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Dey P, Ray SD, Kochiganti VHS, Pukazhenthi BS, Koepfli KP, Singh RP. Mitogenomic Insights into the Evolution, Divergence Time, and Ancestral Ranges of Coturnix Quails. Genes (Basel) 2024; 15:742. [PMID: 38927678 PMCID: PMC11202683 DOI: 10.3390/genes15060742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/29/2024] [Accepted: 06/01/2024] [Indexed: 06/28/2024] Open
Abstract
The Old-World quails, Coturnix coturnix (common quail) and Coturnix japonica (Japanese quail), are morphologically similar yet occupy distinct geographic ranges. This study aimed to elucidate their evolutionary trajectory and ancestral distribution patterns through a thorough analysis of their mitochondrial genomes. Mitogenomic analysis revealed high structural conservation, identical translational mechanisms, and similar evolutionary pressures in both species. Selection analysis revealed significant evidence of positive selection across the Coturnix lineage for the nad4 gene tree owing to environmental changes and acclimatization requirements during its evolutionary history. Divergence time estimations imply that diversification among Coturnix species occurred in the mid-Miocene (13.89 Ma), and their current distributions were primarily shaped by dispersal rather than global vicariance events. Phylogenetic analysis indicates a close relationship between C. coturnix and C. japonica, with divergence estimated at 2.25 Ma during the Pleistocene epoch. Ancestral range reconstructions indicate that the ancestors of the Coturnix clade were distributed over the Oriental region. C. coturnix subsequently dispersed to Eurasia and Africa, and C. japonica to eastern Asia. We hypothesize that the current geographic distributions of C. coturnix and C. japonica result from their unique dispersal strategies, developed to evade interspecific territoriality and influenced by the Tibetan Plateau's geographic constraints. This study advances our understanding of the biogeographic and evolutionary processes leading to the diversification of C. coturnix and C. japonica, laying important groundwork for further research on this genus.
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Affiliation(s)
- Prateek Dey
- Sálim Ali Centre for Ornithology and Natural History (South India Centre of Wildlife Institute of India), Anaikatti, Coimbatore 641108, Tamil Nadu, India; (P.D.); (S.D.R.)
- Bharathiar University, Coimbatore 641046, Tamil Nadu, India
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630, USA;
| | - Swapna Devi Ray
- Sálim Ali Centre for Ornithology and Natural History (South India Centre of Wildlife Institute of India), Anaikatti, Coimbatore 641108, Tamil Nadu, India; (P.D.); (S.D.R.)
| | | | - Budhan S. Pukazhenthi
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630, USA;
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA 22630, USA
| | - Ram Pratap Singh
- Department of Life Science, Central University of South Bihar, Gaya 824236, Bihar, India
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Volkova NA, Romanov MN, Abdelmanova AS, Larionova PV, German NY, Vetokh AN, Shakhin AV, Volkova LA, Anshakov DV, Fisinin VI, Narushin VG, Griffin DK, Sölkner J, Brem G, McEwan JC, Brauning R, Zinovieva NA. Genotyping-by-Sequencing Strategy for Integrating Genomic Structure, Diversity and Performance of Various Japanese Quail ( Coturnix japonica) Breeds. Animals (Basel) 2023; 13:3439. [PMID: 38003057 PMCID: PMC10668688 DOI: 10.3390/ani13223439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/23/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Traces of long-term artificial selection can be detected in genomes of domesticated birds via whole-genome screening using single-nucleotide polymorphism (SNP) markers. This study thus examined putative genomic regions under selection that are relevant to the development history, divergence and phylogeny among Japanese quails of various breeds and utility types. We sampled 99 birds from eight breeds (11% of the global gene pool) of egg (Japanese, English White, English Black, Tuxedo and Manchurian Golden), meat (Texas White and Pharaoh) and dual-purpose (Estonian) types. The genotyping-by-sequencing analysis was performed for the first time in domestic quails, providing 62,935 SNPs. Using principal component analysis, Neighbor-Net and Admixture algorithms, the studied breeds were characterized according to their genomic architecture, ancestry and direction of selective breeding. Japanese and Pharaoh breeds had the smallest number and length of homozygous segments indicating a lower selective pressure. Tuxedo and Texas White breeds showed the highest values of these indicators and genomic inbreeding suggesting a greater homozygosity. We revealed evidence for the integration of genomic and performance data, and our findings are applicable for elucidating the history of creation and genomic variability in quail breeds that, in turn, will be useful for future breeding improvement strategies.
