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Seven new dolphin mitochondrial genomes and a time-calibrated phylogeny of whales.

Xiong Y, Brandley MC, Xu S, Zhou K, Yang G - BMC Evol. Biol. (2009)

Bottom Line: The ambiguous and conflicting results of multiple phylogenetic studies may be the result of the use of too little data, phylogenetic methods that do not adequately capture the complex nature of DNA evolution, or both.Additionally, there is statistically significant support for the paraphyly of Tursiops (bottlenose dolphins) and Stenella (spotted dolphins).Our results indicate that a rapid radiation of lineages explains the lack of support the placement of Platanistidae and Lipotidae.

View Article: PubMed Central - HTML - PubMed

Affiliation: Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, PR China. xiongye2006@163.com

ABSTRACT

Background: The phylogeny of Cetacea (whales) is not fully resolved with substantial support. The ambiguous and conflicting results of multiple phylogenetic studies may be the result of the use of too little data, phylogenetic methods that do not adequately capture the complex nature of DNA evolution, or both. In addition, there is also evidence that the generic taxonomy of Delphinidae (dolphins) underestimates its diversity. To remedy these problems, we sequenced the complete mitochondrial genomes of seven dolphins and analyzed these data with partitioned Bayesian analyses. Moreover, we incorporate a newly-developed "relaxed" molecular clock to model heterogenous rates of evolution among cetacean lineages.

Results: The "deep" phylogenetic relationships are well supported including the monophyly of Cetacea and Odontoceti. However, there is ambiguity in the phylogenetic affinities of two of the river dolphin clades Platanistidae (Indian River dolphins) and Lipotidae (Yangtze River dolphins). The phylogenetic analyses support a sister relationship between Delphinidae and Monodontidae + Phocoenidae. Additionally, there is statistically significant support for the paraphyly of Tursiops (bottlenose dolphins) and Stenella (spotted dolphins).

Conclusion: Our phylogenetic analysis of complete mitochondrial genomes using recently developed models of rate autocorrelation resolved the phylogenetic relationships of the major Cetacean lineages with a high degree of confidence. Our results indicate that a rapid radiation of lineages explains the lack of support the placement of Platanistidae and Lipotidae. Moreover, our estimation of molecular divergence dates indicates that these radiations occurred in the Middle to Late Oligocene and Middle Miocene, respectively. Furthermore, by collecting and analyzing seven new mitochondrial genomes, we provide strong evidence that the delphinid genera Tursiops and Stenella are not monophyletic, and the current taxonomy masks potentially interesting patterns of morphological, physiological, behavioral, and ecological evolution.

Show MeSH
Recent hypotheses of the interrelationships of the major cetacean lineages. Clade support values, when available in the original study, are provided. Decimal numbers represent posterior probabilities and numbers between 50 and 100 represent nonparametric bootstrap proportions.
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Figure 1: Recent hypotheses of the interrelationships of the major cetacean lineages. Clade support values, when available in the original study, are provided. Decimal numbers represent posterior probabilities and numbers between 50 and 100 represent nonparametric bootstrap proportions.

Mentions: However, many of the phylogenetic relationships inferred by the aforementioned studies strongly conflict. Perhaps the most obvious incongruencies are the interrelationships of the major odontocete (toothed whales) clades (Fig. 1). All published phylogenies disagree on the phylogenetic placement of one or more families, and many of these incongruencies are strongly supported with high bootstrap proportions or posterior probabilities (Fig. 1). Thus, we have little confidence in the "deeper" relationships of odontocetes and this situation limits the power of any comparative analyses that incorporate phylogenetic information.


Seven new dolphin mitochondrial genomes and a time-calibrated phylogeny of whales.

Xiong Y, Brandley MC, Xu S, Zhou K, Yang G - BMC Evol. Biol. (2009)

Recent hypotheses of the interrelationships of the major cetacean lineages. Clade support values, when available in the original study, are provided. Decimal numbers represent posterior probabilities and numbers between 50 and 100 represent nonparametric bootstrap proportions.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2656474&req=5

Figure 1: Recent hypotheses of the interrelationships of the major cetacean lineages. Clade support values, when available in the original study, are provided. Decimal numbers represent posterior probabilities and numbers between 50 and 100 represent nonparametric bootstrap proportions.
Mentions: However, many of the phylogenetic relationships inferred by the aforementioned studies strongly conflict. Perhaps the most obvious incongruencies are the interrelationships of the major odontocete (toothed whales) clades (Fig. 1). All published phylogenies disagree on the phylogenetic placement of one or more families, and many of these incongruencies are strongly supported with high bootstrap proportions or posterior probabilities (Fig. 1). Thus, we have little confidence in the "deeper" relationships of odontocetes and this situation limits the power of any comparative analyses that incorporate phylogenetic information.

Bottom Line: The ambiguous and conflicting results of multiple phylogenetic studies may be the result of the use of too little data, phylogenetic methods that do not adequately capture the complex nature of DNA evolution, or both.Additionally, there is statistically significant support for the paraphyly of Tursiops (bottlenose dolphins) and Stenella (spotted dolphins).Our results indicate that a rapid radiation of lineages explains the lack of support the placement of Platanistidae and Lipotidae.

View Article: PubMed Central - HTML - PubMed

Affiliation: Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, PR China. xiongye2006@163.com

ABSTRACT

Background: The phylogeny of Cetacea (whales) is not fully resolved with substantial support. The ambiguous and conflicting results of multiple phylogenetic studies may be the result of the use of too little data, phylogenetic methods that do not adequately capture the complex nature of DNA evolution, or both. In addition, there is also evidence that the generic taxonomy of Delphinidae (dolphins) underestimates its diversity. To remedy these problems, we sequenced the complete mitochondrial genomes of seven dolphins and analyzed these data with partitioned Bayesian analyses. Moreover, we incorporate a newly-developed "relaxed" molecular clock to model heterogenous rates of evolution among cetacean lineages.

Results: The "deep" phylogenetic relationships are well supported including the monophyly of Cetacea and Odontoceti. However, there is ambiguity in the phylogenetic affinities of two of the river dolphin clades Platanistidae (Indian River dolphins) and Lipotidae (Yangtze River dolphins). The phylogenetic analyses support a sister relationship between Delphinidae and Monodontidae + Phocoenidae. Additionally, there is statistically significant support for the paraphyly of Tursiops (bottlenose dolphins) and Stenella (spotted dolphins).

Conclusion: Our phylogenetic analysis of complete mitochondrial genomes using recently developed models of rate autocorrelation resolved the phylogenetic relationships of the major Cetacean lineages with a high degree of confidence. Our results indicate that a rapid radiation of lineages explains the lack of support the placement of Platanistidae and Lipotidae. Moreover, our estimation of molecular divergence dates indicates that these radiations occurred in the Middle to Late Oligocene and Middle Miocene, respectively. Furthermore, by collecting and analyzing seven new mitochondrial genomes, we provide strong evidence that the delphinid genera Tursiops and Stenella are not monophyletic, and the current taxonomy masks potentially interesting patterns of morphological, physiological, behavioral, and ecological evolution.

Show MeSH