centre University of Pécs Pécs Hungary
| | - Gábor Csorba
- Department of Zoology Hungarian Natural History Museum Budapest Hungary
| | - Satoru Arai
- Infectious Disease Surveillance Center National Institute of Infectious Diseases Shinjuku, Tokyo Japan
| | - Fuka Kikuchi
- Infectious Disease Surveillance Center National Institute of Infectious Diseases Shinjuku, Tokyo Japan
- Tokyo University of Science Shinjuku, Tokyo Japan
- Research and Education Center for Prevention of Global Infectious Diseases of Animals Tokyo University of Agriculture and Technology Fuchu, Tokyo Japan
| | - Dai Fukui
- The University of Tokyo Hokkaido Forest Graduate School of Agricultural and Life Sciences The University of Tokyo Hokkaido Japan
| | - Daisuke Koyabu
- Jockey Club College of Veterinary Medicine and Life Sciences City University of Hong Kong Kowloon Hong Kong
- Department of Molecular Craniofacial Embryology Graduate School of Medical and Dental Sciences Tokyo Medical and Dental University Bunkyo‐ku, Tokyo Japan
| | - Neil M. Furey
- Fauna & Flora International, Cambodia Programme Chamkarmorn, Phnom Penh Cambodia
- Harrison InstituteBowerwood House Sevenoaks Kent UK
| | - Saw Bawm
- University of Veterinary Science Yezin, Nay Pyi Taw Myanmar
| | - Kyaw San Lin
- University of Veterinary Science Yezin, Nay Pyi Taw Myanmar
| | - Phillip Alviola
- Institute of Biological Sciences and Museum of Natural History University of the Philippines Los Banos Laguna Philippines
| | - Chu Thi Hang
- Institute of Ecology and Biological Resources Vietnam Academy of Science and Technology Hanoi Vietnam
- Graduate University of Science and TechnologyVietnam Academy of Science and Technology Hanoi Vietnam
| | - Nguyen Truong Son
- Institute of Ecology and Biological Resources Vietnam Academy of Science and Technology Hanoi Vietnam
- Graduate University of Science and TechnologyVietnam Academy of Science and Technology Hanoi Vietnam
| | - Tran Anh Tuan
- Institute of Ecology and Biological Resources Vietnam Academy of Science and Technology Hanoi Vietnam
- Graduate University of Science and TechnologyVietnam Academy of Science and Technology Hanoi Vietnam
| | - Alexandre Hassanin
- Institut de Systématique, Évolution, Biodiversité (ISYEB) Sorbonne UniversitéMNHNCNRSEPHE, UA ‐ Muséum National d’Histoire Naturelle Paris France
- Service de Systématique Moléculaire UMS 2700 Muséum national d’Histoire naturelle Paris France
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Curaudeau M, Rozzi R, Hassanin A. The genome of the lowland anoa (Bubalus depressicornis) illuminates the origin of river and swamp buffalo. Mol Phylogenet Evol 2021; 161:107170. [PMID: 33798669 DOI: 10.1016/j.ympev.2021.107170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/12/2021] [Accepted: 03/25/2021] [Indexed: 10/21/2022]
Abstract
Two types of domestic water buffalo are currently recognized: the river buffalo from the Indian subcontinent and Mediterranean countries and the swamp buffalo from China and Southeast Asia. To test the hypothesis of two separate species of water buffalo, we sequenced the genome of the lowland anoa, Bubalus depressicornis, which is a dwarf wild buffalo endemic to Sulawesi, and two genomes of swamp buffalo, and made comparisons with 12 additional genomes. Three genomic data sets were constructed to infer phylogenetic relationships: the mitochondrial genome (15,468 bp; maternal transmission), two concatenated Y-chromosomal genes, AMELY and DDX3Y (20,036 bp; paternal transmission), and a selection of 30 nuclear genes representing all cattle chromosomes (364,887 bp; biparental transmission). The comparisons between our 30 nuclear gene sequences obtained by read mapping and those directly extracted from Bos taurus and Bubalus bubalis genome assemblies show that the mapping approach revealed higher levels of heterozygosity at both nucleotide sites and indels (insertions and deletions) (0.09-0.15%), as well as several sequence errors (0.07%). Our phylogenetic and molecular dating analyses provide strong evidence that the lowland anoa, river buffalo, and swamp buffalo are three distinct taxa which separated rapidly from each other during the Pleistocene epoch. We therefore conclude that two species of domestic water buffalo should be distinguished: Bubalus bubalis for the river buffalo and Bubalus kerabau for the swamp buffalo. The new classification can have deep implications for understanding the evolution and selection of domesticated forms and for the conservation and management of wild buffalo populations in South and Southeast Asia.
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Affiliation(s)
- Manon Curaudeau
- Institut Systématique Evolution Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, UA, 57 rue Cuvier, CP 51, 75005 Paris, France
| | - Roberto Rozzi
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Synthesis Centre for Biodiversity Sciences (sDiv), Puschstr. 4, D-04103 Leipzig, Germany; Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, 10115 Berlin, Germany
| | - Alexandre Hassanin
- Institut Systématique Evolution Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, UA, 57 rue Cuvier, CP 51, 75005 Paris, France.
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Qing X, Kulkeaw K, Wongkamchai S, Tsui SKW. Mitochondrial Genome of Brugia malayi Microfilariae Isolated From a Clinical Sample. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.637805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Lymphatic filariasis is a neglected parasitic disease that is a leading cause of long-term disability. Information obtained from genome sequencing of filarial worm can help us identify systems in the worm that are likely to be useful for novel drug design. Brugia (B.) malayi is still the only lymphatic-dwelling filarial parasite with a nearly complete, fully annotated, and published genome. However, most previous studies were based on the FR3 strain of B. malayi, which originally was isolated from a human patient, and was adapted to the rodent model, then maintained in laboratories for more than 60 years. It is uncertain whether genetic variation exists, thus, sequencing of clinical isolates of lymphatic dwelling filarial parasites is a high priority. Here, we report for the first time the complete mitochondrial genome of B. malayi microfilariae from clinical isolate. Complete mitochondrial (mt) genome of the microfilariae isolated from a blood sample taken from a Thai subject living in Narathiwat Province, which is an endemic area of brugian filariasis, was assembled with sequencing reads obtained by Illumina sequencing. Gene annotation, phylogenetic analysis and single nucleotide polymorphism (SNP) were deployed. A complete 13,658-bp mt genome of B. malayi microfilaria was obtained, and it shows 68x coverage. Based on gene annotation, the mt genome consists of 12 protein-coding, two rRNA, and 23 tRNA genes. Phylogenetic analysis using all protein sequences of DNA sequences of mt genome or cytochrome c oxidase subunit I (COX1) revealed a close relationship among three lymphatic filariae (i.e., B. timori, zoonotic B. pahangi, and Wuchereria spp.). The SNPs in the COX1 gene can differentiate microfilariae of B. malayi in human from those found in canine. Furthermore, the number, order and transcription, and direction of B. malayi microfilariae mitochondrial genes were the same as those found in the FR3 strain of B. malayi. The comparison on mitochondrial genome of B. malayi could have important implications on the development of a new intervention or vaccine to treat or prevent this disease in endemic areas/regions around the world.
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Zhang K, Lenstra JA, Zhang S, Liu W, Liu J. Evolution and domestication of the Bovini species. Anim Genet 2020; 51:637-657. [PMID: 32716565 DOI: 10.1111/age.12974] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2020] [Indexed: 12/17/2022]
Abstract
Domestication of the Bovini species (taurine cattle, zebu, yak, river buffalo and swamp buffalo) since the early Holocene (ca. 10 000 BCE) has contributed significantly to the development of human civilization. In this study, we review recent literature on the origin and phylogeny, domestication and dispersal of the three major Bos species - taurine cattle, zebu and yak - and their genetic interactions. The global dispersion of taurine and zebu cattle was accompanied by population bottlenecks, which resulted in a marked phylogeographic differentiation of the mitochondrial and Y-chromosomal DNA. The high diversity of European breeds has been shaped through isolation-by-distance, different production objectives, breed formation and the expansion of popular breeds. The overlapping and broad ranges of taurine and zebu cattle led to hybridization with each other and with other bovine species. For instance, Chinese gayal carries zebu mitochondrial DNA; several Indonesian zebu descend from zebu bull × banteng cow crossings; Tibetan cattle and yak have exchanged gene variants; and about 5% of the American bison contain taurine mtDNA. Analysis at the genomic level indicates that introgression may have played a role in environmental adaptation.
