Genome-Wide Convergence during Evolution of Mangroves from Woody Plants

Xu, Shaohua; He, Ziwen; Guo, Zixiao; Zhang, Zhang; Wyckoff, Gerald J.; Greenberg, Anthony J.; Wu, Chung‐I; Shi, Suhua

doi:10.1093/molbev/msw277

Cited by 55 publications

(108 citation statements)

References 48 publications

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“…According to our observations, elimination of most mobile elements leading to a reduced TE load and genome size may be a convergent strategy employed by mangrove hosts adapting to new stressful environments. This is in addition to convergent change in amino acid composition in mangrove genomes (Xu et al ., ). Furthermore, this pattern reveals that although the activities of a few TEs could have been induced by abiotic and biotic stress (Grandbastien, ; Feschotte et al ., ), long‐term selection pressures seem to have counteracted this effect.…”

Section: Discussionmentioning

confidence: 97%

Convergent adaptive evolution in marginal environments: unloading transposable elements as a common strategy among mangrove genomes

Lyu

et al. 2017

New Phytologist

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117

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SummarySeveral clades of mangrove trees independently invade the interface between land and sea at the margin of woody plant distribution. As phenotypic convergence among mangroves is common, the possibility of convergent adaptation in their genomes is quite intriguing.To study this molecular convergence, we sequenced multiple mangrove genomes. In this study, we focused on the evolution of transposable elements (TEs) in relation to the genome size evolution. TEs, generally considered genomic parasites, are the most common components of woody plant genomes. Analyzing the long terminal repeat-retrotransposon (LTR-RT) type of TE, we estimated their death rates by counting solo-LTRs and truncated elements.We found that all lineages of mangroves massively and convergently reduce TE loads in comparison to their nonmangrove relatives; as a consequence, genome size reduction happens independently in all six mangrove lineages; TE load reduction in mangroves can be attributed to the paucity of young elements; the rarity of young LTR-RTs is a consequence of fewer births rather than access death.In conclusion, mangrove genomes employ a convergent strategy of TE load reduction by suppressing element origination in their independent adaptation to a new environment.

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Section: Discussionmentioning

confidence: 97%

Convergent adaptive evolution in marginal environments: unloading transposable elements as a common strategy among mangrove genomes

Lyu

et al. 2017

New Phytologist

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117

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“…One caveat of study on convergent evolution is false positive (Bigham et al 2015;Foote et al 2015;Zou and Zhang 2015;Xu et al 2017). Signal of convergent evolution may be observed frequently between control groups, such as lowland populations in this study.…”

Section: Shared Targets Of Positive Selection For Local Adaptation Ofmentioning

confidence: 76%

Convergent genomic signatures of high altitude adaptation among domestic mammals

Yang

Wang

et al. 2019

Preprint

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Abundant and diverse domestic mammals living on the Tibetan Plateau provide useful materials for investigating adaptive evolution and genetic convergence.Here, we utilized 327 genomes from horses, sheep, goats, cattle, pigs and dogs living at both high and low altitudes, including 73 genomes generated for this study, to disentangle the genetic mechanisms underlying local adaptation of domestic mammals. Although molecular convergence is comparatively rare at the DNA sequence level, we found convergent signature of positive selection at the gene level, particularly EPAS1 gene in these Tibetan domestic mammals. We also reported a potential function in response to hypoxia for the gene C10orf67, which underwent positive selection in three of the domestic mammals. Our data provides insight into adaptive evolution of high-altitude domestic mammals, and should facilitate the search for additional novel genes involved in the hypoxia response pathway.

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“…This ever-shifting pressure to adapt is reminiscent of the metaphor of the "Red Queen" effect (Van Valen 1973;Salathé et al 2008;Liow et al 2011). In the Red Queen landscape, adaptive evolution does not always resemble the large-scale and stable adaptive changes; for example, when terrestrial woody plants invade the intertidal habitats (Xu et al 2017a;Xu et al 2017b) or mammals migrate to the high-altitude terrains (Yi et al 2010). Instead, adaptations may often be transient, small-scale and local.…”

Section: Discussionmentioning

confidence: 99%

Mechanisms of gene death in the Red Queen race revealed by the analysis ofde novomicroRNAs

Lu¹,

Zhao²,

Lan³

et al. 2018

Preprint

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The prevalence of de novo coding genes is controversial due to the length and coding constraints. Non-coding genes, especially small ones, are freer to evolve de novo by comparison. The best examples are microRNAs (miRNAs), a large class of regulatory molecules ~22 nt in length. Here, we study 6 de novo miRNAs in Drosophila which, like most new genes, are testis-specific. We ask how and why de novo genes die because gene death must be sufficiently frequent to balance the many new births. By knocking out each miRNA gene, we could analyze their contributions to each of the 9 components of male fitness (sperm production, length, competitiveness etc.). To our surprise, the knockout mutants often perform better in some components, and slightly worse in others, than the wildtype. When two of the younger miRNAs are assayed in long-term laboratory populations, their total fitness contributions are found to be essentially zero. These results collectively suggest that adaptive de novo genes die regularly, not due to the loss of functionality, but due to the canceling-out of positive and negative fitness effects, which may be characterized as "quasi-neutrality". Since de novo genes often emerge adaptively and become lost later, they reveal ongoing period-specific adaptations, reminiscent of the "Red-Queen" metaphor for long term evolution. peptide of Drosophila melanogaster: female post-mating responses analyzed by using RNA interference. Proc Natl Acad Sci U S A 100: 9923.

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Genome-Wide Convergence during Evolution of Mangroves from Woody Plants

Cited by 55 publications

References 48 publications

Convergent adaptive evolution in marginal environments: unloading transposable elements as a common strategy among mangrove genomes

Convergent adaptive evolution in marginal environments: unloading transposable elements as a common strategy among mangrove genomes

Convergent genomic signatures of high altitude adaptation among domestic mammals

Mechanisms of gene death in the Red Queen race revealed by the analysis ofde novomicroRNAs

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