Population genetics and phylogeographic history of the insular lizard
Podarcis lilfordi (Gunther, 1874) from the Balearic Islands based on
genome-wide polymorphic data
Abstract
Islands provide a great system to explore the processes that maintain
genetic diversity and promote local adaptation. We explored the genomic
diversity of the Balearic lizard Podarcis lilfordi, an endemic species
characterized by numerous small insular populations with large
phenotypic diversity. Using the newly available genome for this species,
we characterized more than 300,000 SNPs, merging Genotype by Sequencing
(GBS) data with previously published Restriction-site associated DNA
sequencing (RADSeq) data, providing a dataset of 16 island populations
(191 individuals) across the range of species distribution (Menorca,
Mallorca, and Cabrera). Results indicate that each islet hosts a
well-differentiated population (Fst=0.2470.09), with no recent
immigration/translocation events. Contrary to expectations, most
populations harbor a considerable genetic diversity (mean nucleotide
diversity, Pi=0.1440.021), characterized by overall low inbreeding
values (Fis<0.1). While the genetic diversity significantly
decreased with decreasing islet surface, maintenance of substantial
genetic diversity even in tiny islets suggests variable selection or
other mechanisms that buffer genetic drift. Maximum-likelihood tree
based on concatenated SNP data confirmed the existence of the two major
independent lineages of Menorca and Mallorca/Cabrera. Multiple lines of
evidence, including admixture and root testing, robustly placed the
origin of the species in the Mallorca Island, rather than in Menorca.
Outlier analysis mainly retrieved a strong signature of genome
differentiation between the two major archipelagos, especially in the
sexual chromosome Z. A set of proteins were target of multiple outliers
and primarily associated with binding and catalytic activity, providing
interesting candidates for future selection studies. This study provides
the framework to explore crucial aspects of the genetic basis of
phenotypic divergence and insular adaptation.