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Not all is black and white: phylogeography and population genetics of the endemic blackbuck (Antilope cervicapra). CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01479-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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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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Phylogeography of sika deer (Cervus nippon) inferred from mitochondrial cytochrome-b gene and microsatellite DNA. Gene 2020; 772:145375. [PMID: 33359125 DOI: 10.1016/j.gene.2020.145375] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/07/2020] [Accepted: 12/15/2020] [Indexed: 11/24/2022]
Abstract
The genetic diversity and phylogenetic relationships of sika deer of different subspecies are uncertain. In order to explore the phylogenetic relationship of different sika deer subspecies, this study used a wider sample collection to analyze mitochondrial sequences and nuclear microsatellites of sika deer. The full lengths of cytochrome-b gene of 134 sika deer were sequenced, and 16 haplotypes were obtained. Based on phylogenetic and haplotype networks analysis, the sika deer was not clustered according to subspecies but was divided into four lineages. Lineage I includes individuals from C.n.kopschi, C.n.sichuanicus, and C.n.hortulorum subspecies; Lineage II includes individuals from C.n.hortulorum subspecies; Lineage III includes individuals from C.n.centralis, C.n.yakushime, C.n.mageshimae, and C.n.keramae subspecies, namely southern Japanese population; Lineage IV includes individuals from C.n.centralis and C.n.yesoensis subspecies, namely northern Japanese population. The microsatellite analysis showed that the sika deer in China and Japan originated independently. The three subspecies of China have significant genetic differentiation, while the three subspecies of Japan have no significant differentiation. This study provides reference for the research of genetic diversity and phylogenetic relationship of sika deer, and also provides scientific data for the evaluation, protection, and utilization of sika deer resources.
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Reiner G, Weber T, Nietfeld F, Fischer D, Wurmser C, Fries R, Willems H. A genome-wide scan study identifies a single nucleotide substitution in MC1R gene associated with white coat colour in fallow deer (Dama dama). BMC Genet 2020; 21:126. [PMID: 33213385 PMCID: PMC7678172 DOI: 10.1186/s12863-020-00950-3] [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: 02/07/2020] [Accepted: 11/10/2020] [Indexed: 11/10/2022] Open
Abstract
Background The coat colour of fallow deer is highly variable and even white animals can regularly be observed in game farming and in the wild. Affected animals do not show complete albinism but rather some residual pigmentation resembling a very pale beige dilution of coat colour. The eyes and claws of the animals are pigmented. To facilitate the conservation and management of such animals, it would be helpful to know the responsible gene and causative variant. We collected 102 samples from 22 white animals and from 80 animals with wildtype coat colour. The samples came from 12 different wild flocks or game conservations located in different regions of Germany, at the border to Luxembourg and in Poland. The genomes of one white hind and her brown calf were sequenced. Results Based on a list of colour genes of the International Federation of Pigment Cell Societies (http://www.ifpcs.org/albinism/), a variant in the MC1R gene (NM_174108.2:c.143 T > C) resulting in an amino acid exchange from leucine to proline at position 48 of the MC1R receptor protein (NP_776533.1:p.L48P) was identified as a likely cause of coat colour dilution. A gene test revealed that all animals of the white phenotype were of genotype CC whereas all pigmented animals were of genotype TT or TC. The study showed that 14% of the pigmented (brown or dark pigmented) animals carried the white allele. Conclusions A genome-wide scan study led to a molecular test to determine the coat colour of fallow deer. Identification of the MC1R gene provides a deeper insight into the mechanism of dilution. The gene marker is now available for the conservation of white fallow deer in wild and farmed animals. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-020-00950-3.
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Affiliation(s)
- Gerald Reiner
- Department for Veterinary Clinical Science, Justus-Liebig-University, Frankfurter Strasse 112, D-35392, Giessen, Germany. .,Arbeitskreis Wildbiologie e.V., Justus-Liebig-University, Giessen, Germany.