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Affiliation(s)
- Natalia A. Volkova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Michael N. Romanov
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK;
| | - Alexandra S. Abdelmanova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Polina V. Larionova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Nadezhda Yu. German
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Anastasia N. Vetokh
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Alexey V. Shakhin
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Ludmila A. Volkova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Dmitry V. Anshakov
- Breeding and Genetic Center Zagorsk Experimental Breeding Farm—Branch of the Federal Research Centre, All-Russian Poultry Research and Technological Institute, Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia;
| | - Vladimir I. Fisinin
- Federal Research Center “All-Russian Poultry Research and Technological Institute” of the Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia;
| | - Valeriy G. Narushin
- Research Institute for Environment Treatment, 69032 Zaporizhya, Ukraine;
- Vita-Market Co., Ltd., 69032 Zaporizhya, Ukraine
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK;
| | - Johann Sölkner
- Institute of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences Vienna, 1180 Vienna, Austria;
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, 1210 Vienna, Austria;
| | - John C. McEwan
- AgResearch, Invermay Agricultural Centre, Mosgiel 9053, New Zealand; (J.C.M.); (R.B.)
| | - Rudiger Brauning
- AgResearch, Invermay Agricultural Centre, Mosgiel 9053, New Zealand; (J.C.M.); (R.B.)
| | - Natalia A. Zinovieva
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
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Kardum Hjort C, Paris JR, Olsson P, Herbertsson L, de Miranda JR, Dudaniec RY, Smith HG. Genomic divergence and a lack of recent introgression between commercial and wild bumblebees ( Bombus terrestris). Evol Appl 2022; 15:365-382. [PMID: 35386397 PMCID: PMC8965379 DOI: 10.1111/eva.13346] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/08/2021] [Accepted: 01/17/2022] [Indexed: 11/27/2022] Open
Abstract
The global movement of bees for agricultural pollination services can affect local pollinator populations via hybridization. When commercial bumblebees are of the same species but of different geographic origin, intraspecific hybridization may result in beneficial integration of new genetic variation, or alternatively may disrupt locally adapted gene complexes. However, neither the existence nor the extent of genomic introgression and evolutionary divergence between wild and commercial bumblebees is fully understood. We obtained whole-genome sequencing data from wild and commercial Bombus terrestris collected from sites in Southern Sweden with and without long-term use of commercially imported B. terrestris. We search for evidence of introgression, dispersal and genome-wide differentiation in a comparative genomic analysis of wild and commercial bumblebees. Commercial B. terrestris were found in natural environments near sites where commercial bumblebees were used, as well as drifting wild B. terrestris in commercial bumblebee colonies. However, we found no evidence for widespread, recent genomic introgression of commercial B. terrestris into local wild conspecific populations. We found that wild B. terrestris had significantly higher nucleotide diversity (Nei's pi, π), while the number of segregating sites (Watterson's theta, θw) was higher in commercial B. terrestris. A highly divergent region on chromosome 11 was identified in commercial B. terrestris and found to be enriched with structural variants. The genes present in this region are involved in flight muscle contraction and structure and pathogen immune response, providing evidence for differing evolutionary processes operating in wild and commercial B. terrestris. We did not find evidence for recent introgression, suggesting that co-occurring commercial B. terrestris have not disrupted evolutionary processes in wild B. terrestris populations.
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Affiliation(s)
- Cecilia Kardum Hjort
- Department of BiologyLund UniversityLundSweden
- School of Natural SciencesMacquarie UniversitySydneyAustralia
| | - Josephine R. Paris
- BiosciencesCollege of Life and Environmental ScienceUniversity of ExeterExeterUK
| | | | - Lina Herbertsson
- Centre for Environmental and Climate ScienceLund UniversityLundSweden
| | | | | | - Henrik G. Smith
- Department of BiologyLund UniversityLundSweden
- Centre for Environmental and Climate ScienceLund UniversityLundSweden
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Ogada S, Otecko NO, Moraa Kennedy G, Musina J, Agwanda B, Obanda V, Lichoti J, Peng M, Ommeh S. Demographic history and genetic diversity of wild African harlequin quail ( Coturnix delegorguei delegorguei) populations of Kenya. Ecol Evol 2021; 11:18562-18574. [PMID: 35003693 PMCID: PMC8717324 DOI: 10.1002/ece3.8458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 11/24/2021] [Accepted: 11/30/2021] [Indexed: 11/24/2022] Open
Abstract
Hunting wild African harlequin quails (Coturnix delegorguei delegorguei) using traditional methods in Western Kenya has been ongoing for generations, yet their genetic diversity and evolutionary history are largely unknown. In this study, the genetic variation and demographic history of wild African harlequin quails were assessed using a 347bp mitochondrial DNA (mtDNA) control region fragment and 119,339 single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing (GBS) data. Genetic diversity analyses revealed that the genetic variation in wild African harlequin quails was predominantly among individuals than populations. Demographic analyses indicated a signal of rapid demographic expansion, and the estimated time since population expansion was found to be 150,000-350,000 years ago, corresponding to around the Pliocene-Pleistocene boundary. A gradual decline in their effective population size was also observed, which raised concerns about their conservation status. These results provide the first account of the genetic diversity of wild African harlequin quails of Siaya, thereby creating a helpful foundation in their biodiversity conservation.
