Conservation Genomics Of A Critically Endangered Bird, The Siberian Crane (Leucogeranus Leucogeranus)

Climate changes and human activities have led to endangerment or even extinction of many species.Meanwhile,genetic factors also affect extinction risk of species.The Siberian crane(Leucogeranus leucogeranus)is an IUCN Critically Endangered species,the East Asian(EA)population is increasing,while the Western/Central Asian(WCA)population is almost extinct.There have been few studies on genetics of the Siberian crane,and adaptive evolution,genetics signatures,endangerment process and reason of the Siberian cranes are still unclear.Thus,related studies were carried out based on comparative genomics and population genomics methods.We firstly assembled and annotated a whole genome of the Siberian crane using de novo sequencing.Then,adaptive evolution was explored based on the coding region sequences of the Siberian crane and 12 other bird species collected from NCBI.Finally,we explored the genetic structure,demographic history,and the genomic signatures shaped by population fluctuation.We used the reference genome and resequencing data of twelve EA individuals and five WCA individuals.The main results and conclusions are as follows:(1)The entire genome size of the Siberian crane was 1.31 Gb and contig N50 was21.54 Mb.A total of 16,383 genes and 152.61 Mb of repeating elements were identified,repeating elements accounted for 11.64% of the genome,the continuity and integrity of assembled genome were good.(2)Phylogenetic tree results suggested that the Siberian crane,whooping crane(Grus americana)and Grey-crowned crane(Balearica regulorum)formed a sperate clade.The divergence time between the Siberian crane and the Whooping crane was at the beginning of Pliocene,and the divergence time between the grey-crowned crane and the Siberian crane was at the middle Miocene.The Siberian crane had 1,158 expanded gene families,mainly involved into the olfactory receptor activity,ion exchange and cells components.It had 46 positively selected genes(PSG)are mainly associated with energy metabolism,growth development and immune.The expanded gene families and positively selected genes may be related to adaptive evolution of the Siberian crane,including foraging behavior,long-distance migration and resistance to harsh environment.(3)There was genetic divergence between the two populations based on population genetic structure analysis,but the divergence level was relatively shallow.This result suggested that it is feasible to reintroduction of the WCA population using individuals derived from the EA population.(4)The results of reconstructing demographic histories suggested that the Siberian crane experienced drastic population fluctuations during the Pleistocene,and then undergone a continuous decline since the Last Glacial Period.The EA population and WCA population diverged during the Last Glacial Period(～38 Kya).Climatic oscillations from the Pleistocene to the Holocene may have contributed to the fluctuations of the Siberian crane populations,and human interference may have further exacerbated the recent population decline.(5)The results of genomic signatures showed the long-term and continuous declines of the two populations may have caused their low genetic diversities,which led to the poor adaptive potential to environmental changes of the Siberian crane.The genetic diversity of the WCA population and the EA population was similar,which suggested that the WCA population had not suffered severe genomic erosion even near extinction,but its relatively high inbreeding and genetic drift could still threaten its long-term survival.The WCA population had higher inbreeding level than the EA population,but the accumulation degree of deleterious mutations was more severe in the EA population.The results indicated that the WCA population could experience genetic purging,which may reduce the impacts of genetic load.The EA population has been increasing in recent years,but its low genetic diversity,high genetic drift and high accumulation of deleterious mutations may still negatively affect its long-term survival.In conclusion,the results of our study help to elucidate the endangerment mechanism of the Siberian crane,and provide a scientific basis for the formation of effective conservation strategies.Based on these results,we proposed some conservation suggestions.It is necessary to monitor population dynamics continuously,and protect and manage the living environment of this species.For the WCA population,it is essential to reintroduce individuals with low inbreeding levels and genetic load,and monitor continuously its genetic characters,so that it can escape from extinction.