Molecular phylogenetics and the origins of placental mammals

  title={Molecular phylogenetics and the origins of placental mammals},
  author={William J. Murphy and Eduardo Eizirik and Warren E. Johnson and Ya Ping Zhang and Oliver A. Ryder and Stephen J. O’Brien},
The precise hierarchy of ancient divergence events that led to the present assemblage of modern placental mammals has been an area of controversy among morphologists, palaeontologists and molecular evolutionists. Here we address the potential weaknesses of limited character and taxon sampling in a comprehensive molecular phylogenetic analysis of 64 species sampled across all extant orders of placental mammals. We examined sequence variation in 18 homologous gene segments (including nearly 10… 

Rodent phylogeny and a timescale for the evolution of Glires: evidence from an extensive taxon sampling using three nuclear genes.

Molecular datings based on three nuclear genes suggest that the rodent radiation took place at the transition between Paleocene and Eocene, and the association of Rodentia with Lagomorpha (the Glires clade), and a Glires + Euarchonta (Primates, Dermoptera, and Scandentia) clade is supported.

Mammalian mitogenomic relationships and the root of the eutherian tree

A mitogenomic study based on the set of protein-coding genes from complete mt genomes of 60 mammalian species finds that the previously unrepresented order Dermoptera (flying lemurs) fell within Primates as the sister group of Anthropoidea, making Primates paraphyletic.

Mitogenomic analyses of eutherian relationships

The study corroborated recent findings that have identified a sister-group relationship between Anthropoidea and Dermoptera (flying lemurs), thereby making their own order, Primates, a paraphyletic assembly.

A Molecular Phylogeny of Living Primates

The resolution of the primate phylogeny provides an essential evolutionary framework with far-reaching applications including: human selection and adaptation, global emergence of zoonotic diseases, mammalian comparative genomics, primate taxonomy, and conservation of endangered species.

A phylogenetic foundation for comparative mammalian genomics.

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.

Molecular phylogeny of living xenarthrans and the impact of character and taxon sampling on the placental tree rooting.

Maximum likelihood and Bayesian phylogenetic analyses of a 47 placental taxa data set resolved the phylogeny of Xenarthra with some evidence for two radiation events in armadillos and provided a strongly supported picture of placental interordinal relationships.

In quest for a phylogeny of Mesozoic mammals

A phylogeny of all major groups of Mesozoic mammals based on phylogenetic analyses of 46 taxa and 275 osteological and dental characters, using parsimony methods is proposed, suggesting that the “obtuse−angle symmetrodonts” are paraphyletic, and that they lack reliable and unambiguous synapomorphies.

Relationships of Cetacea (Artiodactyla) Among Mammals: Increased Taxon Sampling Alters Interpretations of Key Fossils and Character Evolution

The phylogenetic position of †Indohyus suggests that the cetacean stem lineage included herbivorous and carnivorous aquatic species, and the taxonomy of living and extinct artiodactylans is revised and proposes explicit node and stem-based definitions for the ingroup.

Using genomic data to unravel the root of the placental mammal phylogeny.

The genome sequence assemblies of human, armadillo, elephant, and opossum are analyzed to identify informative coding indels that would serve as rare genomic changes to infer early events in placental mammal phylogeny and suggest Afrotheria and Xenarthra diverged from other placental mammals approximately 103 (95-114) million years ago.

Early History of Mammals Is Elucidated with the ENCODE Multiple Species Sequencing Data

The sequence data of the ENCODE consortium, which include 1% of mammalian genomes in 18 species belonging to all main mammalian lineages, support the Afrotheria hypothesis; however, none can reject both of the remaining topological alternatives.



Biomolecular Systematics of Eutherian Mammals: Phylogenetic Patterns and Classification

The higher-level systematics of the mammalian infraclass Eutheria is investigated with protein sequences of seven polypeptide types combined in an extended tandem alignment. Evolutionary trees

Parallel adaptive radiations in two major clades of placental mammals

Two independent molecular data sets, having aligned lengths of DNA of 5,708 and 2,947 base pairs, respectively, are analysed for all orders of placental mammals to resolve placental orders into four groups: Xenarthra, Afrotheria, Laurasiatheria, and Euarchonta plus Glires.

Molecular evolution of the nuclear von Willebrand factor gene in mammals and the phylogeny of rodents.

The aim of this study was to test if inclusion of an increased taxonomic diversity in molecular analyses would shed light on three uncertainties concerning rodent phylogeny, and to obtain a robust answer to the question of Rodentia monophyly.

Molecular evidence for multiple origins of Insectivora and for a new order of endemic African insectivore mammals.

The traditional views regarding the mammalian order Insectivora are that the group descended from a single common ancestor and that it is comprised of the following families: Soricidae (shrews),

The phylogenetic position of the Talpidae within eutheria based on analysis of complete mitochondrial sequences.

The analyses of complete mtDNAs challenge the maintenance of the order Lipotyphla as a taxonomic unit and support the elevation of the Soricomorpha to the level of an order, as previously proposed in some morphological studies.

Phylogenetic position of the order Lagomorpha (rabbits, hares and allies)

It is shown that Lagomorpha is significantly more closely related to Primates and Scandentia (tree shrews) than it is to rodents, which raises the possibility that the ancestral eutherian morphotype may have possessed many rodent-like morphological characters.

Highly congruent molecular support for a diverse superordinal clade of endemic African mammals.

Congruent and convincing evidence is presented from four disparate nuclear protein coding genes and from a tandem alignment of the 12S-16S mitochondrial region for a superordinal clade of endemic African mammals that includes elephant shrews, aardvarks, golden mole, elephants, sirenians, and hyraxes.

Continental breakup and the ordinal diversification of birds and mammals

THE classical hypothesis for the diversification of birds and mammals proposes that most of the orders diverged rapidly in adaptive radiations after the Cretaceous/Tertiary (K/T) extinction event 65

A molecular timescale for vertebrate evolution

The clock-like accumulation of sequence differences in some genes provides an alternative method by which the mean divergence time can be estimated, and the molecular times agree with most early and late fossil-based times, but indicate major gaps in the Mesozoic fossil record.

The pattern of mammalian evolution and the relative rate of molecular evolution.

The assumption of a star phylogeny that underlies Kimura's test for molecular evolutionary rate variation is shown to be invalid for eutherian mammals and excess variance in nucleotide or amino acid differences between mammalian orders is explained better by variation in divergence time than by variationIn evolutionary rate.