| | - Tim Weber
- Department for Veterinary Clinical Science, Justus-Liebig-University, Frankfurter Strasse 112, D-35392, Giessen, Germany
| | - Florian Nietfeld
- Department for Veterinary Clinical Science, Justus-Liebig-University, Frankfurter Strasse 112, D-35392, Giessen, Germany
| | - Dominik Fischer
- Arbeitskreis Wildbiologie e.V., Justus-Liebig-University, Giessen, Germany
| | - Christine Wurmser
- Department of Animal Breeding, Technical University of Munich, Liesel-Beckmann-Strasse 1, D-85354, Freising-Weihenstephan, Germany
| | - Ruedi Fries
- Department of Animal Breeding, Technical University of Munich, Liesel-Beckmann-Strasse 1, D-85354, Freising-Weihenstephan, Germany
| | - Hermann Willems
- Department for Veterinary Clinical Science, Justus-Liebig-University, Frankfurter Strasse 112, D-35392, Giessen, Germany
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Takagi T, Matsumoto Y, Koda R, Tamate HB. Bi-Directional Movement of Deer between Tomogashima Islands and the Western Part of the Kii Peninsula, Japan, with Special Reference to Hybridization between the Japanese Sika Deer (Cervus nippon centralis) and the Introduced Exotic Deer. MAMMAL STUDY 2020. [DOI: 10.3106/ms2019-0048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Toshihito Takagi
- Graduate School of Science and Engineering, Yamagata University, Kojirakawa 1-4-12, Yamagata City, Yamagata 990-8560, Japan
| | - Yuki Matsumoto
- Research and Development Section, Anicom Specialty Medical Institute Inc., 2-6-3 Chojamachi 4F, Yokohamashi-Nakaku, Kanagawa 231-0033, Japan
| | - Ryosuke Koda
- Research Institute of Environment, Agriculture and Fisheries, Osaka Prefecture, 10-4 Koyamotomachi, Neyagawa, Osaka 572-0088, Japan
| | - Hidetoshi B. Tamate
- Faculty of Science, Yamagata University, Kojirakawa 1-4-12, Yamagata City, Yamagata 990-8560, Japan
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A genome-wide scan study identifies a single nucleotide substitution in the tyrosinase gene associated with white coat colour in a red deer (Cervus elaphus) population. BMC Genet 2020; 21:14. [PMID: 32041521 PMCID: PMC7011275 DOI: 10.1186/s12863-020-0814-0] [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: 04/15/2019] [Accepted: 01/20/2020] [Indexed: 12/19/2022] Open
Abstract
Background Red deer with very pale coat colour are observed sporadically. In the red deer (Cervus elaphus) population of Reinhardswald in Germany, about 5% of animals have a white coat colour that is not associated with albinism. In order to facilitate the conservation of the animals, it should be determined whether and to what extent brown animals carry the white gene. For this purpose, samples of one white hind and her brown calf were available for whole genome sequencing to identify the single nucleotide polymorphism(s) responsible for the white phenotype. Subsequently, samples from 194 brown and 11 white animals were genotyped. Results Based on a list of colour genes of the International Federation of Pigment Cell Societies, a non-synonymous mutation with exchange of a glycine residue at position 291 of the tyrosinase protein by arginine was identified as the cause of dilution of the coat colour. A gene test led to exactly matching genotypes in all examined animals. The study showed that 14% of the brown animals carry the white gene. This provides a simple and reliable way of conservation for the white animals. However, results could not be transferred to another, unrelated red deer population with white animals. Although no brown animals with a white tyrosinase genotype were detected, the cause for the white colouring in this population was different. Conclusions A gene test for the conservation of white red deer is available for the population of the Reinhardswald. While mutations in the tyrosinase are commonly associated with oculocutaneous albinism type 1, the amino acid exchange at position 291 was found to be associated with coat colour dilution in Cervus elaphus.
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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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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: 4.2] [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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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: 2.3] [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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Yang W, Zheng J, Jia B, Wei H, Wang G, Yang F. Isolation of novel microsatellite markers and their application for genetic diversity and parentage analyses in sika deer. Gene 2017; 643:68-73. [PMID: 29223356 DOI: 10.1016/j.gene.2017.12.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 11/21/2017] [Accepted: 12/06/2017] [Indexed: 01/30/2023]
Abstract
Every part of the sika deer (Cervus nippon) body is valuable traditional Chinese medicine. And sika deer is the most important semi-domestic medicinal animal that is widely bred in Jilin province northeast of China. But few studies had been conducted to characterize the microsatellite markers derived from sika deer. We firstly used IlluminaHiSeq™2500 sequencing technology obtained 125Mbp genomic data of sika deer. Using microsatellite identification tool (MISA), 22,479 microsatellites were identified. From these data, 100 potential primers were selected for further polymorphic validation, finally, 76 primer pairs were successfully amplified and 29 primer pairs were found to be obvious polymorphic in 8 different individuals. Using those polymorphic microsatellite markers, we analyzed the genetic diversity of Jilin sika deer population. The mean number of alleles of the 29 loci is 9.31 based on genotyping blood DNA from 96 Jilin sika deer; The mean expected heterozygosity and polymorphic information content (PIC) value of the 29 loci is 0.72 and 0.68 respectively, and among which 26 loci are highly polymorphic (PIC>0.50). According to the electrophoretic results and PIC value of these 29 loci, 10 loci with combined paternity exclusion probabilities>99.99% were selected to use in parentage verification for 16 sika deer. All the offspring of a family could be successfully assigned to their biological father. These microsatellite markers generated in this study could greatly facilitate future studies of molecular breeding in sika deer.
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Affiliation(s)
- Wanyun Yang
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Junjun Zheng
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China.
| | - Boyin Jia
- School of Animal Science & Technology, Jilin Agricultural University, Changchun 130118, China
| | - Haijun Wei
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Guiwu Wang
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China.
| | - Fuhe Yang
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China.
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Radko A, Zalewski D, Rubiś D, Szumiec A. Genetic differentiation among 6 populations of red deer (Cervus elaphus L.) in Poland based on microsatellite DNA polymorphism. ACTA BIOLOGICA HUNGARICA 2014; 65:414-27. [PMID: 25475981 DOI: 10.1556/abiol.65.2014.4.6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Recently, there has been considerable interest in genetic differentiation in the Cervidae family. A common tool used to determine genetic variation in different species, breeds and populations is DNA analysis, which allows for direct determination of the differences and changes within a group of animals. Because the analysis of microsatellite polymorphism in different Cervidae populations revealed considerable genetic variability in individual populations, it was important to test a set of markers in animals from these populations.The study was performed with muscle tissue and blood samples collected from a total of 793 red deer. Six groups (subpopulations) of red deer were defined according to region: Masurian (330 animals), Bieszczady (194 animals), Małopolska (80 animals), Sudety (76 animals), Lower Silesian (62 animals) and Lubusz (51 animals). The analysis involved 12 STR markers (BM1818, OarAE129, OarFCB5, OarFCB304, RM188, RT 1, RT 13, T26, T156, T193, T501, TGLA53), for which conditions for simultaneous amplification were established.Based on this study, it is concluded that the chosen set of 12 microsatellite markers could be used to evaluate the genetic structure and to monitor changes in Poland's red deer population.
