The tammar wallaby, Macropus eugenii: a model kangaroo for the study of developmental and reproductive biology

The structure of the TH/INS locus and the parental allele expressed are not conserved between mammals

Parent-of-origin-specific expression of imprinted genes is critical for successful mammalian growth and development. Insulin, coded by the INS gene, is an important growth factor expressed from the paternal allele in the yolk sac placenta of therian mammals. The tyrosine hydroxylase gene TH encodes an enzyme involved in dopamine synthesis. TH and INS are closely associated in most vertebrates, but the mouse orthologues, Th and Ins2, are separated by repeated DNA. In mice, Th is expressed from the maternal allele, but the parental origin of expression is not known for any other mammal so it is unclear whether the maternal expression observed in the mouse represents an evolutionary divergence or an ancestral condition. We compared the length of the DNA segment between TH and INS across species and show that separation of these genes occurred in the rodent lineage with an accumulation of repeated DNA. We found that the region containing TH and INS in the tammar wallaby produces at least five distinct RNA transcripts: TH, TH-INS1, TH-INS2, lncINS and INS. Using allele-specific expression analysis, we show that the TH/INS locus is expressed from the paternal allele in pre- and postnatal tammar wallaby tissues. Determining the imprinting pattern of TH/INS in other mammals might clarify if paternal expression is the ancestral condition which has been flipped to maternal expression in rodents by the accumulation of repeat sequences.

Principles of 3D chromosome folding and evolutionary genome reshuffling in mammals

Studying the similarities and differences in genomic interactions between species provides fertile grounds for determining the evolutionary dynamics underpinning genome function and speciation. Here, we describe the principles of 3D genome folding in vertebrates and show how lineage-specific patterns of genome reshuffling can result in different chromatin configurations. We (1) identified different patterns of chromosome folding in across vertebrate species (centromere clustering versus chromosomal territories); (2) reconstructed ancestral marsupial and afrotherian genomes analyzing whole-genome sequences of species representative of the major therian phylogroups; (3) detected lineage-specific chromosome rearrangements; and (4) identified the dynamics of the structural properties of genome reshuffling through therian evolution. We present evidence of chromatin configurational changes that result from ancestral inversions and fusions/fissions. We catalog the close interplay between chromatin higher-order organization and therian genome evolution and introduce an interpretative hypothesis that explains how chromatin folding influences evolutionary patterns of genome reshuffling.

Postnatal and Adult Neurogenesis in Mammals, Including Marsupials

In mammals, neurogenesis occurs during both embryonic and postnatal development. In eutherians, most brain structures develop embryonically; conversely, in marsupials, a number of brain structures develop after birth. The exception is the generation of granule cells in the dentate gyrus, olfactory bulb, and cerebellum of eutherian species. The formation of these structures starts during embryogenesis and continues postnatally. In both eutherians and marsupials, neurogenesis continues in the subventricular zone of the lateral ventricle (SVZ) and the dentate gyrus of the hippocampal formation throughout life. The majority of proliferated cells from the SVZ migrate to the olfactory bulb, whereas, in the dentate gyrus, cells reside within this structure after division and differentiation into neurons. A key aim of this review is to evaluate advances in understanding developmental neurogenesis that occurs postnatally in both marsupials and eutherians, with a particular emphasis on the generation of granule cells during the formation of the olfactory bulb, dentate gyrus, and cerebellum. We debate the significance of immature neurons in the piriform cortex of young mammals. We also synthesize the knowledge of adult neurogenesis in the olfactory bulb and the dentate gyrus of marsupials by considering whether adult-born neurons are essential for the functioning of a given area.

Sexual conflict in action: An antagonistic relationship between maternal and paternal sex allocation in the tammar wallaby, Notamacropus eugenii

Sex ratio biases are often inconsistent, both among and within species and populations. While some of these inconsistencies may be due to experimental design, much of the variation remains inexplicable. Recent research suggests that an exclusive focus on mothers may account for some of the inconsistency, with an increasing number of studies showing variation in sperm sex ratios and seminal fluids. Using fluorescent in-situ hybridization, we show a significant population-level Y-chromosome bias in the spermatozoa of wild tammar wallabies, but with significant intraindividual variation between males. We also show a population-level birth sex ratio trend in the same direction toward male offspring, but a weaning sex ratio that is significantly female-biased, indicating that males are disproportionately lost during lactation. We hypothesize that sexual conflict between parents may cause mothers to adjust offspring sex ratios after birth, through abandonment of male pouch young and reactivation of diapaused embryos. Further research is required in a captive, controlled setting to understand what is driving and mechanistically controlling sperm sex ratio and offspring sex ratio biases and to understand the sexually antagonistic relationship between mothers and fathers over offspring sex. These results extend beyond sex allocation, as they question studies of population processes that assume equal input of sex chromosomes from fathers, and will also assist with future reproduction studies for management and conservation of marsupials.

