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Abstract Understanding the genetic mechanism of how animals adapt to extreme conditions is fundamental to determine the relationship between molecular evolution and changing environments. Goat is one of the first domesticated species and has evolved rapidly to adapt to diverse environments, including harsh high-altitude conditions with low temperature and poor oxygen supply but strong ultraviolet radiation. Here, we analyzed 331 genomes of domestic goats and wild caprid species living at varying altitudes (high > 3000 m above sea level and low < 1200 m), along with a reference-guided chromosome-scale assembly (contig-N50: 90.4 Mb) of a female Tibetan goat genome based on PacBio HiFi long reads, to dissect the genetic determinants underlying their adaptation to harsh conditions on the Qinghai-Tibetan Plateau (QTP). Population genomic analyses combined with genome-wide association studies (GWAS) revealed a genomic region harboring the 3′-phosphoadenosine 5′-phosphosulfate synthase 2 (PAPSS2) gene showing strong association with high-altitude adaptability (PGWAS = 3.62 × 10−25) in Tibetan goats. Transcriptomic data from 13 tissues revealed that PAPSS2 was implicated in hypoxia-related pathways in Tibetan goats. We further verified potential functional role of PAPSS2 in response to hypoxia in PAPSS2-deficient cells. Introgression analyses suggested that the PAPSS2 haplotype conferring the high-altitude adaptability in Tibetan goats originated from a recent hybridization between goats and a wild caprid species, the markhor (Capra falconeri). In conclusion, our results uncover a hitherto unknown contribution of PAPSS2 to high-altitude adaptability in Tibetan goats on QTP, following interspecific introgression and natural selection.

Background Pistachio ( Pistacia vera ), one of the most important commercial nut crops worldwide, is highly adaptable to abiotic stresses and is tolerant to drought and salt stresses. Results Here, we provide a draft de novo genome of pistachio as well as large-scale genome resequencing. Comparative genomic analyses reveal stress adaptation of pistachio is likely attributable to the expanded cytochrome P450 and chitinase gene families. Particularly, a comparative transcriptomic analysis shows that the jasmonic acid (JA) biosynthetic pathway plays an important role in salt tolerance in pistachio. Moreover, we resequence 93 cultivars and 14 wild P. vera genomes and 35 closely related wild Pistacia genomes, to provide insights into population structure, genetic diversity, and domestication. We find that frequent genetic admixture occurred among the different wild Pistacia species. Comparative population genomic analyses reveal that pistachio was domesticated about 8000 years ago and suggest that key genes for domestication related to tree and seed size experienced artificial selection. Conclusions Our study provides insight into genetic underpinning of local adaptation and domestication of pistachio. The Pistacia genome sequences should facilitate future studies to understand the genetic basis of agronomically and environmentally related traits of desert crops.

Genetic introgression not only provides material for adaptive evolution but also confounds our understanding of evolutionary history. This is particularly true for canids, a species complex in which genome sequencing and analysis has revealed a complex history of admixture and introgression. Here, we sequence 19 new whole genomes from high-altitude Tibetan and Himalayan wolves and dogs and combine these into a larger data set of 166 whole canid genomes. Using these data, we explore the evolutionary history and adaptation of these and other canid lineages. We find that Tibetan and Himalayan wolves are closely related to each other, and that ∼39% of their nuclear genome is derived from an as-yet-unrecognized wolf-like lineage that is deeply diverged from living Holarctic wolves and dogs. The EPAS1 haplotype, which is present at high frequencies in Tibetan dog breeds and wolves and confers an adaptive advantage to animals living at high altitudes, was probably derived from this ancient lineage. Our study underscores the complexity of canid evolution and demonstrates how admixture and introgression can shape the evolutionary trajectories of species.

Much like other indigenous domesticated animals, Tibetan chickens living at high altitudes (2,200–4,100 m) show specific physiological adaptations to the extreme environmental conditions of the Tibetan Plateau, but the genetic bases of these adaptations are not well characterized. Here, we assembled a de novo genome of a Tibetan chicken and resequenced whole genomes of 32 additional chickens, including Tibetan chickens, village chickens, game fowl, and Red Junglefowl, and found that the Tibetan chickens could broadly be placed into two groups. Further analyses revealed that several candidate genes in the calcium-signaling pathway are possibly involved in adaptation to the hypoxia experienced by these chickens, as these genes appear to have experienced directional selection in the two Tibetan chicken populations, suggesting a potential genetic mechanism underlying high altitude adaptation in Tibetan chickens. The candidate selected genes identified in this study, and their variants, may be useful targets for clarifying our understanding of the domestication of chickens in Tibet, and might be useful in current breeding efforts to develop improved breeds for the highlands.