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Affiliation(s)
- Anna Radko
- National Research Institute of Animal Production Department of Animal Cytogenetics and Molecular Genetics Krakowska 1 32-083 Balice Poland
| | - D Zalewski
- University of Warmia and Mazury in Olsztyn Department of Fur-bearing Animal Breeding and Game Management Oczapowskiego 5 10-719 Olsztyn Poland
| | - Dominika Rubiś
- National Research Institute of Animal Production Department of Animal Cytogenetics and Molecular Genetics Krakowska 1 32-083 Balice Poland
| | - Agnieszka Szumiec
- National Research Institute of Animal Production Department of Animal Cytogenetics and Molecular Genetics Krakowska 1 32-083 Balice Poland
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12
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Genetic diversity analysis by microsatellite markers in four captive populations of the sika deer (Cervus nippon). BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.07.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Vietoris V, Czako P, Mendelová A, Remeňová Z, Závracký M. Relations between must clarification and organoleptic attributes of wine varietes. POTRAVINARSTVO 2014. [DOI: 10.5219/359] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Blowdown musts is important operation performed in winemaking, which can have a major impact on the future quality of the wine. Blowdown of the wine removes components that may carry elements that negatively affect the hygienic and sensory quality of the wine. Fining of musts and wines is carried either by a static method or using different fining preparations. The aim of this work was to evaluate the effect of different methods of decanting on the wine quality varieties of Sauvignon. The overall sensory quality was evaluated (100 - points system, and semantic differential) and the aromatic profile (profile method). All sensory evaluations were practiced by skilled sensory panel in controled conditions of Faculty sensory lab. Wine samples were clarified by static manner or with the assistance of the preparation applied to the clarification of wine in two different doses. By the results and their visualization of flavour and smell profile by spider plots we could conclude that pure cultures have positive effect on processed wine. Based on the results we found a beneficial effect of clearing by the clarification of the preparation based on cellulose, polyvinylpolypyrrolidone, gelatin and mineral adsorbents at 100 g.100 L-1 of the sensory quality of the wine.
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Yamashiro A, Yamashiro T, Mori K, Kamada M. Indirect estimation of Recent Sika Deer (Cervus nippon) Migration in Tsurugi Quasi-National Park, Shikoku, Japan. MAMMAL STUDY 2014. [DOI: 10.3106/041.039.0203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Maršálková L, Židek R, Pokoradi J, Golian J, Belej Ľ. Genetic diversity and relatedness among seven red deer (Cervus elaphus) populations. POTRAVINARSTVO 2014. [DOI: 10.5219/320] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Deer (Cervidae) recently belongs to the most important species. The aim of presenting study was evaluation of genetic diversity and relationship within and among seven red deer populations from different origins - Czech Republic, Hungary, hybrids Hungary x New Zealand, Lithuania, New Zealand, Poland and Slovak Republic. This study was conducted to determine the levels of genetic variability and relationships among deer populations from a total of 637 animals originating from seven countries Czech Republic (50), Hungary (35), Hungary x New Zealand hybrids (67), Lithuania (26), New Zealand (82), Poland (347) and Slovak Republic (30). We used the hair bulbs as a source of DNA. In total, 213 alleles were observed from the 10 loci surveyed. The number of alleles per locus ranged from 11 (IOBT965) to 35 (T156, RT13). Genetic diversity and relatedness among red deer populations has been performed on a total of 637 animals. A panel of 10 microsatellite markers used in deer were optimized. On the basis of this panel of microsatellites we were investigated genetic variability and relationships by using statistical and graphical programmes. We evaluated how close populations are to each other and their genetic admixture. Molecular genetic data combined with evaluation in statistical programmes could lead to a complex view of populations.
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Smith SL, Carden RF, Coad B, Birkitt T, Pemberton JM. A survey of the hybridisation status of Cervus deer species on the island of Ireland. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0582-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Tsubono K, Taniguchi Y, Matsuda H, Yamada T, Sugiyama T, Homma K, Kaneko Y, Yamagishi S, Iwaisaki H. Identification of novel genetic markers and evaluation of genetic structure in a population of Japanese crested ibis. Anim Sci J 2013; 85:356-64. [PMID: 24330458 DOI: 10.1111/asj.12155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 09/03/2013] [Indexed: 11/28/2022]
Abstract
Japanese population of the Japanese crested ibis Nipponia nippon was founded by five individuals gifted from the People's Republic of China. In order to exactly evaluate genetic structure, we first performed development of novel genetic makers using 89 microsatellite primer pairs of related species for cross-amplification. Of these, only three primer pairs were useful for the genetic markers. Additionally, we sequenced allelic PCR products of these three markers together with 10 markers previously identified. Most markers showed typical microsatellite repeat units, but two markers were not simple microsatellites. Moreover, over half of the markers did not have the same repeat units as those of the original species. These results suggested that development of novel genetic markers in this population by cross-amplification is not efficient, partly because of low genetic diversity. Furthermore, the cluster analysis by STRUCTURE program using 17 markers showed that the five founders were divided into two clusters. However, the genetic relationships among the founders indicated by the clustering seemed to be questionable, because the analysis relied largely on a small number of triallelic markers, in spite of the addition of the three useful markers. Therefore, more efficient methods for identifying large numbers of single nucleotide polymorphisms are desirable.
