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Pérez-González J, Carranza J, Anaya G, Broggini C, Vedel G, de la Peña E, Membrillo A. Comparative Analysis of Microsatellite and SNP Markers for Genetic Management of Red Deer. Animals (Basel) 2023; 13:3374. [PMID: 37958129 PMCID: PMC10650148 DOI: 10.3390/ani13213374] [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: 09/23/2023] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
The analysis of population genetic structure and individual multilocus heterozygosity are crucial for wildlife management and conservation. Microsatellite markers have traditionally been used to assess these genetic parameters. However, single-nucleotide polymorphisms (SNPs) are becoming increasingly popular. Our goal here was to determine to what extent SNPs can provide better insights than microsatellites into the overall genetic status and population genetic processes in the species. To this end, we genotyped 210 red deer (Cervus elaphus) in the Spanish wild population with both 11 microsatellites and 31,712 SNPs. We compared parameters related to population genetic structure and individual multilocus heterozygosity obtained with both types of markers. Our results showed correlations between parameters measured using both microsatellites and SNPs, particularly those related to the level of genetic diversity and genetic differentiation. However, we found notably lower precision of microsatellites in measuring the distribution of genetic diversity among individuals. We conclude that microsatellites can be used to monitor the overall genetic status and detect broad patterns in red deer populations. Nevertheless, the greater precision of SNPs in inferring genetic structure and multilocus heterozygosity leads us to encourage scientists and wildlife managers to prioritize their use whenever possible.
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Affiliation(s)
- Javier Pérez-González
- Biology and Ethology Unit, Veterinary Faculty, University of Extremadura, 10003 Caceres, Spain
| | - Juan Carranza
- Wildlife Research Unit (UIRCP), University of Córdoba, 14071 Cordoba, Spain; (J.C.); (G.A.); (C.B.); (G.V.); (E.d.l.P.); (A.M.)
| | - Gabriel Anaya
- Wildlife Research Unit (UIRCP), University of Córdoba, 14071 Cordoba, Spain; (J.C.); (G.A.); (C.B.); (G.V.); (E.d.l.P.); (A.M.)
- Department of Genetics, University of Cordoba, 14071 Cordoba, Spain
| | - Camilla Broggini
- Wildlife Research Unit (UIRCP), University of Córdoba, 14071 Cordoba, Spain; (J.C.); (G.A.); (C.B.); (G.V.); (E.d.l.P.); (A.M.)
| | - Giovanni Vedel
- Wildlife Research Unit (UIRCP), University of Córdoba, 14071 Cordoba, Spain; (J.C.); (G.A.); (C.B.); (G.V.); (E.d.l.P.); (A.M.)
| | - Eva de la Peña
- Wildlife Research Unit (UIRCP), University of Córdoba, 14071 Cordoba, Spain; (J.C.); (G.A.); (C.B.); (G.V.); (E.d.l.P.); (A.M.)
- Institute for Game and Wildlife Research (IREC), 13005 Ciudad Real, Spain
| | - Alberto Membrillo
- Wildlife Research Unit (UIRCP), University of Córdoba, 14071 Cordoba, Spain; (J.C.); (G.A.); (C.B.); (G.V.); (E.d.l.P.); (A.M.)
- Department of Specific Didactics, Faculty of Education Sciences, University of Cordoba, 14071 Cordoba, Spain
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Moravčíková N, Kasarda R, Židek R, McEwan JC, Brauning R, Landete-Castillejos T, Chonco L, Ciberej J, Pokorádi J. Traces of Human-Mediated Selection in the Gene Pool of Red Deer Populations. Animals (Basel) 2023; 13:2525. [PMID: 37570333 PMCID: PMC10417186 DOI: 10.3390/ani13152525] [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: 06/10/2023] [Revised: 07/27/2023] [Accepted: 07/30/2023] [Indexed: 08/13/2023] Open
Abstract
In this study, we analysed the effect of human-mediated selection on the gene pool of wild and farmed red deer populations based on genotyping-by-sequencing data. The farmed red deer sample covered populations spread across seven countries and two continents (France, Germany, Hungary, Latvia, New Zealand, Poland, and Slovakia). The Slovak and Spain wild red deer populations (the latter one in a large game estate) were used as control outgroups. The gene flow intensity, relationship and admixture among populations were tested by the Bayesian approach and discriminant analysis of principal components (DAPC). The highest gene diversity (He = 0.19) and the lowest genomic inbreeding (FHOM = 0.04) found in Slovak wild population confirmed our hypothesis that artificial selection accompanied by bottlenecks has led to the increase in overall genomic homozygosity. The Bayesian approach and DAPC consistently identified three separate genetic groups. As expected, the farmed populations were clustered together, while the Slovak and Spanish populations formed two separate clusters. Identified traces of genetic admixture in the gene pool of farmed populations reflected a strong contemporary migration rate between them. This study suggests that even if the history of deer farming has been shorter than traditional livestock species, it may leave significant traces in the genome structure.
