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.

The origin and evolution of vertebrate sex chromosomes and dosage compensation.

In mammals, birds, snakes and many lizards and fish, sex is determined genetically (either male XY heterogamy or female ZW heterogamy), whereas in alligators, and in many reptiles and turtles, the temperature at which eggs are incubated determines sex. Evidently, different sex-determining systems (and sex chromosome pairs) have evolved independently in different vertebrate lineages. Homology shared by Xs and Ys (and Zs and Ws) within species demonstrates that differentiated sex chromosomes were once homologous, and that the sex-specific non-recombining Y (or W) was progressively degraded. Consequently, genes are left in single copy in the heterogametic sex, which results in an imbalance of the dosage of genes on the sex chromosomes between the sexes, and also relative to the autosomes. Dosage compensation has evolved in diverse species to compensate for these dose differences, with the stringency of compensation apparently differing greatly between lineages, perhaps reflecting the concentration of genes on the original autosome pair that required dosage compensation. We discuss the organization and evolution of amniote sex chromosomes, and hypothesize that dosage insensitivity might predispose an autosome to evolving function as a sex chromosome.

Review: Sex chromosome evolution and the expression of sex-specific genes in the placenta.

Sex chromosomes have a disproportionate influence on health and disease. Both the X and Y are atypical in gene content and activity, as a result of their unique evolutionary trajectory. The X and Y chromosomes originated in a pair of autosomes, and differentiated as the Y chromosome degenerated progressively. The Y contains few active genes and is composed largely of repetitive DNA sequences. Most Y genes have copies on the X from which they evolved; this includes even the sex-determining gene SRY as well as several genes required for spermatogenesis. The X contains a disproportionate number of genes that affect reproduction and brain function (or both). It is also subject to inactivation in females, so that females are mosaics composed of patches of tissue that express only the genes on either the maternally or the paternally derived X chromosome. Several widely expressed genes on the Y chromosome code for male-specific proteins that provoke an immune reaction in females; this HY antigen has a measurable effect on maternal-fetal incompatibility. Imprinted paternal X inactivation in rodent extraembryonic tissues would be expected to mitigate the effect of foreign paternal antigens; however, paternal inactivation seems not to occur in the human placenta.

Conservation of a chromosome arm in two distantly related marsupial species.

Marsupials, which diverged from eutherian mammals 150 million years ago (MYA), occupy a phylogenetic position that is very valuable in genome comparisons of mammal and other vertebrate species. Within the marsupials, the Australian and American clades (represented by the tammar wallaby Macropus eugenii, and the opossum Monodelphis domestica) diverged about 70 MYA. G-banding and chromosome painting suggest that tammar wallaby chromosome 6q has homology to opossum chromosome 7q. We tested this conservation by physically mapping the tammar wallaby orthologs of opossum chromosome 7q genes. We isolated 28 tammar wallaby BAC clones that contained orthologs of 16 opossum chromosome 7q genes. We used fluorescence in situ hybridization (FISH) to show that they all mapped specifically to the tammar wallaby chromosome 6q in nearly the same order as their orthologs on opossum chromosome 7q. Thus this chromosome arm is genetically, as well as cytologically, conserved over the 55-80 million years that separate kangaroos and the opossum.

The first cytogenetic map of the tuatara, Sphenodon punctatus.