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Affiliation(s)
- Kanako Tsubono
- Laboratory of Animal Breeding and Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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Ou W, Takekawa S, Yamada T, Terada C, Uno H, Nagata J, Masuda R, Kaji K, Saitoh T. Temporal change in the spatial genetic structure of a sika deer population with an expanding distribution range over a 15-year period. POPUL ECOL 2013. [DOI: 10.1007/s10144-013-0425-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Urano K, Tsubono K, Taniguchi Y, Matsuda H, Yamada T, Sugiyama T, Homma K, Kaneko Y, Yamagishi S, Iwaisaki H. Genetic diversity and structure in the Sado captive population of the Japanese crested ibis. Zoolog Sci 2013; 30:432-8. [PMID: 23721466 DOI: 10.2108/zsj.30.432] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The Japanese crested ibis Nipponia nippon is a critically threatened bird. We assessed genetic diversity and structure in the Sado captive population of the Japanese crested ibis based on 24 and 50 microsatellite markers developed respectively for the same and related species. Of a total of 74 loci, 19 showed polymorphisms in the five founder birds of the population, and therefore were useful for the analysis of genetic diversity and structure. Genetic diversity measures, A, ne, He, Hoand PIC, obtained by genotyping of the 138 descendants were similar to those of other species with population bottlenecks, and thus considerably low. The low level of genetic diversity resulting from such bottlenecks was consistent with the results of lower genetic diversity measures for the Sado captive relative to the Chinese population that is the source population for the Sado group as determined using previously reported data and heterozygosity excess by Hardy-Weinberg equilibrium tests. Further, individual clustering based on the allele-sharing distance and Bayesian model-based clustering revealed that the founder genomes were equally at population in total, and with various admixture patterns at individual levels inherited by the descendants. The clustering results, together with the result of inheritance of all alleles of the microsatellites from the founders to descendants, suggest that planned mating in captive-breeding programs for the population has succeeded in maintaining genetic diversity and minimizing kinship. In addition, the Bayesian model-based clustering assumed two different components of genomes in the Sado captive Japanese crested ibis, supporting a considerably low level of genetic diversity.
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Affiliation(s)
- Kensuke Urano
- Laboratory of Animal Breeding and Genetics, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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Höglund J, Cortazar-Chinarro M, Jarnemo A, Thulin CG. Genetic variation and structure in Scandinavian red deer (Cervus elaphus): influence of ancestry, past hunting, and restoration management. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12049] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jacob Höglund
- Population Biology and Conservation Biology; Department of Ecology and Evolution; EBC; Uppsala University; SE-752 36; Uppsala; Sweden
| | - Maria Cortazar-Chinarro
- Population Biology and Conservation Biology; Department of Ecology and Evolution; EBC; Uppsala University; SE-752 36; Uppsala; Sweden
| | - Anders Jarnemo
- Grimsö Wildlife Research Station; Department of Ecology; Swedish University of Agricultural Sciences; SE-730 91; Riddarhyttan; Sweden
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Matsumoto T, Samuel MD, Bollinger T, Pybus M, Coltman DW. Association mapping of genetic risk factors for chronic wasting disease in wild deer. Evol Appl 2012; 6:340-52. [PMID: 23467626 PMCID: PMC3586622 DOI: 10.1111/eva.12003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 07/11/2012] [Indexed: 01/06/2023] Open
Abstract
Chronic wasting disease (CWD) is a fatal transmissible spongiform encephalopathy affecting North American cervids. We assessed the feasibility of association mapping CWD genetic risk factors in wild white-tailed deer (Odocoileus virginianus) and mule deer (Odocoileus hemionus) using a panel of bovine microsatellite markers from three homologous deer linkage groups predicted to contain candidate genes. These markers had a low cross-species amplification rate (27.9%) and showed weak linkage disequilibrium (<1 cM). Markers near the prion protein and the neurofibromin 1 (NF1) genes were suggestively associated with CWD status in white-tailed deer (P = 0.006) and mule deer (P = 0.02), respectively. This is the first time an association between the NF1 region and CWD has been reported.
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Affiliation(s)
- Tomomi Matsumoto
- Department of Biological Sciences, University of Alberta Edmonton, AB, Canada
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Niedziałkowska M, Jędrzejewska B, Wójcik JM, Goodman SJ. Genetic structure of red deer population in northeastern Poland in relation to the history of human interventions. J Wildl Manage 2012. [DOI: 10.1002/jwmg.367] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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23
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Niedziałkowska M, Fontaine M, Jędrzejewska B. Factors shaping gene flow in red deer (Cervus elaphus) in seminatural landscapes of central Europe. CAN J ZOOL 2012. [DOI: 10.1139/z11-122] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We studied gene flow and connectivity between three subpopulations and nine groups of red deer ( Cervus elaphus L., 1758) occurring in forests in northeastern Poland and western Belarus. The red deer in this region mostly originated from translocated individuals that were introduced primarily in the 19th and 20th centuries. The genetic structure of the population has been identified during the previous study. Using 14 microsatellite loci, we detected 14 first-generation migrants between the three subpopulations and 21 among the nine groups of deer. The number of effective migrants (Nm) was estimated to be 2.5 individuals/generation between the subpopulations and 6.2 individuals/generation between the groups. About 80% of first-generation migrants moved less than 150 km. The gene flow of hinds and stags was similar. A least cost path (LCP) analysis was performed using different habitat types: deciduous and mixed forests, coniferous forests, wetlands, meadows, arable lands, scarce settlements, dense settlements, and waters. No significant barriers to dispersal were detected, but individual dispersal was restricted in space by the significant isolation by distance. The best model, explaining the genetic distance (FST/1 – FST) between the forests, suggested that LCP corridor length limited gene flow and high forest cover within LCP corridors increased gene flow among the forests.