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Affiliation(s)
- K Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht Yalelaan 104, Utrecht, 3584 CM, The Netherlands
| | - S Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - W Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
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Fadakar D, Malekian M, Hemami MR, Lerp H, Rezaei HR, Bärmann EV. Repeated hybridization of two closely related gazelle species ( Gazella bennettii and Gazella subgutturosa) in central Iran. Ecol Evol 2020; 10:11372-11386. [PMID: 33144971 PMCID: PMC7593154 DOI: 10.1002/ece3.6774] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 08/09/2020] [Accepted: 08/11/2020] [Indexed: 12/02/2022] Open
Abstract
Interspecific hybridization increasingly occurs in the course of anthropogenic actions, such as species translocations and introductions, and habitat modifications or occurs in sympatric species due to the shortage of conspecific mates. Compared with anthropogenically caused hybridization, natural hybridization is more difficult to prove, but both play an important role in conservation. In this study, we detected hybridization of two gazelle sister species, Gazella bennettii (adapted to dry areas) and Gazella subgutturosa (adapted to open plains), in five habitat areas, where G. bennettii naturally occur in central Iran. The hybrids have a nuclear genomic identity (based on two introns), habitat preference, and phenotype of G. bennettii, but the mitochondrial identity (based on cyt b) of G. subgutturosa. We suggest that natural hybridization of female G. subgutturosa and male G. bennettii happened twice in central Iran in prehistoric times, based on the haplotype pattern that we found. However, we found indications of recent hybridization between both species under special circumstances, for example, in breeding centers, due to translocations, or in areas of sympatry due to the shortage of conspecific mates. Therefore, these two species must be kept separately in the breeding centers, and introduction of one of them into the habitat of the other must be strictly avoided.
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Affiliation(s)
- Davoud Fadakar
- Department of Natural ResourcesIsfahan University of TechnologyIsfahanIran
| | - Mansoureh Malekian
- Department of Natural ResourcesIsfahan University of TechnologyIsfahanIran
| | - Mahmoud R. Hemami
- Department of Natural ResourcesIsfahan University of TechnologyIsfahanIran
| | - Hannes Lerp
- Natural History CollectionsMuseum WiesbadenWiesbadenGermany
| | - Hamid R. Rezaei
- Department of Fishery and EnvironmentGorgan University of Agricultural Science and Natural ResourcesGorganIran
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The first complete mitochondrial genome sequence of the endangered mountain anoa (Bubalus quarlesi) (Artiodactyla: Bovidae) and phylogenetic analysis. JOURNAL OF ASIA-PACIFIC BIODIVERSITY 2020. [DOI: 10.1016/j.japb.2020.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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16
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Barbhuiya PA, Uddin A, Chakraborty S. Analysis of compositional properties and codon usage bias of mitochondrial CYB gene in anura, urodela and gymnophiona. Gene 2020; 751:144762. [PMID: 32407767 DOI: 10.1016/j.gene.2020.144762] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/24/2020] [Accepted: 05/08/2020] [Indexed: 01/17/2023]
Abstract
We delineated the pattern of synonymous codon usage bias (CUB) and its determinants in mitochondrial CYB gene of respiratory chain across different amphibian groups namely orders anura, urodela and gymnophiona. We observed that CUB was low in CYB gene of amphibia. The gymnophionans had comparatively high bias followed by urodeles and anurans. The codons namely TCA, CCA, CAA, CGA, TGA, AAA and ACA were over-represented in all three orders. The codons such as GCC and TCC were over-represented in anura whereas in urodela, the over-represented codons were TTA, CTA, ATA, GTA, GAA, GGA and GCA. In gymnophiona, GCC, TTA, CTA, ATA, GTA, GAA and GGA codons were over-represented. The regression analysis between effective number of codons (ENC) and nucleobase at the 3rd position revealed that nucleobase A and C influenced CUB positively in order anura, while in urodela and gymnophiona, nucleobase A and T influenced the CUB positively. Mutation pressure and natural selection mutually illustrate the CUB of CYB gene (complex III gene) of amphibia as elucidated by correlation analysis between 3rd nucleotide in a codon and overall nucleotide content of the gene. However, neutrality plot showed that natural selection was the dominant evolutionary factor of CUB.
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Affiliation(s)
- Parvin A Barbhuiya
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India
| | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakand 788150, Assam, India
| | - Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India.
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17
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Petzold A, Hassanin A. A comparative approach for species delimitation based on multiple methods of multi-locus DNA sequence analysis: A case study of the genus Giraffa (Mammalia, Cetartiodactyla). PLoS One 2020; 15:e0217956. [PMID: 32053589 PMCID: PMC7018015 DOI: 10.1371/journal.pone.0217956] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 01/24/2020] [Indexed: 12/25/2022] Open
Abstract
Molecular data are now commonly used in taxonomy for delimiting cryptic species. In the case of giraffes, which were treated as a single species (Giraffa camelopardalis) during half of a century, several molecular studies have suggested a splitting into four to seven species, but the criteria applied for taxonomic delimitation were not fully described. In this study, we have analysed all multi-locus DNA sequences available for giraffes using multispecies coalescent (MSC: *BEAST, BPP and STACEY), population genetic (STRUCTURE, allelic networks, haplotype network and bootstrapping, haplowebs and conspecificity matrix) and phylogenetic (MrBayes, PhyML, SuperTRI) methods to identify the number of species. Our results show that depending on the method chosen, different taxonomic hypotheses, recognizing from two to six species, can be considered for the genus Giraffa. Our results confirm that MSC methods can lead to taxonomic over-splitting, as they delimit geographic structure rather than species. The 3-species hypothesis, which recognizes G. camelopardalis sensu strico A, G. giraffa, and G. tippelskirchi, is highly supported by phylogenetic analyses and also corroborated by most population genetic and MSC analyses. The three species show high levels of nucleotide divergence in both nuclear (0.35-0.51%) and mitochondrial sequences (3-4%), and they are characterised by 7 to 12 exclusive synapomorphies (ES) detected in nine of the 21 nuclear introns analysed for this study. By contrast, other putative species, such as G. peralta, G. reticulata, G. thornicrofti or G. tippelskirchi sensu stricto, do not exhibit any ES in the nuclear genes. A robust mito-nuclear conflict was found for the position and monophyly of G. giraffa and G. tippelskirchi, which is interpreted as the result of a mitochondrial introgression from Masai to southeastern giraffe during the Pleistocene and nuclear gene flow mediated by male dispersal between southern populations (subspecies G. g. giraffa and G. g. angolensis).
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Affiliation(s)
- Alice Petzold
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, Paris, France
- Muséum national d'Histoire naturelle, CP51, Paris, France
| | - Alexandre Hassanin
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, Paris, France
- Muséum national d'Histoire naturelle, CP51, Paris, France
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18
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A Novel Color Image Encryption Algorithm Based on Hyperchaotic Maps and Mitochondrial DNA Sequences. ENTROPY 2020; 22:e22020158. [PMID: 33285933 PMCID: PMC7516571 DOI: 10.3390/e22020158] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 01/25/2020] [Accepted: 01/27/2020] [Indexed: 11/29/2022]
Abstract
Multimedia encryption innovation is one of the primary ways of securely and privately guaranteeing the security of media transmission. There are many advantages when utilizing the attributes of chaos, for example, arbitrariness, consistency, ergodicity, and initial condition affectability, for any covert multimedia transmission. Additionally, many more benefits can be introduced with the exceptional space compliance, unique information, and processing capability of real mitochondrial deoxyribonucleic acid (mtDNA). In this article, color image encryption employs a confusion process based on a hybrid chaotic map, first to split each channel of color images into n-clusters; then to create global shuffling over the whole image; and finally, to apply intrapixel shuffling in each cluster, which results in very disordered pixels in the encrypted image. Then, it utilizes the rationale of human mitochondrial genome mtDNA to diffuse the previously confused pixel values. Hypothetical examination and trial results demonstrate that the anticipated scheme exhibits outstanding encryption, as well as successfully opposes chosen/known plain text, statistical, and differential attacks.
