10.5061/DRYAD.SXKSN032Q
Silva, Sofia
0000-0002-0502-3071
Museu Paraense Emílio Goeldi
Ribas, Camila
National Institute of Amazonian Research
Aleixo, Alexandre
0000-0002-7816-9725
Museu Paraense Emílio Goeldi
Recent population differentiation in the habitat specialist Glossy
Antshrike (Aves: Thamnophilidae) across Amazonian seasonally flooded
forests: Complete matrix
Dryad
dataset
2021
FOS: Biological sciences
Brazilian Research Council*
150657/2017-0; 311732/2020-8
United States Agency for International Development
https://ror.org/01n6e6j62
AID-OAA-A-11-00012
São Paulo Research Foundation
https://ror.org/02ddkpn78
National Science Foundation
https://ror.org/021nxhr62
United States Agency for International Development
https://ror.org/01n6e6j62
National Council for Scientific and Technological Development
https://ror.org/03swz6y49
Brazilian Research Council
150657/2017-0; 311732/2020-8
2021-07-19T00:13:14Z
2022-07-18T00:00:00Z
en
https://doi.org/10.1002/ece3.7951
6073188 bytes
8
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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).
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.