The root of the mammalian tree inferred from whole mitochondrial genomes.

@article{Phillips2003TheRO,
  title={The root of the mammalian tree inferred from whole mitochondrial genomes.},
  author={Matthew J. Phillips and David Penny},
  journal={Molecular phylogenetics and evolution},
  year={2003},
  volume={28 2},
  pages={
          171-85
        }
}

Figures and Tables from this paper

Site specific rates of mitochondrial genomes and the phylogeny of eutheria

TLDR
The results indicate that selection of an appropriate model that accommodates rate heterogeneity across data partitions and proper treatment of RNA genes can result in a mitochondrial genome-based phylogeny of eutherian mammals that is reasonably congruent with recent phylogenies derived from nuclear genes.

Evolution of modern birds revealed by mitogenomics: timing the radiation and origin of major orders.

TLDR
These analyses indicate that by improving the taxonomic sampling, complete mt genomes can solve the evolutionary relationships among major bird groups and support the choice of COX 1 among mt genes as target for developing DNA barcoding approaches in birds.

Mitochondrial data are not suitable for resolving placental mammal phylogeny

TLDR
The suitability of mitochondrial data as a phylogenetic marker in mammal phylogenetics is assessed and its limitations are highlighted, not only for resolving deep divergences and but also for shallow Divergences in the mammal phylogeny.

Comparative sequencing provides insights about the structure and conservation of marsupial and monotreme genomes.

TLDR
Genetic sequence from noneutherian mammals can contribute uniquely to unraveling the functional and evolutionary histories of the mammalian genome, and analyses of the major mammalian lineages reveal distinct patterns with respect to the common presence of evolutionarily conserved vertebrates.

Bird evolution: testing the Metaves clade with six new mitochondrial genomes

TLDR
The phylogenetic hypothesis based on 41 avian mitochondrial genomes rejects monophyly of seven Metaves species and it is concluded that the members of Metaves do not share a common evolutionary history within the Neoaves.

Confirming the Phylogeny of Mammals by Use of Large Comparative Sequence Data Sets

TLDR
The results provide support for rooting the placental mammal tree between Atlantogenata and Afrotheria and Boreoeutheria, illustrate the difficulty in resolving some branches even with large amounts of data, and demonstrate the valuable role that very large comparative sequence data sets can play in refining the understanding of the evolutionary relationships of vertebrates.

The platypus is in its place: nuclear genes and indels confirm the sister group relation of monotremes and Therians.

TLDR
The morphological evidence for a basal position of Monotremata, well separated from Theria, is thus fully supported by the available molecular data from nuclear genes.
...

References

SHOWING 1-10 OF 101 REFERENCES

Phylogenetic relationships within the class mammalia: A study using mitochondrial 12S RNA sequences

TLDR
The results suggest that the monotremes diverged from the living therians only shortly before eutherians and marsupials separated from each other, although there is some evidence for a slowdown in rate of base change in the monotsreme lineage.

Complete mitochondrial genome suggests diapsid affinities of turtles.

  • R. ZardoyaA. Meyer
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1998
TLDR
The results challenge the classic view of turtles as the only survivors of primary anapsid reptiles and imply that turtles might have secondarily lost their skull fenestration.

Mitochondrial versus nuclear gene sequences in deep-level mammalian phylogeny reconstruction.

TLDR
The nuclear exons consistently performed better than mitochondrial protein and rRNA-tRNA coding genes on a per-residue basis in recovering benchmark clades and nuclear genes having appropriate rates of substitution should receive strong consideration in efforts to reconstruct deep-level phylogenetic relationships.

A phylogenetic foundation for comparative mammalian genomics.

TLDR
The largest alignments of amino acid sequence data to date are constructed and a good case is made for the tree shrew as a closer relative of primates than rodents, while also showing a slower rate of evolution in key cell cycle genes.

Phylogenetic Analysis of 18S rRNA and the Mitochondrial Genomes of the Wombat, Vombatus ursinus, and the Spiny Anteater, Tachyglossus aculeatus: Increased Support for the Marsupionta Hypothesis

TLDR
Analysis of new data from the complete mitochondrial genomes of a second monotreme, the spiny anteater, and another marsupial, the wombat yielded clear support for the Marsupionta hypothesis, consistent with a basal split between eutherians and marsupials/monotremes among extant mammals.

Four new mitochondrial genomes and the increased stability of evolutionary trees of mammals from improved taxon sampling.

TLDR
The evolutionary tree for mammals is expected to be resolved quickly, and the stability of trees from independent data sets, as detected from a triplet Markov analysis.

Monotremata, Marsupialia and Placentalia : inferring Phylogenetic relationships from molecular and morphological data : a thesis presented in partial fulfillment of the requirements for the degree of Doctor of Philosophy in evolutionary biology at Massey University

TLDR
A novel incompatibility analysis for examining signal and conflict among characters indicates that homoplasy affecting monotreme placement evolved non-independently among characters, essentially at the level of the anatomical regions.

Amphioxus Mitochondrial DNA , Chordate Phylogeny , and the Limits of Inference Based on Comparisons of Sequences

Ð Analyses of both the nucleotide and am ino acid sequences derived from all 13 m itochondr ial protein-encoding genes (12,234 bp) of 19 metazoan species, including that of the lancelet Branchiostom

Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes.

TLDR
Support is found for a sister relationship between turtles and a bird/crocodilian clade, and for rejecting both the Haemothermia hypothesis and the placement of turtles as basal within the phylogenetic tree for amniote animals.
...