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Yang S, Wang H, Dong Y, Zhao X, Dong S, Wang X, Xing X. Analysis of the genetic diversity of Tahe red deer and population structure of Cervus elaphu/hanglu/canadensis. Gene 2024; 933:148960. [PMID: 39326473 DOI: 10.1016/j.gene.2024.148960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 09/02/2024] [Accepted: 09/19/2024] [Indexed: 09/28/2024]
Abstract
The Tahe red deer is currently the largest breeding population of antlered Cervus elaphus in China. It has unique characteristics such as drought and roughage tolerance, high antler yield and early sexual maturity. It is a high-quality provenance for cultivating high-yield Cervus elaphus breeds and is also the subject of study on the origin, evolution, and classification of Cervus elaphus. The breeding quantity of Tahe red deer has decreased significantly in recent years due to the influence of feeding conditions and consumer market. This has resulted in a serious threat to its genetic resources. To provide a scientific theoretical basis for the protection of the Tahe red deer population, we performed PCR amplification and direct sequencing of the AMELY2, DBY and SRY genes of the Y chromosome, and the ND1, COX1, ATP6, ND5, Cyt b and D-loop regions of the mtDNA, and analysed their genetic diversity and population genetic structure. The results showed high haplotype diversity and low nucleotide diversity in both the Y chromosome and mtDNA genes. The phylogenetic tree and haplotype network diagram, constructed using white-lipped deer as the outgroup, indicate that Tahe red deer has two distinct ancestral types. The phylogenetic tree, based on the Cyt b gene and D-loop region, reveals that the Cervus elaphus/hanglu/canadensis is divided into three clades: western, central, and eastern. Tahe red deer, C.h.bactrianus, and C.h.hanglu are clustered in the central clade. The study results indicate that Tahe red deer has low genetic diversity and two distinct ancestor types. It is speculated that the central clade is either the earliest differentiation from the ancestor species or the closest to it.
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Affiliation(s)
- Sukun Yang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals of Ministry of Agriculture and Rural Affairs, Institute of Specia Animal and Plant Sciences of Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Hongliang Wang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals of Ministry of Agriculture and Rural Affairs, Institute of Specia Animal and Plant Sciences of Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Yimeng Dong
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals of Ministry of Agriculture and Rural Affairs, Institute of Specia Animal and Plant Sciences of Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Xitang Zhao
- Agriculture Development Service Center, Farm No.34 of Agriculture Division No.2 of Xinjiang Corps, Korla 841506, China
| | - Shiwu Dong
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals of Ministry of Agriculture and Rural Affairs, Institute of Specia Animal and Plant Sciences of Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Xinhao Wang
- Guangdong Chimelong Group, Guangzhou 510000, China
| | - Xiumei Xing
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals of Ministry of Agriculture and Rural Affairs, Institute of Specia Animal and Plant Sciences of Chinese Academy of Agricultural Sciences, Changchun 130112, China.
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2
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Tang L, Dong S, Xing X. Comparative Genomics Reveal Phylogenetic Relationship and Chromosomal Evolutionary Events of Eight Cervidae Species. Animals (Basel) 2024; 14:1063. [PMID: 38612302 PMCID: PMC11010878 DOI: 10.3390/ani14071063] [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: 02/26/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Cervidae represents a family that is not only rich in species diversity but also exhibits a wide range of karyotypes. The controversies regarding the phylogeny and classification of Cervidae still persist. The flourishing development of the genomic era has made it possible to address these issues at the genomic level. Here, the genomes of nine species were used to explore the phylogeny and chromosomal evolutionary events of Cervidae. By conducting whole-genome comparisons, we identified single-copy orthologous genes across the nine species and constructed a phylogenetic tree based on the single-copy orthologous genes sequences, providing new insights into the phylogeny of Cervidae, particularly the phylogenetic relationship among sika deer, red deer, wapiti and Tarim red deer. Gene family analysis revealed contractions in the olfactory receptor gene family and expansions in the histone gene family across eight Cervidae species. Furthermore, synteny analysis was used to explore the chromosomal evolutionary events of Cervidae species, revealing six chromosomal fissions during the evolutionary process from Bovidae to Cervidae. Notably, specific chromosomal fusion events were found in four species of Cervus, and a unique chromosomal fusion event was identified in Muntiacus reevesi. Our study further completed the phylogenetic relationship within the Cervidae and demonstrated the feasibility of inferring species phylogeny at the whole-genome level. Additionally, our findings on gene family evolution and the chromosomal evolutionary events in eight Cervidae species lay a foundation for comprehensive research of the evolution of Cervidae.
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Affiliation(s)
| | | | - Xiumei Xing
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (L.T.); (S.D.)
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3
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Heckeberg NS, Zachos FE, Kierdorf U. Antler tine homologies and cervid systematics: A review of past and present controversies with special emphasis on Elaphurus davidianus. Anat Rec (Hoboken) 2023; 306:5-28. [PMID: 35578743 DOI: 10.1002/ar.24956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 01/29/2023]
Abstract
Antlers are the most conspicuous trait of cervids and have been used in the past to establish a classification of their fossil and living representatives. Since the availability of molecular data, morphological characters have generally become less important for phylogenetic reconstructions. In recent years, however, the appreciation of morphological characters has increased, and they are now more frequently used in addition to molecular data to reconstruct the evolutionary history of cervids. A persistent challenge when using antler traits in deer systematics is finding a consensus on the homology of structures. Here, we review early and recent attempts to homologize antler structures and objections to this approach, compare and evaluate recent advances on antler homologies, and critically discuss these different views in order to offer a basis for further scientific exchange on the topic. We further present some developmental aspects of antler branching patterns and discuss their potential for reconstructing cervid systematics. The use of heterogeneous data for reconstructing phylogenies has resulted in partly conflicting hypotheses on the systematic position of certain cervid species, on which we also elaborate here. We address current discussions on the use of different molecular markers in cervid systematics and the question whether antler morphology and molecular data can provide a consistent picture on the evolutionary history of cervids. In this context, special attention is given to the antler morphology and the systematic position of the enigmatic Pere David's deer (Elaphurus davidianus).
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Affiliation(s)
- Nicola S Heckeberg
- Staatliches Museum für Naturkunde Karlsruhe, Karlsruhe, Germany.,Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Frank E Zachos
- Natural History Museum Vienna, Vienna, Austria.,Department of Genetics, University of the Free State, Bloemfontein, South Africa.,Department of Evolutionary Biology, University of Vienna, Vienna, Austria
| | - Uwe Kierdorf
- Department of Biology, University of Hildesheim, Hildesheim, Germany
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4
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Phylogeny and evolution of the genus Cervus (Cervidae, Mammalia) as revealed by complete mitochondrial genomes. Sci Rep 2022; 12:16381. [PMID: 36180508 PMCID: PMC9525267 DOI: 10.1038/s41598-022-20763-x] [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: 03/02/2022] [Accepted: 09/19/2022] [Indexed: 11/24/2022] Open
Abstract
Mitochondrial DNA (mtDNA) lineages are recognized as important components of intra- and interspecific biodiversity, and allow to reveal colonization routes and phylogeographic structure of many taxa. Among these is the genus Cervus that is widely distributed across the Holarctic. We obtained sequences of complete mitochondrial genomes from 13 Cervus taxa and included them in global phylogenetic analyses of 71 Cervinae mitogenomes. The well-resolved phylogenetic trees confirmed Cervus to be monophyletic. Molecular dating based on several fossil calibration points revealed that ca. 2.6 Mya two main mitochondrial lineages of Cervus separated in Central Asia, the Western (including C. hanglu and C. elaphus) and the Eastern (comprising C. albirostris, C. canadensis and C. nippon). We also observed convergent changes in the composition of some mitochondrial genes in C. hanglu of the Western lineage and representatives of the Eastern lineage. Several subspecies of C. nippon and C. hanglu have accumulated a large portion of deleterious substitutions in their mitochondrial protein-coding genes, probably due to drift in the wake of decreasing population size. In contrast to previous studies, we found that the relic haplogroup B of C. elaphus was sister to all other red deer lineages and that the Middle-Eastern haplogroup E shared a common ancestor with the Balkan haplogroup C. Comparison of the mtDNA phylogenetic tree with a published nuclear genome tree may imply ancient introgressions of mtDNA between different Cervus species as well as from the common ancestor of South Asian deer, Rusa timorensis and R. unicolor, to the Cervus clade.