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Affiliation(s)
- M. Niedziałkowska
- Mammal Research Institute, Polish Academy of Sciences, 17-230 Białowieża, Poland
| | - M.C. Fontaine
- Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Université Paris-Sud, Laboratoire Ecologie, Systématique et Evolution, UMR 8079, Orsay CEDEX, F-91405; CNRS, UMR 8079, Orsay CEDEX, F-91405
| | - B. Jędrzejewska
- Mammal Research Institute, Polish Academy of Sciences, 17-230 Białowieża, Poland
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Singh BK, Thakur AK, Tiwari SK, Siddiqui SA, Singh VV, Rai PK. Transferability of Brassica-Derived Microsatellites to Related Genera and their Implications for Phylogenetic Analysis. NATIONAL ACADEMY SCIENCE LETTERS 2012. [DOI: 10.1007/s40009-011-0006-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Genetic diversity, population genetic structure and demographic history of Przewalski’s gazelle (Procapra przewalskii): implications for conservation. CONSERV GENET 2011. [DOI: 10.1007/s10592-011-0244-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Yang J, Jiang Z, Zeng Y, Turghan M, Fang H, Li C. Effect of anthropogenic landscape features on population genetic differentiation of Przewalski's gazelle: main role of human settlement. PLoS One 2011; 6:e20144. [PMID: 21625459 PMCID: PMC3098875 DOI: 10.1371/journal.pone.0020144] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Accepted: 04/26/2011] [Indexed: 11/18/2022] Open
Abstract
Anthropogenic landscapes influence evolutionary processes such as population genetic differentiation, however, not every type of landscape features exert the same effect on a species, hence it is necessary to estimate their relative effect for species management and conservation. Przewalski's gazelle (Procapra przewalskii), which inhabits a human-altered area on Qinghai-Tibet Plateau, is one of the most endangered antelope species in the world. Here, we report a landscape genetic study on Przewalski's gazelle. We used skin and fecal samples of 169 wild gazelles collected from nine populations and thirteen microsatellite markers to assess the genetic effect of anthropogenic landscape features on this species. For comparison, the genetic effect of geographical distance and topography were also evaluated. We found significant genetic differentiation, six genetic groups and restricted dispersal pattern in Przewalski's gazelle. Topography, human settlement and road appear to be responsible for observed genetic differentiation as they were significantly correlated with both genetic distance measures [FST/(1−FST) and F′ST/(1−F′ST)] in Mantel tests. IBD (isolation by distance) was also inferred as a significant factor in Mantel tests when genetic distance was measured as FST/(1−FST). However, using partial Mantel tests, AICc calculations, causal modeling and AMOVA analysis, we found that human settlement was the main factor shaping current genetic differentiation among those tested. Altogether, our results reveal the relative influence of geographical distance, topography and three anthropogenic landscape-type on population genetic differentiation of Przewalski's gazelle and provide useful information for conservation measures on this endangered species.
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Affiliation(s)
- Ji Yang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Zhigang Jiang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
- * E-mail:
| | - Yan Zeng
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Mardan Turghan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Hongxia Fang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Chunwang Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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Weissenberger M, Reichert W, Mattern R. A Multiplex PCR assay to differentiate between dog and red fox. Forensic Sci Int Genet 2010; 5:411-4. [PMID: 20884310 DOI: 10.1016/j.fsigen.2010.08.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Revised: 08/23/2010] [Accepted: 08/26/2010] [Indexed: 10/19/2022]
Abstract
Foxes are frequently the cause of car accidents in Baden-Württemberg (BW, Germany). The domestic dog (Canis familiaris) is in close relation to the red fox (Vulpes vulpes) and the silver fox which is a coat colour variant of the red fox. As insurance claims that involve accidents with animals require authentication, we analyzed frequency distribution and allele sizes in two canine microsatellite loci in 26 dogs (different breeds) and 19 red foxes of the region of BW, Germany. Moreover, sequencing analysis was performed. Red foxes exhibited only 1 allele at each microsatellite locus, whereas in dog 7 alleles at the CPH4 locus and 6 alleles at the CPH12 locus were detected. Sequences of PCR products from the two species revealed several differences between dogs and foxes. We established a sequenced allelic ladder and give population data from dogs and red foxes from the region of BW, Germany. Using microsatellite polymorphisms is efficient in differentiating between dogs and foxes in forensic casework.
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Affiliation(s)
- M Weissenberger
- Institute of Legal Medicine, University of Heidelberg, Voßstr. 2, 69115 Heidelberg, Germany.
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Barrera-Saldaña H, Ascacio-Martínez J, Sifuentes-Rincón A, Arellano-Vera W, Arbiza S. Applications of biotechnology and genomics in goats. Small Rumin Res 2010. [DOI: 10.1016/j.smallrumres.2009.12.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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29
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Silva RW, de Freitas TRO, Sbalqueiro IJ. Evaluation of genetic variability in the collared peccary Pecari tajacu and the white-lipped peccary Tayassu pecari by microsatellite markers. Genet Mol Biol 2010; 33:62-7. [PMID: 21637606 PMCID: PMC3036067 DOI: 10.1590/s1415-47572010005000002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2008] [Accepted: 07/01/2009] [Indexed: 11/26/2022] Open
Abstract
In this study, the microsatellite technique was used to evaluate the genetic variability in populations of collared and white-lipped peccaries kept in captivity. Six primers developed for domestic pigs were used and amplified in both species. They revealed the presence of five polymorphic loci and one monomorphic locus. The polymorphic loci included 4 of the 16 alleles in collared peccaries, and 3 of the 10 alleles in the white-lipped peccaries. Polymorphic information content (PIC) in both species and all the loci was highly informative. The probability of paternity exclusion (PEC), if one of the parents is known, was almost as high in white-lipped peccaries (95.53%) as in the collared (99,48%). The Fst values for collared (0.042) and white-lipped (0.1387) peccaries showed that both populations are not structured. The Fis values for all loci, except ACTG2 in white-lipped peccaries (-0.0275) and in both species (0.1985 to 0.9284 in collared peccaries and 0.3621 to 0.4754 in the white-lipped), revealed a high level of homozygosis, probably caused by inbreeding. Data on heterologous amplification and genetic variability in collared and white-lipped peccaries are presented for the first time.