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Affiliation(s)
- Stephen Ogada
- Institute For Biotechnology ResearchJomo Kenyatta University of Agriculture and TechnologyNairobiKenya
| | - Newton O. Otecko
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic AnimalsKunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- Sino‐Africa Joint Research CenterChinese Academy of SciencesNairobiKenya
| | - Grace Moraa Kennedy
- Institute For Biotechnology ResearchJomo Kenyatta University of Agriculture and TechnologyNairobiKenya
| | - John Musina
- Department of ZoologyNational Museums of KenyaNairobiKenya
| | | | - Vincent Obanda
- Department of Veterinary ServicesKenya Wildlife ServiceNairobiKenya
| | - Jacqueline Lichoti
- Central Veterinary Laboratories KabeteState Department of LivestockMinistry of Agriculture, Livestock and FisheriesNairobiKenya
| | - Min‐Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic AnimalsKunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- Sino‐Africa Joint Research CenterChinese Academy of SciencesNairobiKenya
| | - Sheila Ommeh
- Institute For Biotechnology ResearchJomo Kenyatta University of Agriculture and TechnologyNairobiKenya
- Department of ZoologyNational Museums of KenyaNairobiKenya
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Aliakbari Z, Kayvanfar N, Rajabi‐Maham H, Ghasempouri SM. Evidence for introgressive hybridization of wild black‐necked pheasant with the exotic ring‐necked pheasant during the past 50 years in the Hyrcanian zone, an integrative molecular and morphological approach. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zohreh Aliakbari
- Environmental Science Department Tarbiat Modares University Noor Iran
| | - Nasrin Kayvanfar
- Research Department of Zoological Innovation Faculty of Sciences Institute of Applied Zoology Ferdowsi University of Mashhad Mashhad Iran
| | - Hassan Rajabi‐Maham
- Animal Sciences and Biotechnology Department Faculty of Life Sciences and Biotechnology Shahid Beheshti University Tehran Iran
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Ibrahim NS, El-Sayed MA, Assi HAM, Enab A, Abdel-Moneim AME. Genetic and physiological variation in two strains of Japanese quail. J Genet Eng Biotechnol 2021; 19:15. [PMID: 33474680 PMCID: PMC7817731 DOI: 10.1186/s43141-020-00100-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 12/01/2020] [Indexed: 11/19/2022]
Abstract
Background Detecting the genetic and physiological variations in two Japanese quail strains could be used to suggest a new avian model for future breeding studies. Consequently, two estimations were performed on two Japanese quail strains: gray quail strain (GJQS) and white jumbo quail strain (WJQS). The first estimation was conducted on carcass characteristics, breast muscles, breast concentration of collagen type I, and body measurements. In contrast, blood samples were collected for the second estimation for genomic DNA extraction and genetic analysis. Results A total of 62 alleles out of 97 specific alleles (63.92%) were detected overall loci (14 microsatellite loci) for the two strains. A total of 27 specific alleles of WJQS were observed, and 35 were obtained for GJQS. The percentage of similarity was 48.09% ranged from 4.35 with UBC001 to 100% with GUJ0051. WJQS had greater body weights and a higher value of pectoral muscle and supracoracoideus muscle than GJQS. The breast muscles of GJQS exhibited a higher concentration of type I collagen than the WJQS. Furthermore, males showed higher concentrations of collagen type I than females. WJQS showed a higher body length, chest girth, chest length, thigh length, thigh girth, drumstick length, and drumstick girth (cm) than GJQS. WJQS showed more significant differences in carcass traits compared with GJQS. Conclusion The physiological differences between WJQS and GJQS were ascertained with microsatellite markers, which indicated high polymorphism between these strains. These observations provided a scientific basis for evaluating and utilizing the genetic resources of WJQS and GJQS in a future genetic improvement program.
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Affiliation(s)
- Nashat Saeid Ibrahim
- Biological Application Department, Nuclear Research Center, Egyptian Atomic Energy Authority, P.O. Box 13759, Cairo, Egypt
| | - Mohammed Ahmed El-Sayed
- National Gene Bank, Animal Genetic Resources Department, Agricultural Research Center, Giza, Egypt.
