Background:The Hainan Partridge(Arborophila ardens,Phasianidae,Galliformes) is an endemic species of Hainan Island,China,and it is classified as globally vulnerable species.There are at least 16 species in genus Arbor...Background:The Hainan Partridge(Arborophila ardens,Phasianidae,Galliformes) is an endemic species of Hainan Island,China,and it is classified as globally vulnerable species.There are at least 16 species in genus Arborophila and no genome sequence is available.Methods:The whole genome of Hainan Partridge was de novo sequenced(with shotgun approach on the Illumina 2000 platform) and assembled.Results:The genome size of Arborophila ardens is about 1.05 Gb with a high N50 scaffold length of 8.28 Mb and it is the first high quality genome announced in Arborophila genus.About 9.19% of the genome was identified as repeat sequences and about 5.88 million heterozygous SNPs were detected.A total of 17,376 protein-coding genes were predicted and their functions were annotated.The genome comparison between Hainan Partridge and Red Junglefowl(Gallus gallus) demonstrated a conserved genome structure.The phylogenetic analysis indicated that the Hainan Partridge possessed a basal phylogenetic position in Phasianidae and it was most likely derived from a common ancestor approximately 36.8 million years ago(Mya).We found that the Hainan Partridge population had experienced bottleneck and its effective population decreased from about 1,040,000 individuals 1.5 Mya to about 200,000 individuals 0.2 Mya,and then recovered to about 460,000 individuals.The number of 1:1 orthologous genes that were predicted to have undergone positive selection in the Hainan Partridge was 504 and some environmental adaptation related categories,such as response to ultraviolet radiation were represented in GO distribution analysis.Conclusions:We announced the first high quality genome in Arborophila genus and it will be a valuable genomic resource for the further studies such as evolution,adaption,conservation,not only on Hainan Partridge but also on Arborophila or Phasianidae species.展开更多
Background:Disentangling the relative importance of environmental variables and interspecific interaction in modulating co-occurrence patterns of sympatric species is essential for understanding the mechanisms of comm...Background:Disentangling the relative importance of environmental variables and interspecific interaction in modulating co-occurrence patterns of sympatric species is essential for understanding the mechanisms of community assembly and biodiversity. For the two sympatric Galliformes, Silver Pheasants (Lophura nycthemera) and Whitenecklaced Partridges (Arborophila gingica), we know little about the role of habitat use and interspecific interactions in modulating their coexistence. Methods:We adopted a probabilistic approach incorporating habitat preference and interspecific interaction using occupancy model to account for imperfect detection,and used daily activity pattern analysis to investigate the cooccurrence pattern of these two sympatric Galliformes in wet and dry seasons. Results: We found that the detection probability of Silver Pheasant and White-necklaced Partridge were related to habitat variables and interspecific interaction. The presence of Silver Pheasant increases the detection probability of White-necklaced Partridge in both the wet and dry season. However, the presence of White-necklaced Partridges increases the detection probability of Silver Pheasants in the wet season, but decreases the probability in the dry season. Further, Silver Pheasants were detected frequently in the sites of high values of enhanced vegetable index (EVI) in both the wet and dry season, and in sites away from human residential settlement in the wet season. Whitenecklaced partridges were mainly detected in low EVI sites. The site use probabilities of two Galliformes were best explained by habitat variables, Silver Pheasants and White-necklaced Partridges preferred steeper areas during the wet and dry season. Both species mainly occurred in low EVI areas during the wet season and occupied sites away from the resident settlement during the dry season. Moreover, the site use probabilities of two species had opposite relationships with forest canopy coverage. Silver Pheasants preferred areas with high forest canopy coverage whereas White-necklaced