DOI: 10.5061/dryad.zkh18936g
title: Common barriers, but temporal dissonance: genomic tests suggest ecological and paleo-landscape sieves structure a coastal riverine fish community

description: Assessments of spatial and temporal congruency across taxa from genetic
 data provide insights into the extent to which similar processes structure
 communities. However, for coastal regions that are affected continuously
 by cyclical sea-level changes over the Pleistocene, congruent
 interspecific response will not only depend upon co-distributions, but
 also on similar dispersal histories among taxa. Here, we use SNPs to test
 for concordant genetic structure among four co-distributed taxa of
 freshwater fishes (Teleostei: Characidae) along the Brazilian Atlantic
 coastal drainages. Based on population relationships and hierarchical
 genetic structure analyses, we identify all taxa share the same geographic
 structure suggesting the fish utilized common passages in the past to move
 between river basins. In contrast to this strong spatial concordance,
 model-based estimates of divergence times indicate that despite common
 routes for dispersal, these passages were traversed by each of the taxa at
 different times resulting in varying degrees of genetic differentiation
 across barriers with most divergences dating to the Upper Pleistocene,
 even when accounting for divergence with gene flow. Interestingly, when
 this temporal dissonance is viewed through the lens of the
 species-specific ecologies, it suggests that an ecological sieve
 influenced whether species dispersed readily, with an ecological
 generalist showing the highest propensity for historical dispersal among
 the isolated rivers of the Brazilian coast (i.e., the most recent
 divergence times and frequent gene flow estimated for barriers). We
 discuss how our findings, and in particular what the temporal dissonance,
 despite common geographic passages, suggest about past dispersal
 structuring coastal communities as a function of ecological and
 paleo-landscape sieves.
description: Six double digest Restriction-site Associated DNA (ddRAD)
 libraries were constructed: three libraries contained 118 individuals of
 <i>Mimagoniates microlepis</i> for this study, two libraries
 containing 136 individuals of <i>Hyphessobrycon
 boulengeri</i>, and one library with 87 individuals of
 <i>Bryconamericus</i>. In addition, two libraries with 182
 individuals of <i>Hollandichthys</i> were re-analyzed for this
 study<i> </i>(Thomaz et al., 2017). For all the libraries
 prepared specifically for this study, we followed the protocol of
 Peterson, Weber, Kay, Fisher, & Hoekstra (2012); the two
 previously sequenced libraries of <i>Hollandichthys
 </i>followed the Parchman et al. (2012) protocol (see Thomaz et
 al.<i>,</i> 2017 for preparation details). Genomic data were
 demultiplexed and processed separately for each taxon with the STACKS
 version 1.41 pipeline (Catchen, Hohenlohe, Bassham, Amores, &
 Cresko, 2013). Because of the various requirements of different analyses
 used to characterize the geographic structuring of genomic variation,
 three datasets were generated per taxon varying the amount of missing data
 and the numbers of individuals. One dataset was comprised by one random
 single SNP per locus with maximum of 50% missing data, which was used for
 estimates of population trees using SVSquartets on PAUP. The other dataset
 included loci with maximum 25% missing data after filtering - note that
 for <i>M. microlepis</i> we allowed 35% missing data - and was
 used with a random single SNP per locus in the STRUCTURE analysis.
 Separate datasets were used in FASTSIMCOAL2
 analyses and were generated, when possible, from 20 individuals with the
 smallest amount of missing data from all the populations separated by each
 geographic barrier for each taxon (40 individuals in total), and a single
 variable SNP per RADtag with less than 10% missing data. For all these
 datasets, individuals with considerably fewer SNPs in comparison to other
 individuals of the same population were excluded. All filtering steps were
 performed using the toolset PLINK v.1.90 (Purcell et al., 2007) - see
 Thomaz and Knowles (2020) for details on methodology.
description: Three folders:<br> (1) SVDquartets: contain all input and
 output files from SVSquartets in PAUP.<br> (2) Structure: contain
 all input and output files from structure per taxon and break (central,
 north and south)<br> (3) Fastsimcoal2: four folders with files and
 scripts used to (1) estimation of the SFS, (2) point estimates per model
 tested for each taxon and break, (3) parametric bootstrap, including the
 simulated SFS, and (4) generate Figure 3 in Thomaz and Knowles
 (2020).