First complete genome sequence in Arborophila and comparative genomics reveals the evolutionary adaptation of Hainan Partridge(Arborophila ardens)

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.

Intraspecific variation in microhabitat selection in reintroduced Chinese giant salamanders

Reintroduction of captive-bred Chinese giant salamanders is a primary approach for restoring wild populations.Despite previous studies have investigated the habitat preferences of reintroduced Chinese giant salamanders,the intraspecific variation in their habitat selection has been neglected.In the present study,30 captive-bred Chinese giant salamanders belonging to 3 groups(i.e.,10 males,10 females,and 10 juveniles)were released into a montane stream to explore whether intraspecific variation in habitat selection occurred in this species using radiotelemetry.Our results indicated that linear home range and daily movement of males were significantly higher than those of females and juveniles.Male sedentariness was significantly lower than that of females and juveniles.No significant differences were detected between females and juveniles in these measures.Importantly,we found that males preferred microhabitats with low water conductivity and deep water depth.Females preferred microhabitats with high water conductivity,low dissolved oxygen and ammonium-nitrogen,and slow current velocity,while juveniles occupied microhabitats with low ammonium-nitrogen.In addition,males and juveniles exhibited higher niche breadth than females.Niche overlap was high between adults and juveniles but low between males and females.Our study revealed the presence of spatial segregation in reintroduced Chinese giant salamanders.Males,females,and juveniles exhibited variation in microhabitat selection.These results provide important information for use when planning strategies for conservation of Chinese giant salamanders.