Whole-genome phylogenomics of the tinamous (Aves: Tinamidae): comparing gene tree estimation error between BUSCOs and UCEs illuminates rapid divergence with introgression

Musher, Lukas J.; Catanach, Therese A.; Valqui, Thomas; Brumfield, Robb T.; Aleixo, Alexandre; Johnson, Kevin P.; Weckstein, Jason D.

doi:10.1101/2024.01.22.576737

Cited by 2 publications

(1 citation statement)

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“…ROADIES achieves these impressive results based on three key insights. First , instead of genomic regions with specific characteristics, such as protein-coding genes, ultra-conserved elements (UCEs) 83 , or transposons 63,84–86 . ROADIES is based on a random sampling of loci from input genomes.…”

Section: Discussionmentioning

confidence: 99%

Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES

Gupta,

Mirarab,

Turakhia

2024

Preprint

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Inference of species trees plays a crucial role in advancing our understanding of evolutionary relationships and has immense significance for diverse biological and medical applications. Extensive genome sequencing efforts are currently in progress across a broad spectrum of life forms, holding the potential to unravel the intricate branching patterns within the tree of life. However, estimating species trees starting from raw genome sequences is quite challenging, and the current cutting-edge methodologies require a series of error-prone steps that are neither entirely automated nor standardized. In this paper, we present ROADIES, a novel pipeline for species tree inference from raw genome assemblies that is fully automated, easy to use, scalable, free from reference bias, and provides flexibility to adjust the tradeoff between accuracy and runtime. The ROADIES pipeline eliminates the need to align whole genomes, choose a single reference species, or pre-select loci such as functional genes found using cumbersome annotation steps. Moreover, it leverages recent advances in phylogenetic inference to allow multi-copy genes, eliminating the need to detect orthology. Using the genomic datasets released from large-scale sequencing consortia across three diverse life forms (placental mammals, pomace flies, and birds), we show that ROADIES infers species trees that are comparable in quality with the state-of-the-art approaches but in a fraction of the time. By incorporating optimal approaches and automating all steps from assembled genomes to species and gene trees, ROADIES is poised to improve the accuracy, scalability, and reproducibility of phylogenomic analyses.Code and Data availabilityThe source code of ROADIES is freely available under the MIT License on GitHub (https://github.com/TurakhiaLab/ROADIES), and the documentation for ROADIES is available athttps://turakhia.ucsd.edu/ROADIES/. The details of the input datasets used in the manuscript are listed in Supplementary Tables 1-3. All inferred gene trees and species trees are to be deposited to Dryad with links to be made available on the aforementioned GitHub repository.Contactyturakhia@ucsd.edu

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Section: Discussionmentioning

confidence: 99%

Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES

Gupta,

Mirarab,

Turakhia

2024

Preprint

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Phylogenomics of a genus of ‘Great Speciators’ reveals rampant incomplete lineage sorting, gene flow, and mitochondrial capture in island systems

McCullough,

Eliason,

Hackett

et al. 2024

Preprint

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The flora and fauna of island systems, especially those in the Indo-Pacific, are renowned for their high diversification rates and outsized contribution to the development of evolutionary theories. The total diversity of geographic radiations of many Indo-Pacific fauna is often incompletely sampled in phylogenetic studies due to the difficulty in obtaining single island endemic forms across the Pacific and the relatively poor performance of degraded DNA when using museum specimens for inference of evolutionary relationships. New methods for production and analysis of genome-wide datasets sourced from degraded DNA are facilitating insights into the complex evolutionary histories of these influential island faunas. Here, we leverage whole genome resequencing (20X average coverage) and extensive sampling of all taxonomic diversity within Todiramphus kingfishers, a rapid radiation of largely island endemic "Great Speciators." We find that whole genome datasets do not outright resolve the evolutionary relationships of this clade: four types of molecular markers (UCEs, BUSCOs, SNPs, and mtDNA) and tree building methods did not find a single well-supported and concordant species-level topology. We then uncover evidence of widespread incomplete lineage sorting and both ancient and contemporary gene flow and demonstrate how these factors contribute to conflicting evolutionary histories. Our complete taxonomic sampling allowed us to further identify a novel case of mitochondrial capture between two allopatric species, suggesting a potential historical (but since lost) hybrid zone as islands were successively colonized. Taken together, these results highlight how increased genomic and taxon sampling can reveal complex evolutionary patterns in rapid island radiations.

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Whole-genome phylogenomics of the tinamous (Aves: Tinamidae): comparing gene tree estimation error between BUSCOs and UCEs illuminates rapid divergence with introgression

Cited by 2 publications

References 100 publications

Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES

Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES

Phylogenomics of a genus of ‘Great Speciators’ reveals rampant incomplete lineage sorting, gene flow, and mitochondrial capture in island systems

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