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Genetic insights into an Apennine population of the Italian red deer. MAMMAL RES 2022. [DOI: 10.1007/s13364-022-00637-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
AbstractThe red deer Cervus elephus has been a common species in Italy until the Middle Ages and the Renaissance, when its distribution range started to considerably decrease, due to gradual deforestation and hunting pressure. Afterwards, the red deer has been reintroduced to many regions of the world, including Italy. In the Italian Apennines, the Acquerino-Cantagallo Natural Reserve (ACQUERINO) hosts one of the largest peninsular red deer populations, originated from a series of successful reintroductions. In this study, we meant to detect the level of genetic variability of Acquerino-Cantagallo Natural Reserve deer population and to investigate the genetic relationships with the other Italian and European populations. We identified five mitochondrial DNA control region (D-loop) haplotypes, four falling in lineage A and one falling in lineage C, derived from at least two maternal lineages, confirming that ACQUERINO population should be the result of multiple reintroductions. Haplotype diversity (H = 0.50) and nucleotide (π = 0.004) diversity were low, but included into the deer range values. ACQUERINO population showed low levels of genetic diversity when compared to other European and Mediterranean populations, confirming that this expanding population may have been generated from a low number of founders.
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Molecular Evidence Reveals the Sympatric Distribution of Cervus nippon yakushimae and Cervus nippon taiouanus on Jeju Island, South Korea. Animals (Basel) 2022; 12:ani12080998. [PMID: 35454244 PMCID: PMC9029077 DOI: 10.3390/ani12080998] [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: 03/29/2022] [Revised: 04/09/2022] [Accepted: 04/10/2022] [Indexed: 11/17/2022] Open
Abstract
Non-native species threaten native ecosystems and species, particularly on islands where rates of endemism and vulnerability to threats are high. Understanding species invasion will aid in providing insights into ecological and evolutionary processes. To identify the non-native sika deer (Cervus nippon) population in Jeju, South Korea, and their phylogenetic affinities, we collected tissue samples from roadkill and the World Natural Heritage Headquarters in Jeju. Mitochondrial DNA cytochrome B (CytB) gene sequences were analyzed to determine two distinct CytB haplotypes. Phylogenetic analysis using maximum likelihood tree revealed two haplotypes of CytB clustered into two different groups representing two subspecies: C. n. yakushimae, native to Japan, and C. n. taiouanus, native to Taiwan. The tentative divergence time between the two subspecies was estimated at 1.81 million years. Our study confirmed that the two subspecies of sika deer are sympatric in the natural ecosystem of Jeju Island. This study provides valuable information to help government and conservation agencies understand alien species and determine control policies for conserving native biodiversity in South Korea.
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Gupta SK, Kumar A, van Berkel T, Emsens WJ, Singh B, Puls S, Rin N, Jocque M. Genetic analysis reveals a distinct lineage of hog deer (Axis porcinus) in Kratie province, Cambodia. J Hered 2022; 113:444-452. [PMID: 35373825 DOI: 10.1093/jhered/esac017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 04/01/2022] [Indexed: 11/13/2022] Open
Abstract
The hog deer (Axis porcinus) is an endangered cervid with drastic population declines. There are two recognized subspecies of hog deer: A. p. porcinus, ranging from Punjab Province in Pakistan, Nepal and the Northern part of India to Myanmar, and A. p. annamiticus found in Indo-China, Thailand, Laos, Cambodia and Vietnam. The current geographic range of A. p. annamiticus is still ambiguous. We analyzed variation in the mitochondrial DNA control region (mtDNA CR) to investigate the intra-species structure, differentiation, and demographic history of hog deer from Cambodia (Kratie Province), which we compared with the populations from India and Thailand. We also generated divergence time estimates using a concatenated dataset of complete Cyt b and partial CR. The CR data showed that Cambodian hog deer are genetically differentiated from the mainland Indian and Thai populations, forming a distinct basal clade. The time of divergence indicates that the Cambodian lineage split from the other two hog deer lineages around 0.51 Mya, during the Late Pleistocene. The results also suggest strong phylogeographic structure among hog deer: lineage A extends from Terai Arc (foothills of the Himalayas) to Assam, India (A. p. porcinus), lineage B from Manipur, India to Thailand (A. p. annamiticus), and lineage C is only known from Kratie Province, Cambodia. Lineage A exhibited a higher level of genetic diversity than lineages B and C, with recent demographic stability. Thus, the hog deer population in Kratie Province appears to be a distinct lineage that should be treated as an evolutionarily significant unit.
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Affiliation(s)
- Sandeep Kumar Gupta
- Wildlife Institute of India, Chandrabani, Dehra Dun-248001, Uttarakhand, India
| | - Ajit Kumar
- Wildlife Institute of India, Chandrabani, Dehra Dun-248001, Uttarakhand, India
| | - Tim van Berkel
- Biodiversity Inventory for Conservation (BINCO), Walmersumstraat 44, 3380 Glabbeek, Belgium
| | - Willem-Jan Emsens
- Biodiversity Inventory for Conservation (BINCO), Walmersumstraat 44, 3380 Glabbeek, Belgium.,Ecosystem Management Research Group, Department of Biology, University of Antwerp, Universiteitsplein 1C, 2610 Wilrijk, Belgium
| | - Bhim Singh
- Wildlife Institute of India, Chandrabani, Dehra Dun-248001, Uttarakhand, India
| | - Sam Puls
- Biodiversity Inventory for Conservation (BINCO), Walmersumstraat 44, 3380 Glabbeek, Belgium
| | - Naroeun Rin
- WWF Cambodia, 21 street 322, St 29, Phnom Penh, Cambodia
| | - Merlijn Jocque
- Biodiversity Inventory for Conservation (BINCO), Walmersumstraat 44, 3380 Glabbeek, Belgium.,Aquatic and Terrestrial Ecology (ATECO), Royal Belgian Institute of Natural Sciences (RBINS), Vautierstraat 29, 1000 Brussels, Belgium
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8
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Nagata J, Yasuda M, Yamashiro A. Genetic Analysis of a Newly Established Deer Population Expanding in the Sasebo Area in Nagasaki Prefecture, Japan Reveals No Evidence of Genetic Disturbance by Formosan Sika Deer. MAMMAL STUDY 2021. [DOI: 10.3106/ms2020-0084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Junco Nagata
- Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki 305-8687, Japan
| | - Masatoshi Yasuda
- Kyushu Research Center, Forestry and Forest Products Research Institute, 4-11-16 Kurokami, Chuo-ku, Kumamoto, Kumamoto 860-0862, Japan
| | - Asuka Yamashiro
- Graduate School of Technology, Industrial and Social Science, Tokushima University, 2-1 Minami-josanjima, Tokushima 770-8513, Japan
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9
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Ghazi MG, Hussain SA, Gupta SK. Detection of 40 bp tandem repeat motif and associated insertions and deletions (INDEL) in the mitochondrial DNA control region of Sambar deer (Rusa unicolor). Mol Biol Rep 2021; 48:4129-4135. [PMID: 34041678 DOI: 10.1007/s11033-021-06426-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 05/20/2021] [Indexed: 11/29/2022]
Abstract
Sambar (Rusa unicolor) is the largest oriental deer and has a wide distribution across South and Southeast Asia. Despite its wide distribution range, little information on the genetics of this species is available to date. We examined the genetic variability of Sambar populations using a partial fragment of the mtDNA control region and reconstructed the phylogeographic association of Sambar populations across India. We detected 56 haplotypes with an overall haplotype diversity, Hd = 0.939 ± 0.012 and nucleotide diversity, Pi = 0.029 ± 0.002 in Sambar populations across India. The Sambar populations of Northeast India exhibits 30 localized mtDNA control region haplotypes with no haplotype sharing with other populations of India. We identified a 40 bp tandem repeat motif in the mtDNA control region with variable copy numbers ranging between three to six duplications. The Sambar populations across India exhibited phylogeographic differentiation based on the observed insertion and deletion patterns in the mtDNA control region. The 40 bp tandem repeat motif was associated with patterns of insertions and deletions among different populations of Sambar in India. The findings of this study provide baseline information on the mtDNA genetic variability of Sambar populations across India, which is crucial for future population genetic studies.
