DOI: 10.5061/dryad.2z34tmppp
title: Data from: Linking environmental stability with genetic diversity and population structure in two Atlantic Forest palm trees

description: Spatial patterns of biodiversity in the Atlantic Forest of Brazil are well
 characterized. However, there is no consensus on the biological processes
 underlying these patterns, and multiple competing hypotheses have been
 proposed, several of which center on climatic stability. Here, we ask if
 Late Quaternary climatic stability predicts contemporary population
 structure and genomic-level diversity in two palm species: Syagrus
 botryophora and S. pseudococos (Arecaceae) We first use species occurrence
 data to model the distribution of suitable environments in 62 time-slice
 climate projections over the last 120 thousand years, and summarize
 stability over that period. We then use &gt;25,000 RADseq-generated
 SNPs to i) describe the spatial patterns of genomic variation in both
 species, ii) test how well genomic variation is explained by isolation by
 distance and by the environmental resistance imposed by historical
 instability (isolation by resistance) and iii) test for a correlation
 between genetic diversity and historical stability. The contemporary range
 of S. botryophora has been relatively stable over the last 30 thousand
 years and there are two isolated regions of high stability for S.
 pseudococos. The genomic data recovers a clear pattern of isolation by
 distance in S. botryophora and two structured populations in S.
 pseudococos. Consequently, the contribution of isolation by resistance to
 overall genetic structure is much higher in S. pseudococos. Genetic
 diversity is not significantly correlated with historical stability in
 either species. Based on the concordance between historical stability and
 genetic structure, Late Quaternary climate stability may have maintained
 population connectivity within S. botryophora and promoted intraspecific
 divergence in S. pseudococos. Conversely, historical stability does not
 seem to be driving spatial patterns of genetic diversity. This study
 supports the primary role of climatic stability in determining spatial
 population structure, but not genetic diversity, in the Atlantic Forest.
description: We sampled 11 localities of S.
 botryophora and 13 of S. pseudococos, including at least three individuals
 per locality across the entire range of each species. These data were
 supplimented with occurrences from the Global Biodiversity Information
 Facility (GBIF.org). To ensure taxonomic and locality accuracy, we
 included only those GBIF occurrences based on museum
 specimens. To characterize
 climate stability for each species over time, we built SDMs by combining
 occurrence data for the species of interest with spatial environmental
 data to model how the species occupies geographic space
 (Guisan et al.,
 2017). We used the R package ‘ENMeval’ v2.0.0 to build a
 suite of models, varying the shape of the response curve (linear, or
 linear and quadratic) and model complexity (regularization multipliers
 ranging from 0.1 to 4.5 in increments of 0.1; (Muscarella et al., 2014). For the modeling procedure, we used the machine
 learning algorithm MaxEnt as implemented in the R package ‘dismo’ v1.1-4
 (Hijmans et al.,
 2013), fitting a total of 90
 models. To choose the best model from this suite of SDMs, we prioritized
 those with less model overfitting. First, we selected those models with
 the lowest 10% omission rates, within 0.05 of the minimum 10% omission
 rate. From this subset, we chose the most accurate model as measured by
 the average Area Under the Curve (AUC) of the testing sets
 (Guisan et al.,
 2017).
description: Please refer to ReadMe
 file.