Marsupials and monotremes: A case study in regional collection planning

Cooperative collection planning is critical to the future of zoological parks and aquariums, yet few published models currently exist for collection plan development and implementation. In particular, there has been little discussion about the relationship between regional and institutional collection planning or about what defines a quality regional collection plan (RCP). This article documents the regional collection planning process adopted by the AZA Marsupial and Monotreme Taxon Advisory Group (TAG). More specifically, it outlines the philosophical foundation of the North American RCP for Marsupials and Monotremes, the organizational structure developed by the TAG to facilitate communication, evaluation and institutional participation, and other important details of the planning process. It also documents how the RCP was used by one institution (Los Angeles Zoo) to formulate its Institutional Collection Plan (ICP). Zoo Biol 17:433–451, 1998. © 1998 Wiley-Liss, Inc.     

Marsupials and monotremes possess a novel family of MHC class I genes that is lost from the eutherian lineage

Background

Major histocompatibility complex (MHC) class I genes are found in the genomes of all jawed vertebrates. The evolution of this gene family is closely tied to the evolution of the vertebrate genome. Family members are frequently found in four paralogous regions, which were formed in two rounds of genome duplication in the early vertebrates, but in some species class Is have been subject to additional duplication or translocation, creating additional clusters. The gene family is traditionally grouped into two subtypes: classical MHC class I genes that are usually MHC-linked, highly polymorphic, expressed in a broad range of tissues and present endogenously-derived peptides to cytotoxic T-cells; and non-classical MHC class I genes generally have lower polymorphism, may have tissue-specific expression and have evolved to perform immune-related or non-immune functions. As immune genes can evolve rapidly and are subject to different selection pressure, we hypothesised that there may be divergent, as yet unannotated or uncharacterised class I genes.

Results

Application of a novel method of sensitive genome searching of available vertebrate genome sequences revealed a new, extensive sub-family of divergent MHC class I genes, denoted as UT, which has not previously been characterized. These class I genes are found in both American and Australian marsupials, and in monotremes, at an evolutionary chromosomal breakpoint, but are not present in non-mammalian genomes and have been lost from the eutherian lineage. We show that UT family members are expressed in the thymus of the gray short-tailed opossum and in other immune tissues of several Australian marsupials. Structural homology modelling shows that the proteins encoded by this family are predicted to have an open, though short, antigen-binding groove.

Conclusions

We have identified a novel sub-family of putatively non-classical MHC class I genes that are specific to marsupials and monotremes. This family was present in the ancestral mammal and is found in extant marsupials and monotremes, but has been lost from the eutherian lineage. The function of this family is as yet unknown, however, their predicted structure may be consistent with presentation of antigens to T-cells.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1745-4) contains supplementary material, which is available to authorized users.     

Mammalian genome evolution: new clues from comparisons of eutherians, marsupials and monotremes.

1. Comparisons of chromosomes and gene maps of different mammals are yielding a big picture of the evolution of mammalian genome form and function. It has been particularly instructive to compare gene arrangements on the sex chromosomes between the three major groups of mammals. Eutheria (so-called placental mammals). Metatheria (marsupials) and Prototheria (monotremes), which diverged 150 and 170 Myr BP respectively. 2. A region amounting to 3% of the haploid genome is located on the X chromosome in all three groups, implying that this region must have been part of the original X in a common ancestor. This region comprises the long arm of the human X. 3. A region represented by the short arm of the human X is common to the X in all eutherians, but is autosomal in marsupials and monotremes; thus it was not a part of the original X, and must have been acquired by the X early in the eutherian radiation. 4. This recently acquired region was probably translocated to a pseudoautosomal region shared by the eutherian X and Y. Thus it was originally paired and exempt from X chromosome inactivation; stepwise deletion of this region from the Y and recruitment of the newly unpaired region of the X into the inactivation system could account for some of the peculiarities of this region of the human X. 5. The sex-determining gene TDF must lie on the Y in all mammals in which the Y is male determining. The autosomal location of the candidate gene ZFY in marsupials and monotremes eliminates it from consideration. The recently described candidate gene SRY has yet to pass the "marsupial test".     

