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Naifa Liu - One of the best experts on this subject based on the ideXlab platform.
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Asymmetrical introgression patterns between rusty-necklaced Partridge (Alectoris magna) and Chukar Partridge (Alectoris Chukar) in China.
Integrative Zoology, 2016Co-Authors: Yanke Chen, Naifa LiuAbstract:The rusty-necklaced Partridge (Alectoris magna) and the Chukar Partridge (Alectoris Chukar) are the most common gamebirds in northern China. Previous comparisons of mitochondrial DNA (mtDNA) have revealed an introgression phenomenon between 2 species of Partridge in the Liupan Mountain region of China. mtDNA is maternally inherited, making it difficult to determine the origin of parental genes. We assessed the genetic variation and gene flow between these 2 species of Partridges using 8 microsatellite loci as neutral diagnostic markers in 171 samples from the hybrid zone. Our data revealed an extensive divergence of genetic structure between populations of rusty-necklaced Partridges and Chukar Partridges. In this study, we found that 19 samples had been previously morphologically identified as rusty-necklaced Partridge were genetically identified as hybrids through Bayesian analysis using STRUCTURE analysis. These hybrids exhibited a mosaic of alleles that were derived from both parental lineages. However, Chukar Partridges did not present the genotype of the rusty-necklaced Partridge. Thus, our findings demonstrate that the hybridization between the 2 species was the result of asymmetrical introgression, with gene flow occurring only from the Chukar Partridge to the rusty-necklaced Partridge. In addition, we also note the high linkage disequilibrium in populations of the rusty-necklaced Partridge. These results indicate that although unidirectional introgression did not reduce genetic diversity of the Alectoris Partridges, it affected the balance of gene flow between populations. The data from microsatellite DNA prompted our concern about the genetic integrity of the rusty-necklaced Partridge.
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Phylogeography of Chukar Partridge (Alectoris Chukar) in China based on mtDNA control region
Mitochondrial DNA. Part A DNA mapping sequencing and analysis, 2016Co-Authors: Sen Song, Bo Jiang, Naifa LiuAbstract:The Chukar Partridge (Alectoris Chukar) is distributed in north and northwest of China, in mountainous areas that were heavily affected by cyclic climate and landscape changes during the last Pleistocene glaciations. Some Partridge populations have colonized and expanded their present ranges only after deglaciation and recent deforestation by human. Consequently, Partridges from different areas could be genetically differentiated. In this study, a 1152-1154 bp portion of the mitochondrial DNA control region were analyzed for all 279 specimens collected from 28 populations through their distribution in China. A total number of 91 haplotypes were defined by 113 variable sites. The mean haplotype diversity and nucleotide diversity were 0.939 ± 0.008 and 0.0030 ± 0.0017, respectively, for Chukar. Haplotype diversity among the 28 populations varied from 0.600 ± 0.215 (HH) to 1.000 ± 0.272 (SBC), and nucleotide diversity ranged from 0.0006 ± 0.0007 (HJ) to (0.0071 ± 0.0041) (HEG). The nucleotide diversity of Chukar was descending from west to east and a possible historical scenario might be that A. Chukar inhabited central Asia, and then dispersed eastward. Phylogenetic analyses indicated that there was no distinct phylogeographic structure in Chukar populations in China. Haplotype network of Chukar was star-like with some common haplotypes shared by different samples came from different populations as center. Both unstructured phylogeographic tree and star-like haplotype network are signatures of population expansion.
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Population structure and demographic history of the Chukar Partridge Alectoris Chukar in China
Current Zoology, 2013Co-Authors: Sen Song, Shijie Bao, Ying Wang, Xinkang Bao, Xiaoli Wang, Naifa LiuAbstract:Pleistocene climate fluctuations have shaped the patterns of genetic diversity observed in extant species. Although the effects of recent glacial cycles on genetic diversity have been well studied on species in Europe and North America, genetic legacy of species in the Pleistocene in north and northwest of China where glaciations was not synchronous with the ice sheet development in the Northern Hemisphere or or had little or no ice cover during the glaciations’ period, remains poorly understood. Here we used phylogeographic methods to investigate the genetic structure and population history of the Chukar Partridge Alec-toris Chukar in north and northwest China. A 1,152 – 1,154 bp portion of the mtDNA CR were sequenced for all 279 specimens and a total number of 91 haplotypes were defined by 113 variable sites. High levels of gene flow were found and gene flow estimates were greater than 1 for most population pairs in our study. The AMOVA analysis showed that 81% and 16% of the total genetic variability was found within populations and among populations within groups, respectively. The demographic history of Chukar was examined using neutrality tests and mismatch distribution analyses and results indicated Late Pleistocene population expansion. Results revealed that most populations of Chukar experienced population expansion during 0.027 ? 0.06 Ma. These results are at odds with the results found in Europe and North America, where population expansions occurred after Last Glacial Maximum (LGM, 0.023 to 0.018 Ma). Our results are not consistent with the results from avian species of Tibetan Plateau, either, where species experienced population expansion following the retreat of the extensive glaciation period (0.5 to 0.175 Ma).