Tuatara, Sphenodon punctatus, is the last survivor of the distinctive reptilian order Rhynchocephalia and is a species of extraordinary zoological interest, yet only recently have genomic analyses been undertaken. The karyotype consists of 28 macrochromosomes and 8 microchromosomes. A Bacterial Artificial Chromosome (BAC) library constructed for this species has allowed the first characterization of the tuatara genome. Sequence analysis of 11 fully sequenced BAC clones (approximately 0.03% coverage) increased the estimate of genome wide GC composition to 47.8%, the highest reported for any vertebrate. Our physical mapping data demonstrate discrete accumulation of repetitive elements in large blocks on some chromosomes, particularly the microchromosomes. We suggest that the large size of the genome (5.0 pg/haploid) is due to the accumulation of repetitive sequences. The microchromosomes of tuatara are rich in repetitive sequences, and the observation of one animal that lacked a microchromosome pair suggests that at least this microchromosome is unnecessary for survival. We used BACs bearing orthologues of known genes to construct a low-coverage cytogenetic map containing 21 markers. We identified a region on chromosome 4 of tuatara that shares homology with 7 Mb of chicken chromosome 2, and therefore the orthologous region of the snake Z chromosome. We identified a region on tuatara chromosome 3 that is orthologous to the chicken Z, and a region on chromosome 9 orthologous to the mammalian X. Since the tuatara determines sex by temperature and has no sex chromosomes, this implies that different tuatara autosome regions are homologous with the sex chromosomes of mammals, birds and snakes. We have identified anchor BAC clones that can be used to reliably mark chromosomes 3-7, 10 and 13, some of which are difficult to distinguish based on morphology alone. Fluorescence in situ hybridization mapping of 18S rDNA confirms the presence of a single NOR located on the long arm of chromosome 7, as previously identified by silver staining. Further work to construct a dense physical map will lead to a better understanding of the dynamics of genome evolution and organization in this isolated species.

Sex chromosome evolution in lizards: independent origins and rapid transitions.

Reptiles epitomize the variability of reproductive and sex determining modes and mechanisms among amniotes. These modes include gonochorism (separate sexes) and parthenogenesis, oviparity, viviparity, and ovoviviparity, genotypic sex determination (GSD) with male (XX/XY) and female (ZZ/ZW) heterogamety and temperature-dependent sex determination (TSD). Lizards (order Squamata, suborder Sauria) are particularly fascinating because the distribution of sex-determining mechanisms shows no clear phylogenetic segregation. This implies that there have been multiple transitions between TSD and GSD, and between XY and ZW sex chromosome systems. Approximately 1,000 species of lizards have been karyotyped and among those, fewer than 200 species have sex chromosomes, yet they display remarkable diversity in morphology and degree of degeneration. The high diversity of sex chromosomes as well as the presence of species with TSD, imply multiple and independent origins of sex chromosomes, and suggest that the mechanisms of sex determination are extremely labile in lizards. In this paper, we review the current state of knowledge of sex chromosomes in lizards and the distribution of sex determining mechanisms and sex chromosome forms within and among families. We establish for the first time an association between the occurrence of female heterogamety and TSD within lizard families, and propose mechanisms by which female heterogamety and TSD may have co-evolved. We suggest that lizard sex determination may be much more the result of an interplay between sex chromosomes and temperature than previously thought, such that the sex determination mode is influenced by the nature of heterogamety as well as temperature sensitivity and the stage of sex chromosome degeneration.

Sex determination in mammals--before and after the evolution of SRY.

Therian mammals (marsupials and placentals) have an XX female: XY male sex chromosome system, which is homologous to autosomes in other vertebrates. The testis-determining gene, SRY, is conserved on the Y throughout therians, but is absent in other vertebrates, suggesting that the mammal system evolved about 310 million years ago (MYA). However, recent work on the basal monotreme mammals has completely changed our conception of how and when this change occurred. Platypus and echidna lack SRY, and the therian X and Y are represented by autosomes, implying that SRY evolved in therians after their divergence from monotremes only 166 MYA. Clues to the ancestral mechanism usurped by SRY in therians are provided by the monotremes, whose sex chromosomes are homologous to the ZW of birds. This suggests that the therian X and Y, and the SRY gene, evolved from an ancient bird-like sex chromosome system which predates the divergence of mammals and reptiles 310 MYA.

Reproduction of Blue-black Grassquits in central Brazil.

During the reproductive season Blue-black grassquit (Volatinia jacarina) males are found in clusters, wherein they exhibit a distinctive display that consists of repeated, vertical leaps while simultaneously producing a brief vocalization. The main objective of this study was to describe details of the species' reproductive behavior in a "Cerrado" area of central Brazil and compare these data with some studies carried out in other areas. The data obtained concerning different aspects of nesting, laying and hatching were generally similar to those obtained in previous studies in other areas. However, we found that the typical clutch size of two eggs per nest is lower, and egg and nestling mortality rates higher in our area than what has been reported elsewhere. Our results suggest that males differ in time expended with different activities according to their reproductive condition and also provide extensive parental care. We found that display execution rates peak in the early morning and in the late afternoon and are higher in the middle of the breeding season. We also found that there is an inverse relation between the height of the display leap and the height of the perch.

