Peter Kovalik
Well-known member
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Phasianidae (1 Viewer)
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- Start date
Peter Kovalik
Well-known member
Richard Klim
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Chrysolophus pheasants
Lyu, Päckert, Tietze & Sun (in press). Uncommon paleodistribution patterns of Chrysolophus pheasants in East Asia: explanations and implications. J Avian Biol. [abstract]
McGowan & Kirwan 2013/2014 (HBW Alive):
Lyu, Päckert, Tietze & Sun (in press). Uncommon paleodistribution patterns of Chrysolophus pheasants in East Asia: explanations and implications. J Avian Biol. [abstract]
McGowan & Kirwan 2013/2014 (HBW Alive):
Richard Klim
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Tibetan Snowcock
An, Zhang, Liu & Wang 2015. Refugia persistence of Qinghai-Tibetan Plateau by the cold-tolerant bird Tetraogallus tibetanus (Galliformes: Phasianidae). PLoS ONE 10(3): e0121118. [article] [pdf]
McGowan & Kirwan 2013 (HBW Alive).
An, Zhang, Liu & Wang 2015. Refugia persistence of Qinghai-Tibetan Plateau by the cold-tolerant bird Tetraogallus tibetanus (Galliformes: Phasianidae). PLoS ONE 10(3): e0121118. [article] [pdf]
McGowan & Kirwan 2013 (HBW Alive).
Richard Klim
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Peter Kovalik
Well-known member
Peter Kovalik
Well-known member
Nicholas W. Persons, Peter A. Hosner, Kelly A. Meiklejohn, Edward L. Braun, Rebecca T. Kimball. Sorting out relationships among the grouse and ptarmigan using intron, mitochondrial, and ultra-conserved element sequences. Molecular Phylogenetics and Evolution, In Press, Available online 12 February 2016.
[Abstract]
[Abstract]
Richard Klim
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Golden Pheasant
Zeng, He, Sun, Ma, Ge, Fang & Wan 2016. Balancing selection and recombination as evolutionary forces caused population genetic variations in golden pheasant MHC class I genes. BMC Evol Biol 16: 42. [article & pdf]
Richard Klim
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Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
Their work don't change taxonomy, falcipennis into Falcipennis, canadensis into Canachites and voilà ! Why complicate life ?
Peter Kovalik
Well-known member
Chrysolophus pictus
Ke He, Hong-Yi Liu, Yun-Fa Ge, Shao-Ying Wu, Qiu-Hong Wan. Historical gene flow and profound spatial genetic structure among golden pheasant populations suggested by multi-locus analysis. Molecular Phzlogenetics and Evolution, In Press, Accepted Manuscript, Available online 7 March 2017.
Abstract:
Major histocompatibility complex (MHC) is a good marker system for geographical genetics since they are functional genes in the immune system that are likely to affect the fitness of the individual, and the survival and evolutionary potential of a population in a changing environment. Golden pheasant (Chrysolophus pictus) is a wild Phasianidae distributed in central and north China. In this study, we used a locus-specific genotyping technique for MHC IIB genes of golden pheasant. Combining with microsatellites (simple sequence repeat, SSR) and mitochondrial DNA (mtDNA) D-loop region, we investigated the demographic history and illuminate genetic structure of this bird in detail. SYR (south of Yangtze river) –NYR (north of Yangtze river) lineages, separated by Yangtze River, were defined in genetic structure of MHC IIB. NYR was supposed as refuge during glacial period, suggested by diversity parameters and more ancient alleles in this region. Based on this hypothesis, there was gene flow from NYR to SYR, which was proved by three pieces of evidence: (1) distinct demographic histories of SYR (kept stable) and NYR (experienced expansion); (2) specific affiliation of LC in genetic structure of SSR and MHC genes; (3) significant gene flow from NYR to SYR. Moreover, we also found balancing selection by combination of three Grouping A2’s regions (SC, QL and North) into one in Grouping B4 (NYR) and no pattern of isolation by distance (IBD) found in MHC IIB, whereas for SSR we found a relatively strong and significant IBD. Several mechanisms in the evolution of MHC IIB genes, including recombination, historically positive selection, trans-species evolution and concerted evolution, were shown by molecular and phylogenetic analysis. Overall these results suggest the Yangtze River was inferred to be a geological barrier for this avian and NYR might experience population expansion, which invaded into a neighboring region. This study contributes to the understanding of the effects of geographic features on contemporary patterns of genetic variation in the golden pheasant in China, and helps us to define the adaptive unite (AU) for this avian.
