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Bech N, Barbu CM, Quéméré E, Novoa C, Allienne JF, Boissier J. Pyrenean ptarmigans decline under climatic and human influences through the Holocene. Heredity (Edinb) 2013; 111:402-9. [PMID: 23838689 PMCID: PMC3806021 DOI: 10.1038/hdy.2013.62] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2012] [Revised: 02/20/2013] [Accepted: 04/30/2013] [Indexed: 11/09/2022] Open
Abstract
In Europe, the Quaternary is characterized by climatic fluctuations known to have led to many cycles of contraction and expansion of species geographical ranges. In addition, during the Holocene, historical changes in human occupation such as colonization or abandonment of traditional land uses can also affect habitats. These climatically or anthropically induced geographic range changes are expected to produce considerable effective population size change, measurable in terms of genetic diversity and organization. The rock ptarmigan (Lagopus muta) is a small-bodied grouse occurring throughout Northern hemispheric arctic and alpine tundra. This species is not considered threatened at a continental scale, but the populations in the Pyrenees are of concern because of their small population size, geographical isolation and low genetic diversity. Here, we used 11 microsatellites to investigate genetic variations and differentiations and infer the overall demographic history of Pyrenean rock ptarmigan populations. The low genetic variability found in these populations has been previously thought to be the result of a bottleneck that occurred following the last glacial maximum (i.e., 10,000 years ago) or more recently (i.e., during the last 200 years). Our results clearly indicate a major bottleneck affecting the populations in the last tenth of the Holocene. We discuss how this decline can be explained by a combination of unfavorable and successive events that increased the degree of habitat fragmentation.
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Affiliation(s)
- N Bech
- CNRS, UMR 5244, Evolutionary and Ecology of
Interactions (2EI), University of Perpignan Via Domitia, Perpignan,
France
- University of Perpignan Via Domitia, UMR
5244, Evolutionary and Ecology of Interactions (2EI), CNRS,
Perpignan, France
| | - C M Barbu
- CNRS, UMR 5244, Evolutionary and Ecology of
Interactions (2EI), University of Perpignan Via Domitia, Perpignan,
France
- University of Perpignan Via Domitia, UMR
5244, Evolutionary and Ecology of Interactions (2EI), CNRS,
Perpignan, France
| | - E Quéméré
- INRA-CEFS, Comportement et Ecologie de la
Faune Sauvage, Institut National de la Recherche Agronomique
Castanet-Tolosan Cedex, France
| | - C Novoa
- ONCFS, Direction des Etudes et de la
recherche, Centre National d'Etudes et de Recherches Appliquées, Faune de
Montagne, Prades, France
| | - J F Allienne
- CNRS, UMR 5244, Evolutionary and Ecology of
Interactions (2EI), University of Perpignan Via Domitia, Perpignan,
France
- University of Perpignan Via Domitia, UMR
5244, Evolutionary and Ecology of Interactions (2EI), CNRS,
Perpignan, France
| | - J Boissier
- CNRS, UMR 5244, Evolutionary and Ecology of
Interactions (2EI), University of Perpignan Via Domitia, Perpignan,
France
- University of Perpignan Via Domitia, UMR
5244, Evolutionary and Ecology of Interactions (2EI), CNRS,
Perpignan, France
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Chaves LD, Harry DE, Reed KM. Genome-wide genetic diversity of 'Nici', the DNA source for the CHORI-260 turkey BAC library and candidate for whole genome sequencing. Anim Genet 2009; 40:348-52. [PMID: 19292710 DOI: 10.1111/j.1365-2052.2008.01845.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Vertebrate whole genome sequence assembly can benefit from a priori knowledge of variability in the target genome, with researchers often selecting highly inbred individuals for sequencing. However, for most species highly inbred research lines are lacking, requiring the use of an outbred individual(s). Here we examined the source DNA [Nicholas inbred (Nici)] of the CHORI-260 turkey bacterial artificial chromosome (BAC) library through analysis of microsatellites and BAC sequences. Heterozygosity of Nici was compared with that of individuals from several breeder lines. Seventy-eight microsatellites were screened for polymorphism in a total of 43 birds, identifying an average individual heterozygosity of 0.39, with Nici at 0.35. Additional loci (total of 147) were examined on a subset of individuals to obtain better genome coverage. The mean heterozygosity for this subset was 0.33 with Nici at 0.31. Examination of approximately 200 kb of genome sequence identified SNPs in the order of one per 200 bp in Nici. These data suggest that the heterozygosity of Nici is comparable to other birds of selected breeder lines and that whole genome sequencing would result in an abundant resource of genome-wide polymorphisms.