Plant genome organisation and diversity: the year of the junk!

Having gained a thorough understanding of the structure and organization of model plant genomes, such as those of Arabidopsis thaliana and rice, we have now started to investigate the most interesting aspect of genome structure - its variations. Variation in DNA sequence is responsible for the genetic component of phenotypic variation (i.e. the component upon which both natural and artificial selection act). Recent studies have started to shed light on sequence variation outside of the genic regions, owing mainly to large insertion/deletion (indel) polymorphisms caused by the presence or absence of transposable elements of different classes. In addition to long terminal repeat retrotransposons, DNA transposons have been shown to be responsible for these polymorphisms. These comprise Helitrons, CACTA and Mu-like elements that are capable of acquiring and piecing together fragments of plant genes and are often expressed. Future analyses of the functional roles of intergenic sequence variation will tell us if we will need to pay more attention not only to genes, but also to the 'junk' DNA surrounding them.     

On causal roles and selected effects: our genome is mostly junk

The idea that much of our genome is irrelevant to fitness—is not the product of positive natural selection at the organismal level—remains viable. Claims to the contrary, and specifically that the notion of “junk DNA” should be abandoned, are based on conflating meanings of the word “function”. Recent estimates suggest that perhaps 90% of our DNA, though biochemically active, does not contribute to fitness in any sequence-dependent way, and possibly in no way at all. Comparisons to vertebrates with much larger and smaller genomes (the lungfish and the pufferfish) strongly align with such a conclusion, as they have done for the last half-century.     

Molecular Phylogeny and Evolution of the Neurotrophins from Monotremes and Marsupials

We have investigated the phylogenetic relationships of monotremes and marsupials using nucleotide sequence data from the neurotrophins; nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and neurotrophin-3 (NT-3). The study included species representing monotremes, Australasian marsupials and placentals, as well as species representing birds, reptiles, and fish. PCR was used to amplify fragments encoding parts of the neurotrophin genes from echidna, platypus, and eight marsupials from four different orders. Phylogenetic trees were generated using parsimony analysis, and support for the different tree structures was evaluated by bootstrapping. The analysis was performed with NGF, BDNF, or NT-3 sequence data used individually as well as with the three neurotrophins in a combined matrix, thereby simultaneously considering phylogenetic information from three separate genes. The results showed that the monotreme neurotrophin sequences associate to either therian or bird neurotrophin sequences and suggests that the monotremes are not necessarily related closer to therians than to birds. Furthermore, the results confirmed the present classification of four Australasian marsupial orders based on morphological characters, and suggested a phylogenetic relationship where Dasyuromorphia is related closest to Peramelemorphia followed by Notoryctemorphia and Diprotodontia. These studies show that sequence data from neurotrophins are well suited for phylogenetic analysis of mammals and that neurotrophins can resolve basal relationships in the evolutionary tree. Received: 27 January 1997 / Accepted: 20 March 1997     

Gene mapping in marsupials and monotremes

Somatic cell genetic mapping of marsupial and monotreme species will greatly extend the power of comparative gene mapping to detect ancient mammalian gene arrangements. The use of eutherian-marsupial cell hybrids for such mapping is complicated by the frequent retention of deleted and rearranged marsupial chromosomes. We used staining techniques, involving the fluorochromes Hoechst 33258 and chromomycin A₃, to facilitate rapid and unequivocal identification of marsupial chromosomes and chromosome segments and to make chromosome assignment and regional localization of marsupial genes possible. Chromosome segregation in rodent-macropod hybrids was consistent with preferential loss of the marsupial complement. The extent of loss was very variable. Some hybrids retained 30% of the marsupial complement; some retained small centric fragments; and some, no cytologically identifiable marsupial material. We examined the chromosomes and gene products of a number of rodent-grey kangaroo Macropus giganteus hybrids, and have assigned the genes Pgk-A (phosphoglycerate kinase-A), Hpt (Hypoxanthine phosphoribosyl transferase), and Gpd (Glucose-6-phosphate dehydrogenase) to the long arm of the kangaroo X chromosome, and provisionally established the gene order Pgk-A -Hpt -Gpd.     