Partridges preferred low forest canopy coverage in the dry season, and vice versa in the wet season. Species interaction factor (SIF)corroborated weak evidence of the dependence of the site use of one species on that of the other in the either dry or wet season.Temporally, high overlapping of daily activity pattern indicated no significantly temporal niche differentiation between sympatric Galliformes in both wet and dry seasons. Conclusions:Our results demonstrated that the presence of two species influenced the detection probability interactively and there was no temporal partitioning in activity time between Silver Pheasants and White-necklaced Partridges in the wet and dry seasons.The site use probability of two Galliformes was best explained by habitat variables, especially the forest canopy coverage.Therefore, environmental variables and interspecific interaction are the leading drivers regulating the detection and site use probability and promoting co-occurrence of Silver Pheasants and White-necklaced Partridges.展开更多
四川山鹧鸪Arborophila rufipectus系由R.Boulton于1932年依据F.T.Smith在原西康省某地"Ta Cho Fu"采获的单独一号雄性标本而定名,中国鸟类学家以往多认为该种的模式标本产地为今四川甘洛县的大桥乡。通过对大桥乡所在地理坐...四川山鹧鸪Arborophila rufipectus系由R.Boulton于1932年依据F.T.Smith在原西康省某地"Ta Cho Fu"采获的单独一号雄性标本而定名,中国鸟类学家以往多认为该种的模式标本产地为今四川甘洛县的大桥乡。通过对大桥乡所在地理坐标的实测,并使用GoogleEarth对该地区进行查检,作者提出"Ta Cho Fu"当在今四川汉源县境内,对该地点具体位置的订正和重新定位,使四川山鹧鸪的总分布区域北推了至少100km范围。展开更多
In this study,we report an unusual homing behavior of the Sichuan Partridge(Arborophila rufipectus)at the Laojunshan National Nature Reserve,Sichuan Province,China.Hen Sichuan Partridges led the chicks back to the nes...In this study,we report an unusual homing behavior of the Sichuan Partridge(Arborophila rufipectus)at the Laojunshan National Nature Reserve,Sichuan Province,China.Hen Sichuan Partridges led the chicks back to the nests where they hatched in the evening and roosted there over night.This behavior lasted 6.7±4.3 nights(range=1–15;n=13)after the chicks hatched.At this stage,the hens became very vigilant to predators and human disturbance.If disturbed,they often abandoned the nests immediately and no longer returned thereafter.The ambient temperature at night during the early brooding period of Sichuan Partridge at our study site was^12.4°C.Our findings suggest that hen Sichuan Partridges may make trade-offs between nest predation risks versus the thermoregulatory needs of their young.展开更多
基金supported by the National Natural Science Foundation of China(Grant No.31702017)
文摘Background:The Hainan Partridge(Arborophila ardens,Phasianidae,Galliformes) is an endemic species of Hainan Island,China,and it is classified as globally vulnerable species.There are at least 16 species in genus Arborophila and no genome sequence is available.Methods:The whole genome of Hainan Partridge was de novo sequenced(with shotgun approach on the Illumina 2000 platform) and assembled.Results:The genome size of Arborophila ardens is about 1.05 Gb with a high N50 scaffold length of 8.28 Mb and it is the first high quality genome announced in Arborophila genus.About 9.19% of the genome was identified as repeat sequences and about 5.88 million heterozygous SNPs were detected.A total of 17,376 protein-coding genes were predicted and their functions were annotated.The genome comparison between Hainan Partridge and Red Junglefowl(Gallus gallus) demonstrated a conserved genome structure.The phylogenetic analysis indicated that the Hainan Partridge possessed a basal phylogenetic position in Phasianidae and it was most likely derived from a common ancestor approximately 36.8 million years ago(Mya).We found that the Hainan Partridge population had experienced bottleneck and its effective population decreased from about 1,040,000 individuals 1.5 Mya to about 200,000 individuals 0.2 Mya,and then recovered to about 460,000 individuals.The number of 1:1 orthologous genes that were predicted to have undergone positive selection in the Hainan Partridge was 504 and some environmental adaptation related categories,such as response to ultraviolet radiation were represented in GO distribution analysis.Conclusions:We announced the first high quality genome in Arborophila genus and it will be a valuable genomic resource for the further studies such as evolution,adaption,conservation,not only on Hainan Partridge but also on Arborophila or Phasianidae species.
