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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.

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Chronogram of Cetacea inferred by partitioned Bayesian analyses, enforcing a lognormal relaxed molecular clock, of 12 mitochondrial protein-coding genes. Numbers above the clades represent Bayesian posterior probabilities. Clade letters refer to Table 1. Red boxes indicate nodes for which a prior calibration constraint distribution was used and orange boxes indicate divergence dates estimated without prior calibration constraints for that node. The bounds of the boxes delimit the 95% highest posterior density (HPD) for the clade age. The asterisk indicates that the monophyly of this group was constrained in the phylogenetic analysis.
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Figure 3: Chronogram of Cetacea inferred by partitioned Bayesian analyses, enforcing a lognormal relaxed molecular clock, of 12 mitochondrial protein-coding genes. Numbers above the clades represent Bayesian posterior probabilities. Clade letters refer to Table 1. Red boxes indicate nodes for which a prior calibration constraint distribution was used and orange boxes indicate divergence dates estimated without prior calibration constraints for that node. The bounds of the boxes delimit the 95% highest posterior density (HPD) for the clade age. The asterisk indicates that the monophyly of this group was constrained in the phylogenetic analysis.

Mentions: The two partitioned Bayesian analyses achieved stationarity by 5 million generations, and posterior distributions of each parameter were calculated for the remaining 15 million post burn-in trees. The phylogeny, and 95% credible intervals of divergence times, are provided in Fig. 3. Overall support for the phylogeny is very high with 13 clades strongly (i.e., statistically) supported. The "deeper" relationships of the phylogeny are all well-supported including the monophyly of Cetacea and Odontoceti (toothed whales). The basal divergence within odontocetes is between the physeteroids (sperm whales) and a strongly supported clade (Clade G; PP = 1.0) of remaining odontocete families. The basal relationships within this clade are weakly supported and essentially form a trichotomy including Platanistidae (Indian River dolphins), Ziphiidae (bottlenose whales), and a strongly supported clade (Clade I; PP = 1.0) including other dolphins and porpoises. The relationship between Lipotidae (Yangtze River dolphin) to the two other river dolphin families Pontoporidae (La Plata River dolphins) and Iniidae (Amazon River dolphins) is only weakly supported (PP = 0.61), but support for the sister relationship of the latter two families is significant (PP = 1.0). The remaining marine dolphins and porpoises form a strongly supported clade (Clade L; PP = 1.0), with a basal divergence between a strongly supported Delphinidae (PP = 1.0) and a clade including Phocoenidae (porpoises) and Monodontidae (narwhals and belugas). The interrelationships of G. griseus, L. albirostris, and other delphinid genera are not well supported. Within the strongly supported clade of remaining delphinids (Clade P; PP = 1.0), there is statistically significant support for the paraphyly of Tursiops and Stenella. Stenella attenuata, Sousa chinensis, and T. truncatus form sequentially more exclusive, strongly supported clades (Clades P, Q, and R; PP = 1.0) with the other delphinids. T. aduncus (Indo-Pacific bottlenose dolphin) forms a strongly supported clade (PP = 1.0) with D. capensis and St. coeruleoalba. (but the sister relationship of D. capensis and T. aduncus is highly but not statistically supported [PP = 0.94]).


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)

Chronogram of Cetacea inferred by partitioned Bayesian analyses, enforcing a lognormal relaxed molecular clock, of 12 mitochondrial protein-coding genes. Numbers above the clades represent Bayesian posterior probabilities. Clade letters refer to Table 1. Red boxes indicate nodes for which a prior calibration constraint distribution was used and orange boxes indicate divergence dates estimated without prior calibration constraints for that node. The bounds of the boxes delimit the 95% highest posterior density (HPD) for the clade age. The asterisk indicates that the monophyly of this group was constrained in the phylogenetic analysis.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Chronogram of Cetacea inferred by partitioned Bayesian analyses, enforcing a lognormal relaxed molecular clock, of 12 mitochondrial protein-coding genes. Numbers above the clades represent Bayesian posterior probabilities. Clade letters refer to Table 1. Red boxes indicate nodes for which a prior calibration constraint distribution was used and orange boxes indicate divergence dates estimated without prior calibration constraints for that node. The bounds of the boxes delimit the 95% highest posterior density (HPD) for the clade age. The asterisk indicates that the monophyly of this group was constrained in the phylogenetic analysis.
Mentions: The two partitioned Bayesian analyses achieved stationarity by 5 million generations, and posterior distributions of each parameter were calculated for the remaining 15 million post burn-in trees. The phylogeny, and 95% credible intervals of divergence times, are provided in Fig. 3. Overall support for the phylogeny is very high with 13 clades strongly (i.e., statistically) supported. The "deeper" relationships of the phylogeny are all well-supported including the monophyly of Cetacea and Odontoceti (toothed whales). The basal divergence within odontocetes is between the physeteroids (sperm whales) and a strongly supported clade (Clade G; PP = 1.0) of remaining odontocete families. The basal relationships within this clade are weakly supported and essentially form a trichotomy including Platanistidae (Indian River dolphins), Ziphiidae (bottlenose whales), and a strongly supported clade (Clade I; PP = 1.0) including other dolphins and porpoises. The relationship between Lipotidae (Yangtze River dolphin) to the two other river dolphin families Pontoporidae (La Plata River dolphins) and Iniidae (Amazon River dolphins) is only weakly supported (PP = 0.61), but support for the sister relationship of the latter two families is significant (PP = 1.0). The remaining marine dolphins and porpoises form a strongly supported clade (Clade L; PP = 1.0), with a basal divergence between a strongly supported Delphinidae (PP = 1.0) and a clade including Phocoenidae (porpoises) and Monodontidae (narwhals and belugas). The interrelationships of G. griseus, L. albirostris, and other delphinid genera are not well supported. Within the strongly supported clade of remaining delphinids (Clade P; PP = 1.0), there is statistically significant support for the paraphyly of Tursiops and Stenella. Stenella attenuata, Sousa chinensis, and T. truncatus form sequentially more exclusive, strongly supported clades (Clades P, Q, and R; PP = 1.0) with the other delphinids. T. aduncus (Indo-Pacific bottlenose dolphin) forms a strongly supported clade (PP = 1.0) with D. capensis and St. coeruleoalba. (but the sister relationship of D. capensis and T. aduncus is highly but not statistically supported [PP = 0.94]).

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