Genomic Signatures of Historical Allopatry and Ecological Divergence in an Island Lizard

Abstract

Geographical variation among contiguous populations is frequently attributed to ecological divergence or historical isolation followed by secondary contact. Distinguishing between these effects is key to studies of incipient speciation and could be revealed by different genomic signatures. We used RAD-seq analyses to examine morphologically divergent populations of the endemic lizard (Gallotia galloti) from the volcanic island of Tenerife. Previous analyses have suggested ecological and historical causes to explain the morphological diversity. Analyses of 276,483 single nucleotide polymorphisms (SNPs) from >20 Mbp of the genome revealed one genetically divergent population from Anaga, a region associated with divergent mtDNA lineages in other Tenerife endemics. This population also has a high number of private alleles, and its divergence can be explained by historical isolation. Bayesian outlier analyses identified a small proportion of SNPs as candidates for selection (0.04%) which were strongly differentiated between xeric and mesic habitat types. Individual testing for specific xeric–mesic selection using an alternative approach also supported ecological divergence in a similarly small proportion of SNPs. The study indicates the roles of both historical isolation and ecological divergence in shaping genomic diversity in G. galloti. However, north–south morphological divergence appears solely associated with the latter and likely involves a relatively small proportion of the genome.

Historical volcanism and within-island genetic divergence in the Tenerife skink (Chalcides viridanus)

“…For example, a very recent RADseq study by one of the authors detected evidence of historical isolation in the genome of the Tenerife lizard Gallotia galloti which has a similar divergence time to that observed here (Brown et al, 2016). Posteriors for the distributions of the two "central" clusters.…”

Tempo and mode of allopatric divergence in the weakly electric fish Sternopygus dariensis in the Isthmus of Panama

“…However, allopatric divergence may also be affected by adaptive processes (e.g., local adaptation 55,56 ), which might lead to genomic islands of divergence 57,58 . Distinguishing between these possibilities requires a large number of genetic markers that can be mapped across the genome 59,60 . Although our analysis only included a few individuals per population and a reduced representation of the species’ genome (285 SNPs), the high number of fixed loci between populations, and the broad distribution of these loci across the majority of the species’ chromosomes, is consistent with a model of strict allopatric divergence 38,53 .…”

Morphological species and discordant mtDNA: A genomic analysis of Phrynocephalus lizard lineages on the Qinghai-Tibetan Plateau

“…There have been relatively few examples of multispecies coalescent analyses using SNP data from reduced representation genomic libraries, possibly due to a lack of corresponding statistical approaches. Restriction Associated DNA sequencing (RADseq: Baird et al, 2008;Hohenlohe et al, 2010) and Genotyping By Sequencing (GBS: Elshire et al, 2011) offer genome-wide SNPs from nonmodel species and have already been employed in species/population-level studies (e.g., Brown et al, 2016;Eaton and Ree, 2013;Combosh and Vollmer 2015). Analyses of these data within a coalescent framework will make major contributions to populations genetics.…”