| | | | - Ahmed Enab
- Department of Poultry and Fish Production, Faculty of Agriculture, Menoufia University, Shibin El Kom, Egypt
| | - Abdel-Moneim Eid Abdel-Moneim
- Biological Application Department, Nuclear Research Center, Egyptian Atomic Energy Authority, P.O. Box 13759, Cairo, Egypt
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Guo X, Wang ZC, Wang S, Li HF, Suwannapoom C, Wang JX, Zhang C, Shao Y, Wang MS, Jiang RS. Genetic signature of hybridization between Chinese spot-billed ducks and domesticated ducks. Anim Genet 2020; 51:866-875. [PMID: 33020910 DOI: 10.1111/age.13002] [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: 12/20/2019] [Revised: 08/17/2020] [Accepted: 08/24/2020] [Indexed: 12/27/2022]
Abstract
In this study, we analyzed 93 whole genomes from Chinese spot-billed ducks (CSB), meat-type ducks (MET), and egg and dual purpose-type ducks (EDT) to characterize the genetic material flowing between the CSB and modern ducks. Using a frequency of shared identical-by-descent method, approximately 10.9 Mb introgression segments containing 140 genes were identified showing the signatures of introgression between CSB and EDT. Meanwhile, nearly 10.6 M introgression regions containing 149 genes were identified between CSB and MET. Based on the haplotypes tree of each segment, we found that the introgression between CSB and domesticated ducks was asymmetric with a high level of gene flow from domestic to CSB and a low level of migration in the opposite direction. Moreover, we identified several genes that were introgressions from CSB and showed the signature of positive selection, which may contribute to the breeding of modern ducks. Our results provide new insight into the evolution and breeding history of domestic ducks and may be useful for the future management of wild and domestic duck populations.
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Affiliation(s)
- X Guo
- College of Animal Science and Technology, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Z-C Wang
- College of Animal Science and Technology, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - S Wang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Dong Road, Kunming, Yunnan, 650223, China
| | - H-F Li
- Jiangsu Institute of Poultry Science, Chinese Academy of Agriculture Science, 58 cangjie Rode, Yangzhou, Jiangsu, 225125, China
| | - C Suwannapoom
- School of Agriculture and Natural Resources, University of Phayao, 19 Moo 2 Tambon Maeka, Amphur Muang, Phayao, 56000, Thailand
| | - J-X Wang
- College of Animal Science and Technology, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - C Zhang
- College of Animal Science and Technology, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
| | - Y Shao
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Dong Road, Kunming, Yunnan, 650223, China
| | - M-S Wang
- Howard Hughes Medical Institute, University of California Santa Cruz, 1156 High St, Santa Cruz, CA, 95064, USA.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, 1156 High St, Santa Cruz, CA, 95064, USA
| | - R-S Jiang
- College of Animal Science and Technology, Anhui Agricultural University, 130, Changjiang West Road, Hefei, Anhui, 230036, China
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Lawal RA, Martin SH, Vanmechelen K, Vereijken A, Silva P, Al-Atiyat RM, Aljumaah RS, Mwacharo JM, Wu DD, Zhang YP, Hocking PM, Smith J, Wragg D, Hanotte O. The wild species genome ancestry of domestic chickens. BMC Biol 2020; 18:13. [PMID: 32050971 PMCID: PMC7014787 DOI: 10.1186/s12915-020-0738-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 01/08/2020] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Hybridisation and introgression play key roles in the evolutionary history of animal species. They are commonly observed within several orders in wild birds. The domestic chicken Gallus gallus domesticus is the most common livestock species. More than 65 billion chickens are raised annually to produce meat and 80 million metric tons of egg for global human consumption by the commercial sector. Unravelling the origin of its genetic diversity has major application for sustainable breeding improvement programmes. RESULTS In this study, we report genome-wide analyses for signatures of introgression between indigenous domestic village chicken and the four wild Gallus species. We first assess the genome-wide phylogeny and divergence time across the genus Gallus. Genome-wide sequence divergence analysis supports a sister relationship between the Grey junglefowl G. sonneratii and Ceylon junglefowl G. lafayettii. Both species form a clade that is sister to the Red junglefowl G. gallus, with the Green junglefowl G. varius the most ancient lineage within the genus. We reveal extensive bidirectional introgression between the Grey junglefowl and the domestic chicken and to a much lesser extent with the Ceylon junglefowl. We identify a single case of Green junglefowl introgression. These introgressed regions include genes with biological functions related to development and immune system. CONCLUSIONS Our study shows that while the Red junglefowl is the main ancestral species, introgressive hybridisation episodes have impacted the genome and contributed to the diversity of the domestic chicken, although likely at different levels across its geographic range.
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Affiliation(s)
- Raman Akinyanju Lawal
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
- Present Address: The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA.
| | - Simon H Martin
- Present Address: Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
| | - Koen Vanmechelen
- Open University of Diversity - Mouth Foundation, Hasselt, Belgium
| | - Addie Vereijken
- Technology and Service B.V., Hendrix Genetics, P.O. Box 114, 5830 AC, Boxmeer, The Netherlands
| | - Pradeepa Silva
- Department of Animal Science, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka
| | - Raed Mahmoud Al-Atiyat
- Genetics and Biotechnology, Animal Science Department, Agriculture Faculty, Mutah University, Karak, Jordan
| | | | - Joram M Mwacharo
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5689, ILRI-Ethiopia Campus, Addis Ababa, Ethiopia
| | - Dong-Dong Wu
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Ya-Ping Zhang
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Paul M Hocking
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Jacqueline Smith
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - David Wragg
- Centre for Tropical Livestock Genetics and Health, The Roslin Institute, Edinburgh, EH25 9RG, UK
| | - Olivier Hanotte
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
- Centre for Tropical Livestock Genetics and Health, The Roslin Institute, Edinburgh, EH25 9RG, UK.