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10
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Heckeberg NS. The systematics of the Cervidae: a total evidence approach. PeerJ 2020; 8:e8114. [PMID: 32110477 PMCID: PMC7034380 DOI: 10.7717/peerj.8114] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 10/28/2019] [Indexed: 11/22/2022] Open
Abstract
Systematic relationships of cervids have been controversial for decades. Despite new input from molecular systematics, consensus could only be partially reached. The initial, gross (sub) classification based on morphology and comparative anatomy was mostly supported by molecular data. The rich fossil record of cervids has never been extensively tested in phylogenetic frameworks concerning potential systematic relationships of fossil cervids to extant cervids. The aim of this work was to investigate the systematic relationships of extant and fossil cervids using molecular and morphological characters and make implications about their evolutionary history based on the phylogenetic reconstructions. To achieve these objectives, molecular data were compiled consisting of five nuclear markers and the complete mitochondrial genome of 50 extant and one fossil cervids. Several analyses using different data partitions, taxon sampling, partitioning schemes, and optimality criteria were undertaken. In addition, the most extensive morphological character matrix for such a broad cervid taxon sampling was compiled including 168 cranial and dental characters of 41 extant and 29 fossil cervids. The morphological and molecular data were analysed in a combined approach and other comprehensive phylogenetic reconstructions. The results showed that most Miocene cervids were more closely related to each other than to any other cervids. They were often positioned between the outgroup and all other cervids or as the sister taxon to Muntiacini. Two Miocene cervids were frequently placed within Muntiacini. Plio- and Pleistocene cervids could often be affiliated to Cervini, Odocoileini or Capreolini. The phylogenetic analyses provide new insights into the evolutionary history of cervids. Several fossil cervids could be successfully related to living representatives, confirming previously assumed affiliations based on comparative morphology and introducing new hypotheses. New systematic relationships were observed, some uncertainties persisted and resolving systematics within certain taxa remained challenging.
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Affiliation(s)
- Nicola S. Heckeberg
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
- SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Berlin, Germany
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11
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Hu P, Shao Y, Xu J, Wang T, Li Y, Liu H, Rong M, Su W, Chen B, Cui S, Cui X, Yang F, Tamate H, Xing X. Genome-wide study on genetic diversity and phylogeny of five species in the genus Cervus. BMC Genomics 2019; 20:384. [PMID: 31101010 PMCID: PMC6525406 DOI: 10.1186/s12864-019-5785-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 05/08/2019] [Indexed: 01/01/2023] Open
Abstract
Background Previous investigations of phylogeny in Cervus recovered many clades without whole genomic support. Methods In this study, the genetic diversity and phylogeny of 5 species (21 subspecies/populations from C. unicolor, C. albirostris, C. nippon, C. elaphus and C. eldii) in the genus Cervus were analyzed using reduced-representation genome sequencing. Results A total of 197,543 SNPs were identified with an average sequencing depth of 16 x. A total of 21 SNP matrices for each subspecies/population and 1 matrix for individual analysis were constructed, respectively. Nucleotide diversity and heterozygosity analysis showed that all 21 subspecies/populations had different degrees of genetic diversity. C. eldii, C. unicolor and C. albirostris showed relatively high expected and observed heterozygosity, while observed heterozygosity in C. nippon was the lowest, indicating there was a certain degree of inbreeding rate in these subspecies/populations. Phylogenetic ML tree of all Cervus based on the 21 SNP matrices showed 5 robustly supported clades that clearly separate C. eldii, C. unicolor, C. albirostris, C. elaphus and C. nippon. Within C. elaphus clade, 4 subclades were well differentiated and statistically highly supported: C. elaphus (New Zealand), C. e. yarkandensis, C. c. canadensis and the other grouping the rest of C. canadensis from China. In the C. nippon clade, 2 well-distinct subclades corresponding to C. n. aplodontus and other C. nippon populations were separated. Phylogenetic reconstruction indicated that the first evolutionary event of the genus Cervus occurred approximately 7.4 millions of years ago. The split between C. elaphus and C. nippon could be estimated at around 3.6 millions of years ago. Phylogenetic ML tree of all samples based on individual SNP matrices, together with geographic distribution, have shown that there were 3 major subclades of C. elaphus and C. canadensis in China, namely C. e. yarkandensis (distributed in Tarim Basin), C. c. macneilli/C. c. kansuensis/C. c. alashanicus (distributed in middle west of China), and C. c. songaricus/C. c. sibiricus (distributed in northwest of China). Among them, C. e. yarkandensis was molecularly the most primitive subclade, with a differentiation dating back to 0.8–2.2 Myr ago. D statistical analysis showed that there was high probability of interspecific gene exchange between C. albirostris and C. eldii, C. albirostris and C. unicolor, C. nippon and C. unicolor, and there might be 2 migration events among 5 species in the genus Cervus. Conclusions Our results provided new insight to the genetic diversity and phylogeny of Cervus deer. In view of the current status of these populations, their conservation category will need to be reassessed. Electronic supplementary material The online version of this article (10.1186/s12864-019-5785-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pengfei Hu
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Yuanchen Shao
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Jiaping Xu
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Tianjiao Wang
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Yiqing Li
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Huamiao Liu
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Min Rong
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Weilin Su
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Binxi Chen
- Animal Health Supervision Institute of Hainan Province, Haikou, China
| | - Songhuan Cui
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Xuezhe Cui
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Fuhe Yang
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | | | - Xiumei Xing
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China.
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12
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Matsumoto Y, Takagi T, Koda R, Tanave A, Yamashiro A, Tamate HB. Evaluation of introgressive hybridization among Cervidae in Japan's Kinki District via two novel genetic markers developed from public NGS data. Ecol Evol 2019; 9:5605-5616. [PMID: 31160985 PMCID: PMC6540688 DOI: 10.1002/ece3.5131] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 02/12/2019] [Accepted: 03/08/2019] [Indexed: 01/06/2023] Open
Abstract
Hybridization and backcrossing of native populations with introduced species can lead to introgression and genetic alteration. In this study, we evaluated introgression in 43 deer from a potential hybrid zone around Okinoshima Island, Kinki District, Japan. This region witnessed the migration of a hybrid population (cross between the Formosan sika deer [Cervus nippon taiouanus] and other deer species) that could potentially breed with the native Japanese sika deer (C. n. centralis). We used an existing genetic marker for the mitochondrial cytochrome b gene and two novel markers for nuclear DNA, developed using publicly available next-generation sequencing data. We identified one mainland deer with a mitochondrial haplotype identical to that of the Formosan sika deer as well as nuclear heterozygous sequences identical to those of Formosan and Japanese sika deer. This suggests that the mainland deer is a hybrid offspring of the Okinoshima population and native deer. However, only Japanese sika deer sequences were found in the other 42 samples, indicating limited introgression. Nevertheless, hybridization pre- and postintroduction in the Okinoshima population could cause multispecies introgression among Japanese sika deer, negatively affecting genetic integrity. We developed a simple test based on polymerase chain reaction-restriction fragment length polymorphism to detect introgression in natural populations. Our method can accelerate genetic monitoring of Japanese sika deer in Kinki District. In conclusion, to prevent further introgression and maintain genetic integrity of Japanese sika deer, we recommend establishing fences around Okinoshima Island to limit migration, besides a continued genetic monitoring of the native deer.