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SENN HV, BARTON NH, GOODMAN SJ, SWANSON GM, ABERNETHY KA, PEMBERTON JM. Investigating temporal changes in hybridization and introgression in a predominantly bimodal hybridizing population of invasive sika (Cervus nippon) and native red deer (C. elaphus) on the Kintyre Peninsula, Scotland. Mol Ecol 2010; 19:910-24. [DOI: 10.1111/j.1365-294x.2009.04497.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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31
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Buschiazzo E, Gemmell NJ. Conservation of human microsatellites across 450 million years of evolution. Genome Biol Evol 2010; 2:153-65. [PMID: 20333231 PMCID: PMC2839350 DOI: 10.1093/gbe/evq007] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2010] [Indexed: 11/21/2022] Open
Abstract
The sequencing and comparison of vertebrate genomes have enabled the
identification of widely conserved genomic elements. Chief among these are genes
and cis-regulatory regions, which are often under selective
constraints that promote their retention in related organisms. The conservation
of elements that either lack function or whose functions are yet to be ascribed
has been relatively little investigated. In particular, microsatellites, a class
of highly polymorphic repetitive sequences considered by most to be neutrally
evolving junk DNA that is too labile to be maintained in distant species, have
not been comprehensively studied in a comparative genomic framework. Here, we
used the UCSC alignment of the human genome against those of 11 mammalian and
five nonmammalian vertebrates to identify and examine the extent of conservation
of human microsatellites in vertebrate genomes. Out of 696,016 microsatellites
found in human sequences, 85.39% were conserved in at least one other species,
whereas 28.65% and 5.98% were found in at least one and three nonprimate
species, respectively. An exponential decline of microsatellite conservation
with increasing evolutionary time, a comparable distribution of conserved versus
nonconserved microsatellites in the human genome, and a positive correlation
between microsatellite conservation and overall sequence conservation, all
suggest that most microsatellites are only maintained in genomes by chance,
although exceptionally conserved human microsatellites were also found in
distant mammals and other vertebrates. Our findings provide the first
comprehensive survey of microsatellite conservation across deep evolutionary
timescales, in this case 450 Myr of vertebrate evolution, and provide new tools
for the identification of functional conserved microsatellites, the development
of cross-species microsatellite markers and the study of microsatellite
evolution above the species level.
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Affiliation(s)
- Emmanuel Buschiazzo
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
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McDevitt AD, Edwards CJ, O’Toole P, O’Sullivan P, O’Reilly C, Carden RF. Genetic structure of, and hybridisation between, red (Cervus elaphus) and sika (Cervus nippon) deer in Ireland. Mamm Biol 2009. [DOI: 10.1016/j.mambio.2009.03.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Pérez-Espona S, Pemberton JM, Putman R. Red and sika deer in the British Isles, current management issues and management policy. Mamm Biol 2009. [DOI: 10.1016/j.mambio.2009.01.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Temperley ND, Webster LMI, Adam A, Keller LF, Johnson PCD. Cross-Species Utility of Microsatellite Markers in Trichostrongyloid Nematodes. J Parasitol 2009; 95:487-9. [DOI: 10.1645/ge-1624.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Accepted: 09/09/2008] [Indexed: 11/10/2022] Open
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SENN HELENV, PEMBERTON JOSEPHINEM. Variable extent of hybridization between invasive sika (Cervus nippon) and native red deer (C. elaphus) in a small geographical area. Mol Ecol 2009; 18:862-76. [DOI: 10.1111/j.1365-294x.2008.04051.x] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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36
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Cronin MA, Renecker LA, Patton JC. Genetic variation in domestic and wild elk (Cervus elaphus)1. J Anim Sci 2009; 87:829-34. [DOI: 10.2527/jas.2008-1185] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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PEMBERTON JM, COLTMAN DW, SMITH JA, PILKINGTON JG. Molecular analysis of a promiscuous, fluctuating mating system. Biol J Linn Soc Lond 2008. [DOI: 10.1111/j.1095-8312.1999.tb01170.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Nguyen TT, Genini S, Bui LC, Voegeli P, Stranzinger G, Renard JP, Maillard JC, Nguyen BX. Genomic conservation of cattle microsatellite loci in wild gaur (Bos gaurus) and current genetic status of this species in Vietnam. BMC Genet 2007; 8:77. [PMID: 17986322 PMCID: PMC2190770 DOI: 10.1186/1471-2156-8-77] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2007] [Accepted: 11/06/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The wild gaur (Bos gaurus) is an endangered wild cattle species. In Vietnam, the total number of wild gaurs is estimated at a maximum of 500 individuals. Inbreeding and genetic drift are current relevant threats to this small population size. Therefore, information about the genetic status of the Vietnamese wild gaur population is essential to develop strategies for conservation and effective long-term management for this species. In the present study, we performed cross-species amplification of 130 bovine microsatellite markers, in order to evaluate the applicability and conservation of cattle microsatellite loci in the wild gaur genome. The genetic diversity of Vietnamese wild gaur was also investigated, based on data collected from the 117 successfully amplified loci. RESULTS One hundred-thirty cattle