Background: Previous phylogenetic studies that include the four recognized species of Gallus have resulted in a number of distinct topologies, with little agreement. Several factors could lead to the failure to conver...Background: Previous phylogenetic studies that include the four recognized species of Gallus have resulted in a number of distinct topologies, with little agreement. Several factors could lead to the failure to converge on a consistent topology, including introgression, incomplete lineage sorting, different data types, or insufficient data.Methods: We generated three novel whole genome assemblies for Gallus species, which we combined with data from the published genomes of Gallus gallus and Bambusicola thoracicus(a member of the sister genus to Gallus). To determine why previous studies have failed to converge on a single topology, we extracted large numbers of orthologous exons, introns, ultra-conserved elements, and conserved non-exonic elements from the genome assemblies. This provided more than 32 million base pairs of data that we used for concatenated maximum likelihood and multispecies coalescent analyses of Gallus.Results: All of our analyses, regardless of data type, yielded a single, well-supported topology. We found some evidence for ancient introgression involving specific Gallus lineages as well as modest data type effects that had an impact on support and branch length estimates in specific analyses. However, the estimated gene tree spectra for all data types had a relatively good fit to their expectation given the multispecies coalescent.Conclusions: Overall, our data suggest that conflicts among previous studies probably reflect the use of smaller datasets(both in terms of number of sites and of loci) in those analyses. Our results demonstrate the importance of sampling large numbers of loci, each of which has a sufficient number of sites to provide robust estimates of gene trees. Low-coverage whole genome sequencing, as we did here, represents a cost-effective means to generate the very large data sets that include multiple data types that enabled us to obtain a robust estimate of Gallus phylogeny.展开更多
Background: Little is hitherto known about the breeding ecology of the Tibetan Partridge(Perdix hodgsoniae)which is endemic to the Tibetan plateau. Here we describe nest densities, inter-nest distances and general nes...Background: Little is hitherto known about the breeding ecology of the Tibetan Partridge(Perdix hodgsoniae)which is endemic to the Tibetan plateau. Here we describe nest densities, inter-nest distances and general nest site characteristics in this gallinaceous bird species and explore the possibilities that certain shrub and plant types are preferred as nest surroundings.Method: A total of 56 nests were found over three breeding seasons near Lhasa, Tibet. Nest site characteristics were compared with random control plots and the proportions of specific plant species covering nests were compared with their estimated general occurrence in the study area.Results: Nest density in the two years with highest search effort was estimated at 1.43/km2 and 1.04/km2 but was clearly higher in the part of the study area facing north(1.86–2.35/km2) than that facing south(0.11–0.34/ km2). The average nearest neighbour distance of nests was about 300 m. Nests were situated in relatively lush vegetation and covered by a total of eight shrub species and three herbs. In contrast to previous reports, Caragana shrub did not constitute an important part of the nest habitat. The flowering, non-thorny bush Potentilla fruticosa was significantly over-represented as nest cover, while Rhododendron nivale was similarly under-represented. Nest bush foliage covered a larger area of ground, and the shrub surrounding nests was generally denser, than in control samples. Also, nests were placed closer to paths and in areas with lower densities of Yak(Bos grunniens) dung than in control samples.Except that soil temperatures were lower on nest sites than on control sites, micro-climate variables measured in this study did not differ between nest sites and control plots.Conclusions: Opportunity for nest concealment is probably an important quality of the nest habitat in Tibetan Partridges, yet it is unclear why the species should prefer P. fruticosa as nest cover. It is possible that nest sites are chosen to secure escape exits in the case of appr展开更多
Background: This paper describes the chick plumage of spurfowl(Pternistis) and francolin(Francolinus, Dendroperdix Peliperdix and Scleroptila) chicks, tests its significance for phylogenetic relationships and also exp...Background: This paper describes the chick plumage of spurfowl(Pternistis) and francolin(Francolinus, Dendroperdix Peliperdix and Scleroptila) chicks, tests its significance for phylogenetic relationships and also explores the patterns of character evolution in the francolin and spurfowl lineages.Previously regarded as monophyletic, the two evolutionar?ily distant clades are now divided into five genera.Questions considered were whether chick plumage supports the dichotomy between spurfowls and francolins and what role habitat matching plays.Methods: The study was based mainly on photographs of chick skins from the American Museum of Natural History and the Natural History Museum at Tring.Eight plumage characters were selected for comparative scoring, summa?rised in a matrix.These characters were subsequently analysed phylogenetically and their evolution was traced on the existing molecular phylogeny using a parsimony approach.Results: Based on chick plumage the phylogeny of species groups among francolins and spurfowls, was largely unresolved possibly ascribed to a high degree of symplesiomorphy inherent among the Phasianids.This possibly could have resulted in a high degree of polytomy particularly among the spurfowls and francolins.Furthermore, the ancestral state reconstructions revealed high prevalence of symplesiomorphic states and reversals which do not help in the classification of groups.Although the differences are described that separate some African francolins from spurfowls, other francolins(in Asia and Africa) share remarkably similar characteristics with spurfowls.Plain dark dorsal plumage is probably advantageous for avoiding detection by predators in forests, while facial stripes optimise the breaking of body shapes in dense grass cover(as in Scleroptila spp.) and semi?striped faces are advantageous for stationary camouflage under tree and bush cover(as in Pternistis spp.).Conclusions: Although symplesiomorphy is a hereditary explanation for downy colours and patterns, the traits rel?evant for ha展开更多
基金the Florida International University Tropics Program and the Susan S.Levine Trust.RTK and ELB also received support from the United States National Science Foundation(DEB-1118823 and DEB-1655683).