Ke He, Hong-Yi Liu, Yun-Fa Ge, Shao-Ying Wu, Qiu-Hong Wan. Historical gene flow and profound spatial genetic structure among golden pheasant populations suggested by multi-locus analysis. Molecular Phzlogenetics and Evolution, In Press, Accepted Manuscript, Available online 7 March 2017.
Abstract:
Major histocompatibility complex (MHC) is a good marker system for geographical genetics since they are functional genes in the immune system that are likely to affect the fitness of the individual, and the survival and evolutionary potential of a population in a changing environment. Golden pheasant (Chrysolophus pictus) is a wild Phasianidae distributed in central and north China. In this study, we used a locus-specific genotyping technique for MHC IIB genes of golden pheasant. Combining with microsatellites (simple sequence repeat, SSR) and mitochondrial DNA (mtDNA) D-loop region, we investigated the demographic history and illuminate genetic structure of this bird in detail. SYR (south of Yangtze river) –NYR (north of Yangtze river) lineages, separated by Yangtze River, were defined in genetic structure of MHC IIB. NYR was supposed as refuge during glacial period, suggested by diversity parameters and more ancient alleles in this region. Based on this hypothesis, there was gene flow from NYR to SYR, which was proved by three pieces of evidence: (1) distinct demographic histories of SYR (kept stable) and NYR (experienced expansion); (2) specific affiliation of LC in genetic structure of SSR and MHC genes; (3) significant gene flow from NYR to SYR. Moreover, we also found balancing selection by combination of three Grouping A2’s regions (SC, QL and North) into one in Grouping B4 (NYR) and no pattern of isolation by distance (IBD) found in MHC IIB, whereas for SSR we found a relatively strong and significant IBD. Several mechanisms in the evolution of MHC IIB genes, including recombination, historically positive selection, trans-species evolution and concerted evolution, were shown by molecular and phylogenetic analysis. Overall these results suggest the Yangtze River was inferred to be a geological barrier for this avian and NYR might experience population expansion, which invaded into a neighboring region. This study contributes to the understanding of the effects of geographic features on contemporary patterns of genetic variation in the golden pheasant in China, and helps us to define the adaptive unite (AU) for this avian.
l_raty
laurent raty
Hosner, Tobias, Braun, Kimball. 2017. How do seemingly non-vagile clades accomplish trans-marine dispersal? Trait and dispersal evolution in the landfowl (Aves: Galliformes). Proc. R. Soc. B 284:20170210.
[abstract] [supp.mat.1(FigShare)] [supp.mat.2(Dryad)]
[abstract] [supp.mat.1(FigShare)] [supp.mat.2(Dryad)]
Last edited:
Peter Kovalik
Well-known member
Pheasants
Cai T, Fjeldså J, Wu Y, et al. What makes the Sino-Himalayan mountains the major diversity hotspots for pheasants? J Biogeogr. 2017;00:1–12. https://doi.org/10.1111/jbi.13156
[abstract]
Cai T, Fjeldså J, Wu Y, et al. What makes the Sino-Himalayan mountains the major diversity hotspots for pheasants? J Biogeogr. 2017;00:1–12. https://doi.org/10.1111/jbi.13156
[abstract]
l_raty
laurent raty
Syrmaticus mikado
Lee, Hsieh, Chiang, Chattopadhyay, Li, Lee, Lu, Lai, Lin, Lee, Ding, Tsai, Chen, Chuang. 2018. Whole-genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant. GigaScience, 7(5): giy044.
https://doi.org/10.1093/gigascience/giy044
Abstract
Background
The Mikado pheasant (Syrmaticus mikado) is a nearly endangered species indigenous to high-altitude regions of Taiwan. This pheasant provides an opportunity to investigate evolutionary processes following geographic isolation. Currently, the genetic background and adaptive evolution of the Mikado pheasant remain unclear.