- LiveGene, International Livestock Research Institute (ILRI), P. O. 5689, Addis Ababa, Ethiopia.
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Mitochondrial DNA Diversity in Commercial Lines of Laying-type Japanese Quail. J Poult Sci 2020; 57:253-258. [PMID: 33132724 PMCID: PMC7596030 DOI: 10.2141/jpsa.0190121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The present study aims to investigate the maternal origin and genetic diversity of laying-type Japanese quail lines based on partial sequences (453 base pairs) of a mitochondrial DNA (mtDNA) control region. A total of 478 individuals from 12 lines were sequenced and six different haplotypes with eight variable sites were identified. All haplotypes, two of which were identical to previously reported sequences, were typical for the Japanese quail (Coturnix japonica) and were distinct from those of the common quail (Coturnix coturnix) in a phylogenetic analysis including other published haplotypes. One haplotype was distributed in the majority of individuals (84.9%, 406/478) across all lines. Within each line, 72.5–100% of individuals had this predominant haplotype. The second most common haplotype was detected in 12.8% (61/478) individuals. These two haplotypes accounted for 97.7% of all individuals. The remaining four haplotypes were distributed with a low frequency; these were observed in five, three, two, and one individuals across all lines, respectively. All lines showed a low degree of haplotype diversity ranging from 0.0000 to 0.4321. Genetic differentiation indexes (FST) were not significant in approximately 80% pairwise comparisons of lines. The results suggest limited maternal origin and low mtDNA diversity of laying-type quail lines and may reflect their breeding history where the present gene pool was rooted in a small number of founders.
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Kartout-Benmessaoud Y, Ladjali-Mohammedi K. Banding cytogenetics of chimeric hybrids Coturnixcoturnix × Coturnixjaponica and comparative analysis with the domestic fowl. COMPARATIVE CYTOGENETICS 2018; 12:445-470. [PMID: 30364889 PMCID: PMC6199345 DOI: 10.3897/compcytogen.v12i4.27341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 09/12/2018] [Indexed: 06/08/2023]
Abstract
The Common quail Coturnixcoturnix Linnaeus, 1758 is a wild migratory bird which is distributed in Eurasia and North Africa, everywhere with an accelerating decline in population size. This species is protected by the Bonn and Berne conventions (1979) and by annex II/1 of the Birds Directive (2009). In Algeria, its breeding took place at the hunting centre in the west of the country. Breeding errors caused uncontrolled crosses between the Common quail and Japanese quail Coturnixjaponica Temminck & Schlegel, 1849. In order to help to preserve the natural genetic heritage of the Common quail and to lift the ambiguity among the populations of quail raised in Algeria, it seemed essential to begin to describe the chromosomes of this species in the country since no cytogenetic study has been reported to date. Fibroblast cultures from embryo and adult animal were initiated. Double synchronization with excess thymidine allowed us to obtain high resolution chromosomes blocked at prometaphase stage. The karyotype and the idiogram in GTG morphological banding (G-bands obtained with trypsin and Giemsa) corresponding to larger chromosomes 1-12 and ZW pair were thus established. The diploid set of chromosomes was estimated as 2N=78. Cytogenetic analysis of expected hybrid animals revealed the presence of a genetic introgression and cellular chimerism. This technique is effective in distinguishing the two quail taxa. Furthermore, the comparative chromosomal analysis of the two quails and domestic chicken Gallusgallusdomesticus Linnaeus, 1758 has been conducted. Differences in morphology and/or GTG band motifs were observed on 1, 2, 4, 7, 8 and W chromosomes. Neocentromere occurrence was suggested for Common quail chromosome 1 and Chicken chromosomes 4 and W. Double pericentric inversion was observed on the Common quail chromosome 2 while pericentric inversion hypothesis was proposed for Chicken chromosome 8. A deletion on the short arm of the Common quail chromosome 7 was also found. These results suggest that Common quail would be a chromosomally intermediate species between Chicken and Japanese quail. The appearance of only a few intrachromosomal rearrangements that occurred during evolution suggests that the organization of the genome is highly conserved between these three galliform species.
