DOI: 10.5061/dryad.sxksn032q
title: Recent population differentiation in the habitat specialist Glossy Antshrike (Aves: Thamnophilidae) across Amazonian seasonally flooded forests: Complete matrix

description: We assessed population structure and the spatio-temporal pattern of
 diversification in the Glossy Antshrike Sakesphorus luctuosus (Aves,
 Thamnophilidae) to understand the processes shaping the evolutionary
 history of Amazonian floodplains and address unresolved taxonomic
 controversies surrounding its species limits. By targeting ultraconserved
 elements (UCEs) from 32 specimens of S. luctuosus, we identified
 independent lineages and estimated their differentiation, divergence times
 and migration rates. We also estimated current and past demographic
 histories for each recovered lineage. We found evidence confirming that S.
 luctuosus consists of a single species, comprising at least four
 populations, with some highly admixed individuals and overall similar
 levels of migration between populations. We confirmed the differentiation
 of the Araguaia River basin population (S. l. araguayae), and gathered
 circumstantial evidence indicating that the taxon S. hagmanni may
 represent a highly introgressed population between 3 distinct phylogroups
 of S. luctuosus. Divergence time estimates between populations seem to be
 recent, occurring during the last 183 kya. Signs of population expansions
 were detected for populations attributed to subspecies S. l. luctuosus,
 but the S. l. araguayae population had probably maintained its effective
 size through time. Our results support that S. luctuosus has had a complex
 population history, resulting from a high dependence on southeastern
 “clear-water” habitats and their availability through time. Spatial and
 demographic expansions towards the western “white water” flooded forests
 might still be ongoing. Our study reinforces the view that isolation due
 to absence of suitable habitat has been an important driver of population
 differentiation within Amazonian flooded forests, but also that
 differences between várzeas (“white water” floodplains, mostly in
 southwestern Amazonia) and igapós (“clear- water” floodplains, especially
 located in the east) should be further explored as powerful drivers of
 micro-evolution.
description: Genomic DNA was extracted from tissues of 32 specimens of
 Sakesphorus luctuosus from across its known range and a S. canadensis
 specimen. We used DNeasy Blood & Tissue kit (Qiagen) for DNA
 extraction, and Qubit® 2.0 Fluorometer (Life Technologies) to assess
 quantity and quality of the extracted DNA. Sequence capture and sequencing
 of Ultra Conserved Elements (hereafter UCEs) were performed according to
 Faircloth et al. (2012) by RAPiD Genomics (Gainesville, FL, USA). More
 than 2,300 UCEs and 97 exons were targeted (Harvey, Aleixo, Ribas,
 & Brumfield, 2017; Zucker et al., 2016). We
 followed the PHYLUCE pipeline (Faircloth, 2016, 2017) to first remove
 adapters, barcodes and low quality sequence regions using Illumiprocessor
 2.0.7 (Faircloth, 2013), with the trimming tool Trimmomatic 0.32.1
 (Bolger, Lohse, & Usadel, 2014); and to assemble trimmed reads
 using Trinity (Grabherr et al., 2011). These analyses were performed using
 default parameters. Contigs were blasted against the probe set of exons
 and UCEs using phyluce_match_contigs_to_probes. The annotated set was
 divided by locus, and each was aligned with MAFFT using the scripts
 phyluce_assembly_get_match_counts,
 phyluce_assembly_get_fastas_from_match_counts, and
 phyluce_align_seqcap_align. A complete matrix comprising only loci without
 missing data was obtained following the UCE Phylogenomics tutorial from
 PHYLUCE pipeline (Faircloth, 2016).
description: A complete DNA sequence matrix, comprising loci without missing
 data, from 32 specimens of Sakesphorus luctuosus and 1 specimen of
 Sakesphorus canadensis (sample ID: A16764) is here deposited (Silva, Ribas
 & Aleixo, Ecology and Evolution, doi: 10.1002/ece3.7951). This
 dataset was obtained after sequence capture and sequencing of more than
 2,300 Ultra Conserved Elements and 97 exons. The PHYLUCE pipeline was used
 to remove adapters, barcodes and low quality sequence regions using
 Illumiprocessor 2.0.7, with the trimming tool Trimmomatic 0.32.1; and to
 assemble trimmed reads using Trinity. These analyses were performed using
 default parameters. Contigs were blasted against the probe set of exons
 and UCEs using phyluce_match_contigs_to_probes. The annotated set was
 divided by locus, and each was aligned with MAFFT using the scripts
 phyluce_assembly_get_match_counts,
 phyluce_assembly_get_fastas_from_match_counts, and
 phyluce_align_seqcap_align.