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Kehlmaier C, Zhang X, Georges A, Campbell PD, Thomson S, Fritz U. Mitogenomics of historical type specimens of Australasian turtles: clarification of taxonomic confusion and old mitochondrial introgression. Sci Rep 2019; 9:5841. [PMID: 30967590 PMCID: PMC6456567 DOI: 10.1038/s41598-019-42310-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 03/27/2019] [Indexed: 11/12/2022] Open
Abstract
Diagnosability is central to taxonomy as are type specimens which define taxa. New advances in technologies and the discovery of new informative traits must be matched with previous taxonomic decisions based on name-bearing type specimens. Consequently, the challenge of sequencing highly degraded DNA from historical types becomes an inevitability to resolve the very many taxonomic issues arising from, by modern standards, poor historical species descriptions leading to difficulties to assign names to genetic clusters identified from fresh material. Here we apply high-throughput parallel sequencing and sequence baiting to reconstruct the mitogenomes from 18 type specimens of Australasian side-necked turtles (Chelidae). We resolve a number of important issues that have confused the taxonomy of this family, and analyse the mitogenomes of the types and those of fresh material to improve our understanding of the phylogenetic relationships of this morphologically conservative group. Together with previously published nuclear genomic data, our study provides evidence for multiple old mitochondrial introgressions.
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Affiliation(s)
| | - Xiuwen Zhang
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia
| | - Patrick D Campbell
- Department of Life Sciences, Darwin Centre (DC1), Natural History Museum, London, SW7 5BD, England, UK
| | - Scott Thomson
- Chelonian Research Institute, Oviedo, Florida, USA
- Museu de Zoologia, Universidade de São Paulo, Avenida Nazaré 481, Ipiranga, São Paulo, SP, 04263-000, Brazil
| | - Uwe Fritz
- Museum of Zoology, Senckenberg Dresden, 01109, Dresden, Germany.
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20
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Li Q, Wang Q, Jin X, Chen Z, Xiong C, Li P, Liu Q, Huang W. Characterization and comparative analysis of six complete mitochondrial genomes from ectomycorrhizal fungi of the Lactarius genus and phylogenetic analysis of the Agaricomycetes. Int J Biol Macromol 2019; 121:249-260. [DOI: 10.1016/j.ijbiomac.2018.10.029] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 10/08/2018] [Accepted: 10/08/2018] [Indexed: 01/08/2023]
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21
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Incomplete lineage sorting rather than hybridization explains the inconsistent phylogeny of the wisent. Commun Biol 2018; 1:169. [PMID: 30374461 PMCID: PMC6195592 DOI: 10.1038/s42003-018-0176-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 09/12/2018] [Indexed: 12/30/2022] Open
Abstract
The wisent or European bison is the largest European herbivore and is completely cross-fertile with its American relative. However, mtDNA genome of wisent is similar to that of cattle, which suggests that wisent emerged as a hybrid of bison and an extinct cattle-like species. Here, we analyzed nuclear whole-genome sequences of the bovine species, and found only a minor and recent gene flow between wisent and cattle. Furthermore, we identified an appreciable heterogeneity of the nuclear gene tree topologies of the bovine species. The relative frequencies of various topologies, including the mtDNA topology, were consistent with frequencies of incomplete lineage sorting (ILS) as estimated by tree coalescence analysis. This indicates that ILS has occurred and may well account for the anomalous wisent mtDNA phylogeny as the outcome of a rare event. We propose that ILS is a possible explanation of phylogenomic anomalies among closely related species. Kun Wang et al. present a genomic analysis identifying incomplete lineage sorting and hybridization in the mitochondrial DNA of the European bison (wisent). They find that incomplete lineage sorting is the most feasible explanation for the phylogenetic heterogeneity observed in Bovidae.
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22
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Hassanin A, Houck ML, Tshikung D, Kadjo B, Davis H, Ropiquet A. Multi-locus phylogeny of the tribe Tragelaphini (Mammalia, Bovidae) and species delimitation in bushbuck: Evidence for chromosomal speciation mediated by interspecific hybridization. Mol Phylogenet Evol 2018; 129:96-105. [PMID: 30121341 DOI: 10.1016/j.ympev.2018.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 08/06/2018] [Accepted: 08/06/2018] [Indexed: 10/28/2022]
Abstract
The bushbuck is the most widespread bovid species in Africa. Previous mitochondrial studies have revealed a polyphyletic pattern suggesting the possible existence of two distinct species. To assess this issue, we have sequenced 16 nuclear genes and one mitochondrial fragment (cytochrome b gene + control region) for most species of the tribe Tragelaphini, including seven bushbuck individuals belonging to the two divergent mtDNA haplogroups, Scriptus and Sylvaticus. Our phylogenetic analyses show that the Scriptus lineage is a sister-group of Sylvaticus in the nuclear tree, whereas it is related to Tragelaphus angasii in the mitochondrial tree. This mito-nuclear discordance indicates that the mitochondrial genome of Scriptus was acquired by introgression after one or several past events of hybridization between bushbuck and an extinct species closely related to T. angasii. The division into two bushbuck species is supported by the analyses of nuclear markers and by the karyotype here described for T. scriptus (2n = 57 M/58F), which is strikingly distinct from the one previously found for T. sylvaticus (2n = 33 M/34F). Molecular dating estimates suggest that the two species separated during the Early Pleistocene after an event of interspecific hybridization, which may have mediated massive chromosomal rearrangements in the common ancestor of T. scriptus.
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Affiliation(s)
- Alexandre Hassanin
- Institut Systématique Evolution Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE; 57 rue Cuvier, CP 51, 75005 Paris, France.
| | - Marlys L Houck
- San Diego Zoo Institute for Conservation Research; 15600 San Pasqual Valley Road, Escondido, CA 92027, USA
| | - Didier Tshikung
- Faculté de médicine vétérinaire; Université de Lubumbashi, 243 BP 1825, The Democratic Republic of the Congo
| | - Blaise Kadjo
- Université Félix-Houphouët-Boigny, UFR Biosciences; 22 BP 582, Abidjan 22, Cote d'Ivoire
| | - Heidi Davis
- San Diego Zoo Institute for Conservation Research; 15600 San Pasqual Valley Road, Escondido, CA 92027, USA
| | - Anne Ropiquet
- Middlesex University, Department of Natural Sciences, Faculty of Science and Technology, The Burroughs, Hendon, London NW4 4BT, United Kingdom
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23
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The Evolution and Population Diversity of Bison in Pleistocene and Holocene Eurasia: Sex Matters. DIVERSITY 2018. [DOI: 10.3390/d10030065] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Knowledge about the origin and evolutionary history of the bison has been improved recently owing to several genomic and paleogenomic studies published in the last two years, which elucidated large parts of the evolution of bison populations during the Upper Pleistocene and Holocene in Eurasia. The produced data, however, were interpreted in contradicting manners. Here, we have gathered, reanalyzed and compared previously published or unpublished morphometric and genetic data that have not yet been integrated and that we synthesize in a unified framework. In particular, we re-estimate dates of divergence of mitogenome lineages based on an extended dataset comprising 81 complete ancient bison mitogenomes and we revisit putative gene flow between the Bos and Bison genera based on comparative analyses of ancient and modern bison genomes, thereby questioning published conclusions. Morphometric analyses taking into account sexual dimorphism invalidate a previous claim that Bison schoetensacki was present in France during the Late Pleistocene. Both morphometric and genome analyses reveal that Eurasian bison belonging to different Bison priscus and Bison bonasus lineages maintained parallel evolutionary paths with gene flow during a long period of incomplete speciation that ceased only upon the migration of B. priscus to the American continent establishing the American bison lineage. Our nuclear genome analysis of the evolutionary history of B. bonasus allows us to reject the previous hypothesis that it is a hybrid of B. priscus and Bos primigenius. Based on present-day behavioral studies of European and American bison, we propose that apparently conflicting lines of evidence can be reconciled by positing that female bison drove the specialization of bison populations to different ecological niches while male bison drove regular homogenizing genetic exchanges between populations.
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24
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PAL ARUNA, BANERJEE SAMIDDHA. Mitochondrial replacement therapy - a new remedy for defects in reproduction. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2018. [DOI: 10.56093/ijans.v88i6.80860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Mitochondria is an important subcellular organelle with the prime function being energy metabolism and supply of energy to the body cells for carrying out the vital functions. Energy is the primary requisite for the reproductive organs of both male and female for carrying out the normal functions. In the present article, we have described how mutation in mitochondrial DNA lead to defects in male and female reproduction. Mitochondria is an integral part of the mid-piece of sperm and also has role in other parts of male reproductive system. Similarly, mitochondrial DNA has role in female reproductive system including ovulation, zygote activation, fertilization, oocyte maturation and embryo development. Mitochondrial defect are collectively named as "mystondria" (mysterious diseases of mitochondria) and may be corrected through mitochondrial replacement therapy, popularly known as three parent baby concept, since there are no other scope for cure or treatment. Two approaches for mitochondrial replacement therapy are pronuclear transfer and spindle transfer. The first three parent baby was developed in April 2016 through mitochondrial replacement therapy. The present review is aimed at functional relevance of three-parent baby concept in animal reproduction.
