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Javier MCF, Noblezada AC, Sienes PMQ, Guino-o RS, Palomar-Abesamis N, Malay MCD, del Castillo CS, Ferriols VMEN. Draft genome of the endangered visayan spotted deer ( Rusa alfredi), a Philippine endemic species. GIGABYTE 2025; 2025:gigabyte150. [PMID: 40041424 PMCID: PMC11876970 DOI: 10.46471/gigabyte.150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2024] [Accepted: 02/18/2025] [Indexed: 03/06/2025] Open
Abstract
The Visayan Spotted Deer (VSD), or Rusa alfredi, is an endangered and endemic species in the Philippines. Despite its status, genomic information on R. alfredi, and the genus Rusa in general, is missing. This study presents the first draft genome assembly of the VSD using the Illumina short-read sequencing technology. The resulting RusAlf_1.1 assembly has a 2.52 Gb total length, with a contig N50 of 46 Kb and scaffold N50 size of 75 Mb. The assembly has a BUSCO complete score of 95.5%, demonstrating the genome's completeness, and includes the annotation of 24,531 genes. Our phylogenetic analysis based on single-copy orthologs revealed a close evolutionary relationship between R. alfredi and the genus Cervus. RusAlf_1.1 represents a significant advancement in our understanding of the VSD. It opens opportunities for further research in population genetics and evolutionary biology, potentially contributing to more effective conservation and management strategies for this endangered species.
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Affiliation(s)
- Ma. Carmel F. Javier
- Philippine Genome Center Visayas, University of the Philippines Visayas, Miagao Iloilo, Philippines
| | - Albert C. Noblezada
- Philippine Genome Center Visayas, University of the Philippines Visayas, Miagao Iloilo, Philippines
| | | | - Robert S. Guino-o
- Angelo King Center for Research and Environmental Management, Silliman University, Dumaguete, Philippines
| | | | - Maria Celia D. Malay
- Marine Science Institute, University of the Philippines Diliman, Quezon City, Philippines
| | - Carmelo S. del Castillo
- Institute of Aquaculture, College of Fisheries and Ocean Sciences, University of the Philippines Visayas, Miagao Iloilo, Philippines
- National Institute of Molecular Biology and Biotechnology, University of the Philippines Visayas, Miagao Iloilo, Philippines
| | - Victor Marco Emmanuel N. Ferriols
- Philippine Genome Center Visayas, University of the Philippines Visayas, Miagao Iloilo, Philippines
- Institute of Aquaculture, College of Fisheries and Ocean Sciences, University of the Philippines Visayas, Miagao Iloilo, Philippines
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Reid N, Hughes MF, Hynes RA, Montgomery WI, Prodöhl PA. Bidirectional hybridisation and introgression between introduced European brown hare, Lepus europaeus and the endemic Irish hare, L. timidus hibernicus. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01471-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AbstractIntroduced non-native species can threaten native species through interspecific hybridisation and genetic introgression. We assessed the prevalence of hybridisation and introgression between introduced European brown hare, Lepus europaeus, and the endemic Irish hare, L. timidus hibernicus. Roadkill hares (n = 56) were sequenced for a 379bp section of the mitochondrial DNA D-loop and a 474bp segment of the nuclear transferrin (Tf) gene. A species-specific indel in the transferrin gene was present in L.t. hibernicus and absent in L. europaeus. Excluding three hares from which molecular data could not be recovered, 28 hares (53%) were native L.t. hibernicus, 7 (13%) were non-native L. europaeus and 18 (34%) were hybrids; of which 5 (28%) were first generation (F1) involving bidirectional crosses with mismatched nuclear and mtDNA (3 ♂ europaeus x ♀ hibernicus and 2 ♂ hibernicus x ♀ europaeus). Mixed nuclear transferrin sequences suggested 13 (72%) of hybrids were at least 2nd generation (F2) with 9 (69%) possessing L.t. hibernicus and 4 (31%) L. europaeus mtDNA (the latter indicative of hybrid backcrossing with the non-native). The prevalence of hybridisation at similar mountain-brown hare contact zones throughout Europe is notably lower (4–16%) and typically unidirectional (♂ europaeus x ♀ timidus). A high prevalence of bidirectional hybridisation and introgression (in association with projected climate change) may favour the introduced species over the native. Genetic surveillance and population monitoring are needed to further explore the potential conservation implications of European brown hare in Ireland.
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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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McKiernan F, Flattery A, Browne J, Gray J, Zaid T, O’Connor J, Zintl A. The Prevalence and Genetic Diversity of Babesia divergens in Ixodes ricinus Nymphs Collected from Farm- and Woodland Sites in Ireland. Pathogens 2022; 11:pathogens11030312. [PMID: 35335636 PMCID: PMC8951431 DOI: 10.3390/pathogens11030312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/15/2022] [Accepted: 03/01/2022] [Indexed: 12/04/2022] Open
Abstract
The parasite, Babesia divergens causes redwater fever in cattle and a rare, albeit life-threatening disease in humans. In Ireland, B. divergens has always been considered an important pathogen as the high incidence of redwater fever precluded areas of the country from cattle farming. Moreover a relatively large proportion of human cases were reported here. Red deer (Cervus elaphus), which often harbour babesias that are genetically very similar (if not identical) to B. divergens, are quite widespread. In this study 1369 nymphal Ixodes ricinus ticks collected from various habitats were screened for the presence of B. divergens using TaqMan followed by conventional nested PCR. Fragments of the 18S rRNA gene locus (560 bp) were compared against published Irish B. divergens isolates from cattle, humans and red deer. Overall just 1% of I. ricinus nymphs were infected with B. divergens, with similar infection rates in ticks collected from farm- and woodland. Most (90%) 18S rRNA gene fragments derived from woodland ticks were 100% identical to published sequences from cattle and humans. One differed by a single nucleotide polymorphism (SNP) as did two isolates from ticks collected in bogland. Two isolates derived from nymphs collected in farmland differed by 2 and 4 SNPs respectively.