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Affiliation(s)
- Yuki Matsumoto
- Department of Genetics, School of Life SciencesSOKENDAIShizuokaJapan
- Mouse Genomics Resource LaboratoryNational Institute of GeneticsShizuokaJapan
- Present address:
Research and Development SectionAnicom Specialty Medical Institute Inc.YokohamaJapan
| | - Toshihito Takagi
- Graduate School of Science and EngineeringYamagata UniversityYamagataJapan
| | - Ryosuke Koda
- Research Institute of Environment, Agriculture and FisheriesNeyagawaJapan
| | - Akira Tanave
- Mouse Genomics Resource LaboratoryNational Institute of GeneticsShizuokaJapan
| | - Asuka Yamashiro
- Science and Technology, Graduate School of Technology, Industrial and Social ScienceTokushima UniversityTokushimaJapan
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Queirós J, Acevedo P, Santos JPV, Barasona J, Beltran-Beck B, González-Barrio D, Armenteros JA, Diez-Delgado I, Boadella M, Fernandéz de Mera I, Ruiz-Fons JF, Vicente J, de la Fuente J, Gortázar C, Searle JB, Alves PC. Red deer in Iberia: Molecular ecological studies in a southern refugium and inferences on European postglacial colonization history. PLoS One 2019; 14:e0210282. [PMID: 30620758 PMCID: PMC6324796 DOI: 10.1371/journal.pone.0210282] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 12/19/2018] [Indexed: 01/31/2023] Open
Abstract
The red deer (Cervus elaphus) is a widespread wild ungulate in Europe that has suffered strong anthropogenic impacts over their distribution during the last centuries, but also at the present time, due its economic importance as a game species. Here we focus on the evolutionary history of the red deer in Iberia, one of the three main southern refugial areas for temperate species in Europe, and addressed the hypothesis of a cryptic refugia at higher latitudes during the Last Glacial Maximum (LGM). A total of 911 individuals were sampled, genotyped for 34 microsatellites specifically developed for red deer and sequenced for a fragment of 670 bp of the mitochondrial (mtDNA) D-loop. The results were combined with published mtDNA sequences, and integrated with species distribution models and historical European paleo-distribution data, in order to further examine the alternative glacial refugial models and the influence of cryptic refugia on European postglacial colonization history. Clear genetic differentiation between Iberian and European contemporary populations was observed at nuclear and mtDNA levels, despite the mtDNA haplotypes central to the phylogenetic network are present across western Europe (including Iberia) suggesting a panmictic population in the past. Species distribution models, fossil records and genetic data support a timing of divergence between Iberian and European populations that overlap with the LGM. A notable population structure was also found within the Iberian Peninsula, although several populations displayed high levels of admixture as a consequence of recent red deer translocations. Five D-loop sub-lineages were found in Iberia that belong to the Western European mtDNA lineage, while there were four main clusters based on analysis of nuclear markers. Regarding glacial refugial models, our findings provide detailed support for the hypothesis that red deer may have persisted in cryptic northern refugia in western Europe during the LGM, most likely in southern France, southern Ireland, or in a region between them (continental shelf), and these regions were the source of individuals during the European re-colonization. This evidence heightens the importance of conserving the high mitochondrial and nuclear diversity currently observed in Iberian populations.
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Affiliation(s)
- João Queirós
- Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)/InBio Laboratório Associado, Universidade do Porto, R. Monte-Crasto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Porto, Portugal
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
- * E-mail:
| | - Pelayo Acevedo
- Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)/InBio Laboratório Associado, Universidade do Porto, R. Monte-Crasto, Vairão, Portugal
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - João P. V. Santos
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
- Departamento de Biologia & CESAM, Universidade de Aveiro, Aveiro, Portugal
| | - Jose Barasona
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Beatriz Beltran-Beck
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - David González-Barrio
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Jose A. Armenteros
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Iratxe Diez-Delgado
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Mariana Boadella
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
- SABIOtec. Ed. Polivalente UCLM, Ciudad Real, Spain
| | - Isabel Fernandéz de Mera
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Jose F. Ruiz-Fons
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Joaquin Vicente
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Jose de la Fuente
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, United States of America
| | - Christian Gortázar
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Jeremy B. Searle
- Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)/InBio Laboratório Associado, Universidade do Porto, R. Monte-Crasto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Porto, Portugal
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States of America
| | - Paulo C. Alves
- Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)/InBio Laboratório Associado, Universidade do Porto, R. Monte-Crasto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Porto, Portugal
- Wildlife Biology Program, University of Montana, Missoula, MT, United States of America
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Liu H, Wang T, He J, Tu J, Yang X, Yang F, Xing X. The complete mitochondrial genome of Cervus elaphus kansuensis (Artiodactyla: Cervidae) and its phylogenetic analysis. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1607588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Huitao Liu
- State Key Laboratory for Molecular Biology of Special Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Tianjiao Wang
- State Key Laboratory for Molecular Biology of Special Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Jinming He
- College of Pharmacy, Jilin Agricultural University, Changchun, China
| | - Jianfeng Tu
- State Key Laboratory for Molecular Biology of Special Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Xuzhong Yang
- Gansu Qilianshan Biotechnology Development Co., Ltd, Zhangye, China
| | - Fuhe Yang
- State Key Laboratory for Molecular Biology of Special Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Xiumei Xing
- State Key Laboratory for Molecular Biology of Special Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
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Genetic analysis of endangered hog deer (Axis porcinus) reveals two distinct lineages from the Indian subcontinent. Sci Rep 2018; 8:16308. [PMID: 30397218 PMCID: PMC6218551 DOI: 10.1038/s41598-018-34482-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 10/16/2018] [Indexed: 11/08/2022] Open
Abstract
The hog deer (Axis porcinus) is threatened by habitat alteration, fragmentation, and poaching, which have led to a drastic decline of its wild population. Two subspecies of A. porcinus have been described from its distribution range. A. p. porcinus is reported to occur from Pakistan along the Himalayan foothills through Nepal, India and Myanmar, and A. p. annamiticus is found in Thailand, Indo-China, Laos, Cambodia, and Vietnam. However, the current distribution range of A. p. annamiticus is still unclear. We used the partial control region (CR) of mitochondrial DNA (mtDNA) and seven microsatellite loci to investigate the intra-species structure, differentiation, and demographic history of hog deer populations from three landscapes, the Terai Arc, Northeast, and Indo-Burma (Keibul Lamjao National Park (KLNP), Manipur, India) landscapes. We also carried out divergence time estimation using the complete mitogenome. The level of variation was ~4%, and the time of divergence of the KLNP population and the other Indian populations was about 0.22 Mya, i.e., during the last glaciation periods of the Late Pleistocene/Early Holocene. The KLNP haplotypes of the control region were shared with the Southeast Asian subspecies, A. p. annamiticus. The results of the investigations of the microsatellite loci supported the mtDNA results unambiguously. Two genetically distinct lineages are found in India: one is found from the Terai Arc to Assam (A. p. porcinus) and the other in Manipur (A. p. annamiticus). The genetic diversity in KLNP was low and exhibited a higher degree of genetic differentiation compared with major Indian populations. The Bayesian skyline plots indicated that after a long phase of historic demographic stability, the populations of both the lineages of hog deer suffered pronounced declines during the period from ~800 years BP to 5000 years BP. In summary, our finding provided evidence that the KLNP population is probably a prime, isolated and sustaining stock of A. p. annamiticus and should be managed as evolutionarily significant units (ESUs).
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Doan K, Mackiewicz P, Sandoval-Castellanos E, Stefaniak K, Ridush B, Dalén L, Węgleński P, Stankovic A. The history of Crimean red deer population and Cervus phylogeography in Eurasia. Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx065] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Karolina Doan
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha, Warsaw, Poland
| | - Paweł Mackiewicz
- Department of Genomics, Faculty of Biotechnology, University of Wrocław, Joliot-Curie, Wrocław, Poland
| | - Edson Sandoval-Castellanos
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Krzysztof Stefaniak
- Department of Palaeozoology, University of Wrocław, Sienkiewicza, Wrocław, Poland
| | - Bogdan Ridush
- Department of Physical Geography, Geomorphology and Paleogeography, Yuriy Fedkovych Chernivtsi National University, Kotsubynskogo, Chernivtsi, Ukraine
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Piotr Węgleński
- Centre of New Technologies, University of Warsaw, Banacha, Warsaw, Poland
| | - Ana Stankovic
- Institute of Genetics and Biotechnology, University of Warsaw, Pawińskiego, Warsaw, Poland
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18
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Kumar VP, Thakur M, Rajpoot A, Joshi BD, Nigam P, Ahmad K, Kumar D, Goyal SP. Resolving the phylogenetic status and taxonomic relationships of the Hangul (Cervus elaphus hanglu) in the family Cervidae. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:835-842. [PMID: 27937071 DOI: 10.1080/24701394.2016.1197217] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The Hangul (Cervus elaphus hanglu) is a "Least Concern" deer species, and it is the only survivor of the Red Deer group in the Indian subcontinent. The phylogenetic status of the Hangul relative to the other members of the family Cervidae is not known because sequence data are not available in public databases. Therefore, this study was carried out to determine the phylogenetic status and delineate the genetic boundaries of the Hangul with respect to the other Red Deer subspecies on the basis of cytochrome b gene sequence data (ca 421 bp). There are three major monophyletic groups of the Red Deer in the phylogenetic tree, which are referred to as the western (Hap-01 to Hap-10), eastern (Hap-11 to Hap-20) and tarim (Hap-21 to Hap-25) groups. The overall haplotype diversity and per-site nucleotide diversity were 0.9771 (±0.0523) and 0.0388 (±0.00261), respectively. In the phylogenetic tree, the Hangul clustered with the tarim group (Yarkand and Bactrian Red Deer) with a strong bootstrap support (92%) and was found to be genetically closer to the Bactrian Red Deer than to the Yarkand Red Deer. Our molecular analysis supported the idea that the Hangul diverged from the Bactrian Red Deer and migrated to India from Tajikistan approximately 1.2 MYA.
