Different patterns of selection on the nuclear genes IRBP and DMP-1 affect the efficiency but not the outcome of phylogeny estimation for didelphid marsupials

Development of the ethmoid in Caluromys philander (Didelphidae, Marsupialia) with a discussion on the homology of the turbinal elements in marsupials

Homology of turbinals, or scroll bones, of the mammalian ethmoid bone is poorly known and complicated by a varied terminology. Positionally, there are two main types of ossified adult turbinals known as endoturbinals and ectoturbinals, and their cartilaginous precursors are called ethmoturbinals and frontoturbinals, respectively. Endoturbinals are considered to be serially homologous due to similarity in their developmental patterns. Consequently, endoturbinals from mammals with differing numbers of elements cannot be individually homogenized. In this study, the development of the ethmoid of Caluromys philander, the bare-tailed woolly opossum, is described based on serial sections of six pouchlings ranging in age from 20 to 84 days postnatal (PND-84), and computed tomography images of an adult skull. I found that four ethmoturbinals initially develop as seen in PND-20 and PND-30 individuals but by PND-64 an interturbinal (corresponding to endoturbinal III in adults) is present between ethmoturbinals II and III. This developmental pattern is identical to that of Monodelphis domestica, the gray short-tailed opossum, and is probably also present in the marsupials Didelphis marsupialis, and Thylacinus cynocephalus based on work of previous authors. These data suggest that endoturbinal III has a developmental pattern that differs from other endoturbinals, and the name interturbinal should be retained for the adult structure in recognition of this difference. These results may prove useful for homologizing this individual turbinal element across marsupials, the majority of which have five endoturbinals as adults. This might also explain the presumed placental ancestral condition of four endoturbinals if the marsupial interturbinal is lost.

Mammals from 'down under': a multi-gene species-level phylogeny of marsupial mammals (Mammalia, Metatheria)

Marsupials or metatherians are a group of mammals that are distinct in giving birth to young at early stages of development and in having a prolonged investment in lactation. The group consists of nearly 350 extant species, including kangaroos, koala, possums, and their relatives. Marsupials are an old lineage thought to have diverged from early therian mammals some 160 million years ago in the Jurassic, and have a remarkable evolutionary and biogeographical history, with extant species restricted to the Americas, mostly South America, and to Australasia. Although the group has been the subject of decades of phylogenetic research, the marsupial tree of life remains controversial, with most studies focusing on only a fraction of the species diversity within the infraclass. Here we present the first Methaterian species-level phylogeny to include 80% of the extant marsupial species and five nuclear and five mitochondrial markers obtained from Genbank and a recently published retroposon matrix. Our primary goal is to provide a summary phylogeny that will serve as a tool for comparative research. We evaluate the extent to which the phylogeny recovers current phylogenetic knowledge based on the recovery of “benchmark clades” from prior studies—unambiguously supported key clades and undisputed traditional taxonomic groups. The Bayesian phylogenetic analyses recovered nearly all benchmark clades but failed to find support for the suborder Phalagiformes. The most significant difference with previous published topologies is the support for Australidelphia as a group containing Microbiotheriidae, nested within American marsupials. However, a likelihood ratio test shows that alternative topologies with monophyletic Australidelphia and Ameridelphia are not significantly different than the preferred tree. Although further data are needed to solidify understanding of Methateria phylogeny, the new phylogenetic hypothesis provided here offers a well resolved and detailed tool for comparative analyses, covering the majority of the known species richness of the group.

Delphinid systematics and biogeography with a focus on the current genus Lagenorhynchus: multiple pathways for antitropical and trans-oceanic radiation

The six species currently classified within the genus Lagenorhynchus exhibit a pattern of antitropical distribution common among marine taxa. In spite of their morphological similarities they are now considered an artificial grouping, and include both recent and the oldest representatives of the Delphinidae radiation. They are, therefore, a good model for studying questions about the evolutionary processes that have driven dolphin speciation, dispersion and distribution. Here we used two different approaches. First we constructed a multigenic phylogeny with a minimum amount of missing data (based on 9 genes, 11,030bp, using the 6 species of the genus and their closest relatives) to infer their relationships. Second, we built a supermatrix phylogeny (based on 33 species and 27 genes) to test the effect of taxon sampling on the phylogeny of the genus, to provide inference on biogeographic history, and provide inference on the main events shaping the dispersion and radiation of delphinids. Our analyses suggested an early evolutionary history of marine dolphins in the North Atlantic Ocean and revealed multiple pathways of migration and radiation, probably guided by paleoceanographic changes during the Miocene and Pliocene. L. acutus and L. albirostris likely shared a common ancestor that arose in the North Atlantic around the Middle Miocene, predating the radiation of subfamilies Delphininae, Globicephalinae and Lissodelphininae.