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Affiliation(s)
- Fiona McKiernan
- UCD Veterinary Sciences Centre, University College Dublin, D04 V1W8 Dublin, Ireland; (F.M.); (A.F.); (T.Z.)
| | - Amie Flattery
- UCD Veterinary Sciences Centre, University College Dublin, D04 V1W8 Dublin, Ireland; (F.M.); (A.F.); (T.Z.)
| | - John Browne
- UCD School of Agriculture and Food Science, University College Dublin, D04 V1W8 Dublin, Ireland;
| | - Jeremy Gray
- UCD School of Biology and Environmental Science, University College Dublin, D04 V1W8 Dublin, Ireland;
| | - Taher Zaid
- UCD Veterinary Sciences Centre, University College Dublin, D04 V1W8 Dublin, Ireland; (F.M.); (A.F.); (T.Z.)
| | - Jack O’Connor
- MSD Ireland, South County Business Park, D18 X5R3 Dublin, Ireland;
| | - Annetta Zintl
- UCD Veterinary Sciences Centre, University College Dublin, D04 V1W8 Dublin, Ireland; (F.M.); (A.F.); (T.Z.)
- Correspondence: ; Tel.: +353-1-7166121
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Zenke P, Zorkóczy OK, Lehotzky P, Ózsvári L, Pádár Z. Molecular Sexing and Species Detection of Antlered European Hunting Game for Forensic Purposes. Animals (Basel) 2022; 12:ani12030246. [PMID: 35158570 PMCID: PMC8833381 DOI: 10.3390/ani12030246] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 11/25/2022] Open
Abstract
Simple Summary The reasons behind illegal hunting can be widely different. There are also tricky methods that hunters use in the attempt to legalize their illegally-acquired trophies, specifically, introducing them in later seasons, and registering the eviscerated corpses as hinds. During certain periods of the year, hunters are only able to acquire a license for the shooting of female deer exclusively, with the male-hunting season beginning later. The eviscerated and decapitated carcass of the animal delivered to the wild game processing house cold store can be falsely registered as a female based on phenotype. If the hunting association suspects that the animal’s sex has been falsely reported, a forensic genetic investigation can be proposed. In other criminal events, there are no carcasses at all. When several biological remains left on the crime scene need to be tested, a fast and cost-effective detection of a given species or species-group might be substantial before subsequent analysis. Therefore, sex and species detection can provide an early-stage credibility to the resolution of illegal activities related to trophy animals, and additionally may disclose potential poaching disputes. Abstract Molecular sexing techniques are widely applied in conservation biology, although the range of forensically validated methods is fairly limited. The primary aim of this work was to develop forensically validated assays, using two PCR panels for sex and species assignment for the abundant antlered European game species: red deer (Cervus elaphus), roe deer (Capreolus capreolus) and fallow deer (Dama dama). Segments of the SRY and Amelogenin X/Y genes for sex determination, additionally species-specific cytochrome b regions for species detection were targeted and separately amplified in two multiplex reactions. These assays can reliably analyze trace amounts of DNA. The results of both can easily be visualized and interpreted practically, either on agarose gel or by capillary electrophoresis. These simple, fast molecular assays are able to affect the early-stage resolution of disputed or unsolved poaching cases, without the need of individualization or sequencing of forensic samples.
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Affiliation(s)
- Petra Zenke
- Department of Animal Breeding and Genetics, University of Veterinary Medicine Budapest, István u. 2., H-1078 Budapest, Hungary;
- Correspondence:
| | - Orsolya Krisztina Zorkóczy
- Department of Animal Breeding and Genetics, University of Veterinary Medicine Budapest, István u. 2., H-1078 Budapest, Hungary;
| | - Pál Lehotzky
- Hungarian Hunters’ National Chamber, Medve u. 34-40., H-1027 Budapest, Hungary;
| | - László Ózsvári
- Department of Veterinary Forensics and Economics, University of Veterinary Medicine Budapest, István u. 2., H-1078 Budapest, Hungary;
| | - Zsolt Pádár
- Department of Forensic Medicine, Medical School, University of Pécs, Szigeti út 12., H-7624 Pecs, Hungary;
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Fan H, Wang T, Li Y, Liu H, Dong Y, Zhang R, Wang H, Shang L, Xing X. Development and validation of a 1 K sika deer (Cervus nippon) SNP Chip. BMC Genom Data 2021; 22:35. [PMID: 34535071 PMCID: PMC8447661 DOI: 10.1186/s12863-021-00994-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 09/09/2021] [Indexed: 11/10/2022] Open
Abstract
Background China is the birthplace of the deer family and the country with the most abundant deer resources. However, at present, China’s deer industry faces the problem that pure sika deer and hybrid deer cannot be easily distinguished. Therefore, the development of a SNP identification chip is urgently required. Results In this study, 250 sika deer, 206 red deer, 23 first-generation hybrid deer (F1), 20 s-generation hybrid deer (F2), and 20 third-generation hybrid deer (F3) were resequenced. Using the chromosome-level sika deer genome as the reference sequence, mutation detection was performed on all individuals, and a total of 130,306,923 SNP loci were generated. After quality control filtering was performed, the remaining 31,140,900 loci were confirmed. From molecular-level and morphological analyses, the sika deer reference population and the red deer reference population were established. The Fst values of all SNPs in the two reference populations were calculated. According to customized algorithms and strict screening principles, 1000 red deer-specific SNP sites were finally selected for chip design, and 63 hybrid individuals were determined to contain red deer-specific SNP loci. The results showed that the gene content of red deer gradually decreased in subsequent hybrid generations, and this decrease roughly conformed to the law of statistical genetics. Reaction probes were designed according to the screening sites. All candidate sites met the requirements of the Illumina chip scoring system. The average score was 0.99, and the MAF was in the range of 0.3277 to 0.3621. Furthermore, 266 deer (125 sika deer, 39 red deer, 56 F1, 29 F2,17 F3) were randomly selected for 1 K SNP chip verification. The results showed that among the 1000 SNP sites, 995 probes were synthesized, 4 of which could not be typed, while 973 loci were polymorphic. PCA, random forest and ADMIXTURE results showed that the 1 K sika deer SNP chip was able to clearly distinguish sika deer, red deer, and hybrid deer and that this 1 K SNP chip technology may provide technical support for the protection and utilization of pure sika deer species resources. Conclusion We successfully developed a low-density identification chip that can quickly and accurately distinguish sika deer from their hybrid offspring, thereby providing technical support for the protection and utilization of pure sika deer germplasm resources. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-00994-z.
