DOI: 10.5061/dryad.4qrfj6qbf
title: Data from: Functional connectivity in sympatric spiny rats reflects different dimensions of Amazonian forest-association

description: Aim: Understanding how the landscape influences gene flow is important in
 explaining biodiversity, especially when co-distributed taxa across
 heterogeneous landscapes exhibit species-specific habitat associations.
 Here, we test predictions about the effects of forest-type on population
 connectivity in two sympatric species of spiny rats that differ in their
 forest associations. Specifically, we evaluate the hypothesis that
 seasonal floodplain forests (várzea) provide linear connectivity,
 facilitating gene flow among individuals, while non-flooded forests
 (terra-firme) may diminish the functional connectivity. Location: Western
 Amazon, South America. Taxon: Proechimys simonsi (non-flooded forests,
 terra-firme) and Proechimys steerei (seasonal floodplain forests, várzea).
 Methods: We analyze about 13,000 SNPs along with characterizations of
 landscape heterogeneity for two forest types to test for differences in
 the functional connectivity. Influence of the landscape and environmental
 variables are quantified using maximum-likelihood population effect (MLPE)
 models to identify the relative importance of variables in explaining the
 gene flow. Results: There are significant differences in functional
 connectivity between species. However, the genomic data does not support
 the conventional hypotheses of higher connectivity for inhabitants of
 várzea than those of terra-firme. Stronger genetic structure in P. steerei
 than P. simonsi based on IBD models suggests reduced gene flow in species
 associated with várzea forests. Isolation by resistance reinforces that
 wetland habitats inhibit and promote the functional connectivity in P.
 simonsi and P. steerei, respectively, although large distances along the
 rivers can prevent gene flow in P. steerei. Main conclusions: Interpreting
 differences between connectivity in taxa apparent from genetic analyses
 through the lens of a single dimension of Amazonian heterogeneity – that
 is, forest type – may be an oversimplification. Our statistical modeling
 and fit of the data to different models points to specific environmental
 and habitat differences between the ecological divergent spiny rat species
 that may contribute to differences in the genetic structure of these
 sympatric taxa.
description: Supporting Information for the manuscript: Functional
 connectivity in sympatric spiny rats reflects different dimensions of
 Amazonian forest-association Including:<br>-Raw
 Data: Fastq files by individuals after Stacks processing reads
 (.fq.gz);<br>-Genetic Data: Raw and Filtered VCF by species
 (.vcf);<br>-Spatial Data: coordinates of all localities by the
 individuals (.csv);<br>-MLPE Tables: input for IBR analyses in MLPE
 mixed models (.csv);<br>-Supporting_Information: Table S1.1 with
 details on geographic information for each individual (.csv); and the
 Supporting Information file (Appendix S1, S2, and S3) in a single file
 (.pdf); R scripts are available
 in:<br>https://github.com/jdalapicolla/LanGen_pipeline_version2<br>https://github.com/jdalapicolla/IBD_models.R<br>https://github.com/jdalapicolla/MLPE.R
description: # Data from: Functional connectivity in sympatric spiny rats reflects
 different dimensions of Amazonian forest-association
 [https://doi.org/10.5061/dryad.4qrfj6qbf](https://doi.org/10.5061/dryad.4qrfj6qbf) ## Description of the data and file structure Supporting Information files for the paper "Functional connectivity in sympatric spiny rats reflects different dimensions of Amazonian forest-association" ([https://doi.org/10.1111/jbi.14281](https://doi.org/10.1111/jbi.14281)) **1) Raw Data:** Fastq files by individuals after Stacks processing reads (.fq.gz). Samples were sequenced using the ddRAD-Seq technique in one lane of a HiSeq2500 (Illumina, San Diego, CA, USA) at the Center for Applied Genomics in Toronto, Canada to generate 150 bp, single-end reads. More details can be found in "Functional connectivity in sympatric spiny rats reflects different dimensions of Amazonian forest-association" ([https://doi.org/10.1111/jbi.14281](https://doi.org/10.1111/jbi.14281)) **2) Genetic Data:** Raw and Filtered VCF by species (.vcf); **3) Spatial Data:** coordinates of all localities by the individuals (.csv); **4) MLPE Tables:** input for IBR analyses in MLPE mixed models (.csv); **5) Supporting_Information:** Table S1.1 with details on geographic information for each individual (.csv); **6) Appendix S1, S2, and S3:** Supporting Information files in a single file (.pdf). ## Code/Software R scripts are available in: [https://github.com/jdalapicolla/LanGen_pipeline_version2](https://github.com/jdalapicolla/LanGen_pipeline_version2) [https://github.com/jdalapicolla/IBD_models.R](https://github.com/jdalapicolla/IBD_models.R) [https://github.com/jdalapicolla/MLPE.R](https://github.com/jdalapicolla/MLPE.R)