Sex and differentiation: population genetic divergence and sexual dimorphism in Mexican goodeid fish.

Genetic differentiation arises due to the interaction between natural and sexual selection, migration and genetic drift. A potential role of sexual selection in speciation has received much interest, although comparative studies are inconsistent in finding supporting evidence. A poorly tested prediction is that species subject to a higher intensity of sexual selection should show greater genetic differentiation amongst populations because females from these populations should be more choosy in mate choice. The Goodeinae is a group of endemic Mexican fishes in which female choice has driven some species to be morphologically sexually dimorphic, whereas others are relatively monomorphic. Here, we measured population divergence, using microsatellite loci, within four goodeid species which show contrasting levels of sexual dimorphism. We found higher levels of differentiation between populations of the more dimorphic species, implying less gene flow between populations. We also found evidence of higher levels of genetic differences between the sexes within populations of the dimorphic species, consistent with greater dispersal in males. Adjusted for geographic distance, the mean F(ST) for the dimorphic species is 0.25 compared with 0.16 for the less dimorphic species. We conclude that population differentiation is accelerated in more sexually dimorphic species, and that comparative phylogeography may provide a more powerful approach to detecting processes, such as an influence of sexual selection on differentiation, than broad-scale comparative studies.

A new look at the evolution of avian sex chromosomes.

Birds have a ubiquitous, female heterogametic, ZW sex chromosome system. The current model suggests that the Z chromosome and its degraded partner, the W chromosome, evolved from an ancestral pair of autosomes independently from the mammalian XY male heteromorphic sex chromosomes--which are similar in size, but not gene content (Graves, 1995; Fridolfsson et al., 1998). Furthermore the degradation of the W has been proposed to be progressive, with the basal clade of birds (the ratites) possessing virtually homomorphic sex chromosomes and the more recently derived birds (the carinates) possessing highly heteromorphic sex chromosomes (Ohno, 1967; Solari, 1993). Recent findings have suggested an alternative to independent evolution of bird and mammal chromosomes, in which an XY system took over directly from an ancestral ZW system. Here we examine recent research into avian sex chromosomes and offer alternative suggestions as to their evolution.

Reproduction of Blue-black Grassquits in central Brazil

During the reproductive season Blue-black grassquit (Volatinia jacarina) males are found in clusters, wherein they exhibit a distinctive display that consists of repeated, vertical leaps while simultaneously producing a brief vocalization. The main objective of this study was to describe details of the species' reproductive behavior in a "Cerrado" area of central Brazil and compare these data with some studies carried out in other areas. The data obtained concerning different aspects of nesting, laying and hatching were generally similar to those obtained in previous studies in other areas. However, we found that the typical clutch size of two eggs per nest is lower, and egg and nestling mortality rates higher in our area than what has been reported elsewhere. Our results suggest that males differ in time expended with different activities according to their reproductive condition and also provide extensive parental care. We found that display execution rates peak in the early morning and in the late afternoon and are higher in the middle of the breeding season. We also found that there is an inverse relation between the height of the display leap and the height of the perch.