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25
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Pervasive introgression facilitated domestication and adaptation in the Bos species complex. Nat Ecol Evol 2018; 2:1139-1145. [DOI: 10.1038/s41559-018-0562-y] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 04/20/2018] [Indexed: 12/23/2022]
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26
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Characterization of the complete mitochondrial genome of Kunlun Mountain type wild yak (Bos mutus). CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-017-0776-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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27
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Hassanin A, Colombo R, Gembu GC, Merle M, Tu VT, Görföl T, Akawa PM, Csorba G, Kearney T, Monadjem A, Ing RK. Multilocus phylogeny and species delimitation within the genusGlauconycteris(Chiroptera, Vespertilionidae), with the description of a new bat species from the Tshopo Province of the Democratic Republic of the Congo. J ZOOL SYST EVOL RES 2017. [DOI: 10.1111/jzs.12176] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alexandre Hassanin
- Institut de Systématique, Évolution, Biodiversité; Univ Paris 06, MNHN, CNRS; Sorbonne Universités; Muséum National d'Histoire Naturelle; Paris France
- UMS 2700; Muséum national d'Histoire naturelle; Paris France
| | | | - Guy-Crispin Gembu
- Université de Kisangani; Faculté des Sciences; Kisangani République Démocratique du Congo
| | - Marie Merle
- Institut de Systématique, Évolution, Biodiversité; Univ Paris 06, MNHN, CNRS; Sorbonne Universités; Muséum National d'Histoire Naturelle; Paris France
| | - Vuong Tan Tu
- Institut de Systématique, Évolution, Biodiversité; Univ Paris 06, MNHN, CNRS; Sorbonne Universités; Muséum National d'Histoire Naturelle; Paris France
- Institute of Ecology and Biological Resources; Vietnam Academy of Science and Technology; Cau Giay District Hanoi Vietnam
| | | | - Prescott Musaba Akawa
- Université de Kisangani; Faculté des Sciences; Kisangani République Démocratique du Congo
| | | | - Teresa Kearney
- Ditsong National Museum of Natural History; Pretoria South Africa
- School of Animal, Plant and Environmental Sciences; University of the Witwatersrand; Wits South Africa
| | - Ara Monadjem
- Department of Biological Sciences; University of Swaziland; Kwaluseni Swaziland
- Department of Zoology & Entomology; Mammal Research Institute; University of Pretoria; Pretoria South Africa
| | - Ros Kiri Ing
- Institut Langevin, UMR 7587 CNRS; Université Paris Diderot (Paris 7); Paris France
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28
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Wecek K, Hartmann S, Paijmans JLA, Taron U, Xenikoudakis G, Cahill JA, Heintzman PD, Shapiro B, Baryshnikov G, Bunevich AN, Crees JJ, Dobosz R, Manaserian N, Okarma H, Tokarska M, Turvey ST, Wójcik JM, Zyla W, Szymura JM, Hofreiter M, Barlow A. Complex Admixture Preceded and Followed the Extinction of Wisent in the Wild. Mol Biol Evol 2017; 34:598-612. [PMID: 28007976 PMCID: PMC5356474 DOI: 10.1093/molbev/msw254] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Retracing complex population processes that precede extreme bottlenecks may be impossible using data from living individuals. The wisent (Bison bonasus), Europe’s largest terrestrial mammal, exemplifies such a population history, having gone extinct in the wild but subsequently restored by captive breeding efforts. Using low coverage genomic data from modern and historical individuals, we investigate population processes occurring before and after this extinction. Analysis of aligned genomes supports the division of wisent into two previously recognized subspecies, but almost half of the genomic alignment contradicts this population history as a result of incomplete lineage sorting and admixture. Admixture between subspecies populations occurred prior to extinction and subsequently during the captive breeding program. Admixture with the Bos cattle lineage is also widespread but results from ancient events rather than recent hybridization with domestics. Our study demonstrates the huge potential of historical genomes for both studying evolutionary histories and for guiding conservation strategies.
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Affiliation(s)
- Karolina Wecek
- Department of Comparative Anatomy, Institute of Zoology, Jagiellonian University, Kraków, Poland.,Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Stefanie Hartmann
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | - Ulrike Taron
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | - James A Cahill
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA
| | - Peter D Heintzman
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA.,University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, CA
| | - Gennady Baryshnikov
- Laboratory of Theriology, Zoological Institute of the Russian Academy of Sciences, Petersberg, Russia
| | | | - Jennifer J Crees
- Zoological Society of London, Institute of Zoology, Regent's Park, London, United Kingdom
| | - Roland Dobosz
- Upper Silesian Museum, Bytom, Poland.,Department of Zoology, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Ninna Manaserian
- Institute of Zoology Armenian National Academy of Sciences, Yerevan, Armenia
| | - Henryk Okarma
- Institute of Nature Conservation Polish Academy of Sciences, Kraków, Poland
| | | | - Samuel T Turvey
- Zoological Society of London, Institute of Zoology, Regent's Park, London, United Kingdom
| | - Jan M Wójcik
- Mammal Research Institute Polish Academy of Sciences, Bialowieza, Poland
| | | | - Jacek M Szymura
- Department of Comparative Anatomy, Institute of Zoology, Jagiellonian University, Kraków, Poland
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Axel Barlow
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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29
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The complete mitochondrial genome of Naemorhedus griseus (Artiodactyla: Bovidae) and its phylogenetic implications. CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0794-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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30
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Palacio P, Berthonaud V, Guérin C, Lambourdière J, Maksud F, Philippe M, Plaire D, Stafford T, Marsolier-Kergoat MC, Elalouf JM. Genome data on the extinct Bison schoetensacki establish it as a sister species of the extant European bison (Bison bonasus). BMC Evol Biol 2017; 17:48. [PMID: 28187706 PMCID: PMC5303235 DOI: 10.1186/s12862-017-0894-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 01/26/2017] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The European bison (Bison bonasus), now found in Europe and the Caucasus, has been proposed to originate either from the extinct steppe/extant American bison lineage or from the extinct Bison schoetensacki lineage. Bison schoetensacki remains are documented in Eurasian Middle Pleistocene sites, but their presence in Upper Pleistocene sites has been questioned. Despite extensive genetic studies carried out on the steppe and European bison, no remains from the fossil record morphologically identified as Bison schoetensacki has been analyzed up to now. RESULTS In this paper, we analyzed a 36,000-year-old Bison schoetensaki bone sample from the Siréjol cave (France) and a cave hyena coprolite (fossilized feces) found in a nearby cave and containing large amounts of Bovinae DNA. We show that the Bovinae mitochondrial DNA sequences from both samples, including a complete mitochondrial genome sequence, belong to a clade recently reported in the literature. This clade only includes ancient bison specimens without taxonomic identification and displays a sister relationship with the extant European bison. The genetic proximity of Bison schoetensacki with specimens from this clade is corroborated by the analysis of nuclear DNA single nucleotide polymorphisms. CONCLUSIONS This work provides genetic evidence supporting the continuing presence of Bison schoetensacki up to the Upper Pleistocene. Bison schoetensacki turns out to be a sister species of Bison bonasus, excluding the steppe bison Bison priscus as a direct ancestor of the European bison.
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Affiliation(s)
- Pauline Palacio
- Institute for Integrative Biology of the Cell (I2BC), IBITECS, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Véronique Berthonaud
- Institute for Integrative Biology of the Cell (I2BC), IBITECS, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Claude Guérin
- CNRS-UMR 5276, Laboratoire de Géologie de Lyon: Terre, planètes, environnement, Département des Sciences de la Terre, Université Claude Bernard, Lyon I, 27-43 Boulevard du 11 Novembre, 69622, Villeurbanne cedex, France
| | - Josie Lambourdière
- Service de Systématique Moléculaire, UMS 2700 CNRS-MNHN, CP26, 57 Rue Cuvier, 75231, Paris Cedex 05, France
| | - Frédéric Maksud
- Service Régional de l'Archéologie, 32 rue de la Dalbade, BP811 31080, Toulouse cedex 6, France
| | - Michel Philippe
- Centre de Conservation et d'Étude sur les Collections, 13A rue Bancel, 69007, Lyon, France
| | - Delphine Plaire
- Institute for Integrative Biology of the Cell (I2BC), IBITECS, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.,CNRS-UMR 7206, Eco-anthropologie et Ethnobiologie, Département Hommes, Natures et Sociétés, Musée de l'Homme, 17 place du Trocadéro et du 11 novembre, 75016, Paris, France
| | - Thomas Stafford
- Stafford Research, 200 Acadia Avenue, Lafayette, CO, 80026, USA
| | - Marie-Claude Marsolier-Kergoat
- Institute for Integrative Biology of the Cell (I2BC), IBITECS, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.,CNRS-UMR 7206, Eco-anthropologie et Ethnobiologie, Département Hommes, Natures et Sociétés, Musée de l'Homme, 17 place du Trocadéro et du 11 novembre, 75016, Paris, France
| | - Jean-Marc Elalouf
- Institute for Integrative Biology of the Cell (I2BC), IBITECS, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France. .,CNRS-UMR 7206, Eco-anthropologie et Ethnobiologie, Département Hommes, Natures et Sociétés, Musée de l'Homme, 17 place du Trocadéro et du 11 novembre, 75016, Paris, France.
