The evolution of marsupial and monotreme chromosomes.

Marsupial and monotreme mammals fill an important gap in vertebrate phylogeny between reptile-mammal divergence 310 million years ago (mya) and the eutherian (placental) mammal radiation 105 mya. They possess many unique features including their distinctive chromosomes, which in marsupials are typically very large and well conserved between species. In contrast, monotreme genomes are divided into several large chromosomes and many smaller chromosomes, with a complicated sex chromosome system that forms a translocation chain in male meiosis. The application of molecular cytogenetic techniques has greatly advanced our understanding of the evolution of marsupial chromosomes and allowed the reconstruction of the ancestral marsupial karyotype. Chromosome painting and gene mapping have played a vital role in piecing together the puzzle of monotreme karyotypes, particularly their complicated sex chromosome system. Here, we discuss the significant insight into karyotype evolution afforded by the combination of recently sequenced marsupial and monotreme genomes with cytogenetic analysis, which has provided a greater understanding of the events that have shaped not only marsupial and monotreme genomes, but the genomes of all mammals.

Evaluating phylogenetic informativeness and data-type usage for new protein-coding genes across Vertebrata.

As a resource for vertebrate phylogenetics, we developed 75 new protein-coding genes using a combination of expressed sequence tags (ESTs) available in Genbank, and targeted amplification of complementary DNA (cDNA). In addition, we performed three additional analyses in order to assess the utility of our approach. First, we profiled the phylogenetic informativeness of these new markers using the online program PhyDesign. Next, we compared the utility of four different data-types used in phylogenetics: nucleotides (NUCL), amino acids (AA), 1st and 2nd codon positions only (N12), and modified sequences to account for codon degeneracy (DEGEN1; Regier et al., 2010). Lastly, we use these new markers to construct a vertebrate phylogeny and address the uncertain relationship between higher-level mammal groups: monotremes, marsupials, and placentals. Our results show that phylogenetic informativeness of the 75 new markers varies, both in the amount of phylogenetic signal and optimal timescale. When comparing the four data-types, we find that the NUCL data-type, due to the high level of phylogenetic signal, performs the best across all divergence times. The remaining three data-types (AA, N12, DEGEN1) are less subject to homoplasy, but have greatly reduced levels of phylogenetic signal relative to NUCL. Our phylogenetic inference supports the Theria hypothesis of mammalian relationships, with marsupials and placentals being sister groups.

Independent origins of middle ear bones in monotremes and therians.

A dentary of the oldest known monotreme, the Early Cretaceous Teinolophos trusleri, has an internal mandibular trough, which in outgroups to mammals houses accessory jaw bones, and probable contact facets for angular, coronoid, and splenial bones. Certain of these accessory bones were detached from the mandible to become middle ear bones in mammals. Evidence that the angular (homologous with the mammalian ectotympanic) and the articular and prearticular (homologous with the mammalian malleus) bones retained attachment to the lower jaw in a basal monotreme indicates that the definitive mammalian middle ear evolved independently in living monotremes and therians (marsupials and placentals).

Identification and characterization of amelogenin genes in monotremes, reptiles, and amphibians.

Two features make the tooth an excellent model in the study of evolutionary innovations: the relative simplicity of its structure and the fact that the major tooth-forming genes have been identified in eutherian mammals. To understand the nature of the innovation at the molecular level, it is necessary to identify the homologs of tooth-forming genes in other vertebrates. As a first step toward this goal, homologs of the eutherian amelogenin gene have been cloned and characterized in selected species of monotremes (platypus and echidna), reptiles (caiman), and amphibians (African clawed toad). Comparisons of the homologs reveal that the amelogenin gene evolves quickly in the repeat region, in which numerous insertions and deletions have obliterated any similarity among the genes, and slowly in other regions. The gene organization, the distribution of hydrophobic and hydrophilic segments in the encoded protein, and several other features have been conserved throughout the evolution of the tetrapod amelogenin gene. Clones corresponding to one locus only were found in caiman, whereas the clawed toad possesses at least two amelogenin-encoding loci.

Epipubic bones in eutherian mammals from the late Cretaceous of Mongolia.

An important transformation in the evolution of mammals was the loss of the epipubic bones. These are elements projecting anteriorly from the pelvic girdle into the abdominal region in a variety of Mesozoic mammals, related tritylodonts, marsupials and monotremes but not in living eutherian (placental) mammals. Here we describe a new eutherian from the Late Cretaceous period of Mongolia, and report the first record of epipubic bones in two distinct eutherian lineages. The presence of epipubic bones and other primitive features suggests that these groups occupy a basal position in the Eutheria. It has been argued that the epipubic bones support the pouch in living mammals, but epipubic bones have since been related to locomotion and suspension of the litter mass of several attached, lactating offspring. The loss of the epipubic bones in eutherians can be related to the evolution of prolonged gestation, which would not require prolonged external attachment of altricial young. Thus the occurrence of epipubic bones in two Cretaceous eutherians suggests that the dramatic modifications connected with typical placental reproduction may have been later events in the evolution of the Eutheria.

The complete mitochondrial genome of the wallaroo (Macropus robustus) and the phylogenetic relationship among Monotremata, Marsupialia, and Eutheria.

The complete mitochondrial DNA (mtDNA) (16,896 nt) of the wallaroo (Macropus robustus) was sequenced. The concatenated amino acid sequences of 12 mitochondrial protein-coding genes of the wallaroo plus those of a number of other mammals were included in a phylogenetic study of early mammalian divergences. The analysis joined monotremes and marsupials (the Marsupionta hypothesis) to the exclusion of eutherians. The analysis rejected significantly the commonly acknowledged Theria hypothesis, according to which Marsupialia and Eutheria are grouped together to the exclusion of Monotremata. The region harboring the gene for lysine tRNA (tRNA-Lys) in the mtDNA of other vertebrates is in the wallaroo occupied by a sequence (tRNA-Lys) that lacks both an anticodon loop as well as the anticodon for the amino acid lysine. An alternative tRNA-Lys gene was not identified in any other region of the mtDNA of the wallaroo, suggesting that a tRNA-Lys of nuclear origin is imported into marsupial mitochondria. Previously described RNA editing of tRNA-Asp and rearrangement of some tRNA genes were reconfirmed in the mtDNA of the wallaroo. The divergence between Monotremata/Marsupialia and Eutheria was timed to approximately 130 million years before present (MYBP). The same calculations suggested that Monotremata and Marsupialia diverged approximately 115 MYBP and that Australian and American marsupials separated approximately 75 MYBP. The findings also show that many, probably most, extant eutherian orders had their origin in middle to late Cretaceous times, 115-65 MYBP.

Support for interordinal eutherian relationships with an emphasis on primates and their archontan relatives.

Current knowledge about mammalian interordinal relationships is growing rapidly; thus this contribution is an attempt to summarize the past 5 years of this literature. We have focused on the recent controversies in mammalian phylogenetics including hypotheses concerning the monophyly of Archonta, the diphyly of Chiroptera, and the polyphyly of Rodentia. All of these issues have been proposed recently, challenging these phylogenetic hypotheses. We have attempted to include all of the comprehensive analyses of eutherian mammal systematics with an emphasis on morphological and molecular data sets where discrete characters are listed so they could be compiled and used in support of interordinal relationships. Particular attention is given to determining which of the living eutherian orders is the closest relative to primates. In reviewing relationships among the mammals, we have focused on collating all of the available evidence so that one could know where each of the specific data sets is in support of the various relationships.