Extensive genetic differentiation detected within a model marsupial, the tammar wallaby (Notamacropus eugenii)

The tammar wallaby (Notamacropus eugenii) is one of the most intensively studied of all macropodids and was the first Australasian marsupial to have its genome sequenced. However, comparatively little is known about genetic diversity and differentiation amongst the morphologically distinct allopatric populations of tammar wallabies found in Western (WA) and South Australia (SA). Here we compare autosomal and Y-linked microsatellite genotypes, as well as sequence data (~600 bp) from the mitochondrial DNA (mtDNA) control region (CR) in tammar wallabies from across its distribution. Levels of diversity at autosomal microsatellite loci were typically high in the WA mainland and Kangaroo Island (SA) populations (A = 8.9-10.6; He = 0.77-0.78) but significantly reduced in other endemic island populations (A = 3.8-4.1; He = 0.41-0.48). Autosomal and Y-linked microsatellite loci revealed a pattern of significant differentiation amongst populations, especially between SA and WA. The Kangaroo Island and introduced New Zealand population showed limited differentiation. Multiple divergent mtDNA CR haplotypes were identified within both SA and WA populations. The CR haplotypes of tammar wallabies from SA and WA show reciprocal monophyly and are highly divergent (14.5%), with levels of sequence divergence more typical of different species. Within WA tammar wallabies, island populations each have unique clusters of highly related CR haplotypes and each is most closely related to different WA mainland haplotypes. Y-linked microsatellite haplotypes show a similar pattern of divergence although levels of diversity are lower. In light of these differences, we suggest that two subspecies of tammar wallaby be recognized; Notamacropus eugenii eugenii in SA and N. eugenii derbianus in WA. The extensive neutral genetic diversity and inter-population differentiation identified within tammar wallabies should further increase the species value and usefulness as a model organism.

Characterisation of major histocompatibility complex class I genes at the fetal-maternal interface of marsupials

Major histocompatibility complex class I molecules (MHC-I) are expressed at the cell surface and are responsible for the presentation of self and non-self antigen repertoires to the immune system. Eutherian mammals express both classical and non-classical MHC-I molecules in the placenta, the latter of which are thought to modulate the maternal immune response during pregnancy. Marsupials last shared a common ancestor with eutherian mammals such as humans and mice over 160 million years ago. Since, like eutherians, they have an intra-uterine development dependent on a placenta, albeit a short-lived and less invasive one, they provide an opportunity to investigate the evolution of MHC-I expression at the fetal-maternal interface. We have characterised MHC-I mRNA expression in reproductive tissues of the tammar wallaby (Macropus eugenii) from the time of placental attachment to day 25 of the 26.5 day pregnancy. Putative classical MHC-I genes were expressed in the choriovitelline placenta, fetus, and gravid endometrium throughout the whole of this period. The MHC-I classical sequences were phylogenetically most similar to the Maeu-UC (50/100 clones) and Maeu-UA genes (7/100 clones). Expression of three non-classical MHC-I genes (Maeu-UD, Maeu-UK and Maeu-UM) were also present in placental samples. The results suggest that expression of classical and non-classical MHC-I genes in extant marsupial and eutherian mammals may have been necessary for the evolution of the ancestral therian placenta and survival of the mammalian fetus at the maternal-fetal interface.

Sex-linked and autosomal microsatellites provide new insights into island populations of the tammar wallaby