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Affiliation(s)
- Nina Moravčíková
- Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, 949 76 Nitra, Slovakia;
| | - Radovan Kasarda
- Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, 949 76 Nitra, Slovakia;
| | - Radoslav Židek
- Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, 949 76 Nitra, Slovakia;
| | - John Colin McEwan
- AgResearch, Invermay Agricultural Research Centre, Mosgiel 9024, New Zealand; (J.C.M.); (R.B.)
| | - Rudiger Brauning
- AgResearch, Invermay Agricultural Research Centre, Mosgiel 9024, New Zealand; (J.C.M.); (R.B.)
| | - Tomás Landete-Castillejos
- Instituto de Recursos Cinegéticos-Instituto de Desarrollo Regional, University of Castilla-La Mancha, 02071 Albacete, Spain; (T.L.-C.); (L.C.)
| | - Louis Chonco
- Instituto de Recursos Cinegéticos-Instituto de Desarrollo Regional, University of Castilla-La Mancha, 02071 Albacete, Spain; (T.L.-C.); (L.C.)
| | - Juraj Ciberej
- Department of Breeding and Diseases of Game, Fish and Bees, Ecology and Cynology, University of Veterinary Medicine and Pharmacy, 041 81 Košice, Slovakia
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Spatial genetic structure of European wild boar, with inferences on late-Pleistocene and Holocene demographic history. Heredity (Edinb) 2023; 130:135-144. [PMID: 36639700 PMCID: PMC9981775 DOI: 10.1038/s41437-022-00587-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 01/15/2023] Open
Abstract
European wildlife has been subjected to intensifying levels of anthropogenic impact throughout the Holocene, yet the main genetic partitioning of many species is thought to still reflect the late-Pleistocene glacial refugia. We analyzed 26,342 nuclear SNPs of 464 wild boar (Sus scrofa) across the European continent to infer demographic history and reassess the genetic consequences of natural and anthropogenic forces. We found that population fragmentation, inbreeding and recent hybridization with domestic pigs have caused the spatial genetic structure to be heterogeneous at the local scale. Underlying local anthropogenic signatures, we found a deep genetic structure in the form of an arch-shaped cline extending from the Dinaric Alps, via Southeastern Europe and the Baltic states, to Western Europe and, finally, to the genetically diverged Iberian peninsula. These findings indicate that, despite considerable anthropogenic influence, the deeper, natural continental structure is still intact. Regarding the glacial refugia, our findings show a weaker signal than generally assumed, but are nevertheless suggestive of two main recolonization routes, with important roles for Southern France and the Balkans. Our results highlight the importance of applying genomic resources and framing genetic results within a species' demographic history and geographic distribution for a better understanding of the complex mixture of underlying processes.
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Frank K, Szepesi K, Bleier N, Sugár L, Kusza S, Barta E, Horn P, Orosz L, Stéger V. Genetic traces of dispersal and admixture in red deer (Cervus elaphus) populations from the Carpathian Basin. EUR J WILDLIFE RES 2022. [DOI: 10.1007/s10344-022-01602-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
AbstractAfter the last glacial, the Carpathian Basin was repopulated from either eastward or northward colonisation routes for various species; one of these was the emblematic member of the European megafauna, the red deer, Cervus elaphus. We analysed 303 red deer individuals from the middle of the region, in seven Hungarian game reserves, at ten microsatellite loci (C01, C229, T26, T108, T123, T156, T172, T193, T501, T507), to investigate the genetic diversity of these subpopulations. We discovered high levels of genetic diversity of red deer subpopulations; allelic richness values ranging 4.99–7.01, observed heterozygosity 0.729–0.800, polymorphic information content 0.722–0.806, and Shannon’s information index 1.668–2.064. Multi-locus analyses indicated population admixtures of various degrees that corresponded to geographical location, and complex genetic structures were shown by clustering. Populations in the south-western and the north-eastern parts of the region formed two highly separated groups, and the red deer from populations in between them were highly admixed (in western Pannonia/Transdanubia, where the Danube flows into the Carpathian Basin). This pattern corresponds to the distribution of mitochondrial as well as Y-chromosome lineages. Assignment tests showed that a large fraction of individuals (29.4%) are found outside of their population of origin, indicating that the dispersal of red deer is rather common, which could be expected considering the life course of the species.
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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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Kristjansson D, Bohlin J, Nguyen TT, Jugessur A, Schurr TG. Evolution and dispersal of mitochondrial DNA haplogroup U5 in Northern Europe: insights from an unsupervised learning approach to phylogeography. BMC Genomics 2022; 23:354. [PMID: 35525961 PMCID: PMC9080151 DOI: 10.1186/s12864-022-08572-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 04/20/2022] [Indexed: 12/28/2022] Open
Abstract
Background We combined an unsupervised learning methodology for analyzing mitogenome sequences with maximum likelihood (ML) phylogenetics to make detailed inferences about the evolution and diversification of mitochondrial DNA (mtDNA) haplogroup U5, which appears at high frequencies in northern Europe. Methods Haplogroup U5 mitogenome sequences were gathered from GenBank. The hierarchal Bayesian Analysis of Population Structure (hierBAPS) method was used to generate groups of sequences that were then projected onto a rooted maximum likelihood (ML) phylogenetic tree to visualize the pattern of clustering. The haplogroup statuses of the individual sequences were assessed using Haplogrep2. Results A total of 23 hierBAPS groups were identified, all of which corresponded to subclades defined in Phylotree, v.17. The hierBAPS groups projected onto the ML phylogeny accurately clustered all haplotypes belonging to a specific haplogroup in accordance with Haplogrep2. By incorporating the geographic source of each sequence and subclade age estimates into this framework, inferences about the diversification of U5 mtDNAs were made. Haplogroup U5 has been present in northern Europe since the Mesolithic, and spread in both eastern and western directions, undergoing significant diversification within Scandinavia. A review of historical and archeological evidence attests to some of the population interactions contributing to this pattern. Conclusions The hierBAPS algorithm accurately grouped mitogenome sequences into subclades in a phylogenetically robust manner. This analysis provided new insights into the phylogeographic structure of haplogroup U5 diversity in northern Europe, revealing a detailed perspective on the diversity of subclades in this region and their distribution in Scandinavian populations. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08572-y.
