The platypus is in its place: Nuclear genes and indels confirm the sister group relation of monotremes and therians

Morphological data supports monotremes as the sister group of Theria (extant marsupials + eutherians), but phylogenetic analyses of 12 mitochondrial protein-coding genes have strongly supported the grouping of monotremes With Marsupials: the Marsupionta hypothesis. Various nuclear gees tend to support Theria, but a comprehensive study of long concatenated sequnces and broad taxon Sampling is lacking. We therefore determined sequences from six nuclear genes and obtained additional sequences front the databases to create two large and independent nuclear data sets. One (data set 1) emphasized taxon sampling and comprised five genes, with a concatenated length of 2.793 bp, from 21 species (two monotremes. six 9 marsupials, nine placentals, and four outgroups). The other (data set II) emphasized gene sampling and comprised eight genes and three proteins, with a concatenated length of 10,773 bp or 3,669 amino acids. from five taxa (a monotreme, a marsupial, a rodent, human, and chicken). Both data sets were analyzed by parsimony, evolution, maximum likelihood, and Bayesian methods Using various models and data partitions. Data set I gave bootstrap Support Values for Theria between 55% and 100%, while Support for Marsupionta was at most 12.3%. Taking base compositional bias into account generally increased file Support for Theria. Data set II exclusively Supported Theria, with the highest possible Values and significantly rejected Marsupionta. Independent phylogenetic evidence in support of Theria was obtained front two single amino acid deletions and one insertion. While no supporting insertions and deletions were found for Marsulpionta. On the basis Of Our data sets, the time of divergence between Monotremata and Theria was estimated at 231-217 MYA and between Marsupialia and Eutharia at 193-186 MYA. 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.