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Affiliation(s)
- Ved P Kumar
- a Wildlife Institute of India , Chandrabani , Dehradun , Uttarakhand , India.,b Department of Zoology, Veer Kunwar Singh University , Arrah , Bihar , India
| | - Mukesh Thakur
- c Amity Institute of Wildlife Sciences, Amity University , Noida , Uttar Pradesh , India
| | - Ankita Rajpoot
- d Zoological Survey of India, NRC , Dehradun , Uttarakhand , India
| | - Bhim Dutt Joshi
- a Wildlife Institute of India , Chandrabani , Dehradun , Uttarakhand , India
| | - Parag Nigam
- a Wildlife Institute of India , Chandrabani , Dehradun , Uttarakhand , India
| | - Khursheed Ahmad
- e Centre for Mountain Wildlife Sciences, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology , Srinagar , Jammu & Kashmir , India
| | - Dhyanendra Kumar
- b Department of Zoology, Veer Kunwar Singh University , Arrah , Bihar , India
| | - Surendra P Goyal
- a Wildlife Institute of India , Chandrabani , Dehradun , Uttarakhand , India
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19
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Heckeberg NS, Erpenbeck D, Wörheide G, Rössner GE. Systematic relationships of five newly sequenced cervid species. PeerJ 2016; 4:e2307. [PMID: 27602278 PMCID: PMC4991894 DOI: 10.7717/peerj.2307] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 07/09/2016] [Indexed: 11/20/2022] Open
Abstract
Cervid phylogenetics has been puzzling researchers for over 150 years. In recent decades, molecular systematics has provided new input for both the support and revision of the previous results from comparative anatomy but has led to only partial consensus. Despite all of the efforts to reach taxon-wide species sampling over the last two decades, a number of cervid species still lack molecular data because they are difficult to access in the wild. By extracting ancient DNA from museum specimens, in this study, we obtained partial mitochondrial cytochrome b gene sequences for Mazama bricenii, Mazama chunyi, Muntiacus atherodes, Pudu mephistophiles, and Rusa marianna, including three holotypes. These new sequences were used to enrich the existing mitochondrial DNA alignments and yielded the most taxonomically complete data set for cervids to date. Phylogenetic analyses provide new insights into the evolutionary history of these five species. However, systematic uncertainties within Muntiacus persist and resolving phylogenetic relationships within Pudu and Mazama remain challenging.
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Affiliation(s)
- Nicola S Heckeberg
- Department for Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany; SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany; Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Dirk Erpenbeck
- Department for Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany; GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gert Wörheide
- Department for Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany; SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany; GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gertrud E Rössner
- Department for Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany; SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany; GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
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20
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Amaral DT, Mitani Y, Oliveira G, Ohmiya Y, Viviani VR. Revisiting Coleoptera a + T-rich region: structural conservation, phylogenetic and phylogeographic approaches in mitochondrial control region of bioluminescent Elateridae species (Coleoptera). Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:671-680. [PMID: 27159725 DOI: 10.3109/24701394.2016.1174220] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The control region (CR) or A + T-rich region in Coleoptera mt genome is poorly characterized, including the Elateroidea bioluminescent species. Here, we provided the first attempt to characterize and compare the structure and organization of the CR of different species within Elateridae. We also revisited some sequenced Coleoptera CR and observed consensus T-stretches, non-conserved sequences near the stem-loop and unusual inner tRNAs-like sequences. All these features are probably involved in the replication start of the mt genome. The phylogenetic relationships in Elateridae bioluminescent groups using partial sequence of CR showed the monophyly of Pyrearinus pumilus group and Pyrearinus as a polyphyletic genus, corroborating our previous results. The wider genetic variation obtained by CR analysis could separate two different lineages that occur within P. termitilluminans populations. In Elateridae, the CR exhibited high polymorphism within and between populations, which was also observed in other Coleoptera species, suggesting that the CR could be described as a suitable molecular marker to be applied in phylogenetic and phylogeographic studies.
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Affiliation(s)
- Danilo T Amaral
- a Graduate School of Biotechnology and Environmental Monitoring (UFSCar) , Sorocaba , SP , Brazil.,b Graduate School of Evolutive Genetics and Molecular Biology , Federal University of São Carlos (UFSCar) , São Carlos , SP , Brazil
| | - Yasuo Mitani
- c Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba , Japan
| | - Gabriela Oliveira
- a Graduate School of Biotechnology and Environmental Monitoring (UFSCar) , Sorocaba , SP , Brazil.,b Graduate School of Evolutive Genetics and Molecular Biology , Federal University of São Carlos (UFSCar) , São Carlos , SP , Brazil
| | - Yoshihiro Ohmiya
- d Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba , Japan
| | - Vadim R Viviani
- a Graduate School of Biotechnology and Environmental Monitoring (UFSCar) , Sorocaba , SP , Brazil.,b Graduate School of Evolutive Genetics and Molecular Biology , Federal University of São Carlos (UFSCar) , São Carlos , SP , Brazil
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21
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Escobedo-Morales LA, Mandujano S, Eguiarte LE, Rodríguez-Rodríguez MA, Maldonado JE. First phylogenetic analysis of Mesoamerican brocket deer Mazama pandora and Mazama temama (Cetartiodactyla: Cervidae) based on mitochondrial sequences: Implications for Neotropical deer evolution. Mamm Biol 2016. [DOI: 10.1016/j.mambio.2016.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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22
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Boyce MS, Mao JS, Merrill EH, Fortin D, Turner MG, Fryxell J, Turchin P. Scale and heterogeneity in habitat selection by elk in Yellowstone National Park. ECOSCIENCE 2016. [DOI: 10.1080/11956860.2003.11682790] [Citation(s) in RCA: 187] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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23
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Carranza J, Salinas M, de Andrés D, Pérez‐González J. Iberian red deer: paraphyletic nature at mtDNA but nuclear markers support its genetic identity. Ecol Evol 2016; 6:905-22. [PMID: 26843924 PMCID: PMC4729781 DOI: 10.1002/ece3.1836] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 10/07/2015] [Accepted: 10/21/2015] [Indexed: 01/15/2023] Open
Abstract
Red deer populations in the Iberian glacial refugium were the main source for postglacial recolonization and subspecific radiation in north-western Europe. However, the phylogenetic history of Iberian red deer (Cervus elaphus hispanicus) and its relationships with northern European populations remain uncertain. Here, we study DNA sequences at the mitochondrial control region along with STR markers for over 680 specimens from all the main red deer populations in Spain and other west European areas. Our results from mitochondrial and genomic DNA show contrasting patterns, likely related to the nature of these types of DNA markers and their specific processes of change over time. The results, taken together, bring support to two distinct, cryptic maternal lineages for Iberian red deer that predated the last glacial maximum and that have maintained geographically well differentiated until present. Haplotype relationships show that only one of them contributed to the northern postglacial recolonization. However, allele frequencies of nuclear markers evidenced one main differentiation between Iberian and northern European subspecies although also supported the structure of both matrilines within Iberia. Thus, our findings reveal a paraphyletic nature for Iberian red deer but also its genetic identity and differentiation with respect to northern subspecies. Finally, we suggest that maintaining the singularity of Iberian red deer requires preventing not only restocking practices with red deer specimens belonging to other European populations but also translocations between both Iberian lineages.