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Affiliation(s)
- Dana Kristjansson
- Center for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway. .,Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Bergen, Norway.
| | - Jon Bohlin
- Center for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Method Development and Analytics, Norwegian Institute of Public Health, Oslo, Norway
| | - Truc Trung Nguyen
- IT Systems Bergen, Norwegian Institute of Public Health, Bergen, Norway
| | - Astanand Jugessur
- Center for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA, USA
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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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Genome-wide SNPs detect fine-scale genetic structure in threatened populations of squirrel glider Petaurus norfolcensis. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01435-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractAustralian arboreal mammals are experiencing significant population declines, particularly due to land clearing and resulting habitat fragmentation. The squirrel glider, Petaurus norfolcensis, is a threatened species in New South Wales, with a stronghold population in the Lake Macquarie Local Government Area (LGA) where fragmentation due to urbanization is an ongoing problem for the species conservation. Here we report on the use of squirrel glider mitochondrial (385 bp cytochrome b gene, 70 individuals) and nuclear DNA (6,834 SNPs, 87 individuals) markers to assess their population genetic structure and connectivity across 14 locations sampled in the Lake Macquarie LGA. The mitochondrial DNA sequences detected evidence of a historical genetic bottleneck, while the genome-wide SNPs detected significant population structure in the Lake Macquarie squirrel glider populations at scales as fine as one kilometer. There was no evidence of inbreeding within patches, however there were clear effects of habitat fragmentation and biogeographical barriers on gene flow. A least cost path analysis identified thin linear corridors that have high priority for conservation. These areas should be protected to avoid further isolation of squirrel glider populations and the loss of genetic diversity through genetic drift.
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Golosova OS, Kholodova MV, Volodin IA, Volodina EV, Likhatsky EY, Náhlik A, Tari T. Vocal phenotype of male rutting roars and genetic markers delineate East European red deer (Cervus elaphus) from Central and West European populations. Naturwissenschaften 2021; 108:30. [PMID: 34185170 DOI: 10.1007/s00114-021-01742-0] [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: 12/30/2020] [Revised: 06/08/2021] [Accepted: 06/16/2021] [Indexed: 11/29/2022]
Abstract
This study investigates a population of red deer Cervus elaphus, founded by 10 individuals introduced in the nineteenth century from Germany to the Voronezh region of the European part of Southern Russia and then developed without further introductions. We characterize for the first time the vocal phenotype of the Voronezh red deer male rutting calls in comparison with similar data on the Pannonian (native Central European) and Iberian (native West European) red deer obtained by the authors during preceding studies. In addition, we provide for the first time the genetic data on Pannonian red deer. In Voronezh stags, the number of roars per bout (2.85 ± 1.79) was lower than in Pannonian (3.18 ± 2.17) but higher than in Iberian (2.11 ± 1.71) stags. In Voronezh stags, the duration of main (the longest within bouts) roars was longer (2.46 ± 1.14 s) than in Pannonian (1.13 ± 0.50 s) or Iberian (1.90 ± 0.50 s) stags. The maximum fundamental frequency of main roars was similar between Voronezh (175 ± 60 Hz) and Pannonian (168 ± 61 Hz) but higher in Iberian stags (223 ± 35 Hz). Mitochondrial cytochrome b gene analysis of red deer from the three study populations partially supports the bioacoustical data, of closer similarity between Voronezh and Pannonian populations. In contrast, microsatellite DNA analysis delineates Voronezh red deer from either Pannonian or Iberian red deer. We discuss that population bottlenecking might affect the acoustics of the rutting roars, in addition to genotype.
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Affiliation(s)
- Olga S Golosova
- Department of Molecular Diagnostics Methods, A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Marina V Kholodova
- Department of Molecular Diagnostics Methods, A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Ilya A Volodin
- Department of Behaviour and Behavioural Ecology of Mammals, A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia. .,Department of Vertebrate Zoology, Faculty of Biology, Lomonosov Moscow State University, Vorobievy Gory, 12/1, Moscow, 119234, Russia.
| | - Elena V Volodina
- Department of Behaviour and Behavioural Ecology of Mammals, A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
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Reiner G, Klein C, Lang M, Willems H. Human-driven genetic differentiation in a managed red deer population. EUR J WILDLIFE RES 2021. [DOI: 10.1007/s10344-021-01472-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AbstractNineteen red deer areas in a densely populated region with a huge network of fenced motorways and the division into administrative management units (AMUs) with restricted ecological connectivity were investigated. In the season 2018/2019, a total of 1291 red deer samples (on average 68 per area) were collected and genotyped using 16 microsatellite markers. The results show a clear genetic differentiation between most of the AMUs. Fourteen AMUs may be combined into four regions with a considerable internal genetic exchange. Five areas were largely isolated or showed only a limited gene flow with neighbouring areas. Ten of the 19 AMUs had an effective population size below 100. Effective population sizes greater than 500–1000, required to maintain the evolutionary potential and a long-term adaptation potential, were not achieved by any of the studied AMUs, even when AMUs with an appreciable genetic exchange were aggregated. Substantial genetic differentiation between areas can be associated with the presence of landscape barriers hindering gene flow, but also with the maintenance of ‘red deer–free’ areas. Efforts to sustainably preserve the genetic diversity of the entire region should therefore focus on measures ensuring genetic connectivity. Opportunities for this goal arise from the establishment of game bridges over motorways and from the protection of young male stags migrating through the statutory ‘red deer–free’ areas.