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Population structure and demographic history of the Chukar Partridge Alectoris Chukar in China
Oxford University Press, 2013Co-Authors: Sen Song, Shijie Bao, Ying Wang, Xinkang Bao, Xiaoli Wang, Naifa LiuAbstract:Pleistocene climate fluctuations have shaped the patterns of genetic diversity observed in extant species. Although the effects of recent glacial cycles on genetic diversity have been well studied on species in Europe and North America, genetic legacy of species in the Pleistocene in north and northwest of China where glaciations was not synchronous with the ice sheet development in the Northern Hemisphere or or had little or no ice cover during the glaciations’ period, remains poorly understood. Here we used phylogeographic methods to investigate the genetic structure and population history of the Chukar Partridge Alectoris Chukar in north and northwest China. A 1,152 – 1,154 bp portion of the mtDNA CR were sequenced for all 279 specimens and a total number of 91 haplotypes were defined by 113 variable sites. High levels of gene flow were found and gene flow estimates were greater than 1 for most population pairs in our study. The AMOVA analysis showed that 81% and 16% of the total genetic variability was found within populations and among populations within groups, respectively. The demographic history of Chukar was examined using neutrality tests and mismatch distribution analyses and results indicated Late Pleistocene population expansion. Results revealed that most populations of Chukar experienced population expansion during 0.027 ‒ 0.06 Ma. These results are at odds with the results found in Europe and North America, where population expansions occurred after Last Glacial Maximum (LGM, 0.023 to 0.018 Ma). Our results are not consistent with the results from avian species of Tibetan Plateau, either, where species experienced population expansion following the retreat of the extensive glaciation period (0.5 to 0.175 Ma) [Current Zoology 59 (4): 458–474, 2013]
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Introgressive hybridization and population genetic diversity between rusty-necklaced Partridge and Chukar Partridge in northwestern China
Belgian Journal of Zoology, 2009Co-Authors: Zuhao Huang, Zhisong Yang, Jiao Zhang, Naifa LiuAbstract:Introgressive hybridization is a common feature of the contact zone between divergent Partridges of the genus Alec- toris . The rusty-necklaced Partridge ( Alectoris magna ) is paralleled with the Chukar Partridge ( A. Chukar ) along the Liupan Moun- tain in northwestern China, and hybridization between the two species has been detected in the contact zone within this region. We examined nine populations of rusty-necklaced Partridge and eight populations of Chukar Partridge to determine the extent and nature of the hybridization between them. A total of 458 nucleotides of mitochondrial DNA control-region were sequenced, reveal- ing a strong asymmetry in introgression between the two taxa. The hybrids, morphologically identified as A. magna , were partly introgressed with genetic material from A. Chukar . The haplotype diversity and nucleotide diversity decreased with increasing hybrid ratio among hybrid populations. The genetic integrity of the rusty-necklaced Partridge is shown to be at risk from the intro- gressive hybridization.
Livia Lucentini - One of the best experts on this subject based on the ideXlab platform.
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New Evidences of Mitochondrial DNA Heteroplasmy by Putative Paternal Leakage between the Rock Partridge (Alectoris graeca) and the Chukar Partridge (Alectoris Chukar).
PloS one, 2017Co-Authors: Andrea Gandolfi, Barbara Crestanello, Anna Fagotti, Francesca Simoncelli, Stefania Chiesa, Matteo Girardi, Eleonora Giovagnoli, Carla Marangoni, Ines Di Rosa, Livia LucentiniAbstract:The rock Partridge, Alectoris graeca, is a polytypic species declining in Italy mostly due to anthropogenic causes, including the massive releases of the closely related allochthonous Chukar Partridge Alectoris Chukar which produced the formation of hybrids. Molecular approaches are fundamental for the identification of evolutionary units in the perspective of conservation and management, and to correctly select individuals to be used in restocking campaigns. We analyzed a Cytochrome oxidase I (COI) fragment of contemporary and historical A. graeca and A. Chukar samples, using duplicated analyses to confirm results and nuclear DNA microsatellites to exclude possible sample cross-contamination. In two contemporary specimens of A. graeca, collected from an anthropogenic hybrid zone, we found evidence of the presence of mtDNA heteroplasmy possibly associated to paternal leakage and suggesting hybridization with captive-bred exotic A. Chukar. These results underline significant limitations in the reliability of mtDNA barcoding-based species identification and could have relevant evolutionary and ecological implications that should be accounted for when interpreting data aimed to support conservation actions.
