Using citizen science data to improve regional bird species list:A case study in Shaanxi,China

An accurate and updated regional bird species checklist is the foundation for biodiversity research and conservation.However,with ongoing climate and landscape changes,tracking the distributions of bird species is challenging,and expert-curated species lists are often limited regarding survey area and timeliness.Birdwatching in China is becoming increasingly popular,and observations recorded by citizen birders are quickly increasing as well.Assessing the value of these data for improving regional species lists and studying bird distribution needs a detailed and quantitative comparison of citizen science data and expert-curated data.We collected observation reports from the China Bird Report Center,the largest online open platform for sharing bird sightings in China.We focused on reports from 2016 to 2019 in Shaanxi Province.For expert-curated species lists,we used three sources:the latest bird field guide published by local ornithologists,the province list from Avibase,and a list generated from overlaying distribution range from BirdLife International with the outline of Shaanxi Province.In addition,we also compared the bird sighting coordinates with the species distribution maps from BirdLife International.Surprisingly,species checklists from different sources have considerable discrepancies,even among lists based on expert knowledge.Including birdwatching data,there are 616 bird species in total,but less than half of the species(294)appear in all checklists,and 17.2%of species are unique to one list.One hundred sixty-three species lack birdwatching records,but birdwatching identified 39 species new to the province.One hundred thirty-six bird species have sighting locations outside the distribution ranges from BirdLife International,suggesting that updates might be needed.The data also showed a clear trend of bird species shifting to higher latitudes than their traditional distributions.While being inadequate for generating a regional species checklist on its own,birdwatching data in China can be a valuable source for complementing expert knowledge.In particular,the coordinate information of bird sighting can help track species distribution shifts.On the other hand,comparing expert-curated lists to birdwatching data can generate a species list for targeted birdwatching and monitoring,which will improve the quality of the birdwatching data in the future.

Multi-omic Analyses Shed Light on The Genetic Control of High-altitude Adaptation in Sheep

Sheep were domesticated in the Fertile Crescent and then spread globally,where they have been encountering various environmental conditions.The Tibetan sheep has adapted to high altitudes on the Qinghai-Tibet Plateau over the past 3000 years.To explore genomic variants associated with high-altitude adaptation in Tibetan sheep,we analyzed Illumina short-reads of 994 whole genomes representing∼60 sheep breeds/populations at varied altitudes,PacBio High fidelity(HiFi)reads of 13 breeds,and 96 transcriptomes from 12 sheep organs.Association testing between the inhabited altitudes and 34,298,967 variants was conducted to investigate the genetic architecture of altitude adaptation.Highly accurate HiFi reads were used to complement the current ovine reference assembly at the most significantly associatedβ-globin locus and to validate the presence of two haplotypes A and B among 13 sheep breeds.The haplotype A carried two homologous gene clusters:(1)HBE1,HBE2,HBB-like,and HBBC,and(2)HBE1-like,HBE2-like,HBB-like,and HBB;while the haplotype B lacked the first cluster.The high-altitude sheep showed highly frequent or nearly fixed haplotype A,while the low-altitude sheep dominated by haplotype B.We further demonstrated that sheep with haplotype A had an increased hemoglobin–O_(2) affinity compared with those carrying haplotype B.Another highly associated genomic region contained the EGLN1 gene which showed varied expression between high-altitude and low-altitude sheep.Our results provide evidence that the rapid adaptive evolution of advantageous alleles play an important role in facilitating the environmental adaptation of Tibetan sheep.

Elevational divergence in the great tit complex revealed by major hemoglobin genes

Gene flow and demographic history can play important roles in the adaptive genetic differentiation of species, which is rarely understood in the high-altitude adaptive evolution of birds. To elucidate genetic divergence of populations in the great tit complex （Parus major, P. minor and P. cinereus） at different elevations, we compared the genetic structure and gene flow in hemoglobin genes with neutral loci. Our results revealed the elevationally divergent structure of αA-globin gene, distinctive from that of the/βA-globin gene and neutral loci. We further investigated gene flow patterns among the populations in the central-northern （〉 1,000 m a.s.l.）, south-eastern （〈 1,000 m a.s.l.） regions and the Southwest Mountains （〉2,000 m a.s.l.） in China. The high-altitude （〉 1,000 m a.s.l.） diverged aA-globin genetic structure coincidαed with higher αA-globin gene flow between highland populations, in contrast to restricted neutral gene flow concordant with the phylogeny. The higher aA-globin gene flow suggests the possibility of adaptive evolution during population divergence, contrary to the lower aA-globin gene flow homogenized by neutral loci during population expantion. In concordance with patterns of historical gene flow, genotypic and allelic profiles provide distinctive patterns of fixation in different high-altitude populations. The fixation of alleles at contrasting elevations may primarily due to highland standing variants aA49Asn/72Asn/108Ala originating from the south-western population. Our findings demonstrate a pattern of genetic divergence with gene flow in major hemoglobin genes depending on population demographic history.

Direct evidence of CRISPR-Cas9-mediated mitochondrial genome editing

Pathogenic mitochondrial DNA(mtDNA)mutations can cause a variety of human diseases.The recent development of genome-editing technologies to manipulate mtDNA,such as mitochondria-targeted DNA nucleases and base editors,offer a promising way for curing mitochondrial diseases caused by mtDNA mutations.The CRISPR-Cas9 system is a widely used tool for genome editing;however,its application in mtDNA editing is still under debate.In this study,we developed a mito-Cas9 system by adding the mitochondria-targeted sequences and 30 untranslated region of nuclear-encoded mitochondrial genes upstream and downstream of the Cas9 gene,respectively.