Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES DOI Creative Commons
Anshu Gupta, Siavash Mirarab, Yatish Turakhia

и другие.

Proceedings of the National Academy of Sciences, Год журнала: 2025, Номер 122(19)

Опубликована: Май 2, 2025

Current genome sequencing initiatives across a wide range of life forms offer significant potential to enhance our understanding evolutionary relationships and support transformative biological medical applications. Species trees play central role in many these applications; however, despite the widespread availability assemblies, accurate inference species remains challenging due limited automation, substantial domain expertise, computational resources required by conventional methods. To address this limitation, we present ROADIES, fully automated pipeline infer starting from raw assemblies. In contrast prominent approach, ROADIES incorporates unique strategy randomly sampling segments input genomes generate gene trees. This eliminates need for predefining set loci, limiting analyses fixed number genes, performing cumbersome annotation and/or whole alignment steps. also orthology leveraging existing discordance-aware methods that allow multicopy genes. Using genomic datasets large-scale efforts four diverse (placental mammals, pomace flies, birds, budding yeasts), show infers are comparable quality state-of-the-art studies but fraction time effort, including on with rampant tree discordance complex polyploidy. With its speed, accuracy, has vastly simplify inference, making it accessible broader scientists

Язык: Английский

Impacts of climatic niche breadth, phylogeny, traits and ploidy on geographical ranges of Betula species DOI Creative Commons
Feifei Yan, Lu Liu,

Junyi Ding

и другие.

Journal of Systematics and Evolution, Год журнала: 2025, Номер unknown

Опубликована: Март 27, 2025

Abstract Geographical range size is a fundamental ecological characteristic of species, and the product complex interactions many factors in its history. Here, we investigate causes variation among 43 species woody plant genus Betula (birches), which each occupy areas between one 20 million square kilometers northern hemisphere. We find their distributions are more affected by temperature variables than precipitation variables. The climatic niche breadth, median latitude, width seed wings, degree bark peeling, ploidy all have significant impacts on variation, but number leaf veins life form do not. Many these attributes, itself, phylogenetic component and, once phylogeny accounted for, no longer has effect size, breadth clearly most important factor. Our results therefore support niche‐breadth hypothesis for to lesser extent also dispersal‐ability Rapoport's rule that decreases toward tropics. likely be key attribute ability avoid decline or extinction under climate change.

Язык: Английский

Процитировано

0
Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES DOI Creative Commons
Anshu Gupta, Siavash Mirarab, Yatish Turakhia

и другие.

Proceedings of the National Academy of Sciences, Год журнала: 2025, Номер 122(19)

Опубликована: Май 2, 2025

Current genome sequencing initiatives across a wide range of life forms offer significant potential to enhance our understanding evolutionary relationships and support transformative biological medical applications. Species trees play central role in many these applications; however, despite the widespread availability assemblies, accurate inference species remains challenging due limited automation, substantial domain expertise, computational resources required by conventional methods. To address this limitation, we present ROADIES, fully automated pipeline infer starting from raw assemblies. In contrast prominent approach, ROADIES incorporates unique strategy randomly sampling segments input genomes generate gene trees. This eliminates need for predefining set loci, limiting analyses fixed number genes, performing cumbersome annotation and/or whole alignment steps. also orthology leveraging existing discordance-aware methods that allow multicopy genes. Using genomic datasets large-scale efforts four diverse (placental mammals, pomace flies, birds, budding yeasts), show infers are comparable quality state-of-the-art studies but fraction time effort, including on with rampant tree discordance complex polyploidy. With its speed, accuracy, has vastly simplify inference, making it accessible broader scientists

Язык: Английский

Процитировано

0