Limits...
Phylogenomic analysis resolves the formerly intractable adaptive diversification of the endemic clade of east Asian Cyprinidae (Cypriniformes).

Tao W, Zou M, Wang X, Gan X, Mayden RL, He S - PLoS ONE (2010)

Bottom Line: For instance, ecomorphological convergence may confound morphology-based phylogenetic inferences, and previous molecular phylogenetic studies based on single genes have often yielded contradictory and poorly supported trees.We provide evidence that the bursts of diversification in this fauna are directly linked to major paleoenvironmental events associated with monsoon evolution occurring from late Miocene to Pliocene.The explicit molecular phylogeny provides a valuable framework for future research in genome evolution, adaptation and speciation of cyprinids.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China.

ABSTRACT
Despite their great diversity and biological importance, evolutionary relationships among the endemic clade of East Asian Cyprinidae remain ambiguous. Understanding the phylogenetic history of this group involves many challenges. For instance, ecomorphological convergence may confound morphology-based phylogenetic inferences, and previous molecular phylogenetic studies based on single genes have often yielded contradictory and poorly supported trees. We assembled a comprehensive data matrix of 100 nuclear gene segments (∼ 71132 base pairs) for representative species of the endemic East Asian cyprinid fauna and recovered a robust phylogeny from this genome-wide signal supported by multiple analytical methods, including maximum parsimony, maximum likelihood and Bayesian inference. Relaxed molecular clock analyses indicated species radiations of this clade concentrated at approximately 1.9-7.6 MYA. We provide evidence that the bursts of diversification in this fauna are directly linked to major paleoenvironmental events associated with monsoon evolution occurring from late Miocene to Pliocene. Ancestral state reconstruction reveals convergent morphological characters are hypothesized to be independent products of similar selective pressures in ecosystems. Our study is the first comprehensive phylogenetic study of the enigmatic East-Asian cyprinids. The explicit molecular phylogeny provides a valuable framework for future research in genome evolution, adaptation and speciation of cyprinids.

Show MeSH
Plots of variable length variation of concatenated dataset and bootstrap values attained for nodes in the inferred simultaneous tree (Figure 2) using variable length bootstrap.Node C was not included due to moderate bootstrap values in the combined analyses.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2958143&req=5

pone-0013508-g003: Plots of variable length variation of concatenated dataset and bootstrap values attained for nodes in the inferred simultaneous tree (Figure 2) using variable length bootstrap.Node C was not included due to moderate bootstrap values in the combined analyses.

Mentions: To assess how large of the data set might be needed to resolve a phylogeny, we explored the relationships between the number of nucleotide sites and phylogenetic resolution. The variable length bootstrap curves clearly demonstrated that improvement of bootstrap values was significant for each node, with the resampling of more sites (Figure 3). Nodes B, D, and E achieved at least a 50% bootstrap support increase with the resampling sites up to 70000 bp. Improvement was significant for all nodes when the length of resampling sites ranged from 2000 bp to 30000 bp. All nodes except node C received 100% bootstrap support when resampling sites was 500000 bp (not shown). Little improvements of bootstrap values were, however, found for node C, even with the resampling sites exceeding 500000 bp (not shown).


Phylogenomic analysis resolves the formerly intractable adaptive diversification of the endemic clade of east Asian Cyprinidae (Cypriniformes).

Tao W, Zou M, Wang X, Gan X, Mayden RL, He S - PLoS ONE (2010)

Plots of variable length variation of concatenated dataset and bootstrap values attained for nodes in the inferred simultaneous tree (Figure 2) using variable length bootstrap.Node C was not included due to moderate bootstrap values in the combined analyses.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2958143&req=5

pone-0013508-g003: Plots of variable length variation of concatenated dataset and bootstrap values attained for nodes in the inferred simultaneous tree (Figure 2) using variable length bootstrap.Node C was not included due to moderate bootstrap values in the combined analyses.
Mentions: To assess how large of the data set might be needed to resolve a phylogeny, we explored the relationships between the number of nucleotide sites and phylogenetic resolution. The variable length bootstrap curves clearly demonstrated that improvement of bootstrap values was significant for each node, with the resampling of more sites (Figure 3). Nodes B, D, and E achieved at least a 50% bootstrap support increase with the resampling sites up to 70000 bp. Improvement was significant for all nodes when the length of resampling sites ranged from 2000 bp to 30000 bp. All nodes except node C received 100% bootstrap support when resampling sites was 500000 bp (not shown). Little improvements of bootstrap values were, however, found for node C, even with the resampling sites exceeding 500000 bp (not shown).

Bottom Line: For instance, ecomorphological convergence may confound morphology-based phylogenetic inferences, and previous molecular phylogenetic studies based on single genes have often yielded contradictory and poorly supported trees.We provide evidence that the bursts of diversification in this fauna are directly linked to major paleoenvironmental events associated with monsoon evolution occurring from late Miocene to Pliocene.The explicit molecular phylogeny provides a valuable framework for future research in genome evolution, adaptation and speciation of cyprinids.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China.

ABSTRACT
Despite their great diversity and biological importance, evolutionary relationships among the endemic clade of East Asian Cyprinidae remain ambiguous. Understanding the phylogenetic history of this group involves many challenges. For instance, ecomorphological convergence may confound morphology-based phylogenetic inferences, and previous molecular phylogenetic studies based on single genes have often yielded contradictory and poorly supported trees. We assembled a comprehensive data matrix of 100 nuclear gene segments (∼ 71132 base pairs) for representative species of the endemic East Asian cyprinid fauna and recovered a robust phylogeny from this genome-wide signal supported by multiple analytical methods, including maximum parsimony, maximum likelihood and Bayesian inference. Relaxed molecular clock analyses indicated species radiations of this clade concentrated at approximately 1.9-7.6 MYA. We provide evidence that the bursts of diversification in this fauna are directly linked to major paleoenvironmental events associated with monsoon evolution occurring from late Miocene to Pliocene. Ancestral state reconstruction reveals convergent morphological characters are hypothesized to be independent products of similar selective pressures in ecosystems. Our study is the first comprehensive phylogenetic study of the enigmatic East-Asian cyprinids. The explicit molecular phylogeny provides a valuable framework for future research in genome evolution, adaptation and speciation of cyprinids.

Show MeSH