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.城市化正成为日益严峻的问题，其通过降低野生种群的遗传多样性、施加影响诸多关键适合度性状的新型选择压力，对种群的进化潜力构成挑战。然而迄今为止，城市化的基因组印迹尚未得到足够的研究关注。本研究采用限制性位点相关DNA测序（Restriction-site Associated DNA sequencing, RAD sequencing）技术，对采自城市化水平梯度分明的140只成年大山雀（Parus major）样本展开分析，样本采集地涵盖从天然森林到法国蒙彼利埃市高度城市化区域的一系列生境，旨在探究城市化对中性及适应性基因组多样性的全基因组效应。相较于乡村样地，城市化程度更高的区域其基因组杂合度略低。研究发现，城市化对遗传分化存在微弱但显著的影响，且该效应仅体现在样地水平而非巢群水平，这一结果揭示了城市化影响的地理尺度，以及即便存在基因流，种群仍具备本地适应的潜力。基因-环境关联分析检测到分布于全基因组的大量单核苷酸多态性（Single Nucleotide Polymorphism, SNPs），这些位点与城市化存在微弱关联；其中97个SNPs组成的子集可解释高达81%的城市化表型方差，整体表明城市化环境下的自然选择存在多基因响应模式。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富有启发性的研究方向，以进一步探究城市化对遗传多样性空间分布的影响一致性，以及基因与城市化关联的多基因本质。