DOI: 10.5061/dryad.cc000
title: Data from: Linking micro- and macroevolutionary perspectives to evaluate the role of Quaternary sea-level oscillations in island diversification

description: With shifts in island area, isolation, and cycles of island
 fusion-fission, the role of Quaternary sea-level oscillations as drivers
 of diversification is complex and not well understood. Here we conduct
 parallel comparisons of population and species divergence between two
 island areas of equivalent size that have been affected differently by
 sea-level oscillations, with the aim to understand the micro- and
 macroevolutionary dynamics associated with sea-level change. Using
 genome-wide datasets for a clade of seven Amphiacusta ground cricket
 species endemic to the Puerto Rico Bank (PRB), we found consistently
 deeper interspecific divergences and higher population differentiation
 across the unfragmented Western PRB, in comparison to the currently
 fragmented Eastern PRB that has experienced extreme changes in island area
 and connectivity during the Quaternary. We evaluate alternative hypotheses
 related to the microevolutionary processes (population splitting,
 extinction and merging) that regulate the frequency of completed
 speciation across the PRB. Our results suggest that under certain
 combinations of archipelago characteristics and taxon traits the repeated
 changes in island area and connectivity may create an opposite effect to
 the hypothesized “species pump” action of oscillating sea levels. Our
 study highlights how a microevolutionary perspective can complement
 current macroecological work on the Quaternary dynamics of island
 biodiversity.
description: Interspecific dataset of
 35,585 SNPs for phylogenetic analysesThis dataset contains
 35,585 putatively unlinked SNPs from 121 individuals, representing 16
 populations and 7 Amphiacusta species. This dataset was used for species
 tree and phylogenetic analyses.Amphiacusta_35585unlinkedSNPs.nexIntraspecific dataset of Amphiacusta laresIntraspecific dataset of Amphiacusta lares in vcf format, as exported from Stacks. This dataset was used for estimating genetic diversity and population differentiation, for assessing population structure and for demographic inference, after filtering the data and converting to appropriate input formats as described in the methods section of the manuscript.Amphiacusta_lares.vcfIntraspecific dataset of Amphiacusta pronautaIntraspecific dataset of Amphiacusta pronauta in vcf format, as exported from Stacks. This dataset was used for estimating genetic diversity and population differentiation, for assessing population structure and for demographic inference, after filtering the data and converting to appropriate input formats as described in the methods section of the manuscript.Amphiacusta_pronauta.vcfIntraspecific dataset of Amphiacusta sanctaecrucisIntraspecific dataset of Amphiacusta sanctaecrucis in vcf format, as exported from Stacks. This dataset was used for estimating genetic diversity and population differentiation, for assessing population structure and for demographic inference, after filtering the data and converting to appropriate input formats as described in the methods section of the manuscript.Amphiacusta_sanctaecrucis.vcfInterspecific dataset of 171,528 SNPs for species tree analysesThis dataset contains 171,528 putatively unlinked SNPs from 121 individuals, representing 16 populations and 7 Amphiacusta species. This dataset was used for species tree analyses.Amphiacusta_171528unlinkedSNPs.nex