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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.

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Molecular dating of the East Asian groups of cyprinids.The fossil-based constraints are indicated with black dots. Branch lengths are proportional to divergence times (in million of years). The East Asian cyprinids originated mostly in Piocene but some occurred more recently. “S” indicates possible weakening of the Indian and East Asian summer monsoons and continued strengthening of the East Asian winter monsoon, an important time of climatic change and habitat modification that existed during the evolution of the lacustrine species.
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pone-0013508-g004: Molecular dating of the East Asian groups of cyprinids.The fossil-based constraints are indicated with black dots. Branch lengths are proportional to divergence times (in million of years). The East Asian cyprinids originated mostly in Piocene but some occurred more recently. “S” indicates possible weakening of the Indian and East Asian summer monsoons and continued strengthening of the East Asian winter monsoon, an important time of climatic change and habitat modification that existed during the evolution of the lacustrine species.

Mentions: A significant difference (P<0.001) between the log likelihood values of clock-like versus non-clock-like behavior justified the use of the relaxed molecular clock model for the clade of East Asian Cyprinidae. Our results indicated that the endemic East Asian cyprinids diverged from other cyprinids ∼9 MYA (Figure 4). Of the four famous carp species in China, My. piceus and Ct. idella diverged from their most recent common ancestor ∼3.95 MYA, and the divergence between H. molitrix and H. nobilis occurred ∼ 3.41 MYA. The crown radiation of lacustrine species began ∼2.27 MYA and probably experienced effects from possible weakening of Indian and East Asian summer monsoon and continued strengthening of East Asian winter monsoon [26].


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)

Molecular dating of the East Asian groups of cyprinids.The fossil-based constraints are indicated with black dots. Branch lengths are proportional to divergence times (in million of years). The East Asian cyprinids originated mostly in Piocene but some occurred more recently. “S” indicates possible weakening of the Indian and East Asian summer monsoons and continued strengthening of the East Asian winter monsoon, an important time of climatic change and habitat modification that existed during the evolution of the lacustrine species.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0013508-g004: Molecular dating of the East Asian groups of cyprinids.The fossil-based constraints are indicated with black dots. Branch lengths are proportional to divergence times (in million of years). The East Asian cyprinids originated mostly in Piocene but some occurred more recently. “S” indicates possible weakening of the Indian and East Asian summer monsoons and continued strengthening of the East Asian winter monsoon, an important time of climatic change and habitat modification that existed during the evolution of the lacustrine species.
Mentions: A significant difference (P<0.001) between the log likelihood values of clock-like versus non-clock-like behavior justified the use of the relaxed molecular clock model for the clade of East Asian Cyprinidae. Our results indicated that the endemic East Asian cyprinids diverged from other cyprinids ∼9 MYA (Figure 4). Of the four famous carp species in China, My. piceus and Ct. idella diverged from their most recent common ancestor ∼3.95 MYA, and the divergence between H. molitrix and H. nobilis occurred ∼ 3.41 MYA. The crown radiation of lacustrine species began ∼2.27 MYA and probably experienced effects from possible weakening of Indian and East Asian summer monsoon and continued strengthening of East Asian winter monsoon [26].

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