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Exploration of Plastid Phylogenomic Conflict Yields New Insights into the Deep Relationships of Leguminosae.


ABSTRACT: Phylogenomic analyses have helped resolve many recalcitrant relationships in the angiosperm tree of life, yet phylogenetic resolution of the backbone of the Leguminosae, one of the largest and most economically and ecologically important families, remains poor due to generally limited molecular data and incomplete taxon sampling of previous studies. Here, we resolve many of the Leguminosae's thorniest nodes through comprehensive analysis of plastome-scale data using multiple modified coding and noncoding data sets of 187 species representing almost all major clades of the family. Additionally, we thoroughly characterize conflicting phylogenomic signal across the plastome in light of the family's complex history of plastome evolution. Most analyses produced largely congruent topologies with strong statistical support and provided strong support for resolution of some long-controversial deep relationships among the early diverging lineages of the subfamilies Caesalpinioideae and Papilionoideae. The robust phylogenetic backbone reconstructed in this study establishes a framework for future studies on legume classification, evolution, and diversification. However, conflicting phylogenetic signal was detected and quantified at several key nodes that prevent the confident resolution of these nodes using plastome data alone. [Leguminosae; maximum likelihood; phylogenetic conflict; plastome; recalcitrant relationships; stochasticity; systematic error.].

SUBMITTER: Zhang R 

PROVIDER: S-EPMC7302050 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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Exploration of Plastid Phylogenomic Conflict Yields New Insights into the Deep Relationships of Leguminosae.

Zhang Rong R   Wang Yin-Huan YH   Jin Jian-Jun JJ   Stull Gregory W GW   Bruneau Anne A   Cardoso Domingos D   De Queiroz Luciano Paganucci LP   Moore Michael J MJ   Zhang Shu-Dong SD   Chen Si-Yun SY   Wang Jian J   Li De-Zhu DZ   Yi Ting-Shuang TS  

Systematic biology 20200701 4


Phylogenomic analyses have helped resolve many recalcitrant relationships in the angiosperm tree of life, yet phylogenetic resolution of the backbone of the Leguminosae, one of the largest and most economically and ecologically important families, remains poor due to generally limited molecular data and incomplete taxon sampling of previous studies. Here, we resolve many of the Leguminosae's thorniest nodes through comprehensive analysis of plastome-scale data using multiple modified coding and  ...[more]

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