基金supported by the National Key Research and Development Program of China(2017YFC0503802)China Postdoctoral Science Foundation(2017M 620905)
文摘Background:Disentangling the relative importance of environmental variables and interspecific interaction in modulating co-occurrence patterns of sympatric species is essential for understanding the mechanisms of community assembly and biodiversity. For the two sympatric Galliformes, Silver Pheasants (Lophura nycthemera) and Whitenecklaced Partridges (Arborophila gingica), we know little about the role of habitat use and interspecific interactions in modulating their coexistence. Methods:We adopted a probabilistic approach incorporating habitat preference and interspecific interaction using occupancy model to account for imperfect detection,and used daily activity pattern analysis to investigate the cooccurrence pattern of these two sympatric Galliformes in wet and dry seasons. Results: We found that the detection probability of Silver Pheasant and White-necklaced Partridge were related to habitat variables and interspecific interaction. The presence of Silver Pheasant increases the detection probability of White-necklaced Partridge in both the wet and dry season. However, the presence of White-necklaced Partridges increases the detection probability of Silver Pheasants in the wet season, but decreases the probability in the dry season. Further, Silver Pheasants were detected frequently in the sites of high values of enhanced vegetable index (EVI) in both the wet and dry season, and in sites away from human residential settlement in the wet season. Whitenecklaced partridges were mainly detected in low EVI sites. The site use probabilities of two Galliformes were best explained by habitat variables, Silver Pheasants and White-necklaced Partridges preferred steeper areas during the wet and dry season. Both species mainly occurred in low EVI areas during the wet season and occupied sites away from the resident settlement during the dry season. Moreover, the site use probabilities of two species had opposite relationships with forest canopy coverage. Silver Pheasants preferred areas with high forest canopy coverage whereas White-necklaced Partridges preferred low forest canopy coverage in the dry season, and vice versa in the wet season. Species interaction factor (SIF)corroborated weak evidence of the dependence of the site use of one species on that of the other in the either dry or wet season.Temporally, high overlapping of daily activity pattern indicated no significantly temporal niche differentiation between sympatric Galliformes in both wet and dry seasons. Conclusions:Our results demonstrated that the presence of two species influenced the detection probability interactively and there was no temporal partitioning in activity time between Silver Pheasants and White-necklaced Partridges in the wet and dry seasons.The site use probability of two Galliformes was best explained by habitat variables, especially the forest canopy coverage.Therefore, environmental variables and interspecific interaction are the leading drivers regulating the detection and site use probability and promoting co-occurrence of Silver Pheasants and White-necklaced Partridges.
文摘四川山鹧鸪Arborophila rufipectus系由R.Boulton于1932年依据F.T.Smith在原西康省某地"Ta Cho Fu"采获的单独一号雄性标本而定名,中国鸟类学家以往多认为该种的模式标本产地为今四川甘洛县的大桥乡。通过对大桥乡所在地理坐标的实测,并使用GoogleEarth对该地区进行查检,作者提出"Ta Cho Fu"当在今四川汉源县境内,对该地点具体位置的订正和重新定位,使四川山鹧鸪的总分布区域北推了至少100km范围。
基金This work was supported by the National Natural Science Foundation of China(31872961 and 31272330)the biodiversity survey and assessment project of the Ministry of Ecology and Environment of China(2019HB2096001006)the National Forestry and Grassland Administration of China.
文摘In this study,we report an unusual homing behavior of the Sichuan Partridge(Arborophila rufipectus)at the Laojunshan National Nature Reserve,Sichuan Province,China.Hen Sichuan Partridges led the chicks back to the nests where they hatched in the evening and roosted there over night.This behavior lasted 6.7±4.3 nights(range=1–15;n=13)after the chicks hatched.At this stage,the hens became very vigilant to predators and human disturbance.If disturbed,they often abandoned the nests immediately and no longer returned thereafter.The ambient temperature at night during the early brooding period of Sichuan Partridge at our study site was^12.4°C.Our findings suggest that hen Sichuan Partridges may make trade-offs between nest predation risks versus the thermoregulatory needs of their young.