The dentin matrix acidic phosphoprotein 1 (DMP1) in the light of mammalian evolution

Dentin matrix acidic phosphoprotein 1 (DMP1) is an acidic, highly phosphorylated, noncollagenous protein secreted during dentin and bone formation. Previous functional studies of DMP1 have revealed various motifs playing a role in either mineralization or cell differentiation. We performed an evolutionary analysis of DMP1 to identify residues and motifs that were conserved during 220 millions years (Ma) of mammalian evolution, and hence have an important function. In silico search provided us with 41 sequences that were aligned and analyzed using the Hyphy program. We showed that DMP1 contains 55 positions that were kept unchanged for 220 Ma. We also defined in a more precise manner some motifs that were already known (i.e., cleavage sites, RGD motif, ASARM peptide, glycosaminoglycan chain attachment site, nuclear localization signal sites, and dentin sialophosphoprotein-binding site), and we found five, highly conserved, new functional motifs. In the near future, functional studies could be performed to understand the role played by them.

Identificação de marsupiais do Rio Grande do Sul através da microestrutura dos pelos-guarda

A análise dos padrões microscópicos de pelos de mamíferos é uma técnica não-invasiva que pode auxiliar na identificação dos marsupiais brasileiros. O objetivo deste trabalho foi identificar padrões microscópicos dos pelos-guarda (cutícula e medula) de marsupiais ocorrentes no Rio Grande do Sul (RS), propondo uma chave dicotômica para sua identificação a partir dessas estruturas. Além disso, nós apresentamos, com detalhes, os padrões tricológicos de espécimes do gênero Monodelphis, um gênero ainda taxonomicamente obscuro que requer revisão no RS. Obtivemos o material analisado por meio da coleta de pelos de marsupiais capturados em campo ou provenientes de coleções de diferentes instituições. Identificamos os padrões dos pelos de dez espécies de marsupiais: Caluromys lanatus, Chironectes minimus, Didelphis aurita, Didelphis albiventris, Cryptonanus guahybae, Gracilinanus agilis, Gracilinanus microtarsus, Lutreolina crassicaudata, Micoureus paraguayanus e Philander frenatus. Os indivíduos do gênero Monodelphis foram analisados em conjunto, como parte do grupo dimidiata. Encontramos três padrões dentro desse grupo, sugerindo que possa haver uma terceira espécie além das duas normalmente reconhecidas (M. brevicaudis e M. dimidiata). A análise dos padrões microscópicos dos pelos possibilitou a identificação, com sucesso, da grande maioria das espécies à que pertencem os marsupiais do Rio Grande do Sul. Os resultados obtidos sugerem que as duas espécies de Monodelphis grupo dimidiata possam ocorrer com uma distribuição distinta no estado, estando uma presente principalmente na porção norte e a outra na porção leste do RS, com sobreposição na região central.

Phylogeny and adaptive evolution of the brain-development gene microcephalin (MCPH1) in cetaceans

BACKGROUND

Representatives of Cetacea have the greatest absolute brain size among animals, and the largest relative brain size aside from humans. Despite this, genes implicated in the evolution of large brain size in primates have yet to be surveyed in cetaceans.

RESULTS

We sequenced ~1240 basepairs of the brain development gene microcephalin (MCPH1) in 38 cetacean species. Alignments of these data and a published complete sequence from Tursiops truncatus with primate MCPH1 were utilized in phylogenetic analyses and to estimate ω (rate of nonsynonymous substitution/rate of synonymous substitution) using site and branch models of molecular evolution. We also tested the hypothesis that selection on MCPH1 was correlated with brain size in cetaceans using a continuous regression analysis that accounted for phylogenetic history. Our analyses revealed widespread signals of adaptive evolution in the MCPH1 of Cetacea and in other subclades of Mammalia, however, there was not a significant positive association between ω and brain size within Cetacea.

CONCLUSION

In conjunction with a recent study of Primates, we find no evidence to support an association between MCPH1 evolution and the evolution of brain size in highly encephalized mammalian species. Our finding of significant positive selection in MCPH1 may be linked to other functions of the gene.

Expressed sequence tags as a tool for phylogenetic analysis of placental mammal evolution

BACKGROUND

We investigate the usefulness of expressed sequence tags, ESTs, for establishing divergences within the tree of placental mammals. This is done on the example of the established relationships among primates (human), lagomorphs (rabbit), rodents (rat and mouse), artiodactyls (cow), carnivorans (dog) and proboscideans (elephant).

