ArticleBMC bioinformatics2017
Integrated pipeline for inferring the evolutionary history of a gene family embedded in the species tree: a case study on the STIMATE gene family.
Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed, 7 citations in OpenAlex.
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- Expression and functional divergence of a type-A response regulator paralog pair formed by dispersed duplication during Populus deltoides evolution.Communications biology · 2024Article
- Whole-genome analysis reveals distinct adaptation signatures to diverse environments in Chinese domestic pigs.Journal of animal science and biotechnology · 2024Article
- Genomic Analysis ofG3 (Bethesda, Md.) · 2019Article
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Authors and funding
6 authors at 2 institutions in 2 countries.
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Abstract
backgroundBecause phylogenetic inference is an important basis for answering many evolutionary problems, a large number of algorithms have been developed. Some of these algorithms have been improved by integrating gene evolution models with the expectation of accommodating the hierarchy of evolutionary processes. To the best of our knowledge, however, there still is no single unifying model or algorithm that can take all evolutionary processes into account through a stepwise or simultaneous method.
resultsOn the basis of three existing phylogenetic inference algorithms, we built an integrated pipeline for inferring the evolutionary history of a given gene family; this pipeline can model gene sequence evolution, gene duplication-loss, gene transfer and multispecies coalescent processes. As a case study, we applied this pipeline to the STIMATE (TMEM110) gene family, which has recently been reported to play an important role in store-operated Ca
conclusionsBy integrating three tree reconstruction algorithms with diverse evolutionary models, a pipeline for inferring the evolutionary history of a gene family was developed, and its application was demonstrated.
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