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Affiliation(s)
- Huanhuan Fan
- Key Laboratory of Molecular Biology of Special Economic Animals, Institute of Special Products, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Tianjiao Wang
- Key Laboratory of Molecular Biology of Special Economic Animals, Institute of Special Products, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Yang Li
- Key Laboratory of Molecular Biology of Special Economic Animals, Institute of Special Products, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Huitao Liu
- Key Laboratory of Molecular Biology of Special Economic Animals, Institute of Special Products, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Yimeng Dong
- Key Laboratory of Molecular Biology of Special Economic Animals, Institute of Special Products, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Ranran Zhang
- Key Laboratory of Molecular Biology of Special Economic Animals, Institute of Special Products, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Hongliang Wang
- Key Laboratory of Molecular Biology of Special Economic Animals, Institute of Special Products, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Liyuan Shang
- Jilin Animal Husbandry and Veterinary Research Institute Changchun, Changchun, 130112, China
| | - Xiumei Xing
- Key Laboratory of Molecular Biology of Special Economic Animals, Institute of Special Products, Chinese Academy of Agricultural Sciences, Changchun, 130112, China.
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Howard-McCombe J, Ward D, Kitchener AC, Lawson D, Senn HV, Beaumont M. On the use of genome-wide data to model and date the time of anthropogenic hybridisation: An example from the Scottish wildcat. Mol Ecol 2021; 30:3688-3702. [PMID: 34042240 DOI: 10.1111/mec.16000] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 11/28/2022]
Abstract
While hybridisation has long been recognised as an important natural phenomenon in evolution, the conservation of taxa subject to introgressive hybridisation from domesticated forms is a subject of intense debate. Hybridisation of Scottish wildcats and domestic cats is a good example in this regard. Here, we developed a modelling framework to determine the timescale of introgression using approximate Bayesian computation (ABC). Applying the model to ddRAD-seq data from 129 individuals, genotyped at 6546 loci, we show that a population of wildcats genetically distant from domestic cats is still present in Scotland. These individuals were found almost exclusively within the captive breeding programme. Most wild-living cats sampled were introgressed to some extent. The demographic model predicts high levels of gene-flow between domestic cats and Scottish wildcats (13% migrants per generation) over a short timeframe, the posterior mean for the onset of hybridisation (T1 ) was 3.3 generations (~10 years) before present. Although the model had limited power to detect signals of ancient admixture, we found evidence that significant recent hybridisation may have occurred subsequent to the founding of the captive breeding population (T2 ). The model consistently predicts T1 after T2 , estimated here to be 19.3 generations (~60 years) ago, highlighting the importance of this population as a resource for conservation management. Additionally, we evaluate the effectiveness of current methods to classify hybrids. We show that an optimised 35 SNP panel is a better predictor of the ddRAD-based hybrid score in comparison with a morphological method.
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Affiliation(s)
| | - Daniel Ward
- School of Mathematics, University of Bristol, Bristol, UK
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh, UK
| | - Daniel Lawson
- School of Mathematics, University of Bristol, Bristol, UK
| | - Helen V Senn
- RZSS WildGenes Laboratory, Royal Zoological Society of Scotland, Edinburgh, UK
| | - Mark Beaumont
- School of Biological Sciences, University of Bristol, Bristol, UK
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A Microsatellite Genotyping-Based Genetic Study of Interspecific Hybridization between the Red and Sika Deer in the Western Czech Republic. Animals (Basel) 2021; 11:ani11061701. [PMID: 34200330 PMCID: PMC8229882 DOI: 10.3390/ani11061701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 12/29/2022] Open
Abstract
Simple Summary The sika deer is a very flexible invasive species, capable of living dynamically in both large forests and mixed environment characterized by a prevalence of agricultural land. The Japanese sika deer was introduced to the Czech Republic at the end of the 19th century. The success of an introduced alien species may consist in their hybridizing with closely related taxa. Where few barriers to gene flow exist, rapid introgression of genetic traits from one species into another frequently occurs. The current Czech sika populations embody the most abundant and expanding group in continental Europe. In western Bohemia, we confirmed the interspecific hybridization with the native red deer. In this context, the red deer gene pool is endangered. The animals proliferate steadily in all directions and will most probably spread all over the Czech Republic if no major, timely changes in game management are adopted. Abstract Although inter-species hybrids between the red and sika deer can be phenotypically determined only exceptionally, there is the eventuality of identification via molecular genetic analysis. We used bi-parentally inherited microsatellite markers and a Bayesian statistical framework to re-examine the proportion of hybrids in the Czech red and sika deer populations. In total, 123 samples were collected, and the nuclear dataset consisted of 2668 allelic values. The number of alleles per locus ranged from 10 (BM1818) to 22 (BM888 and T193), yielding the mean of 16 alleles per locus across the deer. The mean allelic diversity of the red deer markedly exceeded that of the Japanese sika deer. Interspecific hybrids were detected, enabling us to confirm the genetic introgression of the sika deer into the red deer populations and vice versa in western Bohemia. The mean hybrid score equaled 10.6%, with 14.3% of the hybrids being among red deer–like individuals and 6.7% among sika-like ones. At two western Bohemian locations, namely, Doupovské hory and Slavkovský les, the total percentages of hybrid animals equaled 18.8 and 8.9, respectively. No red deer alleles were detected in the sika populations of the subregions of Kladská, Žlutice, and Lány. The NeighborNet network clearly separated the seven red and sika deer sampling populations according to the geography. The knowledge gained from the evaluated data is applicable in hunting management to reduce hybridization with the European deer.