METHODOLOGY/PRINCIPAL FINDINGS

We have produced 2000 ESTs (1.2 mega bases) from a marsupial mouse and characterized the data for their use in phylogenetic analysis. The sequences were used to identify putative orthologous sequences from whole genome projects. Although most ESTs stem from single sequence reads, the frequency of potential sequencing errors was found to be lower than allelic variation. Most of the sequences represented slowly evolving housekeeping-type genes, with an average amino acid distance of 6.6% between human and mouse. Positive Darwinian selection was identified at only a few single sites. Phylogenetic analyses of the EST data yielded trees that were consistent with those established from whole genome projects.

CONCLUSIONS

The general quality of EST sequences and the general absence of positive selection in these sequences make ESTs an attractive tool for phylogenetic analysis. The EST approach allows, at reasonable costs, a fast extension of data sampling from species outside the genome projects.

Base-compositional heterogeneity in the RAG1 locus among didelphid marsupials: implications for phylogenetic inference and the evolution of GC content

Although theoretical studies have suggested that base-compositional heterogeneity can adversely affect phylogenetic reconstruction, only a few empirical examples of this phenomenon, mostly among ancient lineages (with divergence dates > 100 Mya), have been reported. In the course of our phylogenetic research on the New World marsupial family Didelphidae, we sequenced 2790 bp of the RAG1 exon from exemplar species of most extant genera. Phylogenetic analysis of these sequences recovered an anomalous node consisting of two clades previously shown to be distantly related based on analyses of other molecular data. These two clades show significantly increased GC content at RAG1 third codon positions, and the resulting convergence in base composition is strong enough to overwhelm phylogenetic signal from other genes (and morphology) in most analyses of concatenated datasets. This base-compositional convergence occurred relatively recently (over tens rather than hundreds of millions of years), and the affected gene region is still in a state of evolutionary disequilibrium. Both mutation rate and substitution rate are higher in GC-rich didelphid taxa, observations consistent with RAG1 sequences having experienced a higher rate of recombination in the convergent lineages.

Cranial endocasts from a growth series ofMonodelphis domestica (Didelphidae, Marsupialia): A study of individual and ontogenetic variation

Intraspecific variation (e.g., ontogenetic, individual, sexual dimorphic) is rarely examined among cranial endocasts (infillings of the braincase cavity) because of the difficulty in obtaining multiple specimens of a species, particularly fossil taxa. We extracted digital cranial endocasts from CT scans of a growth series of skulls of Monodelphis domestica, the gray short-tailed opossum, as a preliminary assessment of the amount of intraspecific variation in mammalian endocranial morphology. The goals of this study were 1) to provide an anatomical description to document developmental changes in endocranial morphology of M. domestica and 2) to examine ontogenetic and individual variation with respect to phylogenetic characters of endocranial cavities that are known to be variable between different mammalian taxa. In this study, "ontogenetic variation" refers to variation between specimens of different ages whereas "individual variation" (i.e., polymorphism) is restricted to variation between specimens of comparable age. Aside from size, changes in shape account for the greatest amount of morphological variation between the endocasts of different ages. Endocast length, width, and volume increase with age for the growth series. Relative olfactory bulb cast size increases with age in the growth series, but the relative size of the parafloccular casts shows a slight negative allometric trend through ontogeny. More than one-third of the phylogenetic characters of the endocranial cavity we examined showed some sort of variation (ontogenetic, individual, or both). This suggests that although endocasts are potentially informative for systematics, both ontogenetic and individual variation affect how endocranial characters are scored for phylogenetic analysis. Further studies such as this are necessary to determine the taxonomic extent of significant intraspecific variation of these endocranial characters.

Status and applications of genomic resources for the gray, short-tailed opossum, Monodelphis domestica, an American marsupial model for comparative biology

Owing to its small size, favourable reproductive characteristics, and simple husbandry, the gray, short-tailed opossum, Monodelphis domestica, has become the most widely distributed and intensively utilised laboratory-bred research marsupial in the world today. This article provides an overview of the current state and future projections of genomic resources for this species and discusses the potential impact of this growing resource base on active research areas that use M. domestica as a model system. The resources discussed include: fully arrayed, bacterial artificial chromosome (BAC) libraries; an expanding linkage map; developing full-genome BAC-contig and chromosomal fluorescence in situ hybridisation maps; public websites providing access to the M. domestica whole-genome-shotgun sequence trace database and the whole-genome sequence assembly; and a new project underway to create an expressed-sequence database and microchip expression arrays for functional genomics applications. Major research areas discussed span a variety of genetic, evolutionary, physiologic, reproductive, developmental, and behavioural topics, including: comparative immunogenetics; genomic imprinting; reproductive biology; neurobiology; photobiology and carcinogenesis; genetics of lipoprotein metabolism; developmental and behavioural endocrinology; sexual differentiation and development; embryonic and fetal development; meiotic recombination; genome evolution; molecular evolution and phylogenetics; and more.