Results
We present the draft genome of the Mikado pheasant, which consists of 1.04 Gb of DNA and 15,972 annotated protein-coding genes. The Mikado pheasant displays expansion and positive selection of genes related to features that contribute to its adaptive evolution, such as energy metabolism, oxygen transport, hemoglobin binding, radiation response, immune response, and DNA repair. To investigate the molecular evolution of the major histocompatibility complex (MHC) across several avian species, 39 putative genes spanning 227 kb on a contiguous region were annotated and manually curated. The MHC loci of the pheasant revealed a high level of synteny, several rapidly evolving genes, and inverse regions compared to the same loci in the chicken. The complete mitochondrial genome was also sequenced, assembled, and compared against four long-tailed pheasants. The results from molecular clock analysis suggest that ancestors of the Mikado pheasant migrated from the north to Taiwan about 3.47 million years ago.
Conclusions
This study provides a valuable genomic resource for the Mikado pheasant, insights into its adaptation to high altitude, and the evolutionary history of the genus Syrmaticus, which could potentially be useful for future studies that investigate molecular evolution, genomics, ecology, and immunogenetics.
Lee, Hsieh, Chiang, Chattopadhyay, Li, Lee, Lu, Lai, Lin, Lee, Ding, Tsai, Chen, Chuang. 2018. Whole-genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant. GigaScience, 7(5): giy044.
https://doi.org/10.1093/gigascience/giy044
Abstract
Background
The Mikado pheasant (Syrmaticus mikado) is a nearly endangered species indigenous to high-altitude regions of Taiwan. This pheasant provides an opportunity to investigate evolutionary processes following geographic isolation. Currently, the genetic background and adaptive evolution of the Mikado pheasant remain unclear.
Results
We present the draft genome of the Mikado pheasant, which consists of 1.04 Gb of DNA and 15,972 annotated protein-coding genes. The Mikado pheasant displays expansion and positive selection of genes related to features that contribute to its adaptive evolution, such as energy metabolism, oxygen transport, hemoglobin binding, radiation response, immune response, and DNA repair. To investigate the molecular evolution of the major histocompatibility complex (MHC) across several avian species, 39 putative genes spanning 227 kb on a contiguous region were annotated and manually curated. The MHC loci of the pheasant revealed a high level of synteny, several rapidly evolving genes, and inverse regions compared to the same loci in the chicken. The complete mitochondrial genome was also sequenced, assembled, and compared against four long-tailed pheasants. The results from molecular clock analysis suggest that ancestors of the Mikado pheasant migrated from the north to Taiwan about 3.47 million years ago.
Conclusions
This study provides a valuable genomic resource for the Mikado pheasant, insights into its adaptation to high altitude, and the evolutionary history of the genus Syrmaticus, which could potentially be useful for future studies that investigate molecular evolution, genomics, ecology, and immunogenetics.
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l_raty
laurent raty
Coturnix japonica
Wu, Zhang, Hou, Fan, Pi, Sun, Chen, Liu, Du, Shen, Hu, Chen, Pan, Yin, Chen, Pu, Zhang, Liang, Jian, Zhang, Wu, Sun, Chen, Tao, Yang, Xiao, Yang, Zheng, Bai, Fang, Burt, Wang, Li, Xu, Li, Yang, Wang, Yang, Liu, Du. 2018. Population genomic data reveal genes related to important traits of quail. GigaScience, 7(5): giy049.
https://doi.org/10.1093/gigascience/giy049
Abstract
Background
Japanese quail (Coturnix japonica), a recently domesticated poultry species, is important not only as an agricultural product, but also as a model bird species for genetic research. However, most of the biological questions concerning genomics, phylogenetics, and genetics of some important economic traits have not been answered. It is thus necessary to complete a high-quality genome sequence as well as a series of comparative genomics, evolution, and functional studies.
Results
Here, we present a quail genome assembly spanning 1.04 Gb with 86.63% of sequences anchored to 30 chromosomes (28 autosomes and 2 sex chromosomes Z/W). Our genomic data have resolved the long-term debate of phylogeny among Perdicinae (Japanese quail), Meleagridinae (turkey), and Phasianinae (chicken). Comparative genomics and functional genomic data found that four candidate genes involved in early maturation had experienced positive selection, and one of them encodes follicle stimulating hormone beta (FSHβ), which is correlated with different FSHβ levels in quail and chicken. We re-sequenced 31 quails (10 wild, 11 egg-type, and 10 meat-type) and identified 18 and 26 candidate selective sweep regions in the egg-type and meat-type lines, respectively. That only one of them is shared between egg-type and meat-type lines suggests that they were subject to an independent selection. We also detected a haplotype on chromosome Z, which was closely linked with maroon/yellow plumage in quail using population resequencing and a genome-wide association study. This haplotype block will be useful for quail breeding programs.