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Affiliation(s)
- Yasmine Kartout-Benmessaoud
- University of Sciences and Technology Houari Boumediene, Faculty of Biological Sciences, Laboratory of Cellular and Molecular Biology, Team of Developmental Genetics. USTHB, PO box 32 El-Alia, Bab-Ezzouar, 16110 Algiers, AlgeriaUniversity of Sciences and Technology Houari BoumedieneBab-EzzouarAlgeria
- University of Bejaia, Faculty of Nature and Life Sciences, Department of Physico-Chemical Biology, 06000, Bejaia, AlgeriaUniversity of BejaiaBejaiaAlgeria
| | - Kafia Ladjali-Mohammedi
- University of Sciences and Technology Houari Boumediene, Faculty of Biological Sciences, Laboratory of Cellular and Molecular Biology, Team of Developmental Genetics. USTHB, PO box 32 El-Alia, Bab-Ezzouar, 16110 Algiers, AlgeriaUniversity of Sciences and Technology Houari BoumedieneBab-EzzouarAlgeria
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Bai JY, Pang YZ, Zhang XH, Yun YX, Qi YX. Microsatellite Analysis of Genetic Diversity in Quail Populations from China. BRAZILIAN JOURNAL OF POULTRY SCIENCE 2016. [DOI: 10.1590/1806-9061-2015-0101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- JY Bai
- Henan University of Science and Technology, China
| | - YZ Pang
- Henan University of Science and Technology, China
| | - XH Zhang
- Henan University of Science and Technology, China
| | - YX Yun
- Henan University of Science and Technology, China
| | - YX Qi
- Henan University of Science and Technology, China
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Nguyen-Phuc H, Fulton JE, Berres ME. Genetic variation of major histocompatibility complex (MHC) in wild Red Junglefowl (Gallus gallus). Poult Sci 2016; 95:400-11. [PMID: 26839415 DOI: 10.3382/ps/pev364] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 10/27/2015] [Indexed: 01/09/2023] Open
Abstract
The major histocompatibility complex (MHC) is a multi-family gene cluster that encodes proteins with immuno-responsive function. While studies of MHC in domesticated poultry are relatively common, very little is known about this highly polymorphic locus in wild Red Junglefowl (Gallus gallus), the natural progenitor of domestic chickens. We investigated the diversity of MHC within and among four wild Red Junglefowl populations across diversified natural habitats in South Central Vietnam. Based on a SNP panel of 84 sites spanning 210 Kb of the MHC-B locus, we identified 310 unique haplotypes in 398 chromosomes. None of these haplotypes have been described before and we did not observe any of the wild Red Junglefowl haplotypes in domesticated chickens. Analysis of molecular variance (AMOVA) revealed that 94.51% of observed haplotype variation was accounted for at the within individual level. Little genetic variance was apportioned within and among populations, the latter accounting only for 0.83%. We also found evidence of increased recombination, including numerous hotspots, and limited linkage disequilibrium among the 84 SNP sites. Compared to an average haplotype diversity of 3.55% among seventeen lines of domestic chickens, our results suggest extraordinarily high haplotype diversity remains in wild Red Junglefowl and is consistent with a pattern of balancing selection. Wild Red Junglefowl in Vietnam, therefore, represent a rich resource of natural genomic variation independent from artificial selection.
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Affiliation(s)
- Hoa Nguyen-Phuc
- University of Wisconsin-Madison, Department of Animal Sciences, Madison, WI
| | | | - Mark E Berres
- University of Wisconsin-Madison, Department of Animal Sciences, Madison, WI
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Biosa D, Scandura M, Tagliavini J, Luccarini S, Mattioli L, Apollonio M. Patterns of genetic admixture between roe deer of different origin in central Italy. J Mammal 2015. [DOI: 10.1093/jmammal/gyv098] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15
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A quantitative assessment of the release of farm-reared red-legged partridges (Alectoris rufa) for shooting in central Spain. EUR J WILDLIFE RES 2014. [DOI: 10.1007/s10344-014-0861-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Johnson JR, Ryan ME, Micheletti SJ, Shaffer HB. Short pond hydroperiod decreases fitness of nonnative hybrid salamanders in California. Anim Conserv 2013. [DOI: 10.1111/acv.12029] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- J. R. Johnson
- Department of Biology; Western Kentucky University; Bowling Green KY USA
| | - M. E. Ryan
- Department of Civil and Environmental Engineering; University of Washington; Seattle WA USA
| | - S. J. Micheletti
- School of Biological Sciences; Washington State University; Pullman WA USA
| | - H. B. Shaffer
- Department of Ecology and Evolutionary Biology; University of California; Los Angeles CA USA
- La Kretz Center for California Conservation Science; Institute of the Environment and Sustainability; University of California; Los Angeles CA USA
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Champagnon J, Crochet PA, Kreisinger J, Čížková D, Gauthier-Clerc M, Massez G, Söderquist P, Albrecht T, Guillemain M. Assessing the genetic impact of massive restocking on wild mallard. Anim Conserv 2012. [DOI: 10.1111/j.1469-1795.2012.00600.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