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Affiliation(s)
- L D Chaves
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St Paul, MN 55108, USA.
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Reed KM, Faile GM, Kreuth SB, Chaves LD, Sullivan LM. Association and in silico assignment of sequences from turkey BACs. Anim Biotechnol 2008; 19:80-3. [PMID: 18432398 DOI: 10.1080/10495390701876209] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Bacterial artificial chromosomes (BACs) provide an important resource in genetic mapping. An initial set of BACs corresponding to microsatellite markers in the turkey (Meleagris gallopavo) was isolated from the CHORI-260 turkey BAC library. The selected markers were distributed on both macro- and microchromosomes and included a genetically unlinked marker. End sequences were obtained for a subset of the recovered BACs and compared to the chicken whole genome sequence. Close association of the turkey BAC-end sequences and original marker sequences was generally conserved in the chicken genome. Gene content of the turkey BACs is predicted from the comparative sequence alignments.
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Affiliation(s)
- Kent M Reed
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota 55108, USA.
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Reed KM, Sullivan LR, Foster LK, Chaves LD, Ponce de León FA. Assignment of linkage groups to turkey chromosome 1 (MGA1). Cytogenet Genome Res 2006; 115:176-8. [PMID: 17065800 DOI: 10.1159/000095239] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2006] [Accepted: 04/13/2006] [Indexed: 11/19/2022] Open
Abstract
Previous genetic mapping identified three linkage groups (M1, M18 and M26) in the turkey corresponding to chicken chromosome 1 (GGA1). This is inconsistent with previously described chromosomal differences between these species. FISH analysis of BAC clones corresponding to microsatellite markers from each of the three turkey linkage groups, assigned all three linkage groups to a single chromosome (MGA1).
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Affiliation(s)
- K M Reed
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN 55108, USA.
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Chaves LD, Knutson TP, Krueth SB, Reed KM. Using the chicken genome sequence in the development and mapping of genetic markers in the turkey (Meleagris gallopavo). Anim Genet 2006; 37:130-8. [PMID: 16573527 DOI: 10.1111/j.1365-2052.2005.01396.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The efficacy of employing the chicken genome sequence in developing genetic markers and in mapping the turkey genome was studied. Eighty previously uncharacterized microsatellite markers were identified for the turkey using BLAST alignment to the chicken genome. The chicken sequence was then used to develop primers for polymerase chain reaction where the turkey sequence was either unavailable or insufficient. A total of 78 primer sets were tested for amplification and polymorphism in the turkey, and informative markers were genetically mapped. Sixty-five (83%) amplified turkey genomic DNA, and 33 (42%) were polymorphic in the University of Minnesota/Nicholas Turkey Breeding Farms mapping families. All but one marker genetically mapped to the position predicted from the chicken genome sequence. These results demonstrate the usefulness of the chicken sequence for the development of genomic resources in other avian species.
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Affiliation(s)
- L D Chaves
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St Paul, MN 55108, USA
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Affiliation(s)
- K M Reed
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St Paul, MN 55108, USA.
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Reed KM, Chaves LD, Hall MK, Knutson TP, Harry DE. A comparative genetic map of the turkey genome. Cytogenet Genome Res 2006; 111:118-27. [PMID: 16103652 DOI: 10.1159/000086380] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2005] [Accepted: 02/01/2005] [Indexed: 11/19/2022] Open
Abstract
Genetic markers (microsatellites and SNPs) were used to create and compare maps of the turkey and chicken genomes. A physical map of the chicken genome was built by comparing sequences of turkey markers with the chicken whole-genome sequence by BLAST analysis. A genetic linkage map of the turkey genome (Meleagris gallopavo) was developed by segregation analysis of genetic markers within the University of Minnesota/Nicholas Turkey Breeding Farms (UMN/NTBF) resource population. This linkage map of the turkey genome includes 314 loci arranged into 29 linkage groups. An additional 40 markers are tentatively placed within linkage groups based on two-point LOD scores and 16 markers remain unlinked. Total map distance contained within linkage groups is 2,011 cM with the longest linkage group (47 loci) measuring 413.3 cM. Average marker interval over the 29 linkage groups was 6.4 cM. All but one turkey linkage group could be aligned with the physical map of the chicken genome. The present genetic map of the turkey provides a comparative framework for future genomic studies.