Marsupials from space: fluctuating asymmetry, geographical information systems and animal conservation

We report the development of a new quantitative method of assessing the effects of anthropogenic impacts on living beings; this method allows us to assess actual impacts and to travel backwards in time to assess impacts. In this method, we have crossed data on fluctuating asymmetry (FA, a measure of environmental or genetic stress), using Didelphis albiventris as a model, with geographical information systems data relating to environmental composition. Our results show that more impacted environments resulted in statistically higher levels of FA. Our method appears to be a useful and flexible conservation tool for assessing anthropogenic impacts.     

The Cardiogastric Gland and Alimentary Tract of Caenolestid Marsupials

The stomach of the South American marsupial family Caenolestidae has a gland on its lesser curvature around the cardia. This cardiogastric gland is bi-lobed, typically 11times5 mm and bears a distinctive, highly folded mucosa which forms sac-like invaginations. These open into the stomach lumen via 40–60 slit-like orifices. The gland mucosa contains unbranched gastric glands which are considerably longer than those of other gastric glands present elsewhere in the stomach. The cells within the cardiogastric gland show intense eosinophilic staining properties, with the parietal cells being larger than those found in other regions of the stomach, as well as being arranged in clusters. Argentaffin cells are not present in the stomach mucosa. The gross morphology of the stomach and intestine is similar to that found in small carnivorous marsupials.     

Identification of a Novel PNMA-MS1 Gene in Marsupials Suggests the LTR Retrotransposon-Derived PNMA Genes Evolved Differently in Marsupials and Eutherians

Two major gene families derived from Ty3/Gypsy long terminal repeat (LTR) retrotransposons were recently identified in mammals. The sushi-ichi retrotransposon homologue (SIRH) family comprises 12 genes: 11 in eutherians including Peg10 and Peg11/Rtl1 that have essential roles in the eutherian placenta and 1 that is marsupial specific. Fifteen and 12 genes were reported in the second gene family, para-neoplastic antigen MA (PNMA), in humans and mice, respectively, although their biological functions and evolutionary history remain largely unknown. Here, we identified two novel candidate PNMA genes, PNMA-MS1 and -MS2 in marsupials. Like all eutherian-specific PNMA genes, they exhibit the highest homology to a Gypsy12_DR (DR, Danio rerio) Gag protein. PNMA-MS1 is conserved in both Australian and South American marsupial species, the tammar wallaby and grey short-tailed opossum. However, no PNMA-MS1 orthologue was found in eutherians, monotremes or non-mammalian vertebrates. PNMA-MS1 was expressed in the ovary, mammary gland and brain during development and growth in the tammar, suggesting that PNMA-MS1 may have acquired a marsupial-specific function. However, PNMA-MS2 seems to be a pseudogene. The absence of marsupial orthologues of eutherian PNMA genes suggests that the retrotransposition events of the Gypsy12_DR-related retrotransposons that gave rise to the PNMA family occurred after the divergence of marsupials and eutherians.     

Phylogenetic Studies on Didelphid Marsupials I. Introduction and Preliminary Results from Nuclear IRBP Gene Sequences

