Arctic introgression and chromatin regulation facilitated rapid Qinghai-Tibet Plateau colonization by an avian predator

Gut microbiota contribute to cold adaptation in mammals-primates and ungulates

Gut microbiota play an influential role in how animals adapt to extreme environments. Two phylogenetically distant mammals, Yunnan snub-nosed monkey and reindeer both adapted to frigid environments. Metagenomic analyses revealed they developed similar cold adaptation strategies in response to food scarcity (enhanced fiber degradation and nitrogen balance maintenance), energy shortages (increased short-chain fatty acid [SCFA] synthesis), and a constant body temperature sustainment (stimulation of non-shivering thermogenesis [NST]). Moreover, they evolved distinct adaptation strategies to cope with different cold ecosystems. Yunnan snub-nosed monkey adapt to high-altitude hypoxia environment through enhancing ability to synthesize lactate and metabolize purine, while reindeer adapt to extreme cold environment through increasing blood flow, strengthening urea cycling, and enriching fat storage associated bacteria. Notably, reindeer microbiota uniquely enriched cholesterol-degrading bacteria, potentially mitigating cardiovascular risks from lipid storage. Our study expands the knowledge of how gut microbiome promotes cold adaptation through shared and specialized mechanisms shaped by different phylogenetic and ecological contexts.

Characterization and comparative transcriptomic analysis of high-altitude adaptation in Tibetan chicken using RNA-sequencing

Tibetan chicken, an indigenous breed, inhabit highland regions and are crucial livestock for local Tibetans. Compared with other chicken breeds that have migrated from lowlands to highlands, Tibetan chicken exhibits superior physiological adaptations to high-altitude environments. However, the genetic mechanisms underlying these adaptations remain unclear. Herein, we generated high-quality RNA-sequencing data from the heart samples of 19 adult lowland and Tibetan chickens subjected to hypoxic and normoxic conditions for 5 weeks. We explored the relationships between chicken populations and the environment using different expression gene detection and weighted gene co-expression network analysis (WGCNA). The Tibetan chicken genome was analyzed for positive selection pressures associated with high-altitude adaptation, to reveal 63 candidate genes primarily involved in heart development and apoptotic signaling pathways, including PARK7, which was then validated using quantitative real-time polymerase chain reaction (qRT-PCR). Further hypoxia-induced cardiomyocyte model tests showed the cardioprotective function of PARK7 by cell viability assay, indicating the cardioprotective function of PARK7 in chickens under low-oxygen conditions. Our findings provided new insights into the genetic basis of high-altitude adaptation in Tibetan chickens and offered values for breeding programs aimed at enhancing the resilience of livestock in challenging environments.

Crop rotation increases Tibetan barley yield and soil quality on the Tibetan Plateau

Tibetan barley (Hordeum vulgare) accounts for over 70% of the total food production in the Tibetan Plateau. However, continuous cropping of Tibetan barley causes soil degradation, reduces soil quality and causes yield decline. Here we explore the benefits of crop rotation with wheat and rape to improve crop yield and soil quality. We conducted 39 field experiments on the Tibetan Plateau, comparing short-term (≤5 years), 5-10 years and long-term (≥10 years) continuous cropping with rotation of Tibetan barley with wheat or rape. Results showed that Tibetan barley-wheat and Tibetan barley-rape rotations increased yields by 17% and 12%, respectively, while improving the soil quality index by 11% and 21%, compared with long-term continuous cropping. Both Tibetan barley rotations with wheat and rape improved soil quality and consequently yield, mainly by increasing soil microbial biomass nitrogen and microbial biomass carbon and decreasing pH. By contrast, long-term continuous cropping led to decreased soil organic matter, lower microbial biomass nitrogen and increased pH, contributing to yield decline. The benefits of rotations on crop yield and soil quality increased over time. Implementing crop rotation with wheat or rape thus offers a sustainable agricultural strategy for improving food security on the Tibetan Plateau.

Recent selection and introgression facilitated high-altitude adaptation in cattle

During the past 3000 years, cattle on the Qinghai-Xizang Plateau have developed adaptive phenotypes under the selective pressure of hypoxia, ultraviolet (UV) radiation, and extreme cold. The genetic mechanism underlying this rapid adaptation is not yet well understood. Here, we present whole-genome resequencing data for 258 cattle from 32 cattle breeds/populations, including 89 Tibetan cattle representing eight populations distributed at altitudes ranging from 3400 m to 4300 m. Our genomic analysis revealed that Tibetan cattle exhibited a continuous phylogeographic cline from the East Asian taurine to the South Asian indicine ancestries. We found that recently selected genes in Tibetan cattle were related to body size (HMGA2 and NCAPG) and energy expenditure (DUOXA2). We identified signals of sympatric introgression from yak into Tibetan cattle at different altitudes, covering 0.64%-3.26% of their genomes, which included introgressed genes responsible for hypoxia response (EGLN1), cold adaptation (LRP11), DNA damage repair (LATS1), and UV radiation resistance (GNPAT). We observed that introgressed yak alleles were associated with noncoding variants, including those in present EGLN1. In Tibetan cattle, three yak introgressed SNPs in the EGLN1 promoter region reduced the expression of EGLN1, suggesting that these genomic variants enhance hypoxia tolerance. Taken together, our results indicated complex adaptation processes in Tibetan cattle, where recently selected genes and introgressed yak alleles jointly facilitated rapid adaptation to high-altitude environments.

