Phylogenomic prediction of interaction networks in the presence of gene duplication

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 8, 2024

Abstract Assigning gene function from genome sequences is a rate-limiting step in molecular biology research. A protein’s position within an interaction network can potentially provide insights into its mechanisms. Phylogenetic analyses of evolutionary rate covariation (ERC) have been shown to be effective for large-scale prediction functional interactions protein sequence data. However, duplication, loss, and other sources phylogenetic incongruence are barriers analyzing ERC on genome-wide basis. Here, we developed ERCnet , bioinformatic program designed overcome these challenges, facilitating efficient all-vs-all large datasets. We compiled sample set 35 angiosperm genomes test the performance ERCnet, including sensitivity user-defined analysis parameters such as input dataset size, branch-length measurement strategy, significance threshold defining hits. find that our novel ‘branch-by-branch’ length measurements outperforms ‘root-to-tip’ approaches most cases, offering valuable new strategy performing even presence extensive duplication. Further, demonstrate number species composition both profound effects genes predicted interact. Our systematic exploration provides roadmap design future predict wide array genomic code freely available at https://github.com/EvanForsythe/ERCnet .

Language: Английский

Evolution of the skull in arvicoline cricetids (Rodentia) according to 3D morphometric insights: Part 1. Morphological disparity of the palato-spheno-pterygoid complex

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 9, 2024

ABSTRACT Our paper is the first contribution to comprehensive analysis of complicated evolution cranial and mandibular parts connected by pterygoid muscles, as part more global investigation into adaptive Arvicolinae. The was performed on 90 micro-computed-tomography–scanned specimens from 33 species 19 genera Arvicolinae well two Cricetinae an outgroup. We revised 11 morphological traits “palato-spheno-pterygoid” complex, including key features palatine that are highly important for defining taxa according micro-computed-tomography data. also homologized characters posterior palatal margin categorized composition elements main morphotypes: morphotype “A” unique Clethrionomyini “B” subdivided three additional types found occur in outgroup (cricetines), voles (B2), lemmings (B3). Morphospace palato-spheno-pterygoid complex means three-dimensional dataset revealed a mode transformation “B2.” A separate task development protocol preparation data subsequent evaluation genotype–phenotype relationships using specialized software applications (e.g., RERconverge).

Language: Английский