Genomic signatures of drift and selection driven by predation and human pressure in an insular lizard

Abstract

Genomic divergence was studied in 10 small insular populations of the endangered Balearic Islands lizard (Podarcis lilfordi) using double digest restriction-site associated DNA sequencing. The objectives were to establish levels of divergence among populations, investigate the impact of population size on genetic variability and to evaluate the role of different environmental factors on local adaptation. Analyses of 72,846 SNPs supported a highly differentiated genetic structure, being the populations with the lowest population size (Porros, Foradada and Esclatasang islets) the most divergent, indicative of greater genetic drift. Outlier tests identified ~ 2% of loci as candidates for selection. Genomic divergence-Enviroment Association analyses were performed using redundancy analyses based on SNPs putatively under selection, detecting predation and human pressure as the environmental variables with the greatest explanatory power. Geographical distributions of populations and environmental factors appear to be fundamental drivers of divergence. These results support the combined role of genetic drift and divergent selection in shaping the genetic structure of these endemic island lizard populations.

Finding the adaptive needles in a population‐structured haystack: A case study in a New Zealand mollusc

“…Such adaptive loci (or their linked markers) are expected to have a distribution of allele or genotype frequencies among populations that do not fit the neutral expectation (Ahrens et al, 2018). The distribution of allele frequencies among populations can also be used as a response variable in tests of association with environmental factors relevant to the ecology of the organism: loci with significant associations are interpreted as being under natural selection due to the focal (or correlated) environmental factors (Ahrens et al, 2018; Bassitta et al, 2021; Dalongeville et al, 2018; Hoban et al, 2016; Liggins et al, 2020; Rellstab et al, 2015; Yadav et al, 2019).…”

Population expansion, divergence, and persistence in Western Fence Lizards (Sceloporus occidentalis) at the northern extreme of their distributional range

“…Increasing coastal development around the Puget Sound threatens to further reduce genetic diversity within subpopulations. Although patterns are highly taxon specific, urban fragmentation typically leads to increased genetic drift within fragmented populations and reduced gene flow among them 69 , 70 . This suggests that the future of the northern S. occidentalis populations could be contingent on a balance between increased suitable habitat with climate change and decreased access to or destruction of this habitat with anthropogenic development.…”

Population genetics and phylogeographic history of the insular lizardPodarcis lilfordi(Gunther, 1874) from the Balearic Islands based on genome-wide polymorphic data

“…Genetic analyses of this species have been long limited to mtDNA, few nuclear genes (Brown et al, 2008; Terrasa et al, 2009) and microsatellites for few populations (Bloor et al, 2011; Rotger et al, 2021). A recent study based on single nucleotide polymorphisms (SNPs) data by Restriction Site Associated DNA Sequencing (RADSeq) (Bassitta et al, 2021) has expanded on previous knowledge on genetic diversity and phylogeographic pattern of this species, confirming the existence of two well-discriminated genetic lineages separating populations from the major archipelagos of Menorca and Mallorca/Cabrera (Brown et al, 2008; Terrasa et al, 2009. Recently, the P. lilfordi genome has been sequenced (Gomez-Garrido et al, 2023) providing the framework for a comprehensive exploration of population-level genomics of this species.…”