Unraveling the gut microbiota of Tibetan chickens: insights into highland adaptation and ecological advantages

Tibetan animals have several unique advantages owing to the harsh ecological conditions under which they live. However, compared to Tibetan mammals, understanding of the advantages and underlying mechanisms of the representative high-latitude bird, the Tibetan chicken (Gallus gallus, TC), remains limited. The gut microbiota of animals has been conclusively shown to be closely related to both host health and host environmental adaptation. This study aimed to explore the relationships between the cecal microbiome and the advantages of TCs based on comparisons among three populations: native TCs residing on the plateau, domestic TCs living in the plain, and one native plain species. Metatranscriptomic sequencing revealed a significant enrichment of active Bacteroidetes but a loss of active Firmicutes in native TCs. Additionally, the upregulated expression of genes in the cecal microbiome of native TCs showed enriched pathways related to energy metabolism, glycan metabolism, and the immune response. Furthermore, the expression of genes involved in the biosynthesis of short-chain fatty acids (SCFAs) and secondary bile acids (SBAs) was upregulated in the cecal microbiome of native TCs. Data from targeted metabolomics further confirmed elevated levels of certain SCFAs and SBAs in the cecum of native TCs. Based on the multi-omics association analysis, we proposed that the higher ratio of active Bacteroidetes/Firmicutes may be attributed to the efficient energy metabolism and stronger immunological activity of native TCs. Our findings provide a better understanding of the interactions between gut microbiota and highland adaptation, and novel insights into the mechanisms by which Tibetan chickens adapt to the plateau hypoxic environment.

IMPORTANCE

The composition and function of the active cecal microbiome were significantly different between the plateau Tibetan chicken population and the plain chicken population. Higher expression genes related to energy metabolism and immune response were found in the cecal microbiome of the plateau Tibetan chicken population. The cecal microbiome in the plateau Tibetan chicken population exhibited higher biosynthesis of short-chain fatty and secondary bile acids, resulting in higher cecal content of these metabolites. The active Bacteroidetes/Firmicutes ratio in the cecal microbiome may contribute to the high-altitude adaptive advantage of the plateau Tibetan chicken population.

Land Use and Climate Change Accelerate the Loss of Habitat and Ecological Corridor to Reeves's Pheasant (Syrmaticus reevesii) in China

Human activity and climate change are widely considered to be primarily responsible for the extinction of Galliformes birds. Due to a decline in population, the Reeves's pheasant (Syrmaticus reevesii), a member of the Galliformes family, was recently elevated to first-class national protected status in China. However, determining the causal factors of their extinction and carrying out protection measures appear to be challenging owing to a lack of long-term data with high spatial and temporal resolutions. Here, based on a national field survey, we used habitat suitability models and integrated data on geographical environment, road development, land use, and climate change to predict the potential changes in the distribution and connectivity of the habitat of Reeves's pheasant from 1995 to 2050. Furthermore, ecological corridors were identified using the minimum cumulative resistance (MCR) model. The prioritized areas for habitat restoration were determined by integrating the importance indices of ecological sources and corridors. Our results indicated that both land use and climate change were linked to the increased habitat loss for the Reeves's pheasant. In more recent decades, road construction and land use changes have been linked to a rise in habitat loss, and future climate change has been predicted to cause the habitat to become even more fragmented and lose 89.58% of its total area. The ecological corridor for Reeves's pheasant will continue to decline by 88.55%. To counteract the negative effects of human activity and climate change on the survivorship of Reeves's pheasant, we recommend taking immediate actions, including bolstering cooperation among provincial governments, restoring habitats, and creating ecological corridors among important habitats.