The emerging availability of microsatellite markers from mammalian sex chromosomes provides opportunities to investigate both male- and female-mediated gene flow in wild populations, identifying patterns not apparent from the analysis of autosomal markers alone. Tammar wallabies (Macropus eugenii), once spread over the southern mainland, have been isolated on several islands off the Western Australian and South Australian coastlines for between 10,000 and 13,000 years. Here, we combine analyses of autosomal, Y-linked and X-linked microsatellite loci to investigate genetic variation in populations of this species on two islands (Kangaroo Island, South Australia and Garden Island, Western Australia). All measures of diversity were higher for the larger Kangaroo Island population, in which genetic variation was lowest at Y-linked markers and highest at autosomal markers (θ=3.291, 1.208 and 0.627 for autosomal, X-linked and Y-linked data, respectively). Greater relatedness among females than males provides evidence for male-biased dispersal in this population, while sex-linked markers identified genetic lineages not apparent from autosomal data alone. Overall genetic diversity in the Garden Island population was low, especially on the Y chromosome where most males shared a common haplotype, and we observed high levels of inbreeding and relatedness among individuals. Our findings highlight the utility of this approach for management actions, such as the selection of animals for translocation or captive breeding, and the ecological insights that may be gained by combining analyses of microsatellite markers on sex chromosomes with those derived from autosomes.

Ultrasonography of wallaby prenatal development shows that the climb to the pouch begins in utero

Marsupials have a functional placenta for a shorter period of time compared to that of eutherian species, and their altricial young reach the teats without any help from the mother. We have monitored the short intrauterine development of one marsupial, the tammar wallaby, with high-resolution ultrasound from reactivation of the 100-cell diapausing blastocyst to birth. The expanding blastocyst could be visualized when it had reached a diameter of 1.5 mm. From at least halfway through pregnancy, there are strong undulating movements of the endometrium that massage the expanding vesicle against the highly secretory endometrial surface. These unique movements possibly enhance exchange of uterine secretions and gases between the mother and embryo. There was a constant rate of development measured ultrasonographically from mid-gestation, regardless of when the blastocyst reactivated. Interestingly climbing movements by the fetus began in utero about 3 days before birth, mimicking those required to climb to the pouch.

Early cell lineage specification in a marsupial: a case for diverse mechanisms among mammals

Early cell lineage specification in eutherian mammals results in the formation of a pluripotent inner cell mass (ICM) and trophoblast. By contrast, marsupials have no ICM. Here, we present the first molecular analysis of mechanisms of early cell lineage specification in a marsupial, the tammar wallaby. There was no overt differential localisation of key lineage-specific transcription factors in cleavage and early unilaminar blastocyst stages. Pluriblast cells (equivalent to the ICM) became distinguishable from trophoblast cells by differential expression of POU5F1 and, to a greater extent, POU2, a paralogue of POU5F1. Unlike in the mouse, pluriblast-trophoblast differentiation coincided with a global nuclear-to-cytoplasmic transition of CDX2 localisation. Also unlike in the mouse, Hippo pathway factors YAP and WWTR1 showed mutually distinct localisation patterns that suggest non-redundant roles. NANOG and GATA6 were conserved as markers of epiblast and hypoblast, respectively, but some differences to the mouse were found in their mode of differentiation. Our results suggest that there is considerable evolutionary plasticity in the mechanisms regulating early lineage specification in mammals.

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

BACKGROUND

We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development.

RESULTS

The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements.

CONCLUSIONS

Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution.

Surgery on tammar wallaby (Macropus eugenii) pouch young

Two features of marsupial young make them ideal for developmental studies: (1) Their immune system, like that of the thyroid and thermoregulation, develops relatively late after birth, and (2) they tolerate xenografts. This late development allows transplants to grow and survive in the recipient for at least 150 d without the use of immunosuppressants. The immaturity of the organ systems and the tiny size of the neonate pose difficulties for anesthesia. However, because the pouch young are completely heterothermic until at least 3 mo of age, cooling can be used as an anesthetic agent. In practice, however, we use hypothermia for neonates and young up to the age of 25-30 d, and injectable anethetics thereafter. Healing is remarkably rapid. This tolerance of xenografts and the ability and ease with which hypothermia can be applied to marsupial young provides a unique approach to understanding developmental processes that normally take place in utero in eutherians. This protocol describes surgical procedures and post-surgical care performed on tammar wallaby (Macropus eugenii) pouch young (PY).

Performing surgery on tammar wallaby (Macropus eugenii) adults

Adult tammar wallabies (Macropus eugenii) are very tolerant of surgery if it is conducted with care. Adult females weigh ~4‐5 kg, males ~7‐8 kg. Routine surgery performed in our laboratory and described in this protocol includes castration, laparotomy (to visualize the reproductive tract), ovariectomy, and hysterectomy (for embryo collection). All surgery is conducted under aseptic conditions. For most reproductive surgery on females, the optimum surgical approach is via the inside of the pouch. Any pouch young must be removed before surgery.

