Phylogeographic and demographic patterns reveal congruent histories in seven Amazonian white-sand ecosystems birds

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 analy..., We used the phyluce 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 illumiprocessor and trimmomatic using phyluce v1.5.0 default parameters (Bolger et al., 2014; Faircloth et al., 2012). Next, the data was assembled into contigs using trinity and called from within the phyluce pipeline using phyluce_assembly_assemblo_trinity with default parameters (--KMER_SIZE set to 25) (Grabherr et al., 2011). Finally, we used the phyluce code to find, extract, and align (using mafft; 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.,