Data from: The role of glacial‐interglacial climate change in shaping the genetic structure of eastern subterranean termites in the southern Appalachian Mountains, USA

Hyseni C, Garrick RC

Date Published: April 16, 2019

DOI: https://doi.org/10.5061/dryad.5hr7f31

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Title EnvironmentalFactors_EasternUS
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Description Raster maps of present-day and historical environmental factors for the Eastern United States. The environmental factors are the outcome of factor analysis on 19 bioclimatic variables (Worldclim 1.4), resulting in four factors capturing: temperature range, summer temperature, dry- and wet-season precipitation. The temporal scale includes the present (1960-1990), the Mid-Holocene (~6,000 years ago), the Last Glacial Maximum (~22,000 years ago), and the Last Inter-glacial (~120,000-140,000 years ago). The spatial scale covers a large part of the Eastern United States (28-41 N, 74-91 W).
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Title Species distribution modeling projections
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Description Species distribution models (SDMs) were constructed using the ‘biomod2’ package in R. We first ran a rectilinear surface range envelope model, and then, from outside the area predicted as suitable habitat, we picked 20 independent sets of 100 pseudo-absence points, each of which were combined with the same 91 presence records. Four modeling algorithms were run: artificial neural networks, generalized boosted models or boosted regression trees, random forest, and maximum entropy. We used 5 cross-validation runs per algorithm, for a total of 400 runs (4 algorithms x 5 cross-validations x 20 datasets), with 5,000 iterations per run. To assess model performance, 75% of the data were used for training, with 25% set aside as "out-of-bag" test data. To maximize the accuracy of presence/absence classification, we used the True Skill Statistic (TSS = sum of sensitivity and specificity – 1), where SDMs with mean TSS above 0.2 were retained. We then used the ensemble framework to obtain a weighted average of all SDMs, where SDMs were weighted according to TSS values. Projections: present-day SDMs were based on mean climatological data spanning 1960–1990, and historical distributions were modeled for the Mid-Holocene (~6,000 years ago), the Last Glacial Maximum (~22,000 years ago), and the Last Inter-glacial (~120,000–140,000 years ago).
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Title DIYABC_files
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Description DIYABC approximate Bayesian computation input file and settings (scenarios and parameters)
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Title AppendicesS1-S8
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Description Supplementary Methods: Appendix S1. Population sampling. Appendix S2. DNA isolation and genetic markers. Appendix S3. Construction of species distribution models. Appendix S4. Comparison of scenarios using approximate Bayesian computation. Supplementary Results: Appendix S5. Environmental factors used in species distribution models. Appendix S6. Genetic divergence, environment, and spatial structure. Appendix S7. Phylogeographic scenarios: error rates and parameter estimates. Appendix S8. Population size changes: standard and compound neutrality tests.
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Title Approximate Bayesian computation - Posterior Probabilities and Error Rates
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Description Posterior probabilities of phylogeographic scenarios in two-tier comparisons, type I (alpha, false positive) and type II (beta, false negative) error rates for "winning" scenarios (with highest posterior probabilities) in each step of each tier. The first tier has two steps (step 1: refugial scenarios; step 2: distributional shift scenarios). Tier 2 only has one step, but the winning scenarios from tier 1 are compared including or excluding a third scenario, vicariance. For the former (including vicariance), we computed type I and II error rates for all three scenarios, rather than just the winning scenario.
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Title BEAST_files
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Description Input files for BEAST analyses. BEAST was run with (Ret) and without (Rf) the out-group Reticulitermes taxa.
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Title BAPS_files
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Description Input files for BAPS analyses, including a file that shows the mtDNA COI+COII locus haplotypes for each data point. To determine the number of geographically cohesive genetic groups of R. flavipes, we analyzed geo-referenced mtDNA sequences in BAPS v.6.0. We assessed values of K (i.e., the number of clusters) ranging from 2–20, with 10 replicate runs each.
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When using this data, please cite the original publication:

Hyseni C, Garrick RC (2019) The role of glacial‐interglacial climate change in shaping the genetic structure of eastern subterranean termites in the southern Appalachian Mountains, USA. Ecology and Evolution, online in advance of print. https://doi.org/10.1002/ece3.5065

Additionally, please cite the Dryad data package:

Hyseni C, Garrick RC (2019) Data from: The role of glacial‐interglacial climate change in shaping the genetic structure of eastern subterranean termites in the southern Appalachian Mountains, USA. Dryad Digital Repository. https://doi.org/10.5061/dryad.5hr7f31
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