Influence of alignment on the mtDNA phylogeny of Cetacea: questionable support for a Mysticeti/Physeteroidea clade.

  title={Influence of alignment on the mtDNA phylogeny of Cetacea: questionable support for a Mysticeti/Physeteroidea clade.},
  author={Salvatore Cerchio and Paul Tucker},
  journal={Systematic biology},
  volume={47 2},
Cetacea has traditionally been divided into Odontoceti, the toothed whales, and Mysticeti, the baleen whales. These groups have been considered monophy? letic, although their origins and age have been historically debated. Recently, Mil? inkovitch et al. (1993, 1994) reported a revised phylogeny for Cetacea, based upon phylogenetic analysis of mitochon? drial DNA (mtDNA), that challenges the classical assumption of odontocete mono? phyly. Their phylogenetic hypotheses were based initially on… 

Figures and Tables from this paper

The Mitochondrial Genome of the Sperm Whale and a New Molecular Reference for Estimating Eutherian Divergence Dates

The complete mitochondrial genome of an odontocete, the sperm whale, is sequenced and included in phylogenetic analyses together with the previously sequenced complete mtDNAs of two mysticetes and a number of other mammals, making both Artiodactyla and Suiformes (pigs, peccaries, and hippopotamuses) paraphyletic.

Morphological Evidence for the Phylogeny of Cetacea

Many of the clades within Odontoceti in the most parsimonious trees of this study are at odds with recent phylogenetic analyses, indicating that additional analyses, which include molecular and anatomical data as well as extant and extinct taxa, are needed.

Cytochrome b and Bayesian inference of whale phylogeny.

Molecular Phylogenetics of the Chiropteran Family Vespertilionidae

Overall, this study offers a robust working hypothesis for vespertilionid relationships and provides a good starting point for new investigations into the evolutionary history of Vespertilionidae.

A complete phylogeny of the whales, dolphins and even‐toed hoofed mammals (Cetartiodactyla)

The present species‐level tree of the Cetartiodactyla provides the first opportunity to examine comparative hypotheses across entirely aquatic and terrestrial species within a single mammalian order.

Phylogenetic signal and the utility of 12S and 16S mtDNA in frog phylogeny

Although 12S and 16S rRNA genes seem to carry some phylogenetic signal of deep (Mesozoic) splitting events the signal was not strong enough to resolve consistently the inter-relationships of major clades within the Anura under varied methods and parameter settings.

Diversity Measures in Environmental Sequences Are Highly Dependent on Alignment Quality—Data from ITS and New LSU Primers Targeting Basidiomycetes

The results suggest that ITS should not be used when calculating phylogenetic trees from genetically distant sequences obtained from environmental DNA extractions and that it is inadvisable to define OTUs on the basis of very heterogeneous alignments.

Molecular Systematics and Evolution: Theory and Practice

The use of physiological data to corroborate cospeciation events in symbiosis and reexamining microbial evolution through the lens of horizontal transfer are examined.



Phylogeny of all major groups of cetaceans based on DNA sequences from three mitochondrial genes.

A molecular phylogeny based on 1,352 base pairs of two mitochondrial ribosomal gene segments and the mitochondrial cytochrome b gene for all major groups of cetaceans contradicts this long-accepted taxonomic subdivision and suggests a more recent origin of baleen whales than has been previously assumed.

Phylogeny of whales: dependence of the inference on species sampling.

It is now highly likely that artiodactyles are the closest relatives of whales, and the PROTML program is used in the package MOLPHY, for the maximum likelihood inference of protein phylogeny.

Cytochrome b nucleotide sequences and the identification of five primary lineages of extant cetaceans.

The level of divergence among the five cetacean lineages, and that seen between cetraceans and artiodactyls, suggests that cetACEans andArtiodactylls had a common ancestor approximately 60 Mya.

Novel phylogeny of whales revisited but not revised.

The major finding was the suggestion that the suborder Odontoceti (toothed whales) is paraphyletic and, more specifically, that the sperm whales are more closely related to baleen whales (suborder Mysticeti) than to any other group of toothed whales.


The results of this analysis unambiguously support a monophyletic Odontoceti including the sperm whales, and the fossil evidence refutes a sperm whale/baleen whale clade.

Molecular phylogeny of cetaceans prompts revision of morphological transformations.

Relationship of baleen whales established by cytochrome b gene sequence comparison

A more comprehensive phylogenetic analysis demonstrates the monophyly of mysticetes and identifies no particular affinity between the sperm whales and rorquals.


  • K. Bremer
  • Biology
    Evolution; international journal of organic evolution
  • 1988
Cladistic analysis of amino acid sequence data, including evaluation of all equally or almost equally parsimonious cladograms, shows that much homoplasy (parallelisms and reversals) is present and that few or no well supported monophyletic groups of families can be demonstrated.

Effects of character weighting and species sampling on phylogeny reconstruction: a case study based on DNA sequence data in cetaceans.

It is the contention that this sensitivity analysis identifies portions of the multidimensional parameter space where phylogenetic signal is most reliably recovered, and simple rules are given to guide the choice of settings.

Alignment-ambiguous nucleotide sites and the exclusion of systematic data.

A replicable methodology in which the comparison of several multiple sequence alignments can be used to eliminate regions of unstable sequence alignment is explored.