Yanke Chen - One of the best experts on this subject based on the ideXlab platform.
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Asymmetrical introgression patterns between rusty-necklaced Partridge (Alectoris magna) and Chukar Partridge (Alectoris Chukar) in China.
Integrative Zoology, 2016Co-Authors: Yanke Chen, Naifa LiuAbstract:The rusty-necklaced Partridge (Alectoris magna) and the Chukar Partridge (Alectoris Chukar) are the most common gamebirds in northern China. Previous comparisons of mitochondrial DNA (mtDNA) have revealed an introgression phenomenon between 2 species of Partridge in the Liupan Mountain region of China. mtDNA is maternally inherited, making it difficult to determine the origin of parental genes. We assessed the genetic variation and gene flow between these 2 species of Partridges using 8 microsatellite loci as neutral diagnostic markers in 171 samples from the hybrid zone. Our data revealed an extensive divergence of genetic structure between populations of rusty-necklaced Partridges and Chukar Partridges. In this study, we found that 19 samples had been previously morphologically identified as rusty-necklaced Partridge were genetically identified as hybrids through Bayesian analysis using STRUCTURE analysis. These hybrids exhibited a mosaic of alleles that were derived from both parental lineages. However, Chukar Partridges did not present the genotype of the rusty-necklaced Partridge. Thus, our findings demonstrate that the hybridization between the 2 species was the result of asymmetrical introgression, with gene flow occurring only from the Chukar Partridge to the rusty-necklaced Partridge. In addition, we also note the high linkage disequilibrium in populations of the rusty-necklaced Partridge. These results indicate that although unidirectional introgression did not reduce genetic diversity of the Alectoris Partridges, it affected the balance of gene flow between populations. The data from microsatellite DNA prompted our concern about the genetic integrity of the rusty-necklaced Partridge.
Pilar Arana - One of the best experts on this subject based on the ideXlab platform.
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Mitochondrial DNA sequence variability in red-legged Partridge, Alectoris rufa, Spanish populations and the origins of genetic contamination from A. Chukar
Conservation Genetics, 2008Co-Authors: María Martínez-fresno, Nuno Henriques-gil, Pilar AranaAbstract:The analysis of 135 mitochondrial D-loop sequences of the Iberian autochthonous red-legged Partridge ( Alectoris rufa ) from wild population hunting bags from various locations and fowl runs in Spain yielded 37 different haplotypes. Among these, three haplotypes correspond to Chukar Partridges ( Alectoris Chukar ), indicating genetic introgression from birds illegally introduced for restocking: three individuals carrying such haplotypes where found in natural populations, one appeared among those sampled on a mass reproduction farm and the remaining 10 in another fowl-run. The geographical origin of the contaminating Chukar haplotypes could be assigned to the most easterly area of the Chukar Partridge geographical distribution in China. Molecular diversity parameters in the A. rufa samples indicate a considerable amount of genetic variation. Φ_ST showed significant differences among populations that are not explained by geographical distance alone. Particularly, one northern population (Palencia) shows a certain degree of genetic differentiation that could reflect a previously suggested subspecies division.
Andrea Gandolfi - One of the best experts on this subject based on the ideXlab platform.
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New Evidences of Mitochondrial DNA Heteroplasmy by Putative Paternal Leakage between the Rock Partridge (Alectoris graeca) and the Chukar Partridge (Alectoris Chukar).
PloS one, 2017Co-Authors: Andrea Gandolfi, Barbara Crestanello, Anna Fagotti, Francesca Simoncelli, Stefania Chiesa, Matteo Girardi, Eleonora Giovagnoli, Carla Marangoni, Ines Di Rosa, Livia LucentiniAbstract:The rock Partridge, Alectoris graeca, is a polytypic species declining in Italy mostly due to anthropogenic causes, including the massive releases of the closely related allochthonous Chukar Partridge Alectoris Chukar which produced the formation of hybrids. Molecular approaches are fundamental for the identification of evolutionary units in the perspective of conservation and management, and to correctly select individuals to be used in restocking campaigns. We analyzed a Cytochrome oxidase I (COI) fragment of contemporary and historical A. graeca and A. Chukar samples, using duplicated analyses to confirm results and nuclear DNA microsatellites to exclude possible sample cross-contamination. In two contemporary specimens of A. graeca, collected from an anthropogenic hybrid zone, we found evidence of the presence of mtDNA heteroplasmy possibly associated to paternal leakage and suggesting hybridization with captive-bred exotic A. Chukar. These results underline significant limitations in the reliability of mtDNA barcoding-based species identification and could have relevant evolutionary and ecological implications that should be accounted for when interpreting data aimed to support conservation actions.