title: Genome-Wide Convergence during Evolution of Mangroves from Woody Plants.
abstract: When living organisms independently invade a new environment, the evolution of similar phenotypic traits is often observed. An interesting but contentious issue is whether the underlying molecular biology also converges in the new habitat. Independent invasions of tropical intertidal zones by woody plants, collectively referred to as mangrove trees, represent some dramatic examples. The high salinity, hypoxia, and other stressors in the new habitat might have affected both genomic features and protein structures. Here, we developed a new method for detecting convergence at conservative Sites (CCS) and applied it to the genomic sequences of mangroves. In simulations, the CCS method drastically reduces random convergence at rapidly evolving sites as well as falsely inferred convergence caused by the misinferences of the ancestral character. In mangrove genomes, we estimated ∼400 genes that have experienced convergence over the background level of convergence in the nonmangrove relatives. The convergent genes are enriched in pathways related to stress response and embryo development, which could be important for mangroves' adaptation to the new habitat.
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China.
authors.forename: Shaohua
authors.initials: S
authors.lastname: Xu
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China.
authors.forename: Ziwen
authors.initials: Z
authors.lastname: He
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China.
authors.forename: Zixiao
authors.initials: Z
authors.lastname: Guo
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China.
authors.forename: Zhang
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Molecular Biology and Biochemistry, University of Missouri-Kansas City, Kansas City, MO.
authors.forename: Gerald J
authors.initials: GJ
authors.lastname: Wyckoff
authors.affiliation: Bayesic Research, Ithaca, NY.
authors.forename: Anthony
authors.initials: A
authors.lastname: Greenberg
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China.|Department of Ecology and Evolution, University of Chicago, Chicago, IL.
authors.forename: Chung-I
authors.initials: CI
authors.lastname: Wu
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China.
authors.forename: Suhua
authors.initials: S
authors.lastname: Shi
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D032407:Avicennia / Q000235:genetics*; D005075:Biological Evolution; D017753:Ecosystem; D004777:Environment; D016678:Genome; D023281:Genomics; D010802:Phylogeny; D010944:Plants / Q000235:genetics; D043982:Rhizophoraceae / Q000235:genetics*; D012641:Selection, Genetic / Q000235:genetics; D014197:Trees / Q000235:genetics; D053833:Wetlands
keywords: adaptive evolution; convergent evolution; genomes; mangroves; marginal environments