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Affiliation(s)
- Juan Carranza
- Ungulate Research UnitCátedra de Recursos Cinegéticos y Piscícolas (CRCP)Universidad de Córdoba14071CórdobaSpain
| | - María Salinas
- Ungulate Research UnitCátedra de Recursos Cinegéticos y Piscícolas (CRCP)Universidad de Córdoba14071CórdobaSpain
| | - Damián de Andrés
- Ungulate Research UnitCátedra de Recursos Cinegéticos y Piscícolas (CRCP)Universidad de Córdoba14071CórdobaSpain
- Instituto de AgrobiotecnologíaCSIC‐UPNA‐Gobierno de Navarra31192MutilvaNavarraSpain
| | - Javier Pérez‐González
- Ungulate Research UnitCátedra de Recursos Cinegéticos y Piscícolas (CRCP)Universidad de Córdoba14071CórdobaSpain
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Quinto CA, Tinoco R, Hellberg RS. DNA barcoding reveals mislabeling of game meat species on the U.S. commercial market. Food Control 2016. [DOI: 10.1016/j.foodcont.2015.05.043] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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25
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Yamashiro A, Endo A, Kuwataka H, Matsumoto Y, Yamashiro T. Geographic Origin and Genetic Structure of Introduced Sika Deer, Kerama Deer (Cervus nippon keramae) on Ryukyus Inferred from Mitochondrial DNA Sequences. MAMMAL STUDY 2015. [DOI: 10.3106/041.040.0306] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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26
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Lorenzini R, Garofalo L. Insights into the evolutionary history of Cervus
(Cervidae, tribe Cervini) based on Bayesian analysis of mitochondrial marker sequences, with first indications for a new species. J ZOOL SYST EVOL RES 2015. [DOI: 10.1111/jzs.12104] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rita Lorenzini
- Istituto Zooprofilattico Sperimentale delle Regioni Lazio e Toscana; Centro di Referenza Nazionale per la Medicina Forense Veterinaria; Rieti Italy
| | - Luisa Garofalo
- Istituto Zooprofilattico Sperimentale delle Regioni Lazio e Toscana; Centro di Referenza Nazionale per la Medicina Forense Veterinaria; Rieti Italy
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Species identification and molecular sexing from feces of Kashmir stag (Cervus elaphus hanglu). CONSERV GENET RESOUR 2015. [DOI: 10.1007/s12686-015-0475-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Kumar VP, Sharma LK, Shukla M, Sathyakumar S. Pragmatic perspective on conservation genetics and demographic history of the last surviving population of Kashmir red deer (Cervus elaphus hanglu) in India. PLoS One 2015; 10:e0117069. [PMID: 25671567 PMCID: PMC4324630 DOI: 10.1371/journal.pone.0117069] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 12/18/2014] [Indexed: 11/30/2022] Open
Abstract
The hangul (Cervus elaphus hanglu) is of great conservation concern because it represents the easternmost and only hope for an Asiatic survivor of the red deer species in the Indian subcontinent. Despite the rigorous conservation efforts of the Department of Wildlife Protection in Jammu & Kashmir, the hangul population has experienced a severe decline in numbers and range contraction in the past few decades. The hangul population once abundant in the past has largely become confined to the Dachigam landscape, with a recent population estimate of 218 individuals. We investigated the genetic variability and demographic history of the hangul population and found that it has shown a relatively low diversity estimates when compared to other red deer populations of the world. Neutrality tests, which are used to evaluate demographic effects, did not support population expansion, and the multimodal pattern of mismatch distribution indicated that the hangul population is under demographic equilibrium. Furthermore, the hangul population did not exhibit any signature of bottleneck footprints in the past, and Coalescent Bayesian Skyline plot analysis revealed that the population had not experienced any dramatic changes in the effective population size over the last several thousand years. We observed a strong evidence of sub-structuring in the population, wherein the majority of individuals were assigned to different clusters in Bayesian cluster analysis. Population viability analysis demonstrated insignificant changes in the mean population size, with a positive growth rate projected for the next hundred years. We discuss the phylogenetic status of hangul for the first time among the other red deer subspecies of the world and strongly recommend to upgrade hangul conservation status under IUCN that should be discrete from the other red deer subspecies of the world to draw more conservation attention from national and international bodies.
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Affiliation(s)
- Ved P Kumar
- Wildlife Institute of India, Chandrabani, Dehradun 248 001, Uttarakhand, India
| | - Lalit K Sharma
- Wildlife Institute of India, Chandrabani, Dehradun 248 001, Uttarakhand, India
| | - Malay Shukla
- Gujarat Forensic Sciences University, Gandhinagar 382007, Gujarat, India
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Matsumoto Y, Ju YT, Yamashiro T, Yamashiro A. Evidence of pre-introduction hybridization of Formosan sika deer (Cervus nippon taiouanus) on Okinoshima, Wakayama Prefecture, Japan, based on mitochondrial and nuclear DNA sequences. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0675-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Zhou CL, Turdy R, Halik M. Genetic differentiation between red deer from different sample sites on the Tianshan Mountains (Cervus elaphus), China. MITOCHONDRIAL DNA 2014; 26:101-11. [PMID: 25431826 DOI: 10.3109/19401736.2014.984165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
About 273 individuals were identified from 471 fecal samples from six different red deer populations in China. The genetic structure showed that the red deer from the western and eastern Tianshan Mountains was different. A total number of 12 haplotypes were defined by 97 variable sites by the control region (CR), and 10 haplotypes were defined by 34 variable sites by cytochrome b. There was no haplotype sharing between red deer populations from western and eastern Tianshan Mountains by the CR and the cytochrome b. The red deer populations from west were clade with wapiti from North American and red deer from Siberia, while red deer populations from east were clade with red deer from Crimea in Pleistocene rather than west at present. The result of NETWORK also showed that red deer populations from western and eastern Tianshan Mountains were different. The haplotype and the Fst value between western and eastern Tianshan red deer were significantly different. The AMOVA analysis showed that 97.34% and 1.14% of the total genetic variability were found within populations and among populations within groups, respectively, by microsatellite. AMOVA for mitochondria showed that most of the variance was explained among-group. The Fst, pairwise distance, and phylogenetic relationship result showed that red deer between western and eastern Tianshan were more different than some of the red deer from North-Asia, South-Asia, East-Asia, and wapiti. All data from this study do support that the genetic characteristics of red deer between western and eastern Tianshan Mountains by microsatellite, control region, and cytochrome b were different.
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Affiliation(s)
- Can-Lin Zhou
- Wildlife Resource Conservation Department, College of Life Science and Technology, Xinjiang University , Urumqi , China and
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Speller C, Kooyman B, Rodrigues A, Langemann E, Jobin R, Yang D. Assessing prehistoric genetic structure and diversity of North American elk ( Cervus elaphus) populations in Alberta, Canada. CAN J ZOOL 2014. [DOI: 10.1139/cjz-2013-0253] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
North American elk (Cervus elaphus L., 1758) are an important component of Canada’s natural ecosystems. Overhunting and habitat decline in the 19th century led to the near eradication of Rocky Mountain elk (Cervus elaphus nelsoni Bailey, 1935) and Manitoban elk (Cervus elaphus manitobensis Millais, 1915) within Alberta. Though elk populations have been restored within provincial and national parks, it is unknown to what degree historic population declines affected overall genetic diversity and population structuring of the two subspecies. This study targeted 551 bp of mitochondrial D-loop DNA from 50 elk remains recovered from 16 archaeological sites (2260 BCE (before common era) to 1920 CE (common era)) to examine the former genetic diversity and population structure of Alberta’s historic elk populations. Comparisons of ancient and modern haplotype and nucleotide diversity suggest that historic population declines reduced the mitochondrial diversity of Manitoban elk, while translocation of animals from Yellowstone National Park in the early 20th century served to maintain the diversity of Rocky Mountain populations. Gene flow between the two subspecies was significantly higher in the past than today, suggesting that the two subspecies previously formed a continuous population. These data on precontact genetic diversity and gene flow in Alberta elk provide essential baseline data integral for elk management and conservation in the province.