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Pérez T, Fernández M, Hammer SE, Domínguez A. Multilocus Intron Trees Reveal Extensive Male-Biased Homogenization of Ancient Populations of Chamois (Rupicapra spp.) across Europe during Late Pleistocene. PLoS One 2017; 12:e0170392. [PMID: 28146581 PMCID: PMC5287467 DOI: 10.1371/journal.pone.0170392] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 01/04/2017] [Indexed: 11/19/2022] Open
Abstract
The inferred phylogenetic relationships between organisms often depend on the molecular marker studied due to the diverse evolutionary mode and unlike evolutionary histories of different parts of the genome. Previous studies have shown conflicting patterns of differentiation of mtDNA and several nuclear markers in chamois (genus Rupicapra) that indicate a complex evolutionary picture. Chamois are mountain caprine that inhabit most of the medium to high altitude mountain ranges of southern Eurasia. The most accepted taxonomical classification considers two species, R. pyrenaica (with the subspecies parva, pyrenaica and ornata) from southwestern Europe and R. rupicapra (with the subspecies cartusiana, rupicapra, tatrica, carpatica, balcanica, asiatica and caucasica) from northeastern Europe. Phylogenies of mtDNA revealed three very old clades (from the early Pleistocene, 1.9 Mya) with a clear geographical signal. Here we analyze a set of 23 autosomal introns, comprising 15,411 nucleotides, in 14 individuals covering the 10 chamois subspecies. Introns offered an evolutionary scenario that contrasts with mtDNA. The nucleotidic diversity was 0.0013± 0.0002, at the low range of what is found in other mammals even if a single species is considered. A coalescent multilocus analysis with *BEAST indicated that introns diversified 88 Kya, in the late Pleistocene, and the effective population size at the root was lower than 10,000 individuals. The dispersal of some few migrant males should have rapidly spread trough the populations of chamois, given the homogeneity of intron sequences. The striking differences between mitochondrial and nuclear markers can be attributed to strong female philopatry and extensive male dispersal. Our results highlight the need of analyzing multiple and varied genome components to capture the complex evolutionary history of organisms.
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Affiliation(s)
- Trinidad Pérez
- Departamento de Biología Funcional, Universidad de Oviedo, Julián Clavería 6, Oviedo, Spain
| | - Margarita Fernández
- Departamento de Biología Funcional, Universidad de Oviedo, Julián Clavería 6, Oviedo, Spain
| | - Sabine E. Hammer
- Department of Pathobiology, Institute of Immunology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, Vienna, Austria
| | - Ana Domínguez
- Departamento de Biología Funcional, Universidad de Oviedo, Julián Clavería 6, Oviedo, Spain
- * E-mail:
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Gautier M, Moazami-Goudarzi K, Levéziel H, Parinello H, Grohs C, Rialle S, Kowalczyk R, Flori L. Deciphering the Wisent Demographic and Adaptive Histories from Individual Whole-Genome Sequences. Mol Biol Evol 2016; 33:2801-2814. [PMID: 27436010 PMCID: PMC5062319 DOI: 10.1093/molbev/msw144] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
As the largest European herbivore, the wisent (Bison bonasus) is emblematic of the continent wildlife but has unclear origins. Here, we infer its demographic and adaptive histories from two individual whole-genome sequences via a detailed comparative analysis with bovine genomes. We estimate that the wisent and bovine species diverged from 1.7 × 106 to 850,000 years before present (YBP) through a speciation process involving an extended period of limited gene flow. Our data further support the occurrence of more recent secondary contacts, posterior to the Bos taurus and Bos indicus divergence (∼150,000 YBP), between the wisent and (European) taurine cattle lineages. Although the wisent and bovine population sizes experienced a similar sharp decline since the Last Glacial Maximum, we find that the wisent demography remained more fluctuating during the Pleistocene. This is in agreement with a scenario in which wisents responded to successive glaciations by habitat fragmentation rather than southward and eastward migration as for the bovine ancestors. We finally detect 423 genes under positive selection between the wisent and bovine lineages, which shed a new light on the genome response to different living conditions (temperature, available food resource, and pathogen exposure) and on the key gene functions altered by the domestication process.
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Affiliation(s)
- Mathieu Gautier
- CBGP, INRA, CIRAD, IRD, Supagro, Montferrier-sur-Lez, France IBC, Institut de Biologie Computationnelle, Montpellier, France
| | | | | | - Hugues Parinello
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, Montpellier, France
| | - Cécile Grohs
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Stéphanie Rialle
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, Montpellier, France
| | - Rafał Kowalczyk
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Laurence Flori
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France INTERTRYP, CIRAD, IRD, Montpellier, France
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Hassanin A, Nesi N, Marin J, Kadjo B, Pourrut X, Leroy É, Gembu GC, Musaba Akawa P, Ngoagouni C, Nakouné E, Ruedi M, Tshikung D, Pongombo Shongo C, Bonillo C. Comparative phylogeography of African fruit bats (Chiroptera, Pteropodidae) provide new insights into the outbreak of Ebola virus disease in West Africa, 2014–2016. C R Biol 2016; 339:517-528. [DOI: 10.1016/j.crvi.2016.09.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/08/2016] [Accepted: 09/13/2016] [Indexed: 11/30/2022]
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Massilani D, Guimaraes S, Brugal JP, Bennett EA, Tokarska M, Arbogast RM, Baryshnikov G, Boeskorov G, Castel JC, Davydov S, Madelaine S, Putelat O, Spasskaya NN, Uerpmann HP, Grange T, Geigl EM. Past climate changes, population dynamics and the origin of Bison in Europe. BMC Biol 2016; 14:93. [PMID: 27769298 PMCID: PMC5075162 DOI: 10.1186/s12915-016-0317-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/11/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Climatic and environmental fluctuations as well as anthropogenic pressure have led to the extinction of much of Europe's megafauna. The European bison or wisent (Bison bonasus), one of the last wild European large mammals, narrowly escaped extinction at the onset of the 20th century owing to hunting and habitat fragmentation. Little is known, however, about its origin, evolutionary history and population dynamics during the Pleistocene. RESULTS Through ancient DNA analysis we show that the emblematic European bison has experienced several waves of population expansion, contraction, and extinction during the last 50,000 years in Europe, culminating in a major reduction of genetic diversity during the Holocene. Fifty-seven complete and partial ancient mitogenomes from throughout Europe, the Caucasus, and Siberia reveal that three populations of wisent (Bison bonasus) and steppe bison (B. priscus) alternately occupied Western Europe, correlating with climate-induced environmental changes. The Late Pleistocene European steppe bison originated from northern Eurasia, whereas the modern wisent population emerged from a refuge in the southern Caucasus after the last glacial maximum. A population overlap during a transition period is reflected in ca. 36,000-year-old paintings in the French Chauvet cave. Bayesian analyses of these complete ancient mitogenomes yielded new dates of the various branching events during the evolution of Bison and its radiation with Bos, which lead us to propose that the genetic affiliation between the wisent and cattle mitogenomes result from incomplete lineage sorting rather than post-speciation gene flow. CONCLUSION The paleogenetic analysis of bison remains from the last 50,000 years reveals the influence of climate changes on the dynamics of the various bison populations in Europe, only one of which survived into the Holocene, where it experienced severe reductions in its genetic diversity. The time depth and geographical scope of this study enables us to propose temperate Western Europe as a suitable biotope for the wisent compatible with its reintroduction.