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McFarlane SE, Senn HV, Smith SL, Pemberton JM. Locus-specific introgression in young hybrid swarms: Drift may dominate selection. Mol Ecol 2021; 30:2104-2115. [PMID: 33638185 DOI: 10.1111/mec.15862] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 02/01/2021] [Accepted: 02/17/2021] [Indexed: 12/17/2022]
Abstract
Closely related species that have previously inhabited geographically separated ranges are hybridizing at an increasing rate due to human disruptions. These human-mediated hybrid zones can be used to study reproductive isolation between species at secondary contact, including examining locus-specific rates of introgression. Introgression is expected to be heterogenous across the genome, reflecting variation in selection. Those loci that introgress especially slowly are good candidates for being involved in reproductive isolation, while those loci that introgress quickly may be involved in adaptive introgression. In the context of conservation, policy makers are especially concerned about introduced alleles moving quickly into the background of a native or endemic species, as these alleles could replace the native alleles in the population, leading to extinction via hybridization. We applied genomic cline analyses to 44,997 SNPs to identify loci introgressing more or less when compared to the genome wide expectation in a human-mediated hybridizing population of red deer and sika in Kintyre Scotland. We found 11.4% of SNPs had cline centres that were significantly different from the genome wide expectation, and 17.6% of all SNPs had excess rates of introgression. Based on simulations, we believe that many of these markers have diverged from the genome-wide average due to drift, rather than because of selection, and we suggest that these simulations can be useful as a null distribution for future studies of genomic clines. Future work on red deer and sika could determine the policy implications of allelic-replacement due to drift rather than selection, and could use replicate, geographically distinct hybrid zones to narrow down those loci that are responding to selection.
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Affiliation(s)
- S Eryn McFarlane
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.,Department of Biology, Lund University, Lund, Sweden
| | - Helen V Senn
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.,WildGenes Laboratory, Royal Zoological Society of Scotland, Edinburgh, UK
| | - Stephanie L Smith
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.,The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, UK
| | - Josephine M Pemberton
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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Queirós J, Gortázar C, Alves PC. Deciphering Anthropogenic Effects on the Genetic Background of the Red Deer in the Iberian Peninsula. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00147] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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McFarlane SE, Hunter DC, Senn HV, Smith SL, Holland R, Huisman J, Pemberton JM. Increased genetic marker density reveals high levels of admixture between red deer and introduced Japanese sika in Kintyre, Scotland. Evol Appl 2020; 13:432-441. [PMID: 31993087 PMCID: PMC6976951 DOI: 10.1111/eva.12880] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 09/01/2019] [Accepted: 10/10/2019] [Indexed: 12/14/2022] Open
Abstract
Hybridization is a natural process at species range boundaries, but increasing numbers of species are hybridizing due to direct or indirect human activities. In such cases of anthropogenic hybridization, subsequent introgression can threaten the survival of native species. To date, many such systems have been studied with too few genetic markers to assess the level of threat resulting from advanced backcrossing. Here, we use 44,999 single nucleotide polymorphisms (SNPs) and the ADMIXTURE program to study two areas of Scotland where a panel of 22 diagnostic microsatellites previously identified introgression between native red deer (Cervus elaphus) and introduced Japanese sika (Cervus nippon). In Kintyre, we reclassify 26% of deer from the pure species categories to the hybrid category whereas in the NW Highlands we only reclassify 2%. As expected, the reclassified individuals are mostly advanced backcrosses. We also investigate the ability of marker panels selected on different posterior allele frequency criteria to find hybrids assigned by the full marker set and show that in our data, ancestry informative markers (i.e. those that are highly differentiated between the species, but not fixed) are better than diagnostic markers (those markers that are fixed between the species) because they are more evenly distributed in the genome. Diagnostic loci are concentrated on the X chromosome to the detriment of autosomal coverage.