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Affiliation(s)
- C.F. Speller
- Department of Archaeology, University of Calgary, Calgary, AB T2N 1N4, Canada
- Ancient DNA Laboratory, Department of Archaeology, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - B. Kooyman
- Department of Archaeology, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - A.T. Rodrigues
- Ancient DNA Laboratory, Department of Archaeology, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - E.G. Langemann
- Cultural Resource Services, Western and Northern Service Centre, Parks Canada, Calgary, AB T2P 3M3, Canada
| | - R.M. Jobin
- Special Investigations and Forensic Services Section, Fish and Wildlife Enforcement Branch, Justice and Solicitor General, Government of Alberta, 7th Floor, OS Longman Building, 6909-116 Street, Edmonton, AB T6H 4P2, Canada
| | - D.Y. Yang
- Ancient DNA Laboratory, Department of Archaeology, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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Ba H, Wu L, Liu Z, Li C. An examination of the origin and evolution of additional tandem repeats in the mitochondrial DNA control region of Japanese sika deer (Cervus Nippon). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:276-81. [PMID: 24621225 DOI: 10.3109/19401736.2014.892077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Tandem repeat units are only detected in the left domain of the mitochondrial DNA control region in sika deer. Previous studies showed that Japanese sika deer have more tandem repeat units than its cousins from the Asian continent and Taiwan, which often have only three repeat units. To determine the origin and evolution of these additional repeat units in Japanese sika deer, we obtained the sequence of repeat units from an expanded dataset of the control region from all sika deer lineages. The functional constraint is inferred to act on the first repeat unit because this repeat has the least sequence divergence in comparison to the other units. Based on slipped-strand mispairing mechanisms, the illegitimate elongation model could account for the addition or deletion of these additional repeat units in the Japanese sika deer population. We also report that these additional repeat units could be occurring in the internal positions of tandem repeat regions, possibly via coupling with a homogenization mechanism within and among these lineages. Moreover, the increased number of repeat units in the Japanese sika deer population could reflect a balance between mutation and selection, as well as genetic drift.
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Affiliation(s)
- Hengxing Ba
- a Institute of Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences , Jilin , People's Republic of China .,b State Key Laboratory for Molecular Biology of Special Economical Animals , Chinese Academy of Agricultural Sciences , Jilin , People's Republic of China , and
| | - Lang Wu
- c Center for Clinical and Translational Science, Mayo Clinic , Rochester , MN , USA
| | - Zongyue Liu
- a Institute of Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences , Jilin , People's Republic of China .,b State Key Laboratory for Molecular Biology of Special Economical Animals , Chinese Academy of Agricultural Sciences , Jilin , People's Republic of China , and
| | - Chunyi Li
- a Institute of Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences , Jilin , People's Republic of China .,b State Key Laboratory for Molecular Biology of Special Economical Animals , Chinese Academy of Agricultural Sciences , Jilin , People's Republic of China , and
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Schellhorn R, Pfretzschner HU. Biometric study of ruminant carpal bones and implications for phylogenetic relationships. ZOOMORPHOLOGY 2013. [DOI: 10.1007/s00435-013-0209-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Ba H, Yang F, Xing X, Li C. Classification and phylogeny of sika deer (Cervus nippon) subspecies based on the mitochondrial control region DNA sequence using an extended sample set. ACTA ACUST UNITED AC 2013; 26:373-9. [DOI: 10.3109/19401736.2013.836509] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Meiri M, Lister AM, Higham TFG, Stewart JR, Straus LG, Obermaier H, González Morales MR, Marín-Arroyo AB, Barnes I. Late-glacial recolonization and phylogeography of European red deer (Cervus elaphusL.). Mol Ecol 2013; 22:4711-22. [DOI: 10.1111/mec.12420] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 06/09/2013] [Accepted: 06/11/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Meirav Meiri
- Department of Zoology; Institute of Archaeology; Tel Aviv University; Tel Aviv 69978 Israel
| | - Adrian M. Lister
- Department of Earth Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
| | - Thomas F. G. Higham
- Research Lab for Archaeology and the History of Art; University of Oxford; Oxford OX1 3QY UK
| | - John R. Stewart
- School of Applied Sciences; Bournemouth University; Poole Dorset BH12 5BB UK
| | - Lawrence G. Straus
- Department of Anthropology; University of New Mexico; Albuquerque NM 87131-0001 USA
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria; Universidad de Cantabria; Santander 39005 Spain
| | - Henriette Obermaier
- Bavarian State Collection for Anthropology and Palaeoanatomy Munich; Munich 80539 Germany
| | - Manuel R. González Morales
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria; Universidad de Cantabria; Santander 39005 Spain
| | - Ana B. Marín-Arroyo
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria; Universidad de Cantabria; Santander 39005 Spain
| | - Ian Barnes
- School of Biological Sciences; Royal Holloway; University of London; Egham Surrey TW20 0EX UK
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Skibiel AL, Downing LM, Orr TJ, Hood WR. The evolution of the nutrient composition of mammalian milks. J Anim Ecol 2013; 82:1254-64. [PMID: 23895187 DOI: 10.1111/1365-2656.12095] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 04/12/2013] [Indexed: 11/29/2022]
Abstract
1. In mammals, nutrient allocation during lactation is a critical component of maternal care as milk intake promotes juvenile growth and survival, and hence maternal and offspring fitness. 2. Milk composition varies widely across mammals and is hypothesized to have arisen via selection pressures associated with environment, diet and life history. These hypotheses have been proposed based on observations and/or cross-species comparisons that did not standardize for stage of lactation and did not consider evolutionary history of the species in analyses. 3. We conducted the largest comparative analysis of milk composition to date accounting for phylogenetic relationships among species in order to understand the selective advantage of producing milk with specific nutritional profiles. We examined four milk constituents in association with species ecology while incorporating phylogeny in analyses. 4. Phylogenetic signal was apparent for all milk constituents examined. After controlling for phylogeny, diet and relative lactation length explained the greatest amount of variation in milk composition. Several aspects of species' ecologies, including adaptation to arid environments, reproductive output and maternal body mass were not associated with milk composition after accounting for phylogeny. 5. Our results suggest that milk composition is largely a function of evolutionary history, maternal nutrient intake and duration of milk production. Arriving at these conclusions was made possible by including the evolutionary relationships among species.
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Affiliation(s)
- Amy L Skibiel
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
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Krojerová-Prokesová J, Baranceková M, Voloshina I, Myslenkov A, Lamka J, Koubek P. Dybowski's sika deer (Cervus nippon hortulorum): genetic divergence between natural primorian and introduced Czech populations. ACTA ACUST UNITED AC 2013; 104:312-26. [PMID: 23454911 DOI: 10.1093/jhered/est006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Dybowski's sika deer (Cervus nippon hortulorum) originally inhabited the majority of the Primorsky Krai in Far Eastern Russia, north-eastern China, and Korean Peninsula. At present, only the Russian population seems to be stable, even though this taxon is still classified as endangered by the Russian Federation. Almost 100 years ago, this subspecies, among others, was imported to several European countries including the Czech Republic. We used both mitochondrial (mtDNA; the cytochrome b gene and the control region) and nuclear DNA markers to examine the actual taxonomic status of modern Czech Dybowski's sika population and to compare the genetic diversity between the introduced and the native populations. Altogether, 124 Czech samples and 109 Primorian samples were used in the analyses. Within the samples obtained from individuals that were all morphologically classified as Dybowski's sika, we detected mtDNA haplotypes of Dybowski's sika (84 samples), as well as those belonging to other sika subspecies: northern Japanese sika (25 samples), southern Japanese sika (6 samples), and south-eastern Chinese sika (8 samples). Microsatellite analysis revealed a certain level of heterozygote deficiency and a high level of inbreeding in both populations. The high number of private alleles, factorial correspondence analysis, and Bayesian clustering analysis indicate a high level of divergence between both populations. The large degree of differentiation and the high number of population-specific alleles could be a result of a founder effect, could be a result of a previously suggested bottleneck within the Primorian population, and could also be affected by the crossbreeding of captive individuals with other sika subspecies.
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Affiliation(s)
- Jarmila Krojerová-Prokesová
- Institute of Vertebrate Biology Academy of Sciences of the Czech Republic, v.v.i., Květná 8, Brno, Czech Republic
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Biedrzycka A, Solarz W, Okarma H. Hybridization between native and introduced species of deer in Eastern Europe. J Mammal 2012. [DOI: 10.1644/11-mamm-a-022.1] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Vidal F, Smith-Flueck JAM, Flueck WT, Bartoš L. Variation in reproduction of a temperate deer, the southern pudu (Pudu puda). ANIMAL PRODUCTION SCIENCE 2012. [DOI: 10.1071/an11364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Pudu (Pudu puda), occurring in the southern cone of Latin America, has been classified as vulnerable by the International Union for Conservation of Nature (IUCN), yet little is known about this animal in the wild, with most knowledge on the breeding behaviour coming from captive animals. For this second-smallest deer in the world, delayed implantation has been suggested to explain the two peaks in the annual cycle of male sexual hormones on the basis of the accepted tenet that the breeding period occurs only once a year, between March and June. However, in the present study, birth dates from fawns born at the Los Canelos semi-captive breeding centre in Chile and male courting behaviour revealed the possibility of two rutting periods: autumn and spring. To our knowledge, this is the first time that late-fall births (May through early June for 17% of fawns in the study population) have been recorded for the southern pudu; two of these four births were conceived by females in the wild. From zoo and captive-animal birth records (n = 97), only three fawns were born in the fall. For all births combined (n = 121), 77% occurred in spring. The roe deer (Capreolus capreolus) and Pere David deer (Elaphurus davidianus) have been considered the only two temperate cervids in which sexual activity is initiated by increasing daylength and which breed in early summer. Yet, the present results indicate a similar response from the southern pudu when under a wild or semi-captive environment, with breeding taking place in spring. These results suggest that this species may either have two reproductive periods per year or retains the capacity to be a breeder for a much more extended period of time than documented by earlier studies. Pudu, like other temperate deer, is responsive to photoperiod for timing its breeding period, but may further optimise its production of offspring by also responding to other environmental cues such as seasonal variation in food supply when climatic conditions are favourable.