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Affiliation(s)
- Diyendo Massilani
- Institut Jacques Monod, UMR7592, CNRS, University Paris Diderot, Epigenome and Paleogenome group, 15 rue Hélène Brion, 75013, Paris, France
| | - Silvia Guimaraes
- Institut Jacques Monod, UMR7592, CNRS, University Paris Diderot, Epigenome and Paleogenome group, 15 rue Hélène Brion, 75013, Paris, France
| | - Jean-Philip Brugal
- CNRS, USR 3336 IFRA (Institut Français de Recherche en Afrique), Nairobi, Kenya.,Aix-Marseille Université, UMR 7269 LAMPEA (Labo.Méd.de Préhistoire, Europe-Afrique) Maison Méditerranéenne des Sciences de l'Homme, BP 674, 13094, Aix-en-Provence, cedex 2, France
| | - E Andrew Bennett
- Institut Jacques Monod, UMR7592, CNRS, University Paris Diderot, Epigenome and Paleogenome group, 15 rue Hélène Brion, 75013, Paris, France
| | - Malgorzata Tokarska
- Mammal Research Institute Polish Academy of Sciences, Genetics and Evolution Department, Waszkiewicza 1, 17-230, Bialowieza, Poland
| | - Rose-Marie Arbogast
- CNRS/UMR 7044/MISHA, 5 allée du Général Rouvillois, 67083, Strasbourg, France
| | - Gennady Baryshnikov
- Zoological Institute, Russian Academy of Sciences, 199034, Saint Petersburg, Russia
| | - Gennady Boeskorov
- Diamond and Precious Metal Geology Institute of the Siberian Branch of the RAS, Yakutsk, Russia
| | - Jean-Christophe Castel
- Muséum d'histoire naturelle de Genève (MHN), Département d'Archéozoologie, Route de Malagnou 1, 1208, Geneva, Switzerland
| | - Sergey Davydov
- North-East Science Station, Pacific Institute of Geography, Far East Branch, Russ. Ac. Sci., 678830, Cherskiy, Russia
| | - Stéphane Madelaine
- Musée national de Préhistoire, 24620, Les Eyzies de Tayac-Sireuil, France
| | - Olivier Putelat
- Archéologie Alsace, 11 rue Jean-François Champollion, 67600, Sélestat, France.,UMR 7041 ArScan - Archéologies environnementales - Maison de l'Archéologie et de l'Ethnologie, 92023, Nanterre, France
| | - Natalia N Spasskaya
- Zoological Museum of Moscow Lomonosow, State University, Bolshaya Nikitskaya Str. 6, Moscow, 125009, Russia
| | - Hans-Peter Uerpmann
- Institut für Ur- und Frühgeschichte und Archäologie des Mittelalters, Abteilung Ältere Urgeschichte und Quartärökologie, Zentrum für Naturwissenschaftliche Archäologie, Rümelinstr. 23, 72070, Tübingen, Germany
| | - Thierry Grange
- Institut Jacques Monod, UMR7592, CNRS, University Paris Diderot, Epigenome and Paleogenome group, 15 rue Hélène Brion, 75013, Paris, France.
| | - Eva-Maria Geigl
- Institut Jacques Monod, UMR7592, CNRS, University Paris Diderot, Epigenome and Paleogenome group, 15 rue Hélène Brion, 75013, Paris, France.
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Di Lorenzo P, Lancioni H, Ceccobelli S, Curcio L, Panella F, Lasagna E. Uniparental genetic systems: a male and a female perspective in the domestic cattle origin and evolution. ELECTRON J BIOTECHN 2016. [DOI: 10.1016/j.ejbt.2016.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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Nicolas V, Martínez-Vargas J, Hugot JP. Molecular data and ecological niche modelling reveal the evolutionary history of the common and Iberian moles (Talpidae) in Europe. ZOOL SCR 2016. [DOI: 10.1111/zsc.12189] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité; ISYEB UMR 7205 - CNRS; MNHN; UPMC; EPHE; Muséum National d'Histoire Naturelle; Sorbonne Universités; Paris France
| | - Jessica Martínez-Vargas
- Departament de Biologia Animal; de Biologia Vegetal i d'Ecologia; Facultat de Biociències; Universitat Autònoma de Barcelona; E-08193 Bellaterra (Cerdanyola del Vallès) Barcelona Spain
| | - Jean-Pierre Hugot
- Institut de Systématique, Evolution, Biodiversité; ISYEB UMR 7205 - CNRS; MNHN; UPMC; EPHE; Muséum National d'Histoire Naturelle; Sorbonne Universités; Paris France
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Khwanmunee J, Leelawatwattana L, Prapunpoj P. Gene structure and evolution of transthyretin in the order Chiroptera. Genetica 2015; 144:71-83. [PMID: 26681450 DOI: 10.1007/s10709-015-9879-5] [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: 05/16/2015] [Accepted: 12/13/2015] [Indexed: 11/26/2022]
Abstract
Bats are mammals in the order Chiroptera. Although many extensive morphologic and molecular genetics analyses have been attempted, phylogenetic relationships of bats has not been completely resolved. The paraphyly of microbats is of particular controversy that needs to be confirmed. In this study, we attempted to use the nucleotide sequence of transthyretin (TTR) intron 1 to resolve the relationship among bats. To explore its utility, the complete sequences of TTR gene and intron 1 region of bats in Vespertilionidae: genus Eptesicus (Eptesicus fuscus) and genus Myotis (Myotis brandtii, Myotis davidii, and Myotis lucifugus), and Pteropodidae (Pteropus alecto and Pteropus vampyrus) were extracted from the retrieved sequences, whereas those of Rhinoluphus affinis and Scotophilus kuhlii were amplified and sequenced. The derived overall amino sequences of bat TTRs were found to be very similar to those in other eutherians but differed from those in other classes of vertebrates. However, missing of amino acids from N-terminal or C-terminal region was observed. The phylogenetic analysis of amino acid sequences suggested bat and other eutherian TTRs lineal descent from a single most recent common ancestor which differed from those of non-placental mammals and the other classes of vertebrates. The splicing of bat TTR precursor mRNAs was similar to those of other eutherian but different from those of marsupial, bird, reptile and amphibian. Based on TTR intron 1 sequence, the inferred evolutionary relationship within Chiroptera revealed more closely relatedness of R. affinis to megabats than to microbats. Accordingly, the paraphyly of microbats was suggested.
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Affiliation(s)
- Jiraporn Khwanmunee
- Department of Biochemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Ladda Leelawatwattana
- Department of Biochemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Porntip Prapunpoj
- Department of Biochemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand.
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Hassanin A, Khouider S, Gembu GC, M. Goodman S, Kadjo B, Nesi N, Pourrut X, Nakouné E, Bonillo C. The comparative phylogeography of fruit bats of the tribe Scotonycterini (Chiroptera, Pteropodidae) reveals cryptic species diversity related to African Pleistocene forest refugia. C R Biol 2015; 338:197-211. [DOI: 10.1016/j.crvi.2014.12.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 12/15/2014] [Accepted: 12/16/2014] [Indexed: 11/25/2022]
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Salces-Ortiz J, González C, Martínez M, Mayoral T, Calvo JH, Serrano MM. Looking for adaptive footprints in the HSP90AA1 ovine gene. BMC Evol Biol 2015; 15:7. [PMID: 25648535 PMCID: PMC4351680 DOI: 10.1186/s12862-015-0280-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 01/05/2015] [Indexed: 11/10/2022] Open
Abstract
Background Climatic factors play an important role in determining species distributions and phenotypic variation of populations over geographic space. Since domestic sheep is managed under low intensive systems animals could have retained some genome adaptive footprints. The gene encoding the Hsp90α has been extensively studied in sheep and some polymorphisms located at its promoter have been associates with differences in the transcription rate of the gene depending on climatic conditions. In this work the relationships among the distribution and frequencies of 11 polymorphisms of the ovine HSP90AA1 gene promoter in 31 sheep breeds and the climatic and geographic variables prevailing in their regions of origin have been studied. Also the promoter sequence has been characterized in 9 species of the Caprinae subfamily. Results Correlations among several climatic variables and allele frequencies of the polymorphisms of the HSP90AA1 gene promoter linked with differences in the transcription activity of the gene under heat stress conditions have been assessed. A group of breeds reared in semi dry climates have high frequencies of the insertion allele of the g.667-668insC associated with the heat stress response. Other group of breeds native to semi arid conditions showed very low frequencies of this same allele. However, in some cases, this previous correlation has not been achieved, revealing the high levels of gene flow among populations occurred following domestication. The Bayesian Test of Beaumont and Balding identified two outlier loci, the g.522A > G and g.703_704del(2)A candidates to balancing and directional selection, respectively. Polymorphisms detected in O. aries are also present in several species of the Caprinae subfamily being C. hircus, O. musimon and O. moschatus those sharing the highest number of them with O. aries. Conclusions Despite domestication, sheep breeds showed some genetic footprints related to climatic variables. Adaptation of breeds to heat climates can suppose a selective advantage to cope with global warming caused by climatic change. Polymorphisms of the HSP90AA1 gene detected in the Ovis aries species are also present in wild species from the Caprinae subfamily, indicating a great antiquity of these mutations and its importance in the adaptation of species to past climatic conditions existing in its native environments. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0280-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Carmen González
- INIA, Carretera de La Coruña Km. 7,5. 280040, Madrid, Spain.
| | - Marta Martínez
- Laboratorio Central de Veterinaria, MAGRAMA, Ctra. M-106 km1.4 28110, Madrid, Spain.
| | - Tomás Mayoral
- Laboratorio Central de Veterinaria, MAGRAMA, Ctra. M-106 km1.4 28110, Madrid, Spain.