| | - P-A. Crochet
- Centre d'Ecologie Fonctionnelle et Evolutive; UMR 5175 - CNRS; Montpellier Cedex 5; France
| | - J. Kreisinger
- Department of Zoology; Faculty of Science; Charles University in Prague; Praha 2; Czech Republic
| | - D. Čížková
- Department of Population Biology; Institute of Vertebrate Biology; Academy of Sciences of the Czech Republic; Brno; Czech Republic
| | | | - G. Massez
- Les Marais du Vigueirat; Arles; France
| | | | | | - M. Guillemain
- Office National de la Chasse et de la Faune Sauvage; CNERA Avifaune Migratrice; Arles; France
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Biedrzycka A, Solarz W, Okarma H. Hybridization between native and introduced species of deer in Eastern Europe. J Mammal 2012. [DOI: 10.1644/11-mamm-a-022.1] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Frésard L, Leroux S, Dehais P, Servin B, Gilbert H, Bouchez O, Klopp C, Cabau C, Vignoles F, Feve K, Ricros A, Gourichon D, Diot C, Richard S, Leterrier C, Beaumont C, Vignal A, Minvielle F, Pitel F. Fine mapping of complex traits in non-model species: using next generation sequencing and advanced intercross lines in Japanese quail. BMC Genomics 2012; 13:551. [PMID: 23066875 PMCID: PMC3534603 DOI: 10.1186/1471-2164-13-551] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 10/08/2012] [Indexed: 11/16/2022] Open
Abstract
Background As for other non-model species, genetic analyses in quail will benefit greatly from a higher marker density, now attainable thanks to the evolution of sequencing and genotyping technologies. Our objective was to obtain the first genome wide panel of Japanese quail SNP (Single Nucleotide Polymorphism) and to use it for the fine mapping of a QTL for a fear-related behaviour, namely tonic immobility, previously localized on Coturnix japonica chromosome 1. To this aim, two reduced representations of the genome were analysed through high-throughput 454 sequencing: AFLP (Amplified Fragment Length Polymorphism) fragments as representatives of genomic DNA, and EST (Expressed Sequence Tag) as representatives of the transcriptome. Results The sequencing runs produced 399,189 and 1,106,762 sequence reads from cDNA and genomic fragments, respectively. They covered over 434 Mb of sequence in total and allowed us to detect 17,433 putative SNP. Among them, 384 were used to genotype two Advanced Intercross Lines (AIL) obtained from three quail lines differing for duration of tonic immobility. Despite the absence of genotyping for founder individuals in the analysis, the previously identified candidate region on chromosome 1 was refined and led to the identification of a candidate gene. Conclusions These data confirm the efficiency of transcript and AFLP-sequencing for SNP discovery in a non-model species, and its application to the fine mapping of a complex trait. Our results reveal a significant association of duration of tonic immobility with a genomic region comprising the DMD (dystrophin) gene. Further characterization of this candidate gene is needed to decipher its putative role in tonic immobility in Coturnix.
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Affiliation(s)
- Laure Frésard
- INRA, UMR444 Laboratoire de Génétique Cellulaire, Castanet-Tolosan, F-31326, France
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Berthouly-Salazar C, Thévenon S, Van TN, Nguyen BT, Pham LD, Chi CV, Maillard JC. Uncontrolled admixture and loss of genetic diversity in a local Vietnamese pig breed. Ecol Evol 2012; 2:962-75. [PMID: 22837841 PMCID: PMC3399162 DOI: 10.1002/ece3.229] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 01/18/2012] [Indexed: 12/25/2022] Open
Abstract
The expansion of intensive livestock production systems in developing countries has increased the introduction of highly productive exotic breeds facilitating indiscriminate crossbreeding with local breeds. In this study, we set out to investigate the genetic status of the Vietnamese Black H'mong pig breed by evaluating (1) genetic diversity and (2) introgression from exotic breeds. Two exotic breeds, namely Landrace and Yorkshire used for crossbreeding, and the H'mong pig population from Ha Giang (HG) province were investigated using microsatellite markers. Within the province, three phenotypes were observed: a White, a Spotted and a Black phenotype. Genetic differentiation between phenotypes was low (0.5-6.1%). The White phenotypes showed intermediate admixture values between exotic breeds and the Black HG population (0.53), indicating a crossbreed status. Management practices were used to predict the rate of private diversity loss due to exotic gene introgressions. After 60 generations, 100% of Black private alleles will be lost. This loss is accelerated if the admixture rate is increased but can be slowed down if the mortality rate (e.g., recruitment rate) is decreased. Our study showed that a large number of markers are needed for accurately identifying hybrid classes for closely related populations. While our estimate of admixture still seems underestimated, genetic erosion can occur very fast even through indiscriminate crossbreeding.
