DOI: 10.5061/dryad.47d7wm3f9
title: Data from: Phylogeographic and demographic patterns reveal congruent histories in seven Amazonian white-sand ecosystems birds

description: Aim: As the most biodiverse region of the world, the drivers of genetic
 diversity in Amazonia are still poorly understood. It has been debated
 that species on distinct ecosystems will show unique biogeographic
 histories tied to their habitats which in turn help understand landscape
 climatic history in Amazonia. We studied bird species associated with
 patchy Amazonian white-sand ecosystems (WSE) to evaluate the occurrence of
 shared patterns and its relationship to species habitat preferences and
 Amazonian environmental and landscape history. Location: Northern South
 America; Amazonia. Taxon: Passerine birds. Methods: We sequenced
 Ultra-conserved Elements (UCEs) from 177 samples of seven bird species
 associated with WSE that have overlapping ranges. We used the SNP matrices
 and sequence data to estimate genetic structure patterns and migration
 surfaces using ‘conStruct’ and eems, perform model-selection to obtain the
 most probable demographic histories on ‘PipeMaster’, and implement
 analyses of shared demography with ecoevolity. Results: Shallow genetic
 structure patterns varied among species with the Amazon river being the
 only barrier shared among them. Population structure dates to no more than
 450,000 years ago. We identified 17 geographically structured populations
 from which nine showed signals of population size changes and eight of
 these occur in Northern Amazonia. Population expansion was inferred at two
 distinct times: ~100,000 years ago and ~50,000 years ago. The timing of
 co-expanding populations is consistent with differences in habitat
 preference, as species that prefer dense scrubby to forested vegetation
 expanded more recently compared to species that prefer open vegetation.
 Main conclusions: We show that WSE species responded in concert to past
 environmental and landscape changes. Past population expansions were
 likely driven by the genesis of new WSE patches and a return to wetter
 conditions after glacial periods. Pleistocene climatic cycles affected the
 distribution and dynamics of open vegetation habitats in Amazonia,
 especially in the Northern region, driving genetic diversity and
 demographic patterns of its associated biota.
description: We used the <em>phyluce</em> v1.5.0 pipeline to
 process the UCEs from the raw reads (Faircloth, 2016; Faircloth et al.,
 2012). First, raw reads were cleaned from adapters and low quality bases
 using<em> illumiprocessor</em> and
 <em>trimmomatic</em> using <em>phyluce</em> v1.5.0
 default parameters (Bolger et al., 2014; Faircloth et al., 2012). Next,
 the data was assembled into contigs using <em>trinity</em> and
 called from within the phyluce pipeline using
 <em>phyluce_assembly_assemblo_trinity</em> with default
 parameters (--<em>KMER_SIZE</em> set to 25) (Grabherr et al.,
 2011). Finally, we used the phyluce code to find, extract, and align
 (using <em>mafft</em>; Katoh & Standley 2013) the UCE
 loci from the assembled reads. This process was done separately for each
 species and generated species-specific alignments of every UCE
 locus.