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Mining the red deer genome (CerEla1.0) to develop X-and Y-chromosome-linked STR markers. PLoS One 2020; 15:e0242506. [PMID: 33226998 PMCID: PMC7986210 DOI: 10.1371/journal.pone.0242506] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 11/03/2020] [Indexed: 12/13/2022] Open
Abstract
Microsatellites are widely applied in population and forensic genetics, wildlife studies and parentage testing in animal breeding, among others, and recently, high-throughput sequencing technologies have greatly facilitated the identification of microsatellite markers. In this study the genomic data of Cervus elaphus (CerEla1.0) was exploited, in order to identify microsatellite loci along the red deer genome and for designing the cognate primers. The bioinformatics pipeline identified 982,433 microsatellite motifs genome-wide, assorted along the chromosomes, from which 45,711 loci mapped to the X- and 1096 to the Y-chromosome. Primers were successfully designed for 170,873 loci, and validated with an independently developed autosomal tetranucleotide STR set. Ten X- and five Y-chromosome-linked microsatellites were selected and tested by two multiplex PCR setups on genomic DNA samples of 123 red deer stags. The average number of alleles per locus was 3.3, and the average gene diversity value of the markers was 0.270. The overall observed and expected heterozygosities were 0.755 and 0.832, respectively. Polymorphic Information Content (PIC) ranged between 0.469 and 0.909 per locus with a mean value of 0.813. Using the X- and Y-chromosome linked markers 19 different Y-chromosome and 72 X-chromosome lines were identified. Both the X- and the Y-haplotypes split to two distinct clades each. The Y-chromosome clades correlated strongly with the geographic origin of the haplotypes of the samples. Segregation and admixture of subpopulations were demonstrated by the use of the combination of nine autosomal and 16 sex chromosomal STRs concerning southwestern and northeastern Hungary. In conclusion, the approach demonstrated here is a very efficient method for developing microsatellite markers for species with available genomic sequence data, as well as for their use in individual identifications and in population genetics studies.
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Funk SM, Guedaoura S, Juras R, Raziq A, Landolsi F, Luís C, Martínez AM, Musa Mayaki A, Mujica F, Oom MDM, Ouragh L, Stranger Y, Vega‐Pla JL, Cothran EG. Major inconsistencies of inferred population genetic structure estimated in a large set of domestic horse breeds using microsatellites. Ecol Evol 2020; 10:4261-4279. [PMID: 32489595 PMCID: PMC7246218 DOI: 10.1002/ece3.6195] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 01/22/2020] [Accepted: 01/27/2020] [Indexed: 11/10/2022] Open
Abstract
STRUCTURE remains the most applied software aimed at recovering the true, but unknown, population structure from microsatellite or other genetic markers. About 30% of structure-based studies could not be reproduced (Molecular Ecology, 21, 2012, 4925). Here we use a large set of data from 2,323 horses from 93 domestic breeds plus the Przewalski horse, typed at 15 microsatellites, to evaluate how program settings impact the estimation of the optimal number of population clusters K opt that best describe the observed data. Domestic horses are suited as a test case as there is extensive background knowledge on the history of many breeds and extensive phylogenetic analyses. Different methods based on different genetic assumptions and statistical procedures (dapc, flock, PCoA, and structure with different run scenarios) all revealed general, broad-scale breed relationships that largely reflect known breed histories but diverged how they characterized small-scale patterns. structure failed to consistently identify K opt using the most widespread approach, the ΔK method, despite very large numbers of MCMC iterations (3,000,000) and replicates (100). The interpretation of breed structure over increasing numbers of K, without assuming a K opt, was consistent with known breed histories. The over-reliance on K opt should be replaced by a qualitative description of clustering over increasing K, which is scientifically more honest and has the advantage of being much faster and less computer intensive as lower numbers of MCMC iterations and repetitions suffice for stable results. Very large data sets are highly challenging for cluster analyses, especially when populations with complex genetic histories are investigated.
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Affiliation(s)
- Stephan Michael Funk
- Centro de Excelencia de Modelación y Computación CientíficaUniversidad de La FronteraTemucoChile
- Nature HeritageSt. LawrenceUK
| | - Sonya Guedaoura
- Faculté des Sciences de la Nature et de la VieUniversité d'El‐TarfEl‐TarfAlgeria
- Faculté de PharmacieUniversité LavalQuébec CityQCCanada
| | - Rytis Juras
- College of Veterinary Medicine and Biomedical ScienceTexas A&M UniversityCollege StationTXUSA
| | - Absul Raziq
- Society of Veterinary, Environment and Agriculture Scientists (SAVES)QuettaPakistan
| | | | - Cristina Luís
- Centro Interuniversitário de História das Ciências e da Tecnologia (CIUHCT)Faculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | | | | | - Fernando Mujica
- Instituto de Producción AnimalUniversidad Austral de ChileValdiviaChile
| | - Maria do Mar Oom
- CE3C – Centre for Ecology, Evolution and Environmental ChangesFaculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | | | | | - Jose Luis Vega‐Pla
- Laboratorio de Investigación AplicadaCrıa Caballar de las Fuerzas ArmadasCordobaSpain
| | - Ernest Gus Cothran
- College of Veterinary Medicine and Biomedical ScienceTexas A&M UniversityCollege StationTXUSA
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Quéméré E, Rossi S, Petit E, Marchand P, Merlet J, Game Y, Galan M, Gilot-Fromont E. Genetic epidemiology of the Alpine ibex reservoir of persistent and virulent brucellosis outbreak. Sci Rep 2020; 10:4400. [PMID: 32157133 PMCID: PMC7064506 DOI: 10.1038/s41598-020-61299-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 02/25/2020] [Indexed: 01/23/2023] Open
Abstract
While it is now broadly accepted that inter-individual variation in the outcomes of host-pathogen interactions is at least partially genetically controlled, host immunogenetic characteristics are rarely investigated in wildlife epidemiological studies. Furthermore, most immunogenetic studies in the wild focused solely on the major histocompatibility complex (MHC) diversity despite it accounts for only a fraction of the genetic variation in pathogen resistance. Here, we investigated immunogenetic diversity of the Alpine ibex (Capra ibex) population of the Bargy massif, reservoir of a virulent outbreak of brucellosis. We analysed the polymorphism and associations with disease resistance of the MHC Class II Drb gene and several non-MHC genes (Toll-like receptor genes, Slc11A1) involved in the innate immune response to Brucella in domestic ungulates. We found a very low neutral genetic diversity and a unique MHC Drb haplotype in this population founded few decades ago from a small number of individuals. By contrast, other immunity-related genes have maintained polymorphism and some showed significant associations with the brucellosis infection status hence suggesting a predominant role of pathogen-mediated selection in their recent evolutionary trajectory. Our results highlight the need to monitor immunogenetic variation in wildlife epidemiological studies and to look beyond the MHC.