Conclusions
This study provided a high-quality quail reference genome, identified quail-specific genes, and resolved quail phylogeny. We have identified genes related to quail early maturation and a marker for plumage color, which is significant for quail breeding. These results will facilitate biological discovery in quails and help us elucidate the evolutionary processes within the Phasianidae family.
Wu, Zhang, Hou, Fan, Pi, Sun, Chen, Liu, Du, Shen, Hu, Chen, Pan, Yin, Chen, Pu, Zhang, Liang, Jian, Zhang, Wu, Sun, Chen, Tao, Yang, Xiao, Yang, Zheng, Bai, Fang, Burt, Wang, Li, Xu, Li, Yang, Wang, Yang, Liu, Du. 2018. Population genomic data reveal genes related to important traits of quail. GigaScience, 7(5): giy049.
https://doi.org/10.1093/gigascience/giy049
Abstract
Background
Japanese quail (Coturnix japonica), a recently domesticated poultry species, is important not only as an agricultural product, but also as a model bird species for genetic research. However, most of the biological questions concerning genomics, phylogenetics, and genetics of some important economic traits have not been answered. It is thus necessary to complete a high-quality genome sequence as well as a series of comparative genomics, evolution, and functional studies.
Results
Here, we present a quail genome assembly spanning 1.04 Gb with 86.63% of sequences anchored to 30 chromosomes (28 autosomes and 2 sex chromosomes Z/W). Our genomic data have resolved the long-term debate of phylogeny among Perdicinae (Japanese quail), Meleagridinae (turkey), and Phasianinae (chicken). Comparative genomics and functional genomic data found that four candidate genes involved in early maturation had experienced positive selection, and one of them encodes follicle stimulating hormone beta (FSHβ), which is correlated with different FSHβ levels in quail and chicken. We re-sequenced 31 quails (10 wild, 11 egg-type, and 10 meat-type) and identified 18 and 26 candidate selective sweep regions in the egg-type and meat-type lines, respectively. That only one of them is shared between egg-type and meat-type lines suggests that they were subject to an independent selection. We also detected a haplotype on chromosome Z, which was closely linked with maroon/yellow plumage in quail using population resequencing and a genome-wide association study. This haplotype block will be useful for quail breeding programs.
Conclusions
This study provided a high-quality quail reference genome, identified quail-specific genes, and resolved quail phylogeny. We have identified genes related to quail early maturation and a marker for plumage color, which is significant for quail breeding. These results will facilitate biological discovery in quails and help us elucidate the evolutionary processes within the Phasianidae family.
Peter Kovalik
Well-known member
Rheinardia ocellata nigrescens
G. W. H. Davison, Peter Boesman, N. J. Collar, C. L. Puan. Species rank for Rheinardia ocellata nigrescens (Phasianidae). Bulletin of the British Ornithologists’ Club, 140(2):182-194 (2020). https://doi.org/10.25226/bboc.v140i2.2020.a9
Abstract:
Crested Argus Rheinardia ocellata has two highly disjunct populations in Vietnam and Lao PDR (nominate ocellata) and Malaysia (subspecies nigrescens). When evidence from the small sample of museum specimens is supplemented by novel photographic and acoustic evidence, Malaysian nigrescens proves to be distinct on a suite of characters: yellower bill with blackish nares, buffier supercilium, throat and breast, different-coloured and -structured crest, different-patterned upperparts and tail, a purer, more fluent, longer, lower Short Call (used by advertising males), markedly divergent from the explosive, nasal, double-noted equivalent in nominate ocellata, and a higher number of loud notes in the Long Call including an unexplained bimodal vs. unimodal pattern (hence either average 8.6 or 14.5 vs. 7.1 loud notes per call). In combination these characters indicate a level of differentiation compatible with species rank for nigrescens, and this is strongly reflected in Tobias criteria scoring. The conservation of the two forms requires urgent reconsideration.
