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

Abstract

The Qinghai-Tibet Plateau (QTP), possesses a climate as cold as that of the Arctic, and also presents uniquely low oxygen concentrations and intense ultraviolet (UV) radiation. QTP animals have adapted to these extreme conditions, but whether they obtained genetic variations from the Arctic during cold adaptation, and how genomic mutations in non-coding regions regulate gene expression under hypoxia and intense UV environment, remain largely unknown. Here, we assemble a high-quality saker falcon genome and resequence populations across Eurasia. We identify female-biased hybridization with Arctic gyrfalcons in the last glacial maximum, that endowed eastern sakers with alleles conveying larger body size and changes in fat metabolism, predisposing their QTP cold adaptation. We discover that QTP hypoxia and UV adaptations mainly involve independent changes in non-coding genomic variants. Our study highlights key roles of gene flow from Arctic relatives during QTP hypothermia adaptation, and cis-regulatory elements during hypoxic response and UV protection.

Genomic architecture underlying morphological and physiological adaptation to high elevation in a songbird

“…Our results showed that the fixed SNPs were under‐represented in coding regions. Therefore, the altitudinal adaptation of rufous‐capped babblers may be dominantly fuelled by mutations in regulatory regions (or with regulatory functions), consistent with the findings for another songbird in Taiwan (Lai et al, 2019) and a raptor on the Qinghai–Tibet Plateau (Hu et al, 2022). Noncoding regions have been found to contribute more to ecological divergence at the initial stage of population divergence or speciation than coding regions (Jones et al, 2012).…”

“…Genomic sequencing provides a powerful tool not only for reconstructing divergence history, but also for testing hypotheses regarding the origin and association of mutations that contribute to physiological and morphological adaptation to new environments (Seehausen et al, 2014), including high elevations (Hu et al, 2022; Lai et al, 2019; Martini et al, 2021; Qu et al, 2013; Qu et al, 2021; Storz, 2021). Studies have shown that the arrangement of mutations in the genome is important to ecological adaptation because structural genomic variations often affect multiple genes together (Malinsky et al, 2015; Zong et al, 2021).…”

“…Studies have shown that the arrangement of mutations in the genome is important to ecological adaptation because structural genomic variations often affect multiple genes together (Malinsky et al, 2015; Zong et al, 2021). Outstanding questions regarding the role of genome architecture in ecological adaptation include whether mutations in coding or noncoding regions tend to be subject to divergent selection for adaptation (Hu et al, 2022; Lai et al, 2019; Malinsky et al, 2015; Nosil & Feder, 2012; Wolf & Ellegren, 2017), whether chromosomal inversions facilitate the accumulation of adaptive genetic differences between diverging lineages (Kirkpatrick & Barton, 2006; Poelstra et al, 2014), and whether genes related to ecological difference tend to be located in sex chromosomes or associated with those under sexual selection that hence facilitate the evolution of reproductive isolation (Bourgeois et al, 2020; Edwards et al, 2015; Malinsky et al, 2015; Qvarnström & Bailey, 2009). These questions remain poorly understood, especially in nonmodel species, and we aim to examine them by studying altitudinal adaptation in species with wide elevational ranges.…”

RNA sampling time on postmortem avian carcasses in the wild

“…Genetic sampling (e.g. RNA) from wild animals in the field is challenging, especially for the birds with strong flight capability and wide-ranging activity (Pan et al 2017, Gu et al 2021, Hu et al 2022). Opportunistic encounters with wild avian carcasses, Page 2 of 9 thus, provide a complementary source for genetic sampling (Camacho-Sanchez et al 2013, Romero et al 2014.…”

“…To address these issues, we designed a field experiment of RNA sampling from domestic chicken Gallus gallus domesticus carcasses on the QTP. As a classical extreme environment, QTP provides us valuable opportunities to study species' gene expression changes in response to extreme conditions characterized by low oxygen levels and temperatures (Pan et al 2017, Hu et al 2022). On the plateau, wild avian species have been found to die of natural (e.g.…”