microsatellite markers were tested on a panel of 11 animals. Efficient amplifications were observed for 117 markers (90%) with a total of 264 alleles, and of these, 68 (58.1%) gave polymorphic band patterns. The number of alleles per locus among the polymorphic markers ranged from two to six. Thirteen loci (BM1314, BM2304, BM6017, BMC2228, BMS332, BMS911, CSSM023, ETH123, HAUT14, HEL11, HEL5, ILSTS005 and INRA189) distributed on nine different cattle chromosomes failed to amplify wild gaur genomic DNA. Three cattle Y-chromosome specific microsatellite markers (INRA124, INRA126 and BM861) were also highly specific in wild gaur, only displaying an amplification product in the males. Genotype data collected from the 117 successfully amplified microsatellites were used to assess the genetic diversity of this species in Vietnam. Polymorphic Information Content (PIC) values varied between 0.083 and 0.767 with a mean of 0.252 while observed heterozygosities (Ho) ranged from 0.091 to 0.909 (mean of 0.269). Nei's unbiased mean heterozygosity and the mean allele number across loci were 0.298 and 2.2, respectively. CONCLUSION Extensive conservation of cattle microsatellite loci in the wild gaur genome, as shown by our results, indicated a high applicability of bovine microsatellites for genetic characterization and population genetic studies of this species. Moreover, the low genetic diversity observed in Vietnamese wild gaur further underlines the necessity of specific strategies and appropriate management plans to preserve this endangered species from extinction.
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Wu HL, Wan QH, Fang SG. Microsatellite analysis of genetic variation and population subdivision for the black muntjac, Muntiacus crinifrons. Biochem Genet 2007; 45:775-88. [PMID: 17939033 DOI: 10.1007/s10528-007-9117-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2006] [Accepted: 07/31/2007] [Indexed: 11/29/2022]
Abstract
The black muntjac (Muntiacus crinifrons) is a rare deer found only in a restricted region in east China. Recent studies of mitochondrial DNA diversity have shown a markedly low level of nucleotide diversity for the species, and the Suichang population was genetically differentiated from the two other populations, in Huangshan and Tianmushan mountains. In this study, we extended the analysis of genetic diversity and population subdivision for the black muntjac using data from 11 highly polymorphic nuclear DNA microsatellite loci. Contrary to the results based on mtDNA data, the microsatellite loci revealed that the black muntjac retained a rather high nuclear genetic diversity (overall average H (E) = 0.78). Nevertheless, both types of markers supported the idea that the extant black muntjac population is genetically disrupted (overall phi (ST) = 0.16 for mtDNA and overall F (ST) = 0.053 for microsatellite, both P < 0.001). The correlation between genetic differentiation and geographic distance was not significant (Mantel test; P > 0.05), implying that the patterns of genetic differentiation observed in this study might result from recent habitat fragmentation or loss. Based on the results from the mtDNA and nuclear DNA data sets, two management units were defined for the species, Huangshan/Tianmushan and Suichang. We also recommend that a new captive population be established with individuals from the Suichang region as a founder source.
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Affiliation(s)
- Hai-Long Wu
- College of Life Sciences, State Conservation Center for Gene Resources of Endangered Wildlife, and Key Lab. of Conservation Genetics and Reproductive Biology for Endangered Wild Animals, Ministry of Education, Zhejiang University, Hangzhou, P.R. China
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Bradshaw CJA, Isagi Y, Kaneko S, Brook BW, Bowman DMJS, Frankham R. Low genetic diversity in the bottlenecked population of endangered non-native banteng in northern Australia. Mol Ecol 2007; 16:2998-3008. [PMID: 17614913 DOI: 10.1111/j.1365-294x.2007.03365.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Undomesticated (wild) banteng are endangered in their native habitats in Southeast Asia. A potential conservation resource for the species is a large, wild population in Garig Gunak Barlu National Park in northern Australia, descended from 20 individuals that were released from a failed British outpost in 1849. Because of the founding bottleneck, we determined the level of genetic diversity in four subpopulations in the national park using 12 microsatellite loci, and compared this to the genetic diversity of domesticated Asian Bali cattle, wild banteng and other cattle species. We also compared the loss of genetic diversity using plausible genetic data coupled to a stochastic Leslie matrix model constructed from existing demographic data. The 53 Australian banteng sampled had average microsatellite heterozygosity (HE) of 28% compared to 67% for outbred Bos taurus and domesticated Bos javanicus populations. The Australian banteng inbreeding coefficient (F) of 0.58 is high compared to other endangered artiodactyl populations. The 95% confidence bounds for measured heterozygosity overlapped with those predicted from our stochastic Leslie matrix population model. Collectively, these results show that Australian banteng have suffered a loss of genetic diversity and are highly inbred because of the initial population bottleneck and subsequent small population sizes. We conclude that the Australian population is an important hedge against the complete loss of wild banteng, and it can augment threatened populations of banteng in their native range. This study indicates the genetic value of small populations of endangered artiodactyls established ex situ.
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Affiliation(s)
- Corey J A Bradshaw
- School for Environmental Research, Institute of Advanced Studies, Charles Darwin University, Darwin, NT 0909, Australia.