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Affiliation(s)
- Erwan Quéméré
- CEFS, INRAE, Université de Toulouse, Castanet-Tolosan, France.
- ESE, Ecology and Ecosystems Health, Agrocampus Ouest, INRAE, 35042 Rennes, France.
| | - Sophie Rossi
- Office Français de la Biodiversité, Unité Sanitaire de la Faune, Gap, France
| | - Elodie Petit
- Office Français de la Biodiversité, Unité Ongulés sauvages, Gières, France
| | - Pascal Marchand
- Office Français de la Biodiversité, Unité Ongulés sauvages, Gières, France
| | - Joël Merlet
- CEFS, INRAE, Université de Toulouse, Castanet-Tolosan, France
| | - Yvette Game
- Laboratoire Départemental d'Analyses Vétérinaires de Savoie, Chambéry, France
| | - Maxime Galan
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Emmanuelle Gilot-Fromont
- Université de Lyon, VetAgro Sup - Campus vétérinaire de Lyon, Marcy l'Étoile, France
- Université de Lyon 1, UMR CNRS 5558 Laboratoire de Biométrie et Biologie Evolutive (LBBE), Villeurbanne, France
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14
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Genetic analysis of red deer (Cervus elaphus) administrative management units in a human-dominated landscape. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01248-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
AbstractRed deer (Cervus elaphus) throughout central Europe are influenced by different anthropogenic activities including habitat fragmentation, selective hunting and translocations. This has substantial impacts on genetic diversity and the long-term conservation of local populations of this species. Here we use genetic samples from 480 red deer individuals to assess genetic diversity and differentiation of the 12 administrative management units located in Schleswig Holstein, the northernmost federal state in Germany. We applied multiple analytical approaches and show that the history of local populations (i.e., translocations, culling of individuals outside of designated red deer zones, anthropogenic infrastructures) potentially has led to low levels of genetic diversity. Mean expected heterozygosity was below 0.6 and we observed on average 4.2 alleles across 12 microsatellite loci. Effective population sizes below the recommended level of 50 were estimated for multiple local populations. Our estimates of genetic structure and gene flow show that red deer in northern Germany are best described as a complex network of asymmetrically connected subpopulations, with high genetic exchange among some local populations and reduced connectivity of others. Genetic diversity was also correlated with population densities of neighboring management units. Based on these findings, we suggest that connectivity among existing management units should be considered in the practical management of the species, which means that some administrative management units should be managed together, while the effective isolation of other units needs to be mitigated.
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15
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Tajchman K, Sawicka-Zugaj W, Greguła-Kania M, Drozd L, Czyżowski P. Effect of Translocations on the Genetic Structure in Populations of the Red Deer (Cervus elaphus) in Poland. RUSS J GENET+ 2020. [DOI: 10.1134/s102279541912010x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Ventrella D, Elmi A, Bertocchi M, Aniballi C, Parmeggiani A, Govoni N, Bacci ML. Progesterone and Cortisol Levels in Blood and Hair of Wild Pregnant Red Deer ( Cervus Elaphus) Hinds. Animals (Basel) 2020; 10:E143. [PMID: 31963117 PMCID: PMC7022734 DOI: 10.3390/ani10010143] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 12/31/2022] Open
Abstract
The red deer (Cervus elaphus L., 1758) is one of the largest deer species in the world. Females are seasonal polyestrous, with negative photoperiod: the increase of the night peak of melatonin determines the secretion of GnRH and, therefore, LH and FSH. To date there is little information regarding the hormonal control during pregnancy for this species; this could be due to the difficulty of sampling wild subjects, while farmed animals' hormonal concentrations may not reflect the physiology of the animal in a natural state. In this study we evaluated the concentration of cortisol and progesterone, extracted from blood and hair, on 10 wild and pregnant red deer females. Belonging to the population of the Bolognese Apennines (Italy), the hinds were sampled in the January-March 2018 period, according to the regional selective hunting plan. Plasma progesterone (P4) ranged from a minimum of 1.9 to a maximum of 7.48 ng/mL; while hair P4 concentrations varied from 41.68 to 153.57 pg/mg. The plasma and hair cortisol ranges are respectively 0.4-2.97 ng/mL and 0.03-0.55 pg/mg; the only significant correlation was found between hair concentration of P4 and the date of death. The results of this preliminary study represent a small step towards a better knowledge of this species' physiology during pregnancy.
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Affiliation(s)
| | | | - Martina Bertocchi
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Ozzano dell’Emilia (BO), Italy; (D.V.); (A.E.); (C.A.); (A.P.); (N.G.); (M.L.B.)