We report and analyze nucleotide sequence variation in the first exon (1158 bp) of the nuclear gene encoding the Interphotoreceptor Retinoid Binding Protein (IRBP) among 21 species representing all 15 currently recognized genera of living didelphids. Six previously published IRBP sequences representing five nondidelphimorph marsupial orders were also analyzed to test didelphid monophyly, and 12 published sequences representing ten placental orders were used as outgroups. No gaps (indels) are necessary to align didelphid sequences, but one short region (35 bp) is alignment-ambiguous among nondidelphids. Uncorrected pairwise sequence divergence ranges from 0.7 to 5.7% among nonconspecific didelphids, from 9.2 to 15.3% between didelphids and nondidelphid marsupials, and from 24.9 to 32.1% between marsupials and placentals. Neither transitions nor transversions exhibit saturation for any codon position at any level of taxonomic comparison. Parsimony analyses of these data provide strong support (bootstrap values >95%, Bremer values 7) for the monophyly of (1) Didelphidae ("caluromyines" + Didelphinae); (2) a group containing Caluromys and Caluromysiops; (3) Didelphinae; (4) a group of large opossums that includes Metachirus; (5) a group containing the remaining large opossums (with 2N = 22 chromosomes); (6) a group containing Marmosa and Micoureus; (7) a group containing Thylamys, Lestodelphys, and Gracilinanus; and (8) a group containing the last three genera plus a monophyletic Marmosops. In addition, we found moderate support (bootstrap values >80%, Bremer values 2) for the monophyly of Thylamys + Lestodelphys and for a sister-group relationship between Monodelphis and Marmosa + Micoureus. Sensitivity analysis suggests that all of these clades, together with their associated levels of bootstrap and Bremer support, are robust to alternative hypotheses of positional homology within the ambiguously alignable region. Although some of the relationships supported by IRBP are not consistent with the results of published morphological analyses, our reassessment of the morphological data suggests that many conflicts are more apparent than real.     

“South American” Marsupials from the Late Cretaceous of North America and the Origin of Marsupial Cohorts

Newly described marsupial specimens of Judithian (late Campanian) and Lancian (Maastrichtian) age in the western interior of North America (Wyoming to Alberta) have dental morphologies consistent with those expected in comparably aged sediments in South America (yet to be found). Three new Lancian species are referable to the didelphimorphian Herpetotheriidae, which suggests that the ameridelphian radiation was well under way by this time. The presence of a polydolopimorphian from Lancian deposits with a relatively plesiomorphic dental morphology and an additional polydolopimorphian taxon from Judithian deposits with a more derived molar form indicate that this lineage of typically South American marsupials was diversifying in the Late Cretaceous of North America. This study indicates that typical South American lineages (e.g. didelphimorphians and polydolopimorphians) are not the result of North American peradectian progenitors dispersing into South America at the end of the Cretaceous (Lancian), or at the beginning of the Paleocene (Puercan), and giving rise to the ameridelphian marsupials. Instead, these lineages, and predictably others as well, had their origins in North America (probably in more southerly latitudes) and then dispersed into South America by the end of the Cretaceous. Geophysical evidence concerning the connections between North and South America in the Late Cretaceous is summarized as to the potential for overland mammalian dispersal between these places at those times. Paleoclimatic reconstructions are considered, as is the dispersal history of hadrosaurine dinosaurs and boid snakes, as to their contribution to an appraisal of mammalian dispersals in the Late Cretaceous. In addition, we present a revision of the South American component of the Marsupialia. One major outcome of this process is that the Polydolopimorphia is placed as Supercohort Marsupialia incertae sedis because no characteristics currently known from this clade securely place it within one of the three named marsupial cohorts. This article contains corrections to the text and a new Figure 11 not incorporated in the originally published version in Vol. 11, Nos. 3/4. For purposes of future citation, the present version (Vol. 12 and Nos. 3/4) should be used.     

Mapping the Prion Protein Distribution in Marsupials: Insights from Comparing Opossum with Mouse CNS

The cellular form of the prion protein (PrP^C) is a sialoglycoprotein widely expressed in the central nervous system (CNS) of mammalian species during neurodevelopment and in adulthood. The location of the protein in the CNS may play a role in the susceptibility of a species to fatal prion diseases, which are also known as the transmissible spongiform encephalopathies (TSEs). To date, little is known about PrP^C distribution in marsupial mammals, for which no naturally occurring prion diseases have been reported. To extend our understanding of varying PrP^C expression profiles in different mammals we carried out a detailed expression analysis of PrP^C distribution along the neurodevelopment of the metatherian South American short-tailed opossum (Monodelphis domestica). We detected lower levels of PrP^C in white matter fiber bundles of opossum CNS compared to mouse CNS. This result is consistent with a possible role for PrP^C in the distinct neurodevelopment and neurocircuitry found in marsupials compared to other mammalian species.