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New cryptic karyotypic differences between cattle (Bos taurus) and goat (Capra hircus). Chromosome Res 2015; 23:225-35. [PMID: 25612562 DOI: 10.1007/s10577-014-9462-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 12/12/2014] [Accepted: 12/18/2014] [Indexed: 10/24/2022]
Abstract
Cattle (Bos taurus) and goat (Capra hircus) belong to the Bovidae family, and they share a common ancestor 19.7-21.5 Ma ago (MYA). The Bovidae family apparently experienced a rapid species radiation in the middle Miocene. The present day cattle and goat possess the same diploid chromosome number (2n = 60) and structurally similar autosomes, except that a small subcentromeric portion of cattle chromosome nine has been translocated to goat chromosome 14. In this study, we adopted a new strategy that involves the use of bioinformatics approach to detect unknown cryptic chromosome divergences between cattle and goat using and subsequent validation using the fluorescence in situ hybridization (FISH) of bacterial artificial chromosome clones. We identified two hypothetical discrepancies between the cattle and goat genome assemblies: an inversion in the goat chromosome 13 and a transposition in the goat chromosome 6. The FISH technique allowed clear validation of the existence of a new 7.4 Mb chromosomal inversion in the goat chromosome 13. Regarding the transposition in the goat chromosome six, FISH analyses revealed that the cattle and goat genomes shared the same organization, with the assembly of the goat genome being the correct one. Moreover, we defined, for the first time, the size and orientation of the translocated fragment involved in the evolutionary translocation between cattle chromosomes 9 and goat chromosome 14. Our results suggest that bioinformatics represents an efficient method for detecting cryptic chromosome divergences among species.
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Mans BJ, Pienaar R, Latif AA. A review of Theileria diagnostics and epidemiology. INTERNATIONAL JOURNAL FOR PARASITOLOGY-PARASITES AND WILDLIFE 2015; 4:104-18. [PMID: 25830110 PMCID: PMC4356873 DOI: 10.1016/j.ijppaw.2014.12.006] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 12/18/2014] [Accepted: 12/19/2014] [Indexed: 11/28/2022]
Abstract
Serological and molecular assays exist for most economic important Theileria species. Molecular assays are constantly being improved with regard to sensitivity and specificity. The concept of what constitute a Theileria species impacts on accurate diagnostics. Analytical specificity of molecular assays are >800 000 parasites/L blood. Parasitemia ranges may determine practical limits of detection.
An extensive range of serological and molecular diagnostic assays exist for most of the economically important Theileira species such as T. annulata, T. equi, T. lestoquardi, T. parva, T. uilenbergi and other more benign species. Diagnostics of Theileria is considered with regard to sensitivity and specificity of current molecular and serological assays and their use in epidemiology. In the case of serological assays, cross-reactivity of genetically closely related species reduces the use of the gold standard indirect fluorescent antibody test (IFAT). Development of antigen-specific assays does not necessarily address this problem, since closely related species will potentially have similar antigens. Even so, serological assays remain an important line of enquiry in epidemiological surveys. Molecular based assays have exploded in the last decade with significant improvements in sensitivity and specificity. In this review, the current interpretation of what constitute a species in Theileria and its impact on accurate molecular diagnostics is considered. Most molecular assays based on conventional or real-time PCR technology have proven to be on standard with regard to analytical sensitivity. However, consideration of the limits of detection in regard to total blood volume of an animal indicates that most assays may only detect >400,000 parasites/L blood. Even so, natural parasitaemia distribution in carrier-state animals seems to be above this limit of detection, suggesting that most molecular assays should be able to detect the majority of infected individuals under endemic conditions. The potential for false-negative results can, however, only be assessed within the biological context of the parasite within its vertebrate host, i.e. parasitaemia range in the carrier-state that will support infection of the vector and subsequent transmission.
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Affiliation(s)
- Ben J Mans
- Parasites, Vectors and Vector-Borne Diseases, Agricultural Research Council-Onderstepoort Veterinary Institute, Onderstepoort 0110, South Africa ; The Department of Veterinary Tropical Diseases, University of Pretoria, Pretoria, South Africa ; Department of Life and Consumer Sciences, University of South Africa, South Africa
| | - Ronel Pienaar
- Parasites, Vectors and Vector-Borne Diseases, Agricultural Research Council-Onderstepoort Veterinary Institute, Onderstepoort 0110, South Africa
| | - Abdalla A Latif
- Parasites, Vectors and Vector-Borne Diseases, Agricultural Research Council-Onderstepoort Veterinary Institute, Onderstepoort 0110, South Africa ; The Department of Veterinary Tropical Diseases, University of Pretoria, Pretoria, South Africa
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Abstract
Cattle are our most important livestock species because of their production and role in human culture. Many breeds that differ in appearance, performance and environmental adaptation are kept on all inhabited continents, but the historic origin of the diverse phenotypes is not always clear. We give an account of the history of cattle by integrating archaeological record and pictorial or written sources, scarce until 300 years ago, with the recent contributions of DNA analysis. We describe the domestication of their wild ancestor, migrations to eventually all inhabited continents, the developments during prehistory, the antiquity and the Middle Ages, the relatively recent breed formation, the industrial cattle husbandry in the Old and New World and the current efforts to preserve the cattle genetic resources. Surveying the available information, we propose three main and overlapping phases during the development of the present genetic diversity: (i) domestication and subsequent wild introgression; (ii) natural adaptation to a diverse agricultural habitat; and (iii) breed development.
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Kulemzina AI, Perelman PL, Grafodatskaya DA, Nguyen TT, Thompson M, Roelke-Parker ME, Graphodatsky AS. Comparative chromosome painting of pronghorn (Antilocapra americana) and saola (Pseudoryx nghetinhensis) karyotypes with human and dromedary camel probes. BMC Genet 2014; 15:68. [PMID: 24923361 PMCID: PMC4061535 DOI: 10.1186/1471-2156-15-68] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 06/09/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pronghorn (Antilocapridae, 2n = 58) and saola (Bovidae, 2n = 50) are members of Pecora, a highly diversified group of even-toed hoofed mammals. Karyotypes of these species were not involved in chromosome painting studies despite their intriguing phylogenetic positions in Pecora. RESULTS To trace the chromosome evolution during very fast radiation of main families from the common Pecoran ancestor, high-resolution comparative chromosome maps of pronghorn and saola with human (HSA) and dromedary camel (CDR) painting probes were established. The human and dromedary camel painting probes revealed 50 and 64 conserved segments respectively in the pronghorn genome, while 51 and 63 conserved segments respectively in the saola genome. Integrative analysis with published comparative maps showed that inversions in chromosomes homologous to CDR19/35/19 (HSA 10/20/10), CDR12/34/12 (HSA12/22/12/22), CDR10/33/10 (HSA 11) are present in representatives of all five living Pecoran families. The pronghorn karyotype could have formed from a putative 2n = 58 Pecoran ancestral karyotype by one fission and one fusion and that the saola karyotype differs from the presumed 2n = 60 bovid ancestral karyotype (2n = 60) by five fusions. CONCLUSION The establishment of high-resolution comparative maps for pronghorn and saola has shed some new insights into the putative ancestral karyotype, chromosomal evolution and phylogenic relationships in Pecora. No cytogenetic signature rearrangements were found that could unite the Antilocapridae with Giraffidae or with any other Pecoran families. Our data on the saola support a separate position of Pseudorigyna subtribe rather than its affinity to either Bovina or Bubalina, but the saola phylogenetic position within Bovidae remains unresolved.