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17
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Bieniek-Kobuszewska M, Borkowski J, Panasiewicz G, Nowakowski JJ. Impact of conservation and hunting on big game species: comparison of the genetic diversity of the red deer population groups from a national park and neighboring hunting areas in northern Poland. THE EUROPEAN ZOOLOGICAL JOURNAL 2020. [DOI: 10.1080/24750263.2020.1822936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- M. Bieniek-Kobuszewska
- Department and Clinic of Dermatology, Sexually Transmitted Diseases and Clinical Immunology, Faculty of Medical Sciences, Collegium Medicum, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - J. Borkowski
- Department of Forestry and Forest Ecology, Faculty of Management and Agriculture Sciences, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - G. Panasiewicz
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - J. J. Nowakowski
- Department of Ecology and Environmental Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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18
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Nebel C, Gamauf A, Haring E, Segelbacher G, Väli Ü, Villers A, Zachos FE. New insights into population structure of the European golden eagle (Aquila chrysaetos) revealed by microsatellite analysis. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz130] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractConnectivity between golden eagle (Aquila chrysaetos) populations is poorly understood. Field studies exploring natal dispersal suggest that this raptor is a philopatric species, but with the ability to roam far. However, little is known about the population structure of the species in Europe. Our study is based on 14 microsatellite loci and is complemented by new and previously published mitochondrial control region DNA data. The present dataset includes 121 eagles from Scotland, Norway, Finland, Estonia, the Mediterranean and Alpine regions. Our sampling focused on the Alpine and Mediterranean populations because both mitochondrial DNA (mtDNA) lineages found in golden eagles, the Holarctic and the Mediterranean, are known to co-occur there. Cluster analyses of nuclear DNA support a shallow split into northern and southern populations in Europe, similar to the distribution of the two mtDNA lineages, with the Holarctic lineage occurring in the north and the Mediterranean lineage predominating in the south. Additionally, Scotland shows significant differentiation and low relative migration levels that indicate isolation from the mainland populations. Alpine and Mediterranean golden eagles do not show nuclear structure corresponding to divergent mtDNA lineages. This indicates that the presence of northern Holarctic mitochondrial haplotypes in the Alps and the Mediterranean is attributable to past admixture rather than recent long-distance dispersal.
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Affiliation(s)
- Carina Nebel
- FitzPatrick Institute of African Ornithology, University of Cape Town, Cape Town, South Africa
- Natural History Museum Vienna, Vienna, Austria
| | - Anita Gamauf
- Natural History Museum Vienna, Vienna, Austria
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
| | - Elisabeth Haring
- Natural History Museum Vienna, Vienna, Austria
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
| | | | - Ülo Väli
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Alexandre Villers
- Centre d’Etudes Biologiques de Chizé, UMR7372, CNRS – Université de la Rochelle, Beauvoir sur Niort, France
- Section of Ecology, Department of Biology, University of Turku, Turku, Finland
- Unité Avifaune Migratrice, Office National de la Chasse et de la Faune Sauvage, Station de Chizé, Villiers-en-Bois, France
| | - Frank E Zachos
- Natural History Museum Vienna, Vienna, Austria
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
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19
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Kotzé A, Smith RM, Moodley Y, Luikart G, Birss C, Van Wyk AM, Grobler JP, Dalton DL. Lessons for conservation management: Monitoring temporal changes in genetic diversity of Cape mountain zebra (Equus zebra zebra). PLoS One 2019; 14:e0220331. [PMID: 31365543 PMCID: PMC6668792 DOI: 10.1371/journal.pone.0220331] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 07/12/2019] [Indexed: 11/23/2022] Open
Abstract
The Cape mountain zebra (Equus zebra zebra) is a subspecies of mountain zebra endemic to South Africa. The Cape mountain zebra experienced near extinction in the early 1900's and their numbers have since recovered to more than 4,800 individuals. However, there are still threats to their long-term persistence. A previous study reported that Cape mountain zebra had low genetic diversity in three relict populations and that urgent conservation management actions were needed to mitigate the risk of further loss. As these suggestions went largely unheeded, we undertook the present study, fifteen years later to determine the impact of management on genetic diversity in three key populations. Our results show a substantial loss of heterozygosity across the Cape mountain zebra populations studied. The most severe losses occurred at De Hoop Nature Reserve where expected heterozygosity reduced by 22.85% from 0.385 to 0.297. This is alarming, as the De Hoop Nature Reserve was previously identified as the most genetically diverse population owing to its founders originating from two of the three remaining relict stocks. Furthermore, we observed a complete loss of multiple private alleles from all populations, and a related reduction in genetic structure across the subspecies. These losses could lead to inbreeding depression and reduce the evolutionary potential of the Cape mountain zebra. We recommend immediate implementation of evidence-based genetic management and monitoring to prevent further losses, which could jeopardise the long term survival of Cape mountain zebra, especially in the face of habitat and climate change and emerging diseases.