Culturing tammar wallaby (Macropus eugenii) pouch young gonads

Tammar wallaby (Macropus eugenii) pouch young (PY) gonads are ideal for studies on gonadal differentiation and germ cell proliferation because, in contrast to the mouse, both of these events occur postnatally in the tammar. In the male, testicular cords start developing at day 2 postpartum (pp), whereas in the female the ovarian cortex and medulla differentiate from ~day 8 pp. In females, meiosis starts from day 25 pp and is complete in most germ cells by day 50 pp. The gonads can be cultured either in grooves within agar or flat on a membrane. The former arrangement maintains the close contact of the gonad and mesonephros better than culturing them flat on a membrane. This protocol provides methods for isolation and culturing of PY gonads.

Collection, handling, fixation, and processing of tammar wallaby (Macropus eugenii) embryos

This protocol describes methods for collecting and handling tammar wallaby (Macropus eugenii) conceptuses. Zygotes, cleavage stages, diapausing blastocysts, and unexpanded blastocysts are ~250 μm in diameter and are collected by flushing either the oviduct or uterus. Later stages are collected by opening the uterus. Late preimplantation stages must be handled carefully because their large size (>2 cm in diameter) results in high surface tension within the yolk sac, especially on the delicate avascular area. When handled too roughly, the embryonic vesicle tends to split and then rapidly collapse; such embryos do not reinflate. If embryos are to be cultured, all steps during collection must be carried out aseptically. In all cases, solutions should be prewarmed to 37°C and embryos should be kept warm by use of a heating stage. Standard fixatives, fixation times, and washing protocols used for mouse embryos are also used for tammar embryos. Methods for embedding tammar conceptuses in paraffin wax depend on the size and stage of the conceptus.

Whole-mount immunohistochemical staining of tammar wallaby (Macropus eugenii) peri-gastrulation embryos

This protocol describes a method for whole-mount immunohistochemical staining of tammar wallaby (Macropus eugenii) peri-gastrulation stage embryos using the avidin-biotin complex system. Tammar embryos are ideal for whole-mount immunostaining because of their morphology: They develop in a planar manner on the surface of the embryonic vesicle and are not covered by any extraembryonic membranes until amnion formation (which occurs during mid-somitogenesis). Tammar embryos are surrounded by a transparent shell coat, which must be opened prior to staining to ensure penetration of solutions and reagents.

Culturing tammar wallaby (Macropus eugenii) peri-gastrulation stage embryos

Tammar wallaby (Macropus eugenii) peri-gastrulation stage embryos can be cultured in complete medium in 95% oxygen for up to 3 d. There is little apparent difference in terms of development between tammar peri-gastrulation stage embryos cultured in DMEM versus Medium 199 with Earle’s salts, or between the supplementation of complete medium with either 10% fetal calf serum (FCS) or 10% wallaby serum (WS). The peri-gastrulation marsupial conceptus is hollow, which means that some techniques, such as grafting, cannot be performed on embryos to be cultured whole because, once punctured, the embryo collapses and does not reinflate. This protocol describes both whole embryo culture and an alternative method of culture. In the latter method, the embryonic disc and some adjoining vascular yolk sac are isolated, laid flat on a membrane, and cultured as a flat mount. Embryos cultured in this way develop to a similar stage as those cultured whole.

Whole-mount immunohistochemical staining of tammar wallaby (Macropus eugenii) cleavage stages and blastocysts

This protocol describes a method for whole-mount immunofluorescence staining of early stages of tammar wallaby (Macropus eugenii) development, including cleavage and unilaminar blastocysts. Conceptuses of these stages are surrounded by a shell coat, which must be removed before staining to ensure proper penetration of all solutions.

Working with tammar wallabies (Macropus eugenii)

It requires practice to become adept at catching and handling tammar wallabies (Macropus eugenii). Although generally not aggressive, tammars do scratch and can also bite. Once caught, tammars will stay quiet in their sacks for several hours. Take care that sacked animals do not overheat by ensuring that they are not left in the sun or piled on top of each other. To avoid the risk of heat stress, do not catch animals when air temperatures are above 25°C. Once handling techniques for adult animals are mastered, procedures such as vaccinations and checking for pouch young (PY) are easily performed, as described in this protocol. Methods for sexing, aging, and handling PY, as well as euthanasia of PY, are also detailed in this protocol. Once removed from the pouch, PY must be kept warm, because they lack the ability to thermoregulate until they are ~6 mo old.