DOI: 10.5061/dryad.pp6bm
title: Data from: Hybridization masks speciation in the evolutionary history of the Galápagos marine iguana

description: The effects of the direct interaction between hybridization and
 speciation—two major contrasting evolutionary processes—are poorly
 understood. We present here the evolutionary history of the Galápagos
 marine iguana (Amblyrhynchus cristatus) and reveal a case of incipient
 within-island speciation, which is paralleled by between-island
 hybridization. In-depth genome-wide analyses suggest that Amblyrhynchus
 diverged from its sister group, the Galápagos land iguanas, around 4.5
 million years ago (Ma), but divergence among extant populations is
 exceedingly young (less than 50 000 years). Despite Amblyrhynchus
 appearing as a single long-branch species phylogenetically, we find strong
 population structure between islands, and one case of incipient speciation
 of sister lineages within the same island—ostensibly initiated by volcanic
 events. Hybridization between both lineages is exceedingly rare, yet
 frequent hybridization with migrants from nearby islands is evident. The
 contemporary snapshot provided by highly variable markers indicates that
 speciation events may have occurred throughout the evolutionary history of
 marine iguanas, though these events are not visible in the deeper
 phylogenetic trees. We hypothesize that the observed interplay of
 speciation and hybridization might be a mechanism by which local
 adaptations, generated by incipient speciation, can be absorbed into a
 common gene pool, thereby enhancing the evolutionary potential of the
 species as a whole.
description: Dataset_CComplete mitochondrial control region sequences (1181 bp) in 1493 marine iguanas (Amblyrynchus cristatus) sampled across the Galapagos archipelago.Datasets_F_G_HData from RAD sequencing for 33 marine iguanas and 8 outgroups. Described as datasets F, G and H in the manuscript. More information available in the ReadMe file.Dataset_A_concatenated_alignmentA concatenated alignment of various squamate sequences for nuclear genes: RAG1, BDNF, R35 and NKTR.Dataset_D_MicrosatsA dataset of 614 marine iguana samples, genotyped at 12 microsatellite loci and used in analysis to determine population structure across the archipelago.Dataset_E_MicrosatData consisting of 474 marine iguanas sampled from the island San Cristobal, genotyped at 18 microsatellite loci. The last 20 samples (highlighted in yellow) are individuals identified as hybrids of migrants from other islands.Dataset_MSVar_BottleneckData from marine iguanas sampled on San Cristobal island, genotyped at 18 microsatellite loci and sorted into two populations: Loberia and Punta Pitt. All individuals with &gt;6% missing data and any possible vargrants or migrants from other islands have been removed.Dataset_B_Mitochondrial5557 bp from seven mitochondrial genes in a representative selection of the three main haplotype lineages within Amblyrhynchus, and all species of Conolophus.Morphometry_AmblyrhynchusMeasurements and scale counts taken from a microsatellite-genotyped marine iguanas from San Cristóbal to investigate morphological differences between diverged lineages