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Affiliation(s)
- Antoinette Kotzé
- National Zoological Garden, South African National Biodiversity Institute, Pretoria, South Africa
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
| | - Rae M. Smith
- National Zoological Garden, South African National Biodiversity Institute, Pretoria, South Africa
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
| | - Yoshan Moodley
- Department of Zoology, University of Venda, Thohoyandou, Republic of South Africa
| | - Gordon Luikart
- Flathead Lake Biological Station, Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
- Wildlife Program, Fish and Wildlife Genomics Group, College of Forestry and Conservation, University of Montana, Missoula, Montana, United States of America
| | | | - Anna M. Van Wyk
- National Zoological Garden, South African National Biodiversity Institute, Pretoria, South Africa
| | - J. Paul Grobler
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
| | - Desiré L. Dalton
- National Zoological Garden, South African National Biodiversity Institute, Pretoria, South Africa
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
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20
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Reiner G, Lang M, Willems H. Impact of different panels of microsatellite loci, different numbers of loci, sample sizes, and gender ratios on population genetic results in red deer. EUR J WILDLIFE RES 2019. [DOI: 10.1007/s10344-019-1262-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Rutting roars in native Pannonian red deer of Southern Hungary and the evidence of acoustic divergence of male sexual vocalization between Eastern and Western European red deer (Cervus elaphus). Mamm Biol 2019. [DOI: 10.1016/j.mambio.2018.10.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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22
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Bhattacharyya S, Ishtiaq F. Noninvasive sampling reveals population genetic structure in the Royle's pika, Ochotona roylei, in the western Himalaya. Ecol Evol 2019; 9:180-191. [PMID: 30680105 PMCID: PMC6342111 DOI: 10.1002/ece3.4707] [Citation(s) in RCA: 5] [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: 01/12/2018] [Revised: 10/11/2018] [Accepted: 10/22/2018] [Indexed: 11/09/2022] Open
Abstract
Understanding population genetic structure of climate-sensitive herbivore species is important as it provides useful insights on how shifts in environmental conditions can alter their distribution and abundance. Herbivore responses to the environment can have a strong indirect cascading effect on community structure. This is particularly important for Royle's pika (Lagomorpha: Ochotona roylei), a herbivorous talus-dwelling species in alpine ecosystem, which forms a major prey base for many carnivores in the Himalayan arc. In this study, we used seven polymorphic microsatellite loci to detect evidence for recent changes in genetic diversity and population structure in Royle's pika across five locations sampled between 8 and 160 km apart in the western Himalaya. Using four clustering approaches, we found the presence of significant contemporary genetic structure in Royle's pika populations. The detected genetic structure could be primarily attributed to the landscape features in alpine habitat (e.g., wide lowland valleys, rivers) that may act as semipermeable barriers to gene flow and distribution of food plants, which are key determinants in spatial distribution of herbivores. Pika showed low inbreeding coefficients (F IS) and a high level of pairwise relatedness for individuals within 1 km suggesting low dispersal abilities of talus-dwelling pikas. We have found evidence of a recent population bottleneck, possibly due to effects of environmental disturbances (e.g., snow melting patterns or thermal stress). Our results reveal significant evidence of isolation by distance in genetic differentiation (F ST range = 0.04-0.19). This is the first population genetics study on Royle's pika, which helps to address evolutionary consequences of climate change which are expected to significantly affect the distribution and population dynamics in this talus-dwelling species.
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Affiliation(s)
| | - Farah Ishtiaq
- Centre for Ecological SciencesIndian Institute of ScienceBangaloreIndia
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23
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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: 1.0] [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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24
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Frantz AC, Zachos FE, Bertouille S, Eloy MC, Colyn M, Flamand MC. Using genetic tools to estimate the prevalence of non-native red deer ( Cervus elaphus) in a Western European population. Ecol Evol 2017; 7:7650-7660. [PMID: 29043022 PMCID: PMC5632609 DOI: 10.1002/ece3.3282] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/30/2017] [Accepted: 06/28/2017] [Indexed: 01/17/2023] Open
Abstract
Game species like the red deer have been subjected to anthropogenic impacts for centuries. Translocations are often carried out—sometimes illegally—not only for sporting purposes, but also to increase trophy quality, reduce inbreeding, or mitigate bottlenecks after excessive persecution. Apart from the blurring of large‐scale genetic structure, translocations without adequate quarantine measure risk introducing pathogens into potentially immunologically naïve populations. It is therefore important to understand the frequency of clandestine translocations. Identification of non‐autochthonous animals and their potential origin is often difficult and, in red deer, has been hampered by the lack of large‐scale genotypic datasets for comparison. In the present study, we make use of a recently published European‐wide microsatellite dataset to detect and quantify the presence of non‐autochthonous red deer in a large population sample (n = 1,780) from Central Europe (Belgium). Using factorial correspondence analysis, assignment tests and Bayesian clustering algorithms we arrive at an estimate of 3.7% non‐autochthonous animals (or their descendants). Some of these animals were assigned to a nearby French population and may have immigrated into Belgium naturally, but the large majority must have been introduced by humans. Our analysis pointed to the British Isles and Germany/Poland as the potential origin of many introduced deer, regions known to have been source populations for translocations in Europe and beyond. We found evidence for recreational hunters using carcasses from farmed deer to fulfill mandatory hunting quotas. Our study is the first to quantify the extent of human‐mediated introductions in a European game species at such a large scale with large and representative sample sizes.