Genetic analysis of Saker Falcon (Falcocherrug) subspecies

Two subspecies of Saker Falcon are commonly accepted - Western (Falcocherrugcherrug) and Eastern (Falcocherrugmilvipes), which are differentiated by their distribution range and phenotype. In Bulgaria, Western Saker Falcons are breeding ex situ in the Wildlife Rehabilitation and Breeding Centre, part of Green Balkans - Stara Zagora NGO, with the aim of restoring the nesting population of the species in the country and both Western and Eastern - in the Breeding Centre for Birds of Prey in Burgas for the purpose of sale for the needs of falconry in the country and abroad. In 2021, a total of 115 birds from the two breeding centres were sampled. The samples were analysed in Bielefeld University (Germany) at nine microsatellite loci. Structure analyses were performed to establish the optimal explanatory number of groups. We compared the putative genetic groups with the known/expected origin of falcons. A separation in two groups best explained the allelic variation between samples. Out of 68 Saker Falcons with putatively Eastern origin, 66 were ascribed to genetic group 2 and two falcons had unclear, mixed or hybrid genetic fingerprints. Out of 42 Sakers with putatively Western origin, 33 were ascribed to genetic group 1, seven to genetic group 2 and two individuals appeared to have a mixed signature of genetic groups 1 and 2 with dominating alleles of group 2. Five known hybrids were scored as mixed signature with dominating genetic cluster 2. This suggests that the two (Eastern and Western) populations of Saker Falcon origin suggested by the subspecies' definitions are also adequate to be considered in breeding programmes. Genetic cluster 1 might represent the ancestral alleles shared with other falcons, while specific novel alleles allow the discrimination of secured Eastern Sakers (group 2), while these populations may be occasionally invaded by individuals from the west.

Genomic structural variation is associated with hypoxia adaptation in high-altitude zokors

Zokors, an Asiatic group of subterranean rodents, originated in lowlands and colonized high-elevational zones following the uplift of the Qinghai-Tibet plateau about 3.6 million years ago. Zokors live at high elevation in subterranean burrows and experience hypobaric hypoxia, including both hypoxia (low oxygen concentration) and hypercapnia (elevated partial pressure of CO2). Here we report a genomic analysis of six zokor species (genus Eospalax) with different elevational ranges to identify structural variants (deletions and inversions) that may have contributed to high-elevation adaptation. Based on an assembly of a chromosome-level genome of the high-elevation species, Eospalax baileyi, we identified 18 large inversions that distinguished this species from congeners native to lower elevations. Small-scale structural variants in the introns of EGLN1, HIF1A, HSF1 and SFTPD of E. baileyi were associated with the upregulated expression of those genes. A rearrangement on chromosome 1 was associated with altered chromatin accessibility, leading to modified gene expression profiles of key genes involved in the physiological response to hypoxia. Multigene families that underwent copy-number expansions in E. baileyi were enriched for autophagy, HIF1 signalling and immune response. E. baileyi show a significantly larger lung mass than those of other Eospalax species. These findings highlight the key role of structural variants underlying hypoxia adaptation of high-elevation species in Eospalax.

Phylogenomic insights into the polyphyletic nature of Altai falcons within eastern sakers (Falco cherrug) and the origins of gyrfalcons (Falco rusticolus)

The Altai falcon from Central Asia always attracted the attention of humans. Long considered a totemic bird in its native area, modern falconers still much appreciated this large-bodied and mighty bird of prey due to its rarity and unique look. The peculiar body characteristics halfway between the saker falcon (Falco cherrug) and the gyrfalcon (F. rusticolus) triggered debates about its contentious taxonomy. The weak phylogenetic signal associated with traditional genetic methods could not resolve this uncertainty. Here, we address the controversial evolutionary origin of Altai falcons by means of a genome-wide approach, Restriction-site Associated DNA sequencing, using sympatric eastern sakers falcons, allopatric western saker falcons and gyrfalcons as outgroup. This approach provided an unprecedented insight into the phylogenetic relationships of the studied populations by delivering 17,095 unlinked SNPs shedding light on the polyphyletic nature of Altai falcons within eastern sakers. Thus we concluded that the former must correspond to a low taxonomic rank, probably an ecotype or form of the latter. Also, we found that eastern sakers are paraphyletic without gyrfalcons, thus, these latter birds are best regarded as the direct sister lineage of the eastern sakers. This evolutionary relationship, corroborated also by re-analyzing the dataset with the inclusion of outgroup samples (F. biarmicus and F. peregrinus), put eastern sakers into a new light as the potential ancestral genetic source of high latitude and altitude adaptation in descendent populations. Finally, conservation genomic values hint at the stable genetic background of the studied saker populations.

The metabolic adaptation in wild vertebrates via omics approaches

Metabolism is the basis for sustaining life and essential to the adaptive evolution of organisms. With the development of high-throughput sequencing technology, genetic mechanisms of adaptive evolution, including metabolic adaptation, have been extensively resolved by omics approaches, but a deep understanding of genetic and epigenetic metabolic adaptation is still lacking. Exploring metabolic adaptations from genetic and epigenetic perspectives in wild vertebrates is vital to understanding species evolution, especially for the early stages of adaptative evolution. Herein, we summarize the advances in our understanding of metabolic adaptations via omics approaches in wild vertebrates based on three types of cases: extreme environment, periodically changing environment, and changes of species characteristics. We conclude that the understanding of the formation of metabolic adaptations at the genetic level alone can well identify the adaptive genetic variation that has developed during evolution, but cannot resolve the potential impact of metabolic adaptations on the adaptative evolution in the future. Thus, it seems imperative to include epigenomics and metabolomics in the study of adaptation, and that in the future genomic and epigenetic data should be integrated to understand the formation of metabolic adaptation of wild vertebrate organisms.