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Jia B, Li RY, Zhao ZS, Yan GQ, Xi JF, Blair HT, Li DQ, Zhang JX, Zhao XT. Analysis of genetic diversity and phylogenetic relationship of red deer subspecies in XinJiang, China. Anim Sci J 2011; 82:517-22. [PMID: 21794008 DOI: 10.1111/j.1740-0929.2011.00885.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Polymorphisms for seven microsatellite loci in three red deer subspecies (9 populations) found in XinJiang were detected by polymerase chain reaction (PCR), 12% nondenaturation polyacrylamide gel electrophoresis and the Sanguinetti silver staining method. Numbers of alleles, average effective numbers of alleles (E) and the average rate of homozygosity, allelic frequencies of seven microsatellite loci, polymorphism information content (PIC), mean heterozygosity (H) and genetic distances among the populations were calculated for each population. Dendrograms were constructed based on genetic distances by the neighbor-joining method (NJ), utilizing molecular evolutionary genetics analysis software PHYLIP (3.6). The phylogenetic tree was constructed based on allelic frequencies using maximum likelihood (ML); the bootstrap value was estimated by bootstrap test in the tree. Lastly, phylogenesis was analyzed. The results showed that four of the seven microsatellite loci were highly polymorphic, but BMS2508 and Celjp0023 showed no polymorphism and BM5004 was a neutral polymorphism. It is our conclusion that the four microsatellite loci are effective DNA markers for the analysis of genetic diversity and phylogenetic relationships among the three red deer subspecies. The mean PIC, H and E-values across the microsatellite loci were 0.5393, 0.5736 and 2.64, which showed that these microsatellite loci are effective DNA markers for the genetic analysis of red deer. C.e. songaricus populations from Regiment 104, 151 and Hami are clustered together. C.e. yarkandensis populations from Regiment 35, Xaya and Alaer are clustered together. These two clusters also cluster together. Lastly, C.e. sibiricus populations from Burqin, Regiment 188 and the first two clusters were clustered together. The phylogenetic relationship among different red deer populations is consistent with the known origin, history of breeding and geographic distributions of populations.
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Affiliation(s)
- Bin Jia
- Animal Science and Technology College, Shihezi University, ShiHeZi, XinJiang, China
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Wada K, Okumura K, Nishibori M, Kikkawa Y, Yokohama M. The complete mitochondrial genome of the domestic red deer (Cervus elaphus) of New Zealand and its phylogenic position within the family Cervidae. Anim Sci J 2010; 81:551-7. [PMID: 20887306 DOI: 10.1111/j.1740-0929.2010.00799.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We determined the complete nucleotide sequence of the mitochondrial genome of the semidomestic red deer (Cervus elaphus) of New Zealand. The genome was 16,357 bp long and contained 13 protein-coding genes, 12SrRNA, 16SrRNA, 22 tRNAs and a D-loop as found in other mammals. Database homology searches showed that the mitochondrial DNA (mtDNA) sequence from the New Zealand semidomestic deer was similar to partial mtDNA sequences from the European, Norwegian (C. e. atlanticus) and Spanish red deer (C. e. hispanicus). Phylogenetic analysis of the mitochondrial protein-coding regions revealed two well-defined monophyletic clades in subfamilies Cervinae and Muntiacinae. However, red deer and Sika deer were not found to be close relatives. The analysis did identify the red deer as a sister taxon of a Samber/Sika deer clade, although it was more closely related to the Samber than the Sika group.
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Affiliation(s)
- Kenta Wada
- Faculty of Bioindustry, Department of Bioproduction Graduate School of Bioindustry, Tokyo University of Agriculture, Abashiri, Japan
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Nilsson MA. The structure of the Australian and South American marsupial mitochondrial control region. ACTA ACUST UNITED AC 2010; 20:126-38. [PMID: 19900062 DOI: 10.3109/19401730903180112] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND AND AIMS The mitochondrial control region (CR) was studied across five marsupialian orders, in order to give a detailed overview of its features. RESULTS The CR is organised into three domains similar to the CR of placental mammals. However, the conservation of different features among the marsupial orders is in general more strict. In the first domain, two conserved blocks extended termination-associated sequences (ETAS 1 and ETAS 2) are present in all marsupial orders. In the third domain, the three conserved sequence blocks (CSB 1, CSB 2 and CSB 3) are present and complete, with CSB 1 being duplicated in four of five marsupial orders. CONCLUSIONS The nucleotide frequency and secondary structures of the repeats were typical for marsupial species. The repeats are generally AT-rich except in Dasyuridae and Paucituberculata, which show a significant increase in GC content.
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Affiliation(s)
- Maria A Nilsson
- Institute for Experimental Pathology/ZMBE, University of Münster, Münster, Germany.
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47
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SENN HELENV, PEMBERTON JOSEPHINEM. Variable extent of hybridization between invasive sika (Cervus nippon) and native red deer (C. elaphus) in a small geographical area. Mol Ecol 2009; 18:862-76. [DOI: 10.1111/j.1365-294x.2008.04051.x] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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NIELSEN ELSEMARIEKRAGH, OLESEN CARSTENRIIS, PERTOLDI CINO, GRAVLUND PETER, BARKER JAMESSF, MUCCI NADIA, RANDI ETTORE, LOESCHCKE VOLKER. Genetic structure of the Danish red deer (Cervus elaphus). Biol J Linn Soc Lond 2008. [DOI: 10.1111/j.1095-8312.2008.01115.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Pérez-Espona S, Pérez-Barbería FJ, Goodall-Copestake WP, Jiggins CD, Gordon IJ, Pemberton JM. Genetic diversity and population structure of Scottish Highland red deer (Cervus elaphus) populations: a mitochondrial survey. Heredity (Edinb) 2008; 102:199-210. [PMID: 19002206 DOI: 10.1038/hdy.2008.111] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The largest population of red deer (Cervus elaphus) in Europe is found in Scotland. However, human impacts through hunting and introduction of foreign deer stock have disturbed the population's genetics to an unknown extent. In this study, we analysed mitochondrial control region sequences of 625 individuals to assess signatures of human and natural historical influence on the genetic diversity and population structure of red deer in the Scottish Highlands. Genetic diversity was high with 74 haplotypes found in our study area (115 x 87 km). Phylogenetic analyses revealed that none of the individuals had introgressed mtDNA from foreign species or subspecies of deer and only suggested a very few localized red deer translocations among British localities. A haplotype network and population analyses indicated significant genetic structure (Phi(ST)=0.3452, F(ST)=0.2478), largely concordant with the geographical location of the populations. Mismatch distribution analysis and neutrality tests indicated a significant population expansion for one of the main haplogroups found in the study area, approximately dated c. 8200 or 16 400 years ago when applying a fast or slow mutation rate, respectively. Contrary to general belief, our results strongly suggest that native Scottish red deer mtDNA haplotypes have persisted in the Scottish Highlands and that the population retains a largely natural haplotype diversity and structure in our study area.
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Affiliation(s)
- S Pérez-Espona
- Institute of Evolutionary Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK.
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Bar-David S, Saltz D, Dayan T, Shkedy Y. Using spatially expanding populations as a tool for evaluating landscape planning: The reintroduced Persian fallow deer as a case study. J Nat Conserv 2008. [DOI: 10.1016/j.jnc.2008.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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