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Resolution of Brassicaceae Phylogeny Using Nuclear Genes Uncovers Nested Radiations and Supports Convergent Morphological Evolution.

ABSTRACT: Brassicaceae is one of the most diverse and economically valuable angiosperm families with widely cultivated vegetable crops and scientifically important model plants, such as Arabidopsis thaliana. The evolutionary history, ecological, morphological, and genetic diversity, and abundant resources and knowledge of Brassicaceae make it an excellent model family for evolutionary studies. Recent phylogenetic analyses of the family revealed three major lineages (I, II, and III), but relationships among and within these lineages remain largely unclear. Here, we present a highly supported phylogeny with six major clades using nuclear markers from newly sequenced transcriptomes of 32 Brassicaceae species and large data sets from additional taxa for a total of 55 species spanning 29 out of 51 tribes. Clade A consisting of Lineage I and Macropodium nivale is sister to combined Clade B (with Lineage II and others) and a new Clade C. The ABC clade is sister to Clade D with species previously weakly associated with Lineage II and Clade E (Lineage III) is sister to the ABCD clade. Clade F (the tribe Aethionemeae) is sister to the remainder of the entire family. Molecular clock estimation reveals an early radiation of major clades near or shortly after the Eocene-Oligocene boundary and subsequent nested divergences of several tribes of the previously polytomous Expanded Lineage II. Reconstruction of ancestral morphological states during the Brassicaceae evolution indicates prevalent parallel (convergent) evolution of several traits over deep times across the entire family. These results form a foundation for future evolutionary analyses of structures and functions across Brassicaceae.

SUBMITTER: Huang CH

PROVIDER: S-EPMC4866547 | biostudies-literature | 2016 Feb

REPOSITORIES: biostudies-literature

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Resolution of Brassicaceae Phylogeny Using Nuclear Genes Uncovers Nested Radiations and Supports Convergent Morphological Evolution.

Huang Chien-Hsun CH Sun Renran R Hu Yi Y Zeng Liping L Zhang Ning N Cai Liming L Zhang Qiang Q Koch Marcus A MA Al-Shehbaz Ihsan I Edger Patrick P PP Pires J Chris JC Tan Dun-Yan DY Zhong Yang Y Ma Hong H

Molecular biology and evolution 20151029 2

Brassicaceae is one of the most diverse and economically valuable angiosperm families with widely cultivated vegetable crops and scientifically important model plants, such as Arabidopsis thaliana. The evolutionary history, ecological, morphological, and genetic diversity, and abundant resources and knowledge of Brassicaceae make it an excellent model family for evolutionary studies. Recent phylogenetic analyses of the family revealed three major lineages (I, II, and III), but relationships amon ...[more]

PMID: 26516094

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Project description:BackgroundThe marine environment is comprised of numerous divergent organisms living under similar selective pressures, often resulting in the evolution of convergent structures such as the fusiform body shape of pelagic squids, fishes, and some marine mammals. However, little is known about the frequency of, and circumstances leading to, convergent evolution in the open ocean. Here, we present a comparative study of the molluscan class Cephalopoda, a marine group known to occupy habitats from the intertidal to the deep sea. Several lineages bear features that may coincide with a benthic or pelagic existence, making this a valuable group for testing hypotheses of correlated evolution. To test for convergence and correlation, we generate the most taxonomically comprehensive multi-gene phylogeny of cephalopods to date. We then create a character matrix of habitat type and morphological characters, which we use to infer ancestral character states and test for correlation between habitat and morphology.ResultsOur study utilizes a taxonomically well-sampled phylogeny to show convergent evolution in all six morphological characters we analyzed. Three of these characters also correlate with habitat. The presence of an autogenic photophore (those relying upon autonomous enzymatic light reactions) is correlated with a pelagic habitat, while the cornea and accessory nidamental gland correlate with a benthic lifestyle. Here, we present the first statistical tests for correlation between convergent traits and habitat in cephalopods to better understand the evolutionary history of characters that are adaptive in benthic or pelagic environments, respectively.DiscussionOur study supports the hypothesis that habitat has influenced convergent evolution in the marine environment: benthic organisms tend to exhibit similar characteristics that confer protection from invasion by other benthic taxa, while pelagic organisms possess features that facilitate crypsis and communication in an environment lacking physical refuges. Features that have originated multiple times in distantly related lineages are likely adaptive for the organisms inhabiting a particular environment: studying the frequency and evolutionary history of such convergent characters can increase understanding of the underlying forces driving ecological and evolutionary transitions in the marine environment.

Project description:BackgroundThe phylogeny of tribe Brassiceae (Brassicaceae) has not yet been resolved because of its complex evolutionary history. This tribe comprises economically relevant species, including the genus Moricandia DC. This genus is currently distributed in North Africa, Middle East, Central Asia and Southern Europe, where it is associated with arid and semi-arid environments. Although some species of Moricandia have been used in several phylogenetic studies, the phylogeny of this genus is not well established.MethodsHere we present a phylogenetic analysis of the genus Moricandia using a nuclear (the internal transcribed spacers of the ribosomal DNA) and two plastidial regions (parts of the NADH dehydrogenase subunit F gene and the trnT-trnF region). We also included in the analyses members of their sister genus Rytidocarpus and from the close genus Eruca.ResultsThe phylogenetic analyses showed a clear and robust phylogeny of the genus Moricandia. The Bayesian inference tree was concordant with the maximum likelihood and timing trees, with the plastidial and nuclear trees showing only minor discrepancies. The genus Moricandia appears to be formed by two main lineages: the Iberian clade including three species, and the African clade including the four species inhabiting the Southern Mediterranean regions plus M. arvensis.DiscussionWe dated the main evolutionary events of this genus, showing that the origin of the Iberian clade probably occurred after a range expansion during the Messinian period, between 7.25 and 5.33 Ma. In that period, an extensive African-Iberian floral and faunal interchange occurred due to the existence of land bridges between Africa and Europa in what is, at present-days, the Strait of Gibraltar. We have demonstrated that a Spanish population previously ascribed to Rytidocarpus moricandioides is indeed a Moricandia species, and we propose to name it as M. rytidocarpoides sp. nov. In addition, in all the phylogenetic analyses, M. foleyi appeared outside the Moricandia lineage but within the genus Eruca. Therefore, M. foleyi should be excluded from the genus Moricandia and be ascribed, at least provisionally, to the genus Eruca.

Dataset Information

Resolution of Brassicaceae Phylogeny Using Nuclear Genes Uncovers Nested Radiations and Supports Convergent Morphological Evolution.

Publications

Resolution of Brassicaceae Phylogeny Using Nuclear Genes Uncovers Nested Radiations and Supports Convergent Morphological Evolution.

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