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Affiliation(s)
- K M Reed
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN 55108, USA.
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Knutson TP, Chaves LD, Hall MK, Reed KM. One hundred fifty-four genetic markers for the turkey (Meleagris gallopavo). Genome 2005; 47:1015-28. [PMID: 15644959 DOI: 10.1139/g04-076] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Identifying and selectively breeding for improved traits is one of the ultimate goals of genetic research in agriculturally important species. Genome characterization and analysis are important first steps in this process. Genetic linkage maps based on the linear order of polymorphic DNA markers are typically developed through statistical analysis of inheritance patterns in pedigreed families. To develop microsatellite markers for further improvement of the turkey genetic linkage map, small-insert genomic libraries were screened for tandem repeats. Oligonuclotide primers were designed to amplify 164 microsatellite-containing fragments from genomic DNA. Genetic polymorphisms at 154 markers were determined by genotyping the F(1) individuals of two resource populations. Markers determined as segregating in the University of Minnesota/Nicholas Turkey Breeding Farms (UMN/NTBF) reference population were used to genotype F(2) individuals and a two-point linkage analysis was performed.
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Affiliation(s)
- Todd P Knutson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, 295 ASVM, 1988 Fitch Ave., University of Minnesota, St. Paul, MN 55108, USA
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Reed KM. In silico comparative mapping of 278 genomic survey sequences from the turkey (Meleagris gallopavo). Anim Genet 2005; 36:438-43. [PMID: 16167991 DOI: 10.1111/j.1365-2052.2005.01326.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- K M Reed
- Department of Veterinary and Biomedical Sciences, University of Minnesota, MN, USA.
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Reed KM, Holm J, Morisson M, Leroux S, Vignal A. Assignment of non-informative turkey genetic markers through comparative approaches. Cytogenet Genome Res 2005; 109:527-32. [PMID: 15905649 DOI: 10.1159/000084214] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2004] [Accepted: 09/08/2004] [Indexed: 11/19/2022] Open
Abstract
Molecular markers such as microsatellites, provide genetic signposts for navigating genomes. In general, genetic markers that are monomorphic or non-informative in mapping populations typically remain unmapped and as such are less likely to be included in future studies. The use of hybrid cell panels and in silico mapping via whole genome sequences allow for positional mapping of non-segregating markers. This study utilizes the INRA ChickRH6 whole-genome radiation hybrid panel and chicken whole-genome shotgun sequence to map microsatellite markers from the turkey (Meleagris gallopavo). Thirty-three of the 41 markers typed on the RH panel had significant linkage to at least one other marker and 83 of 100 sequences returned significant BLAST similarities. Positioning of these markers provides additional sequence tagged sites in the turkey genome and increases the potential use of these markers for future genetic studies.
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Affiliation(s)
- K M Reed
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN 55108, USA.
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Abstract
Genome characterization and analysis is an imperative step in identifying and selectively breeding for improved traits of agriculturally important species. Expressed sequence tags (ESTs) represent a transcribed portion of the genome and are an effective way to identify genes within a species. Downstream applications of EST projects include DNA microarray construction and interspecies comparisons. In this study, 694 ESTs were sequenced and analyzed from a library derived from a 24-day-old turkey embryo. The 437 unique sequences identified were divided into 76 assembled contigs and 361 singletons. The majority of significant comparative matches occurred between the turkey sequences and sequences reported from the chicken. Whole genome sequence from the chicken was used to identify potential exon–intron boundaries for selected turkey clones and intron-amplifying primers were developed for sequence analysis and single nucleotide polymorphism (SNP) discovery. Identified SNPs were genotyped for linkage analysis on two turkey reference populations. This study significantly increases the number of EST sequences available for the turkey.Key words: turkey, cDNA, expressed sequence tag, single nucleotide polymorphism.
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Affiliation(s)
- L D Chaves
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN 55108, USA.
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