Pangenome data for: A landscape-level pangenomic framework reveals climate-driven vulnerability and adaptation based on structural variants in a sedentary bird

<p data-end="962" data-start="323">Structural genetic variants (SVs) are increasingly recognized as important contributors to evolutionary processes, yet their role in adaptation has rarely been evaluated across the full geographic range of a species in a conservation genomics context. The Montezuma quail (<em data-end="617" data-start="596">Cyrtonyx montezumae</em>) is a ground-dwelling bird distributed across arid and montane habitats from southern Mexico to the southwestern United States. Habitat degradation, fragmentation, and climate change threaten populations across much of its range, and peripheral populations in Texas exhibit reduced genetic diversity that may limit their evolutionary potential.</p>

<p data-end="1915" data-start="964">This dataset accompanies a study investigating the genomic basis of climate adaptation and conservation vulnerability in Montezuma quail using a pangenome-based framework. We constructed a species-wide pangenome to capture structural genomic diversity and integrated genomic, environmental, and phenotypic data to investigate patterns of local adaptation. Analyses revealed geographically structured adaptive variation associated primarily with winter climate variables along an east–west climatic gradient. Population structure, adaptive genomic patterns, and gradients of genetic diversity are consistent with a historical ring-like range expansion from southern Mexico, supporting predictions of the central–marginal hypothesis and glacial refugia theory. Genomic offset analyses and forward-time evolutionary simulations further indicate that isolated Central Texas populations are particularly vulnerable under projected climate change scenarios.</p>

<p data-end="2488" data-start="1917">The dataset contains the pangenome graph files generated for this study. Two sets of pangenome files are available. The first set is readily available and includes the initial pangenome constructed from ten long-read-based haplotypes, provided in two formats ("monq-out.pg" and "monq-out.gfa"). The second set is available upon request and contains the final augmented pangenome graphs generated by incorporating short-read data from 91 individuals. These files are provided separately for each chromosome (e.g., "monq_chr1_aug.pg", "monq_chr2_aug.pg", …, "monq_chr30_aug.pg"), where chromosomes 29 and 30 correspond to the Z and W sex chromosomes, respectively. The ".pg" and ".gfa" files can be converted to other formats and utilized using the VG tools (https://github.com/vgteam/vg).</p>

<p data-end="2819" data-start="2490">These data are shared to accompany the associated manuscript and to facilitate reproducibility of the analyses presented therein. The pangenome graph files may also support future research on structural variation, landscape genomics, evolutionary history, and conservation genomics of Montezuma quail and other non-model species.</p>