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Affiliation(s)
- S. Eryn McFarlane
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
- Department of BiologyLund UniversityLundSweden
| | - Darren C. Hunter
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Helen V. Senn
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
- WildGenes LaboratoryRoyal Zoological Society of ScotlandEdinburghUK
| | - Stephanie L. Smith
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
- The Royal (Dick) School of Veterinary StudiesUniversity of EdinburghEaster Bush CampusMidlothian, EdinburghUK
| | - Rebecca Holland
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
| | - Jisca Huisman
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
| | - Josephine M. Pemberton
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
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12
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Hill E, Linacre A, Toop S, Murphy N, Strugnell J. Widespread hybridization in the introduced hog deer population of Victoria, Australia, and its implications for conservation. Ecol Evol 2019; 9:10828-10842. [PMID: 31624584 PMCID: PMC6787866 DOI: 10.1002/ece3.5603] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/31/2019] [Accepted: 08/02/2019] [Indexed: 02/02/2023] Open
Abstract
In Australia, many species have been introduced that have since undergone drastic declines in their native range. One species of note is the hog deer (Axis porcinus) which was introduced in the 1860s to Victoria, Australia, and has since become endangered in its native range throughout South-East Asia. There is increased interest in using non-native populations as a source for genetic rescue; however, considerations need to be made of the genetic suitability of the non-native population. Three mitochondrial markers and two nuclear markers were sequenced to assess the genetic variation of the Victorian population of hog deer, which identified that the Victorian population has hybrid origins with the closely related chital (Axis axis), a species that is no longer present in the wild in Victoria. In addition, the mitochondrial D-loop region within the Victorian hog deer is monomorphic, demonstrating that mitochondrial genetic diversity is very low within this population. This study is the first to report of long-term persistence of hog deer and chital hybrids in a wild setting, and the continual survival of this population suggests that hybrids of these two species are fertile. Despite the newly discovered hybrid status in Victorian hog deer, this population may still be beneficial for future translocations within the native range. However, more in-depth analysis of genetic diversity within the Victorian hog deer population and investigation of hybridization rates within the native range are necessary before translocations are attempted.
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Affiliation(s)
- Erin Hill
- Department of Ecology, Environment and EvolutionSchool of Life SciencesLa Trobe UniversityMelbourneVic.Australia
| | - Adrian Linacre
- College of Science and EngineeringFlinders UniversityAdelaideSAAustralia
| | - Simon Toop
- Game Management AuthorityMelbourneVic.Australia
| | - Nicholas Murphy
- Department of Ecology, Environment and EvolutionSchool of Life SciencesLa Trobe UniversityMelbourneVic.Australia
- Research Centre for Future LandscapesSchool of Life SciencesLa Trobe UniversityMelbourneVic.Australia
| | - Jan Strugnell
- Department of Ecology, Environment and EvolutionSchool of Life SciencesLa Trobe UniversityMelbourneVic.Australia
- Centre for Sustainable Tropical Fisheries and AquacultureJames Cook UniversityTownsvilleQldAustralia
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13
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Iacolina L, Corlatti L, Buzan E, Safner T, Šprem N. Hybridisation in European ungulates: an overview of the current status, causes, and consequences. Mamm Rev 2018. [DOI: 10.1111/mam.12140] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Laura Iacolina
- Department of Chemistry and Bioscience; Aalborg University; Frederik Bajers Vej 7H 9220 Aalborg Denmark
- Aalborg Zoo; Mølleparkvej 63 9000 Aalborg Denmark
| | - Luca Corlatti
- Wildlife Ecology and Management; University of Freiburg; Tennenbacher Straße 4 79106 Freiburg Germany
- Institute of Wildlife Biology and Game Management; University of Natural Resources and Life Sciences Vienna; Gregor-Mendel-Straße 33 1180 Vienna Austria
| | - Elena Buzan
- Department of Biodiversity; Faculty of Mathematics, Natural Sciences and Information Technologies; University of Primorska; Glagoljaška 8 6000 Koper Slovenia
| | - Toni Safner
- Faculty of Agriculture; Department of Plant Breeding, Genetics and Biometrics; University of Zagreb; Svetošimunska cesta 25 10000 Zagreb Croatia
| | - Nikica Šprem
- Faculty of Agriculture; Department of Fisheries, Beekeeping, Game Management and Special Zoology; University of Zagreb; Svetošimunska cesta 25 10000 Zagreb Croatia
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14
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Essl F, Bacher S, Genovesi P, Hulme PE, Jeschke JM, Katsanevakis S, Kowarik I, Kühn I, Pyšek P, Rabitsch W, Schindler S, van Kleunen M, Vilà M, Wilson JRU, Richardson DM. Which Taxa Are Alien? Criteria, Applications, and Uncertainties. Bioscience 2018. [DOI: 10.1093/biosci/biy057] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Franz Essl
- Division of Conservation Biology, Vegetation and Landscape Ecology at the University of Vienna, in Austria; the Department of Biodiversity and Nature Conservation at Environment Agency Austria, in Vienna; and the Centre for Invasion Biology in the Department of Botany and Zoology at Stellenbosch University, in South Africa
| | - Sven Bacher
- Department of Biology at the University of Fribourg, in Switzerland
| | - Piero Genovesi
- Institute for Environmental Protection and Research (ISPRA) and is the chair of the International Union for Conservation of Nature Species Survival Commission Invasive Species Specialist Group, in Rome, Italy
| | - Philip E Hulme
- Bio-Protection Research Centre at Lincoln University, in Christchurch, New Zealand
| | - Jonathan M Jeschke
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB); Freie Universität Berlin; and the Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), in Berlin, Germany
| | - Stelios Katsanevakis
- Department of Marine Sciences at the University of the Aegean, in Mytilene, Greece
| | - Ingo Kowarik
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB) and is chair of ecosystem science/plant ecology at Technische Universität Berlin, in Germany
| | - Ingolf Kühn
