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
Living mammals are divided into three groups, Monotremata, Marsupialia and Placentalia. Complete mitochondrial (mt) genome sequencing has provided a large dataset for inferring phylogenetic relationships between these groups and within Placentalia. Marsupials however, are underrepresented, with only mt genomes from an opossum (Didelphis virginiana) and a wallaroo (Macropus robustus) having been published prior to this study. Herein I report complete mt genome sequences for two further marsupials, a northern brown bandicoot (Isoodon macrourus) and a common brushtail possum (Trichosurus vulpecula). Phylogenetic analysis of the protein-coding and RNA-coding mtDNA sequences provides the first statistically robust support for placing bandicoots within the cohort Australidelphia (Australasian marsupials plus Microbiotheria). Examination of vertebrate mtDNA sequences revealed two major problems for phylogeny reconstruction, (a) nucleotide (particularly cytosine versus thymine) compositional bias among taxa and (b) differences in substitution processes between data partitions (concatenation bias). Both biases enhanced the signal for Marsupionta, a grouping of marsupials and monotremes. When the DNA sequence was RY-coded (lumping C and T, and lumping A and G) and the maximum-likelihood analysis partitioned over subsets of similarly evolving sites the traditional morphology-based Theria hypothesis (marsupials plus placentals) was recovered. The relationships of monotremes, marsupials and placentals to Mesozoic (65-250 mybp) fossil taxa that are known from near-complete skeletons were tested with dental, mandibular, vertebral, basicranial and upper and lower appendicular characters. The null hypothesis for the phylogeny of Mesozoic mammals that retained essentially ancestral mammalian niches (morganucodontids, (eutriconodonts, (spalacotheriids, (eupantotheres, (eutherians, metatherians))))) is strongly supported and congruent with respect to the above anatomical region partitions. The inclusion of the fossorial (echidnas) and semi-aquatic (platypuses) monotremes induces extreme and topologically complex incongruence between the anatomical region partitions. 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. After consideration of monotreme shoulder girdle and forelimb traits, in view of trends among the background phylogeny, it is apparent that correlated reversal of upper appendicular characters has occurred along the monotreme stem lineage. This is consistent with phylogenetic inference from both mtDNA and the other anatomical regions, which together suggest a close relationship between monotremes and therians. As with the molecular data, the major problem affecting phylogeny reconstruction from morphological data is non-stationarity in evolutionary processes, such as functional convergence. Monotreme affinities appear to be affected by a less recognizable non-stationarity problem, in that niche-related modification results in attraction towards outgroup taxa. Comparison of morphological and molecular trees suggests that outgroup-attraction of "morphological long-branches" may be a common problem. Incorporating information on morphological evolutionary processes will be crucial for inferring the relationships of fossil taxa to extant mammals. Nevertheless, it is encouraging that analysis of RY-coded mtDNA data resulted in a placental tree, that unlike previous mtDNA trees, is entirely consistent with interordinal relationships inferred from long nuclear sequences. Furthermore, divergence dates inferred from the mtDNA analysis suggest that as well as monotremes, at least two marsupial and six placental lineages diverged prior to the Cretaceous-Tertiary boundary. However, it seems likely that the phyletic and ecological diversification of modern mammals was not tightly coupled, with the later diversification being largely restricted to the Tertiary period.