Species of the Bos genus, including taurine cattle, zebu, gayal, gaur, banteng, yak, wisent and bison, have been domesticated at least four times and have been an important source of meat, milk and power for many human cultures. We sequence the genomes of gayal, gaur, banteng, wisent and bison, and provide population genomic sequencing of an additional 98 individuals. We use these data to determine the phylogeny and evolutionary history of these species and show that the threatened gayal is an independent species or subspecies. We show that there has been pronounced introgression among different members of this genus, and that it in many cases has involved genes of considerable adaptive importance. For example, genes under domestication selection in cattle (for example, MITF ) were introgressed from domestic cattle to yak. Also, genes in the response-to-hypoxia pathway (for example, EGLN1 , EGLN2 and HIF3a ) have been introgressed from yak to Tibetan cattle, probably facilitating their adaptation to high altitude. We also validate that there is an association between the introgressed EGLN1 allele and haemoglobin and red blood cell concentration. Our results illustrate the importance of introgression as a source of adaptive variation and during domestication, and suggest that the Bos genus evolves as a complex of genetically interconnected species with shared evolutionary trajectories. Genome sequences of Bos species are sequenced and compared to determine their phylogeny and evolutionary history. Introgression pathways for genes under domestication selection are identified.

Background Inbreeding, a central theme in evolutionary and conservation biology, is a crucial practice in breeding to stabilize and enhance the specific traits or to establish inbred lines. It also carries the risk of inbreeding depression, reduced fitness, and increased potential for extinction. Nevertheless, inbreeding has been extensively studied in small and endangered populations but its effects in large domesticated animals are poorly understood. Here, we aim to investigate the genomic consequences of inbreeding in the Banna miniature inbred pig (BN), a breed that has been inbred for over 40 years. Results We have sequenced 41 genomes of BN and Diannan miniature pig (DN) at high-coverage (> 31×) and combined them with published whole-genomes of swine to comprehensively investigate the genetic consequences of inbreeding. We find that BN is genetically closely related to DN, which is consistent with breeding records. All families of BN have undergone an extreme bottleneck due to intensive inbreeding, resulting in higher genomic inbreeding coefficients, reduced genetic diversity, and a lower effective population size ( Ne ) compare to non-inbred pigs. Furthermore, BN and DN exhibit an increased genetic load relative to Asian wild boars. Prolonged inbreeding and bottlenecks have led to some purging of deleterious mutations in BN compared to DN, and a conversion from masked load to realized load. Conclusions We present a comprehensive analysis to understand and assess the consequences of inbreeding in miniature inbred pigs from a perspective of population genomics. Utilizing genomic measurements proves effective in estimating the consequences of inbreeding, especially when a detailed and accurate historical record of pedigree are lacking. Our results provide valuable resources and a detailed perspective on the genomic impacts of inbreeding, potentially guiding efforts in breeding, breed improvement, and conservation.

Duck viral hepatitis (DVH) is an acute, highly lethal infectious disease of ducklings that causes huge losses in the duck industry. Duck hepatitis A virus genotype 3 (DHAV-3) has been one of the most prevalent DVH pathogen in the Asian duck industry in recent years. Here, we investigated the genetic basis of the resistance and susceptibility of ducks to DVH by comparing the genomes and transcriptomes of a resistant Pekin duck flock (Z8) and a susceptible Pekin duck flock (SZ7). Our comparative genomic and transcriptomic analyses suggested that NOD1 showed a strong signal of association with DVH susceptibility in ducks. Then, we found that NOD1 showed a significant expression difference between the livers of susceptible and resistant individuals after infection with DHAV-3, with higher expression in the SZ7 flock. Furthermore, suppression and overexpression experiments showed that the number of DHAV-3 genomic copies in primary duck hepatocytes was influenced by the expression level of NOD1 . In addition, in situ RNAscope analysis showed that the localization of NOD1 and DHAV-3 in liver cells was consistent. Altogether, our data suggested that NOD1 was likely associated with DHAV-3 susceptibility in ducks, which provides a target for future investigations of the pathogenesis of DVH.