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Affiliation(s)
- Anastasia I Kulemzina
- Institute of Molecular and Cellular Biology, SB RAS and Novosibirsk State University, Novosibirsk, Russia.
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Douzery EJP, Scornavacca C, Romiguier J, Belkhir K, Galtier N, Delsuc F, Ranwez V. OrthoMaM v8: A Database of Orthologous Exons and Coding Sequences for Comparative Genomics in Mammals. Mol Biol Evol 2014; 31:1923-8. [DOI: 10.1093/molbev/msu132] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Luo XL, Song HF, Guan JQ. Investigation on mechanism of sterility of male hybrids between yak and cattle. JOURNAL OF APPLIED ANIMAL RESEARCH 2014. [DOI: 10.1080/09712119.2013.875907] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Bai Y, Malania L, Alvarez Castillo D, Moran D, Boonmar S, Chanlun A, Suksawat F, Maruyama S, Knobel D, Kosoy M. Global distribution of Bartonella infections in domestic bovine and characterization of Bartonella bovis strains using multi-locus sequence typing. PLoS One 2013; 8:e80894. [PMID: 24278342 PMCID: PMC3836770 DOI: 10.1371/journal.pone.0080894] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 10/17/2013] [Indexed: 11/18/2022] Open
Abstract
Bartonella bovis is commonly detected in cattle. One B. bovis strain was recently isolated from a cow with endocarditis in the USA, suggesting its role as an animal pathogen. In the present study, we investigated bartonella infections in 893 cattle from five countries (Kenya, Thailand, Japan, Georgia, and Guatemala) and 103 water buffaloes from Thailand to compare the prevalence of the infection among different regions and different bovid hosts. We developed a multi-locus sequence typing (MLST) scheme based on nine loci (16S rRNA, gltA, ftsZ, groEL, nuoG, ribC, rpoB, ssrA, and ITS) to compare genetic divergence of B. bovis strains, including 26 representatives from the present study and two previously described reference strains (one from French cows and another from a cow with endocarditis in the USA). Bartonella bacteria were cultured in 6.8% (7/103) of water buffaloes from Thailand; all were B. bovis. The prevalence of bartonella infections in cattle varied tremendously across the investigated regions. In Japan, Kenya, and the Mestia district of Georgia, cattle were free from the infection; in Thailand, Guatemala, and the Dusheti and Marneuli districts of Georgia, cattle were infected with prevalences of 10-90%. The Bartonella isolates from cattle belonged to three species: B. bovis (n=165), B. chomelii (n=9), and B. schoenbuchensis (n=1), with the latter two species found in Georgia only. MLST analysis suggested genetic variations among the 28 analyzed B. bovis strains, which fall into 3 lineages (I, II, and III). Lineages I and II were found in cattle while lineage III was restricted to water buffaloes. The majority of strains (17/28), together with the strain causing endocarditis in a cow in the USA, belonged to lineage I. Further investigations are needed to determine whether B. bovis causes disease in bovids.
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Affiliation(s)
- Ying Bai
- Bacterial Disease Branch, Division of Vector-Borne Disease, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
- * E-mail:
| | - Lile Malania
- National Center for Disease Control and Public Health, Tbilisi, Republic of Georgia
| | | | - David Moran
- Centro de Estudios en Salud, Universidad del Valle de Guatemala, Guatemala, Guatemala
| | - Sumalee Boonmar
- International Emerging Infectious Program, Thailand MOPH-US CDC Collaboration, Nonthaburi, Thailand
| | | | | | - Soichi Maruyama
- Department of Veterinary Medicine, College of Bioresource Science, Nihon University, Kanagawa, Japan
| | - Darryn Knobel
- Department of Veterinary Tropical Diseases, University of Pretoria, Pretoria, South Africa
- Kenya Medical Research Institute/Centers for Disease Control and Prevention Public Health Collaboration, Kisumu, Kenya
| | - Michael Kosoy
- Bacterial Disease Branch, Division of Vector-Borne Disease, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
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Jacquet F, Nicolas V, Colyn M, Kadjo B, Hutterer R, Decher J, Akpatou B, Cruaud C, Denys C. Forest refugia and riverine barriers promote diversification in the West African pygmy shrew (Crocidura obscuriorcomplex, Soricomorpha). ZOOL SCR 2013. [DOI: 10.1111/zsc.12039] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- François Jacquet
- Muséum National d'Histoire Naturelle, Département Systématique et Evolution, UMR 7205, Laboratoire Mammifères et Oiseaux; 55 rue Buffon 75005 Paris France
| | - Violaine Nicolas
- Muséum National d'Histoire Naturelle, Département Systématique et Evolution, UMR 7205, Laboratoire Mammifères et Oiseaux; 55 rue Buffon 75005 Paris France
| | - Marc Colyn
- Université de Rennes 1, CNRS, Ecobio UMR 6553, Station Biologique; 35380 Paimpont France
| | - Blaise Kadjo
- Université de Cocody-Abidjan-UFR Biosciences, Systématique, Biologie et Ecologie des Mammifères; 22 BP 582 Abidjan 22 Côte d'Ivoire
| | - Rainer Hutterer
- Zoologisches Forschungsmuseum A. Koenig, Section of Mammals; Adenauerallee 160 D-53113 Bonn Germany
| | - Jan Decher
- Zoologisches Forschungsmuseum A. Koenig, Section of Mammals; Adenauerallee 160 D-53113 Bonn Germany
| | - Bertin Akpatou
- Université de Cocody-Abidjan-UFR Biosciences, Systématique, Biologie et Ecologie des Mammifères; 22 BP 582 Abidjan 22 Côte d'Ivoire
| | - Corinne Cruaud
- Génoscope, Centre National de Séquençage; 2 rue Gaston Crémieux CP5706 91057 Evry Cedex France
| | - Christiane Denys
- Muséum National d'Histoire Naturelle, Département Systématique et Evolution, UMR 7205, Laboratoire Mammifères et Oiseaux; 55 rue Buffon 75005 Paris France
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Bibi F. A multi-calibrated mitochondrial phylogeny of extant Bovidae (Artiodactyla, Ruminantia) and the importance of the fossil record to systematics. BMC Evol Biol 2013; 13:166. [PMID: 23927069 PMCID: PMC3751017 DOI: 10.1186/1471-2148-13-166] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 08/06/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Molecular phylogenetics has provided unprecedented resolution in the ruminant evolutionary tree. However, molecular age estimates using only one or a few (often misapplied) fossil calibration points have produced a diversity of conflicting ages for important evolutionary events within this clade. I here identify 16 fossil calibration points of relevance to the phylogeny of Bovidae and Ruminantia and use these, individually and together, to construct a dated molecular phylogeny through a reanalysis of the full mitochondrial genome of over 100 ruminant species. RESULTS The new multi-calibrated tree provides ages that are younger overall than found in previous studies. Among these are young ages for the origin of crown Ruminantia (39.3-28.8 Ma), and crown Bovidae (17.3-15.1 Ma). These are argued to be reasonable hypotheses given that many basal fossils assigned to these taxa may in fact lie on the stem groups leading to the crown clades, thus inflating previous age estimates. Areas of conflict between molecular and fossil dates do persist, however, especially with regard to the base of the rapid Pecoran radiation and the sister relationship of Moschidae to Bovidae. Results of the single-calibrated analyses also show that a very wide range of molecular age estimates are obtainable using different calibration points, and that the choice of calibration point can influence the topology of the resulting tree. Compared to the single-calibrated trees, the multi-calibrated tree exhibits smaller variance in estimated ages and better reflects the fossil record. CONCLUSIONS The use of a large number of vetted fossil calibration points with soft bounds is promoted as a better approach than using just one or a few calibrations, or relying on internal-congruency metrics to discard good fossil data. This study also highlights the importance of considering morphological and ecological characteristics of clades when delimiting higher taxa. I also illustrate how phylogeographic and paleoenvironmental hypotheses inferred from a tree containing only extant taxa can be problematic without consideration of the fossil record. Incorporating the fossil record of Ruminantia is a necessary step for future analyses aiming to reconstruct the evolutionary history of this clade.
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Affiliation(s)
- Faysal Bibi
- Museum für Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity at the Humboldt University Berlin, Invalidenstrasse 43, Berlin 10115, Germany
- Current address: Department of Mammalogy, American Museum of Natural History, 200 Central Park West, New York, NY 10024, USA
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