- Helmholtz Centre for Environmental Research–UFZ in the Department of Community Ecology, in Halle, Germany; the Geobotany and Botanical Garden at Martin Luther University Halle-Wittenberg, in Halle, Germany; and the German Centre for Integrative Biodiversity Research (iDiv), in Leipzig, Germany
| | - Petr Pyšek
- Institute of Botany and the Department of Invasion Ecology at The Czech Academy of Sciences, in Průhonice, Czech Republic, and with the Department of Ecology at Charles University, in Prague, Czech Republic
| | - Wolfgang Rabitsch
- Department of Biodiversity and Nature Conservation at Environment Agency Austria, in Vienna
| | - Stefan Schindler
- Department of Biodiversity and Nature Conservation at Environment Agency Austria, in Vienna
| | - Mark van Kleunen
- Department of Biology at the University of Konstanz, in Germany, and with the Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation at Taizhou University, in China
| | - Montserrat Vilà
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (EBD-CSIC), in Sevilla, Spain
| | - John R U Wilson
- Centre for Invasion Biology in the Department of Botany and Zoology at Stellenbosch University, in South Africa
- South African National Biodiversity Institute at the Kirstenbosch Research Centre, Cape Town, South Africa
| | - David M Richardson
- Centre for Invasion Biology in the Department of Botany and Zoology at Stellenbosch University, in South Africa
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15
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Powell C, Butler F, O’Reilly C. The development of real-time PCR assays for species and sex identification of three sympatric deer species from noninvasive samples. CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-018-1041-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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16
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Smith SL, Senn HV, Pérez‐Espona S, Wyman MT, Heap E, Pemberton JM. Introgression of exotic Cervus ( nippon and canadensis) into red deer ( Cervus elaphus) populations in Scotland and the English Lake District. Ecol Evol 2018; 8:2122-2134. [PMID: 29468030 PMCID: PMC5817139 DOI: 10.1002/ece3.3767] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 11/04/2017] [Accepted: 11/14/2017] [Indexed: 11/10/2022] Open
Abstract
Since the mid-19th century, multiple introductions of Japanese sika deer (Cervus nippon nippon) and North American wapiti (C. canadensis) have taken place in the British Isles. While wapiti have generally been unsuccessful, sika have been very successful, especially in Scotland where they now overlap at least 40% of the range of native red deer (C. elaphus). Hybridization between these two species and red deer has been demonstrated in captivity and in the wild. Using a panel of 22 microsatellite loci that are highly diagnostic between red deer and sika, and moderately diagnostic between red deer and wapiti, we investigated the extent of introgression between these species in 2,943 deer sampled from around Scotland and from the English Lake District using the Bayesian clustering software STRUCTURE. We also used a diagnostic mitochondrial marker for red deer and sika. Our survey extends previous studies indicating little introgression of wapiti nuclear alleles into red deer, in particular in Northern Scotland, Kintyre, and the Lake District. We found a new area of extensive sika introgression in South Kintyre. In the North Highlands, we show for the first time geographically scattered evidence of past hybridization followed by extensive backcrossing, including one red-like individual with sika introgression, two sika-like individuals with red deer introgression, and six individuals that were apparently pure sika at the nuclear markers assessed but which carried red deer mitochondria. However, there has not been a collapse of assortative mating in this region. Similarly, in the English Lake District red deer, we found only traces of past sika introgression. No sika alleles were detected in the Central Highlands or the Hebridean red deer refugia. We make suggestions for management to prevent further spread of sika alleles into red deer and vice versa.
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Affiliation(s)
- Stephanie L. Smith
- Institute of Evolutionary BiologySchool of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Helen V. Senn
- WildGenes LaboratoryRoyal Zoological Society of ScotlandEdinburghUK
| | | | - Megan T. Wyman
- Mammal Vocal Communication and Cognition ResearchSchool of PsychologyUniversity of SussexFalmerUK
| | - Elizabeth Heap
- Institute of Evolutionary BiologySchool of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Josephine M. Pemberton
- Institute of Evolutionary BiologySchool of Biological SciencesUniversity of EdinburghEdinburghUK
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17
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Martins RF, Schmidt A, Lenz D, Wilting A, Fickel J. Human-mediated introduction of introgressed deer across Wallace's line: Historical biogeography of Rusa unicolor and R. timorensis. Ecol Evol 2018; 8:1465-1479. [PMID: 29435225 PMCID: PMC5792523 DOI: 10.1002/ece3.3754] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/23/2017] [Accepted: 11/27/2017] [Indexed: 01/20/2023] Open
Abstract
In this study we compared the phylogeographic patterns of two Rusa species, Rusa unicolor and Rusa timorensis, in order to understand what drove and maintained differentiation between these two geographically and genetically close species and investigated the route of introduction of individuals to the islands outside of the Sunda Shelf. We analyzed full mitogenomes from 56 archival samples from the distribution areas of the two species and 18 microsatellite loci in a subset of 16 individuals to generate the phylogeographic patterns of both species. Bayesian inference with fossil calibration was used to estimate the age of each species and major divergence events. Our results indicated that the split between the two species took place during the Pleistocene, ~1.8 Mya, possibly driven by adaptations of R. timorensis to the drier climate found on Java compared to the other islands of Sundaland. Although both markers identified two well-differentiated clades, there was a largely discrepant pattern between mitochondrial and nuclear markers. While nDNA separated the individuals into the two species, largely in agreement with their museum label, mtDNA revealed that all R. timorensis sampled to the east of the Sunda shelf carried haplotypes from R. unicolor and one Rusa unicolor from South Sumatra carried a R. timorensis haplotype. Our results show that hybridization occurred between these two sister species in Sundaland during the Late Pleistocene and resulted in human-mediated introduction of hybrid descendants in all islands outside Sundaland.