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Affiliation(s)
- Cécile Berthouly-Salazar
- Department of Botany & Zoology, DST-NRF Centre of Excellence for Invasion Biology (C·I·B), University of StellenboschMatieland 7602, South Africa
| | - Sophie Thévenon
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD)UMR INTERTRYP, 34398 Montpellier, France
| | - Thu Nhu Van
- National Institute of Animal Husbandry (NIAH)Tu Liem, Hanoi, Vietnam
| | - Binh Trong Nguyen
- National Institute of Animal Husbandry (NIAH)Tu Liem, Hanoi, Vietnam
| | - Lan Doan Pham
- National Institute of Animal Husbandry (NIAH)Tu Liem, Hanoi, Vietnam
| | - Cuong Vu Chi
- National Institute of Animal Husbandry (NIAH)Tu Liem, Hanoi, Vietnam
| | - Jean-Charles Maillard
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD)UPR AGIRs, 34398 Montpellier, France
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Sanchez-Donoso I, Vilà C, Puigcerver M, Butkauskas D, Caballero de la Calle JR, Morales-Rodríguez PA, Rodríguez-Teijeiro JD. Are farm-reared quails for game restocking really common quails (Coturnix coturnix)?: a genetic approach. PLoS One 2012; 7:e39031. [PMID: 22701745 PMCID: PMC3373495 DOI: 10.1371/journal.pone.0039031] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 05/15/2012] [Indexed: 11/20/2022] Open
Abstract
The common quail (Coturnix coturnix) is a popular game species for which restocking with farm-reared individuals is a common practice. In some areas, the number of released quails greatly surpasses the number of wild breeding common quail. However, common quail are difficult to raise in captivity and this casts suspicion about a possible hybrid origin of the farmed individuals from crosses with domestic Japanese quail (C. japonica). In this study we used a panel of autosomal microsatellite markers to characterize the genetic origin of quails reared for hunting purposes in game farms in Spain and of quails from an experimental game farm which was founded with hybrids that have been systematically backcrossed with wild common quails. The genotypes of these quail were compared to those of wild common quail and domestic strains of Japanese quail. Our results show that more than 85% of the game farm birds were not common quail but had domestic Japanese quail ancestry. In the experimental farm a larger proportion of individuals could not be clearly separated from pure common quails. We conclude that the majority of quail sold for restocking purposes were not common quail. Genetic monitoring of individuals raised for restocking is indispensable as the massive release of farm-reared hybrids could represent a severe threat for the long term survival of the native species.
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Affiliation(s)
- Ines Sanchez-Donoso
- Conservation and Evolutionary Genetics Group, Doñana Biological Station, EBD-CSIC, Seville, Spain.
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MORINHA FRANCISCO, CARVALHO MÁRCIA, FERRO ANABELA, GUEDES-PINTO HENRIQUE, RODRIGUES ROGÉRIO, BASTOS ESTELA. Molecular sexing and analysis of CHD1-Z and CHD1-W sequence variations in wild common quail (Coturnix c. coturnix) and domesticated Japanese quail (Coturnix c. japonica). J Genet 2011. [DOI: 10.1007/s12041-011-0053-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Steeves TE, Maloney RF, Hale ML, Tylianakis JM, Gemmell NJ. Genetic analyses reveal hybridization but no hybrid swarm in one of the world's rarest birds. Mol Ecol 2010; 19:5090-100. [PMID: 21050294 DOI: 10.1111/j.1365-294x.2010.04895.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hybridization facilitated by human activities has dramatically altered the evolutionary trajectories of threatened taxa around the globe. Whereas introduced mammalian predators and widespread habitat loss and degradation clearly imperil the recovery and survival of the New Zealand endemic black stilt or kakī (Himantopus novaezelandiae), the risk associated with hybridization between this critically endangered endemic and its self-introduced congener, the pied stilt or poaka (Himantopus himantopus leucocephalus) is less clear. Here, we combine Bayesian admixture analyses of microsatellite data with mitochondrial DNA sequence data to assess the levels of hybridization and introgression between kakī and poaka. We show that birds classified as hybrids on the basis of adult plumage are indeed of hybrid origin and that hybridization between kakī and poaka is both extensive and bidirectional. Despite this, we found almost no evidence for introgression from poaka to kakī, thus negating the popular belief that kakī represent a hybrid swarm. To our knowledge, ours represents the first comprehensive study to document a lack of widespread introgression for a species at risk despite a recent history of extensive bidirectional human-induced hybridization. We attribute this rather surprising result, in part, to reduced reproductive success in female hybrids combined with a transient male-biased kakī sex ratio. To maximize the evolutionary potential of kakī, we use these data to recommend conservation management activities aimed to maintain the genetic integrity and to maximize the genetic diversity of this iconic rare bird.
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Affiliation(s)
- Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand.
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