Data from: Great tits and the city: distribution of genomic diversity and gene-environment associations along an urbanization gradient

Urbanization is a growing concern challenging the evolutionary potential of wild populations by reducing genetic diversity and imposing new selection regimes affecting many key fitness traits. However, genomic footprints of urbanization have received little attention so far. Using RAD sequencing, we investigated the genome-wide effects of urbanization on neutral and adaptive genomic diversity in 140 adult great tits Parus major collected in locations with contrasted urbanization levels (from a natural forest to highly urbanized areas of a city (Montpellier, France). Heterozygosity was slightly lower in the more urbanized sites compared to the more rural ones. Low but significant effect of urbanization on genetic differentiation was found, at the site-level but not at the nest-level, indicative of the geographic scale of urbanization impact and of the potential for local adaptation despite gene flow. Gene-environment association tests identified numerous SNPs with small association scores to urbanization, distributed across the genome, from which a subset of 97 SNPs explained up to 81% of the variance in urbanization, overall suggesting a polygenic response to selection in the urban environment. These findings open stimulating perspectives for broader applications of high-resolution genomic tools on other cities and larger sample sizes to investigate the consistency of the effects of urbanization on the spatial distribution of genetic diversity and the polygenic nature of gene-urbanization association.

城市化已成为日益严峻的全球性挑战，其通过降低野生种群的遗传多样性、施加全新的选择压力，对诸多关键适合度性状的演化潜力构成威胁。然而，截至目前，针对城市化基因组足迹的相关研究仍较为匮乏。本研究借助限制性位点相关DNA测序（Restriction-site Associated DNA sequencing, RAD sequencing）技术，以采自城市化水平梯度差异显著的140只成年大山雀（Parus major）为研究对象，开展全基因组分析，探究城市化对中性与适应性基因组多样性的整体影响；采样点位覆盖从天然林到法国蒙彼利埃市高度城市化区域的完整梯度。相较于乡村点位，城市化程度更高的区域中个体杂合性略有降低。研究发现，城市化对遗传分化存在微弱但显著的影响，该效应仅在点位尺度下显著，而在巢群尺度下未表现出显著性，这揭示了城市化影响的地理尺度，以及即便存在基因流时本地适应仍具备潜在可能。基因-环境关联分析共鉴定出大量与城市化关联强度较低的单核苷酸多态性（Single Nucleotide Polymorphism, SNP），这些位点广泛分布于整个基因组；其中由97个SNP构成的子集可解释高达81%的城市化相关变异，整体表明城市化环境下的选择存在多基因响应特征。本研究结果为高分辨率基因组工具在更多城市及更大样本量中的推广应用提供了全新研究视角，未来可借此进一步探究城市化对遗传多样性空间分布的影响一致性，以及基因-城市化关联的多基因本质。