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Affiliation(s)
- Renata F. Martins
- Department of Evolutionary GeneticsLeibniz Institute for Zoo and Wildlife ResearchBerlinGermany
| | - Anke Schmidt
- Department of Evolutionary GeneticsLeibniz Institute for Zoo and Wildlife ResearchBerlinGermany
| | - Dorina Lenz
- Department of Evolutionary GeneticsLeibniz Institute for Zoo and Wildlife ResearchBerlinGermany
| | - Andreas Wilting
- Department of Evolutionary GeneticsLeibniz Institute for Zoo and Wildlife ResearchBerlinGermany
| | - Joerns Fickel
- Department of Evolutionary GeneticsLeibniz Institute for Zoo and Wildlife ResearchBerlinGermany
- Institute for Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
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18
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Galarza JA, Sánchez-Fernández B, Fandos P, Soriguer R. Intensive Management and Natural Genetic Variation in Red Deer (Cervus elaphus). J Hered 2017; 108:496-504. [PMID: 28863451 DOI: 10.1093/jhered/esx052] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 05/31/2017] [Indexed: 11/13/2022] Open
Abstract
The current magnitude of big-game hunting has outpaced the natural growth of populations, making artificial breeding necessary to rapidly boost hunted populations. In this study, we evaluated if the rapid increase of red deer (Cervus elaphus) abundance, caused by the growing popularity of big-game hunting, has impacted the natural genetic diversity of the species. We compared several genetic diversity metrics between 37 fenced populations subject to intensive management and 21 wild free-ranging populations. We also included a historically protected population from a national park as a baseline for comparisons. Contrary to expectations, our results showed no significant differences in genetic diversity between wild and fenced populations. Relatively lower genetic diversity was observed in the protected population, although differences were not significant in most cases. Bottlenecks were detected in both wild and fenced populations, as well as in the protected population. Assignment tests identified individuals that did not belong to their population of origin, indicating anthropogenic movement. We discuss the most likely processes, which could have led to the observed high levels of genetic variability and lack of differentiation between wild and fenced populations and suggest cautionary points for future conservation. We illustrate our comparative approach in red deer. However, our results and interpretations can be largely applicable to most ungulates subject to big-game hunting as most of them share a common exploitation-recovery history as well as many ecological traits.
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Affiliation(s)
- Juan A Galarza
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyväskylä, Survontie 9, 40500 Jyväskylä, Finland; Estación Biológica Doñana (CSIC), Seville, Spain; and Agencia de Medio Ambiente y Agua, Seville, Spain
| | - Beatriz Sánchez-Fernández
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyväskylä, Survontie 9, 40500 Jyväskylä, Finland; Estación Biológica Doñana (CSIC), Seville, Spain; and Agencia de Medio Ambiente y Agua, Seville, Spain
| | - Paulino Fandos
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyväskylä, Survontie 9, 40500 Jyväskylä, Finland; Estación Biológica Doñana (CSIC), Seville, Spain; and Agencia de Medio Ambiente y Agua, Seville, Spain
| | - Ramón Soriguer
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyväskylä, Survontie 9, 40500 Jyväskylä, Finland; Estación Biológica Doñana (CSIC), Seville, Spain; and Agencia de Medio Ambiente y Agua, Seville, Spain
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19
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Graham DA, Gallagher C, Carden RF, Lozano JM, Moriarty J, O'Neill R. A survey of free-ranging deer in Ireland for serological evidence of exposure to bovine viral diarrhoea virus, bovine herpes virus-1, bluetongue virus and Schmallenberg virus. Ir Vet J 2017; 70:13. [PMID: 28503294 PMCID: PMC5427525 DOI: 10.1186/s13620-017-0091-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 05/08/2017] [Indexed: 11/24/2022] Open
Abstract
Background Deer are an important wildlife species in both the Republic of Ireland and Northern Ireland having colonised most regions across the island of Ireland. In comparison to cattle and sheep which represent the main farmed ruminant species on the island, there is a lack of data concerning their exposure, as measured by the presence of antibodies, to important viral pathogens of ruminants. A study was therefore undertaken to investigate the seroprevalence of wild deer to four viruses, namely bovine viral diarrhoea virus (BVDV), bovine herpesvirus-1 (BoHV-1), Schmallenberg virus (SBV) and bluetongue virus (BTV). Results Two panels of sera were assembled; Panel 1 comprised 259 samples (202 collected in the Republic of Ireland and 57 in Northern Ireland) between 2013 and 2015, while Panel 2 comprised 131 samples collected in the Republic of Ireland between 2014 and 2015. Overall sika deer (Cervus nippon) were sampled most commonly (54.8%), followed by fallow deer (Dama dama) (35.3%), with red deer (Cervus elaphus) (4.3%) and hybrid species (0.3%) sampled less frequently, with the species not being recorded for the remaining 5.3% of deer sampled. Age was not recorded for 96 of the 390 deer sampled. 196 of the remainder were adults, while 68 and 30 were yearlings and calves, respectively. Using commercially available enzyme-linked immunosorbent assays, true prevalence and 95% confidence intervals were calculated as 9.9%, (6.8-13.0% CI), SBV; 1.5% (0.1-3.0% CI), BoHV-1; 0.0%, 0-1.7% CI), BVDV; and 0.0%, (0.01-0.10% CI), BTV. Conclusions The results indicate a very low seroprevalence for both BVDV and BoHV-1 in the wild deer tested within the study and, are consistent with a very low prevalence in Ireland. While serological cross-reaction with cervid herpesviruses cannot be excluded, the results in both cases suggest that the presence of these viruses in deer is not a significant risk to their control and eradication from the cattle population. This is important given the ongoing programme to eradicate BVDV in Ireland and deliberations on a national eradication programme for BoHV-1. The SBV results show consistency with those reported from cattle and sheep on the island of Ireland, while the BTV results are consistent with this virus remaining exotic to Ireland. The results provide a baseline against which future surveys of either wild or farmed/captive deer populations can be compared.