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41
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Hu J, Pan HJ, Wan QH, Fang SG. Nuclear DNA microsatellite analysis of genetic diversity in captive populations of Chinese water deer. Small Rumin Res 2007. [DOI: 10.1016/j.smallrumres.2005.10.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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42
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Genetic variability in relocated Père David’s deer (Elaphurus davidianus) populations—Implications to reintroduction program. CONSERV GENET 2006. [DOI: 10.1007/s10592-006-9256-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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43
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Genetic structure of introduced European fallow deer (Dama dama dama) in Tasmania, Australia. EUR J WILDLIFE RES 2006. [DOI: 10.1007/s10344-006-0069-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Cronin MA, Macneil MD, Patton JC. Mitochondrial DNA and Microsatellite DNA Variation in Domestic Reindeer (Rangifer tarandus tarandus) and Relationships with Wild Caribou (Rangifer tarandus granti, Rangifer tarandus groenlandicus, and Rangifer tarandus caribou). J Hered 2006; 97:525-30. [PMID: 16837563 DOI: 10.1093/jhered/esl012] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Reindeer (Rangifer tarandus tarandus) in Alaska are semidomestic livestock descended from 1280 animals introduced from Siberia, Russia, approximately 100 years ago. Genetic variation at 18 microsatellite DNA loci and the cytochrome b gene of mitochondrial DNA (mtDNA) was quantified in reindeer from Alaska, Siberia (Russia), and Scandinavia and compared with wild North American caribou. Mean sequence divergence among 15 mtDNA haplotypes in reindeer was 0.007 substitutions per nucleotide site, and reindeer mtDNA is polyphyletic with caribou mtDNA. Microsatellite allele and mtDNA haplotype frequencies are similar between Alaskan and Russian reindeer and differentiated between these and Scandinavian reindeer. The frequencies of microsatellite alleles and mtDNA haplotypes are different in reindeer and wild caribou (Rangifer tarandus granti, Rangifer tarandus groenlandicus, and Rangifer tarandus caribou). Alaskan reindeer have maintained a genetic variation comparable to that in Russia and differentiated from that of wild caribou, >100 years after their introduction to Alaska.
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Affiliation(s)
- Matthew A Cronin
- School of Natural Resources and Agricultural Sciences, University of Alaska, Fairbanks, 533 E. Fireweed Ave., Palmer, AK 99645, USA.
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Diaz A, Hughes S, Putman R, Mogg R, Bond JM. A genetic study of sika (Cervus nippon) in the New Forest and in the Purbeck region, southern England: is there evidence of recent or past hybridization with red deer (Cervus elaphus)? J Zool (1987) 2006. [DOI: 10.1111/j.1469-7998.2006.00130.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Microsatellite investigation of roe deer (Capreolus capreolus) in Scandinavia reveals genetic differentiation of a Baltic Sea Island population. EUR J WILDLIFE RES 2006. [DOI: 10.1007/s10344-006-0047-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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McRae AF, Pemberton JM, Visscher PM. Modeling linkage disequilibrium in natural populations: the example of the Soay sheep population of St. Kilda, Scotland. Genetics 2005; 171:251-8. [PMID: 15965254 PMCID: PMC1456516 DOI: 10.1534/genetics.105.040972] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2005] [Accepted: 05/19/2005] [Indexed: 11/18/2022] Open
Abstract
The use of linkage disequilibrium to localize the genes underlying quantitative traits has received considerable attention in the livestock genetics community over the past few years. This has resulted in the investigation of linkage disequilibrium structures of several domestic livestock populations to assess their potential use in fine-mapping efforts. However, the linkage disequilibrium structure of free-living populations has been less well investigated. As the direct evaluation of linkage disequilibrium can be both time consuming and expensive the use of simulations that include as many aspects of population history as possible is advocated as an alternative. A simulation of the linkage disequilibrium structure of the Soay sheep population of St. Kilda, Scotland, is provided as an example. The simulated population showed significant decline of linkage disequilibrium with genetic distance and low levels of background linkage disequilibrium, indicating that the Soay sheep population is a viable resource for linkage disequilibrium fine mapping of quantitative trait loci.
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Affiliation(s)
- Allan F McRae
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom.
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Abstract
Marker-based estimates of heritability are an attractive alternative to pedigree-based methods for estimating quantitative genetic parameters in field studies where it is difficult or impossible to determine relationships and pedigrees. Here I test the ability of the marker-based method to estimate heritability of a suite of traits in a wild population of bighorn sheep (Ovis canadensis) using marker data from 32 microsatellite loci. I compared marker-based estimates with estimates obtained using a pedigree and the animal model. Marker-based estimates of heritability were imprecise and downwardly biased. The high degree of uncertainty in marker-based estimates suggests that the method may be sufficient to detect the presence of genetic variance for highly heritable traits, but not sufficiently reliable to estimate genetic parameters.
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Affiliation(s)
- David W Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
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Cronin MA, MacNeil MD, Patton JC. VARIATION IN MITOCHONDRIAL DNA AND MICROSATELLITE DNA IN CARIBOU (RANGIFER TARANDUS) IN NORTH AMERICA. J Mammal 2005. [DOI: 10.1644/1545-1542(2005)86[495:vimdam]2.0.co;2] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Evaluation of microsatellites as a potential tool for product tracing of ground beef mixtures. Meat Sci 2005; 70:337-45. [DOI: 10.1016/j.meatsci.2005.01.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2004] [Revised: 01/24/2005] [Accepted: 01/25/2005] [Indexed: 11/22/2022]
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