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- Quaresma, T. F., et al.
(författare)
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Diversification and species limits in scale-backed antbirds (Willisornis: Thamnophilidae), an Amazonian endemic lineage
- 2022
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Ingår i: Zoological Journal of the Linnean Society. - : Oxford University Press (OUP). - 0024-4082 .- 1096-3642. ; 196:4, s. 1408-30
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Tidskriftsartikel (refereegranskat)abstract
- The genus Willisornis is endemic to the Amazon Basin, inhabiting upland terra firme forest, with two species and seven subspecies currently recognized. Despite numerous systematic studies, a taxonomically-dense sampled phylogeny for Willisornis is still lacking, which, combined with evidence of paraphyly and gene flow between its recognized species, underscores the uncertainty concerning species limits and evolutionary history of the genus. Here we present phylogenies and population genetic analyses, including all currently recognized Willisornis taxa, relating them to patterns of plumage variation, and reconstructing the spatiotemporal context of diversification in the genus. Our analyses have uncovered 13 independent genetic lineages in the genus, and the monophyly of all currently named taxa, which also showed robust plumage diagnoses. However, deeply coalesced genetic lineages were also found within most Willisornis taxa, for which no consistent variation in plumage was found. The diversification of the genus Willisornis is related to hydrographic and climate change cycles across Amazonia since the Plio-Pleistocene, with most genetic lineages originating in the past one million years. Based on our findings, we recommend the recognition of a total of six species in Willisornis (one of which polytypic) based on the congruency between deeply coalesced lineages and consistent plumage diagnoses.
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| 2. |
- Ribeiro, C. V. R., et al.
(författare)
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UCEasy: A software package for automating and simplifying the analysis of ultraconserved elements (UCEs)
- 2021
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Ingår i: Biodiversity Data Journal. - 1314-2836. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Background The use of Ultraconserved Elements (UCEs) as genetic markers in phylogenomics has become popular and has provided promising results. Although UCE data can be easily obtained from targeted enriched sequencing, the protocol for in silico analysis of UCEs consist of the execution of heterogeneous and complex tools, a challenge for scientists without training in bioinformatics. Developing tools with the adoption of best practices in research software can lessen this problem by improving the execution of computational experiments, thus promoting better reproducibility. New information We present UCEasy, an easy-to-install and easy-to-use software package with a simple command line interface that facilitates the computational analysis of UCEs from sequencing samples, following the best practices of research software. UCEasy is a wrapper that standardises, automates and simplifies the quality control of raw reads, assembly and extraction and alignment of UCEs, generating at the end a data matrix with different levels of completeness that can be used to infer phylogenetic trees. We demonstrate the functionalities of UCEasy by reproducing the published results of phylogenomic studies of the bird genus Turdus (Aves) and of Adephaga families (Coleoptera) containing genomic datasets to efficiently extract UCEs. © 2021. Ribeiro C et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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