The geographic origin and migration of the brown rat (Rattus norvegicus) remain subjects of considerable debate. In this study, we sequenced whole genomes of 110 wild brown rats with a diverse world-wide representation. We reveal that brown rats migrated out of southern East Asia, rather than northern Asia as formerly suggested, into the Middle East and then to Europe and Africa, thousands of years ago. Comparison of genomes from different geographical populations reveals that many genes involved in the immune system experienced positive selection in the wild brown rat.

Background The remarkable abilities of the human brain are distinctive features that set us apart from other animals. However, our understanding of how the brain has changed in the human lineage remains incomplete, but is essential for understanding cognition, behavior, and brain disorders in humans. Here, we compared the expression trajectory in brain development between humans and rhesus macaques (Macaca mulatta) to explore their divergent transcriptome profiles. Results Results showed that brain development could be divided into two stages, with a demarcation date in a range between 25 and 26 postconception weeks (PCW) for humans and 17-23PCWfor rhesus macaques, rather than birth time that have been widely used as a uniform demarcation time of neurodevelopment across species. Dynamic network biomarker (DNB) analysis revealed that the two demarcation dates were transition phases during brain development, after which the brain transcriptome profiles underwent critical transitions characterized by highly fluctuating DNB molecules. We also found that changes between early and later brain developmental stages (as defined by the demarcation points) were substantially greater in the human brain than in the macaque brain. To explore the molecular mechanism underlying prolonged timing during early human brain development, we carried out expression heterochrony tests. Results demonstrated that compared to macaques, more heterochronic genes exhibited neoteny during early human brain development, consistent with the delayed demarcation time in the human lineage, and proving that neoteny in human brain development could be traced to the prenatal period. We further constructed transcriptional networks to explore the profile of early human brain development and identified the hub gene RBFOX1 as playing an important role in regulating early brain development. We also found RBFOX1 evolved rapidly in its non-coding regions, indicating that this gene played an important role in human brain evolution. Our findings provide evidence that RBFOX1 is a likely key hub gene in early human brain development and evolution. Conclusions By comparing gene expression profiles between humans and macaques, we found divergent expression trajectories between the two species, which deepens our understanding of the evolution of the human brain.

Runs of homozygosity (ROH) are contiguous stretches of identical genomic regions inherited from both parents. Assessment of ROH in livestock species contributes significantly to our understanding of genetic health, population genetic structure, selective pressure and conservation efforts. In this study, whole genome re‐sequencing data from 140 birds of 10 Iranian indigenous chicken ecotypes, 3 commercial chicken breeds and 1 red junglefowl (RJF) population were used to investigate their population genetic structure, ROH characteristics (length and frequency) and genomic inbreeding coefficients (FROH). Additionally, we examined ROH islands for selection footprints in the indigenous chicken populations. Our results revealed distinct genetic backgrounds, among which the White Leghorn breed exhibited the greatest genetic distance from other populations, while the gamecock populations formed a separate cluster. We observed significant differences in ROH characteristics, in which the commercial breeds showed a higher number of ROH compared to indigenous chickens and red junglefowls. Short ROH ranging from 0.1 to 1 Mb were dominant among the populations. The Arian line had the highest mean length of ROH, while the White Leghorn breed showed the highest number of ROH. Among indigenous chickens, the Lari‐Afghani ecotype exhibited the highest FROH, but the Sari inherited the richest genetic diversity. Interestingly, GGA16 carried no ROH in the red junglefowls, whereas GGA22 had the highest FROH across all populations, except in the Isfahan ecotype. We also identified ROH islands associated with genetic adaptations in indigenous ecotypes. These islands harboured immune‐related genes contributing to disease resistance (TLR2, TICAM1, IL22RA1, NOS2, CCL20 and IFNLR1), heat tolerance and oxidative stress response (NFKB1, HSF4, OSGIN1 and BDNF), and muscle development, lipid metabolism and reproduction (MEOX2, CEBPB, CDS2 and GnRH‐I). Overall, this study highlights the genetic potential of indigenous chickens to survive and adapt to their respective environments. There are distinct genetic backgrounds among different chicken populations, with commercial breeds showing a higher number of runs of homozygosity compared to indigenous chickens and their wild ancestors. Indigenous chicken ecotypes have runs of homozygosity islands associated with genetic adaptations, including genes related to disease resistance, heat tolerance, oxidative stress response and muscle development. The White Leghorn breed exhibited the greatest genetic distance from other populations, while gamecock populations formed a separate cluster .