文摘Background: Previous phylogenetic studies that include the four recognized species of Gallus have resulted in a number of distinct topologies, with little agreement. Several factors could lead to the failure to converge on a consistent topology, including introgression, incomplete lineage sorting, different data types, or insufficient data.Methods: We generated three novel whole genome assemblies for Gallus species, which we combined with data from the published genomes of Gallus gallus and Bambusicola thoracicus(a member of the sister genus to Gallus). To determine why previous studies have failed to converge on a single topology, we extracted large numbers of orthologous exons, introns, ultra-conserved elements, and conserved non-exonic elements from the genome assemblies. This provided more than 32 million base pairs of data that we used for concatenated maximum likelihood and multispecies coalescent analyses of Gallus.Results: All of our analyses, regardless of data type, yielded a single, well-supported topology. We found some evidence for ancient introgression involving specific Gallus lineages as well as modest data type effects that had an impact on support and branch length estimates in specific analyses. However, the estimated gene tree spectra for all data types had a relatively good fit to their expectation given the multispecies coalescent.Conclusions: Overall, our data suggest that conflicts among previous studies probably reflect the use of smaller datasets(both in terms of number of sites and of loci) in those analyses. Our results demonstrate the importance of sampling large numbers of loci, each of which has a sufficient number of sites to provide robust estimates of gene trees. Low-coverage whole genome sequencing, as we did here, represents a cost-effective means to generate the very large data sets that include multiple data types that enabled us to obtain a robust estimate of Gallus phylogeny.
基金the late Torstein Solhoy for initiating the projectfunded by the Network for University Co-operation Tibet–Norway
文摘Background: Little is hitherto known about the breeding ecology of the Tibetan Partridge(Perdix hodgsoniae)which is endemic to the Tibetan plateau. Here we describe nest densities, inter-nest distances and general nest site characteristics in this gallinaceous bird species and explore the possibilities that certain shrub and plant types are preferred as nest surroundings.Method: A total of 56 nests were found over three breeding seasons near Lhasa, Tibet. Nest site characteristics were compared with random control plots and the proportions of specific plant species covering nests were compared with their estimated general occurrence in the study area.Results: Nest density in the two years with highest search effort was estimated at 1.43/km2 and 1.04/km2 but was clearly higher in the part of the study area facing north(1.86–2.35/km2) than that facing south(0.11–0.34/ km2). The average nearest neighbour distance of nests was about 300 m. Nests were situated in relatively lush vegetation and covered by a total of eight shrub species and three herbs. In contrast to previous reports, Caragana shrub did not constitute an important part of the nest habitat. The flowering, non-thorny bush Potentilla fruticosa was significantly over-represented as nest cover, while Rhododendron nivale was similarly under-represented. Nest bush foliage covered a larger area of ground, and the shrub surrounding nests was generally denser, than in control samples. Also, nests were placed closer to paths and in areas with lower densities of Yak(Bos grunniens) dung than in control samples.Except that soil temperatures were lower on nest sites than on control sites, micro-climate variables measured in this study did not differ between nest sites and control plots.Conclusions: Opportunity for nest concealment is probably an important quality of the nest habitat in Tibetan Partridges, yet it is unclear why the species should prefer P. fruticosa as nest cover. It is possible that nest sites are chosen to secure escape exits in the case of appr
文摘Background: This paper describes the chick plumage of spurfowl(Pternistis) and francolin(Francolinus, Dendroperdix Peliperdix and Scleroptila) chicks, tests its significance for phylogenetic relationships and also explores the patterns of character evolution in the francolin and spurfowl lineages.Previously regarded as monophyletic, the two evolutionar?ily distant clades are now divided into five genera.Questions considered were whether chick plumage supports the dichotomy between spurfowls and francolins and what role habitat matching plays.Methods: The study was based mainly on photographs of chick skins from the American Museum of Natural History and the Natural History Museum at Tring.Eight plumage characters were selected for comparative scoring, summa?rised in a matrix.These characters were subsequently analysed phylogenetically and their evolution was traced on the existing molecular phylogeny using a parsimony approach.Results: Based on chick plumage the phylogeny of species groups among francolins and spurfowls, was largely unresolved possibly ascribed to a high degree of symplesiomorphy inherent among the Phasianids.This possibly could have resulted in a high degree of polytomy particularly among the spurfowls and francolins.Furthermore, the ancestral state reconstructions revealed high prevalence of symplesiomorphic states and reversals which do not help in the classification of groups.Although the differences are described that separate some African francolins from spurfowls, other francolins(in Asia and Africa) share remarkably similar characteristics with spurfowls.Plain dark dorsal plumage is probably advantageous for avoiding detection by predators in forests, while facial stripes optimise the breaking of body shapes in dense grass cover(as in Scleroptila spp.) and semi?striped faces are advantageous for stationary camouflage under tree and bush cover(as in Pternistis spp.).Conclusions: Although symplesiomorphy is a hereditary explanation for downy colours and patterns, the traits rel?evant for ha