[full article]
G. W. H. Davison, Peter Boesman, N. J. Collar, C. L. Puan. Species rank for Rheinardia ocellata nigrescens (Phasianidae). Bulletin of the British Ornithologists’ Club, 140(2):182-194 (2020). https://doi.org/10.25226/bboc.v140i2.2020.a9
Abstract:
Crested Argus Rheinardia ocellata has two highly disjunct populations in Vietnam and Lao PDR (nominate ocellata) and Malaysia (subspecies nigrescens). When evidence from the small sample of museum specimens is supplemented by novel photographic and acoustic evidence, Malaysian nigrescens proves to be distinct on a suite of characters: yellower bill with blackish nares, buffier supercilium, throat and breast, different-coloured and -structured crest, different-patterned upperparts and tail, a purer, more fluent, longer, lower Short Call (used by advertising males), markedly divergent from the explosive, nasal, double-noted equivalent in nominate ocellata, and a higher number of loud notes in the Long Call including an unexplained bimodal vs. unimodal pattern (hence either average 8.6 or 14.5 vs. 7.1 loud notes per call). In combination these characters indicate a level of differentiation compatible with species rank for nigrescens, and this is strongly reflected in Tobias criteria scoring. The conservation of the two forms requires urgent reconsideration.
[full article]
James Lowther
Well-known member
Ocellata sensu stricto going to be a super difficult species to see presumably. And maybe critically endangered?
James
James
DMW
Well-known member
It was not especially uncommon in suitable areas in central Vietnam when I first visited, and much more accessible than Crested Argus s.l. In Malaysia, but I believe it has undergone a serious decline in the last couple of decades. Probably safe to say that both taxa are now super difficult. Whether the Indochinese birds meet the criteria for CE, I don't know, but not a good place to be a large edible bird.
Peter Kovalik
Well-known member
IOC Updates Diary June 28
Accept split of Malaysian Crested Argus Rheinardia nigrescens from Vietnamese Crested Argus Rheinardia ocellata.
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
Peter A. Hosner Hannah L. Owens Edward L. Braun Rebecca T. Kimball (2020)
Phylogeny and diversification of the gallopheasants (Aves: Galliformes): Testing roles of sexual selection and environmental niche divergence
Abstract
The gallopheasants comprise a clade of 22 species including some of the most elaborately plumaged and highly ornamented birds in the world. They also occupy a remarkable breath of environments and habitats, ranging from lowland rainforests to high grasslands and steppes of the Tibetan plateau. Here, we provide the first well‐resolved species phylogeny of this charismatic group, inferred from ultraconserved elements, nuclear introns and mitochondrial DNA sequences. Unlike previous studies which found unresolvable relationships and suggested a rapid initial burst of diversification, we identified a well‐resolved phylogeny supported in both concatenated and coalescent analytical frameworks, and a steady accrual of lineages through time. Morphological trait reconstructions demonstrated strong phylogenetic signal, not only for highly ornamented males, but also in more cryptically plumaged females. Environmental niche similarly exhibited strong phylogenetic signal. Moreover, evolution of male traits, female traits and environmental niche were all significantly correlated, making it difficult to disentangle their individual roles in gallopheasant diversification
https://onlinelibrary.wiley.com/doi/full/10.1111/zsc.12441
Phylogeny and diversification of the gallopheasants (Aves: Galliformes): Testing roles of sexual selection and environmental niche divergence
Abstract
The gallopheasants comprise a clade of 22 species including some of the most elaborately plumaged and highly ornamented birds in the world. They also occupy a remarkable breath of environments and habitats, ranging from lowland rainforests to high grasslands and steppes of the Tibetan plateau. Here, we provide the first well‐resolved species phylogeny of this charismatic group, inferred from ultraconserved elements, nuclear introns and mitochondrial DNA sequences. Unlike previous studies which found unresolvable relationships and suggested a rapid initial burst of diversification, we identified a well‐resolved phylogeny supported in both concatenated and coalescent analytical frameworks, and a steady accrual of lineages through time. Morphological trait reconstructions demonstrated strong phylogenetic signal, not only for highly ornamented males, but also in more cryptically plumaged females. Environmental niche similarly exhibited strong phylogenetic signal. Moreover, evolution of male traits, female traits and environmental niche were all significantly correlated, making it difficult to disentangle their individual roles in gallopheasant diversification
https://onlinelibrary.wiley.com/doi/full/10.1111/zsc.12441
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