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Affiliation(s)
- Alain C Frantz
- Musée National d'Histoire Naturelle Luxembourg Luxembourg.,Fondation faune-flore Luxembourg Luxembourg
| | | | - Sabine Bertouille
- Département de l'Etude du Milieu naturel et agricole Service Public de Wallonie Gembloux Belgium
| | - Marie-Christine Eloy
- Institut des Sciences de la Vie Université catholique de Louvain Louvain-la-Neuve Belgium
| | - Marc Colyn
- CNRS-UMR 6553 Université de Rennes 1 Paimpont France
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25
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Konishi S, Hata S, Matsuda S, Arai K, Mizoguchi Y. Evaluation of the genetic structure of sika deer (Cervus nippon
) in Japan's Kanto and Tanzawa mountain areas, based on microsatellite markers. Anim Sci J 2017. [DOI: 10.1111/asj.12844] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sayaka Konishi
- Graduate School of Agriculture; Meiji University; Tama-ku Kawasaki Kanagawa Japan
| | - Shoko Hata
- Tokyo Metropolitan Agriculture and Forestry Research Center; Fujimi-cho Tachikawa Tokyo Japan
| | - Sayumi Matsuda
- School of Agriculture; Meiji University; Tama-ku Kawasaki Kanagawa Japan
| | - Kazushi Arai
- Tokyo Metropolitan Agriculture and Forestry Research Center; Fujimi-cho Tachikawa Tokyo Japan
| | - Yasushi Mizoguchi
- School of Agriculture; Meiji University; Tama-ku Kawasaki Kanagawa Japan
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26
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Doan K, Zachos FE, Wilkens B, Vigne JD, Piotrowska N, Stanković A, Jędrzejewska B, Stefaniak K, Niedziałkowska M. Phylogeography of the Tyrrhenian red deer (Cervus elaphus corsicanus) resolved using ancient DNA of radiocarbon-dated subfossils. Sci Rep 2017; 7:2331. [PMID: 28539631 PMCID: PMC5443832 DOI: 10.1038/s41598-017-02359-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/10/2017] [Indexed: 11/12/2022] Open
Abstract
We present ancient mitochondrial DNA analyses of 31 complete cytochrome b gene sequences from subfossil red deer remains from the Tyrrhenian islands (Corsica and Sardinia) and mainland Italy in a European-wide phylogeographic framework. Tyrrhenian and North African red deer, both going back to human introductions, were previously the only red deer to harbour the mitochondrial B lineage whose origin, however, remained unknown. Our ancient Italian samples from the central part of the peninsula that were radiocarbon-dated to an age of ca. 6300 to 15 600 cal BP all showed B haplotypes, closely related or even identical to those found on Sardinia. Genetic diversity in the mainland population was considerably higher than on the islands. Together with palaeontological evidence our genetic results identify the Italian Peninsula as the ultimate origin of the B lineage and thus the Tyrrhenian and North African red deer. This is in line with previous biogeographic findings that uncovered distinct intraspecific phylogeographic lineages in Italian mammals, underlining Italy’s status as a hotspot of European mammalian diversity.
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Affiliation(s)
- K Doan
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Warsaw, Poland
| | - F E Zachos
- Natural History Museum Vienna, 1010, Vienna, Austria.
| | - B Wilkens
- Department of Nature and Environmental Science, University of Sassari, Sassari, Italy
| | - J-D Vigne
- Muséum National d'Histoire Naturelle - CNRS (InEE) - Sorbonne Universités, Archaeozoology, Archaeobotany, Paris, France
| | - N Piotrowska
- Radiocarbon Laboratory Institute of Physics - Center for Science and Education, Silesian University of Technology, 44-100, Gliwice, Poland
| | - A Stanković
- Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland.,Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106, Warsaw, Poland.,The Antiquity of Southeastern Europe Research Centre, University of Warsaw, Warsaw, Poland
| | - B Jędrzejewska
- Mammal Research Institute Polish Academy of Sciences, 17-230, Białowieża, Poland
| | - K Stefaniak
- Department of Palaeozoology, University of Wrocław, 50-335, Wrocław, Poland
| | - M Niedziałkowska
- Mammal Research Institute Polish Academy of Sciences, 17-230, Białowieża, Poland
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27
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Baker KH, Gray HWI, Ramovs V, Mertzanidou D, Akın Pekşen Ç, Bilgin CC, Sykes N, Hoelzel AR. Strong population structure in a species manipulated by humans since the Neolithic: the European fallow deer (Dama dama dama). Heredity (Edinb) 2017; 119:16-26. [PMID: 28353685 PMCID: PMC5520134 DOI: 10.1038/hdy.2017.11] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 02/08/2017] [Accepted: 02/09/2017] [Indexed: 01/24/2023] Open
Abstract
Species that have been translocated and otherwise manipulated by humans may show
patterns of population structure that reflect those interactions. At the same time,
natural processes shape populations, including behavioural characteristics like
dispersal potential and breeding system. In Europe, a key factor is the geography and
history of climate change through the Pleistocene. During glacial maxima throughout
that period, species in Europe with temperate distributions were forced south,
becoming distributed among the isolated peninsulas represented by Anatolia, Italy and
Iberia. Understanding modern patterns of diversity depends on understanding these
historical population dynamics. Traditionally, European fallow deer (Dama dama
dama) are thought to have been restricted to refugia in Anatolia and possibly
Sicily and the Balkans. However, the distribution of this species was also greatly
influenced by human-mediated translocations. We focus on fallow deer to better
understand the relative influence of these natural and anthropogenic processes. We
compared modern fallow deer putative populations across a broad geographic range
using microsatellite and mitochondrial DNA loci. The results revealed highly insular
populations, depauperate of genetic variation and significantly differentiated from
each other. This is consistent with the expectations of drift acting on populations
founded by small numbers of individuals, and reflects known founder populations in
the north. However, there was also evidence for differentiation among (but not
within) physically isolated regions in the south, including Iberia. In those regions
we find evidence for a stronger influence from natural processes than may be expected
for a species with such strong, known anthropogenic influence.
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Affiliation(s)
- K H Baker
- School of Biological and Biomedical Sciences, Durham University, Durham, UK
| | - H W I Gray
- School of Biological and Biomedical Sciences, Durham University, Durham, UK
| | - V Ramovs
- School of Biological and Biomedical Sciences, Durham University, Durham, UK
| | - D Mertzanidou
- Department of Biology, University of Athens, Athens, Greece
| | - Ç Akın Pekşen
- Department of Biology, Middle East Technical University, Ankara, Turkey.,Department of Molecular Biology and Genetics, Yüzüncü Yıl University, Van, Turkey
| | - C C Bilgin
- Department of Biology, Middle East Technical University, Ankara, Turkey
| | - N Sykes
- Department of Archaeology, University of Nottingham, Nottinghamshire, UK
| | - A R Hoelzel
- School of Biological and Biomedical Sciences, Durham University, Durham, UK
| |
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