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Affiliation(s)
- David A Graham
- Animal Health Ireland, 4-5 The Archways, Carrick on Shannon, Co. Leitrim Ireland
| | - Clare Gallagher
- Animal Health Ireland, 4-5 The Archways, Carrick on Shannon, Co. Leitrim Ireland
| | - Ruth F Carden
- Adjunct Research Fellow, School of Archaeology, University College Dublin, Belfield, Dublin 4 Ireland
| | - Jose-Maria Lozano
- Central Veterinary Research Laboratory, Backweston Campus, Celbridge, Ireland
| | - John Moriarty
- Central Veterinary Research Laboratory, Backweston Campus, Celbridge, Ireland
| | - Ronan O'Neill
- Central Veterinary Research Laboratory, Backweston Campus, Celbridge, Ireland
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20
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Kasarda R, Moravčíková N, Trakovická A, Krupová Z, Ondrej K. Genomic variation across cervid species in respect to the estimation of red deer diversity. ACTA VET-BEOGRAD 2017. [DOI: 10.1515/acve-2017-0005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
The aim of this study was to assess the genetic variations and relationships across evolutionary related cervid species in order to estimate the genetic diversity of the Red deer population that inhabits the forest area in the south-western part of Slovakia. The study was based on the application of cross-species SNP genotyping. The genomic data were obtained from a total of 86 individuals representing six genera (Axis, Dama, Cervus, Alces, Rangifer, and Odocoileus) using Illumina BovineSNP50 BeadChip. From 38.85% of successfully genotyped loci up to 1,532 SNPs showed polymorphism and were informative for subsequent analyses of the diversity and interspecific genetic relationships. Generally, a good level of observed heterozygosity was found across all species. The value of FIS (0.23±0.13) signalised the increase of a homozygous proportion within them. The application of molecular variance analysis to the hierarchical population structure showed that most of the variation was conserved within separate species (96%). The performed diversity analysis of Slovak Red deer population and comparative analysis of their phylogenic relationships among subspecies from genus Cervus did not identify a remarkable loss of genetic variability. Also, were not identified any degree of admixture that could be due to the historical background of deer farming in Slovakia or reintroduction and hybridisation by other species from genus Cervus (C. canadensis, and C. nippon) which are the major risk of loss of autochthonous Red deer populations in many areas of Central Europe. The analysis of individual’s ancestry showed consistent results with patterns of evaluated group differentiations which means low migration rates among all species.
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Affiliation(s)
- Radovan Kasarda
- Department of Animal Genetics and Breeding Biology, Slovak University of Agriculture in Nitra, Nitra, Slovak Republic
| | - Nina Moravčíková
- Department of Animal Genetics and Breeding Biology, Slovak University of Agriculture in Nitra, Nitra, Slovak Republic
| | - Anna Trakovická
- Department of Animal Genetics and Breeding Biology, Slovak University of Agriculture in Nitra, Nitra, Slovak Republic
| | - Zuzana Krupová
- Genetics and Breeding of Farm Animals, Institute of Animal Science, Prague, Czech Republic
| | - Kadlečík Ondrej
- Department of Animal Genetics and Breeding Biology, Slovak University of Agriculture in Nitra, Nitra, Slovak Republic
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21
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Wyman MT, Locatelli Y, Charlton BD, Reby D. Female Sexual Preferences Toward Conspecific and Hybrid Male Mating Calls in Two Species of Polygynous Deer, Cervus elaphus and C. nippon. Evol Biol 2015; 43:227-241. [PMID: 27217596 PMCID: PMC4860407 DOI: 10.1007/s11692-015-9357-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Accepted: 10/31/2015] [Indexed: 11/29/2022]
Abstract
The behavioral processes at the basis of hybridization and introgression are understudied in terrestrial mammals. We use a unique model to test the role of sexual signals as a reproductive barrier to introgression by investigating behavioral responses to male sexual calls in estrous females of two naturally allopatric but reproductively compatible deer species, red deer and sika deer. Previous studies demonstrated asymmetries in acoustic species discrimination between these species: most but not all female red deer prefer conspecific over sika deer male calls while female sika deer exhibit no preference differences. Here, we extend this examination of acoustic species discrimination to the role of male sexual calls in introgression between parent species and hybrids. Using two-speaker playback experiments, we compared the preference responses of estrous female red and sika deer to male sexual calls from conspecifics versus red × sika hybrids. These playbacks simulate early secondary contact between previously allopatric species after hybridization has occurred. Based on previous conspecific versus heterospecific playbacks, we predicted that most female red deer would prefer conspecific calls while female sika deer would show no difference in their preference behaviors toward conspecific and hybrid calls. However, results show that previous asymmetries did not persist as neither species exhibited more preferences for conspecific over hybrid calls. Thus, vocal behavior is not likely to deter introgression between these species during the early stages of sympatry. On a wider scale, weak discrimination against hybrid sexual signals could substantially contribute to this important evolutionary process in mammals and other taxa.
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Affiliation(s)
- Megan T. Wyman
- />Mammal Vocal Communication and Cognition Research, School of Psychology, University of Sussex, Falmer, BN1 9QH UK
- />Department of Wildlife, Fish and Conservation Biology, University of California, 1331 Academic Surge Building, One Shields Ave., Davis, CA 95616 USA
| | - Yann Locatelli
- />Muséum National d’Histoire Naturelle, Réserve de la Haute Touche, 36290 Obterre, France
| | - Benjamin D. Charlton
- />School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - David Reby
- />Mammal Vocal Communication and Cognition Research, School of Psychology, University of Sussex, Falmer, BN1 9QH UK
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