Durante a estação reprodutiva, machos de tiziu (Volatinia jacarina) são encontrados agregados e apresentam uma exibição bastante conspícua, que consiste de saltos verticais associados a uma curta vocalização. Através de observações realizadas em uma área de Cerrado na região do Brasil central, este trabalho teve como objetivos detalhar alguns aspectos da biologia reprodutiva de V. jacarina e comparar tais dados com os poucos trabalhos existentes sobre a espécie. Os dados obtidos neste estudo com relação aos diferentes aspectos da nidificação, postura e eclosão dos ovos se mostraram semelhantes, em geral, àqueles encontrados em estudos anteriores, diferindo apenas com relação ao número de ovos por ninho (a maioria dos ninhos com apenas dois ovos) e às taxas de predação, que se mostraram mais elevadas. Os dados mostram ainda que machos variam com relação ao gasto de tempo com diferentes atividades de acordo com a condição reprodutiva e que os mesmos investem parentalmente. Foram encontradas ainda, que as taxas de execução de exibição são mais elevadas no início da manhã e no final da tarde, assim como também tem um pico no meio da estação reprodutiva. Encontramos também uma relação inversa entre a altura do salto da exibição e a altura do poleiro.

Recruitment of old genes to new functions: evidences obtained by comparing the orthologues of human XLMR genes in mouse and chicken.

Gene mapping data indicate that the human X chromosome is enriched in genes that affect both, higher cognitive efficiency and reproductive success. This raises the question whether these functions are ancient, or whether conserved X-linked genes were recruited to new functions. We have studied three X-linked mental retardation (XLMR) genes by RNA in situ hybridization in mouse and in chicken, in which these genes are autosomal: Rho guanine nucleotide exchange factor 6 (ARHGEF6), oligophrenin (OPHN1), and p21 activated kinase 3 (PAK3). In the mouse these genes are specifically expressed in telencephalic regions. Their orthologues in the chicken gave patterns of similar specificity in ancient parts of the brain, i.e. cerebellum and mesencephalon, but were not expressed in the telencephalon. Also in the testes, specific expression was only found in mouse, not in chicken. These data are interpreted such that certain genes on the X chromosome gained novel functions during evolution.

Class I genes have split from the MHC in the tammar wallaby.

Genes within the Major Histocompatibility Complex (MHC) are critical to the immune response and immunoregulation. Comparative studies have revealed that the MHC has undergone many changes throughout evolution yet in tetrapods the three different classes of MHC genes have maintained linkage, suggesting that there may be some functional advantage obtained by maintaining this clustering of MHC genes. Here we present data showing that class II and III genes, the antigen processing gene TAP2, and MHC framework genes are found together in the tammar wallaby on chromosome 2. Surprisingly class I loci were not found on chromosome 2 but were mapped to ten different locations spread across six chromosomes. This distribution of class I loci in the wallaby on nearly all autosomes is not a characteristic of all marsupials and may be a relatively recent phenomenon. It highlights the need for the inclusion of more than one marsupial species in comparative studies and raises questions regarding the functional significance of the clustering of MHC genes.

Mapping platypus SOX genes; autosomal location of SOX9 excludes it from sex determining role.

In the absence of an SRY orthologue the platypus sex determining gene is unknown, so genes in the human testis determining pathway are of particular interest as candidates. SOX9 is an attractive choice because SOX9 deletions cause male-to-female sex reversal in humans and mice, and SOX9 duplications cause female-to-male sex reversal. We have localized platypus SOX9, as well as the related SOX10, to platypus chromosomes 15 and 10, respectively, the first assignments to these platypus chromosomes, and the first comparative mapping markers from human chromosomes 17 and 22. The autosomal localization of platypus SOX9 in this study contradicts the hypothesis that SOX9 acts as the sex determining switch in platypus.

Reassignment of chicken W chromosome sequences to the Z chromosome by fluorescence in situ hybridization (FISH).

There is much interest in the gene content of the small heterochromatic W chromosome of the chicken, on the supposition that it may contain sex-determining genes. A considerable region in the chicken genome has been assigned to the W chromosome on the basis of its repetitive sequences. Using fluorescent in situ hybridization (FISH) we localized five Bacterial Artificial Chromosomes (BACs) onto female chicken metaphase spreads. We physically mapped these BACs to the Z chromosome. The chicken genome database, however, assigned all five BACs to the W chromosome. Our results demonstrate that the 17 genes on these BACs are Z-specific, and points to the inadequacy of assigning regions of the genome based exclusively on repetitive sequences.

Yolk androgens and embryo sex: maternal effects or confounding factors?

Maternal effects occur when offspring phenotype is affected by environmental factors experienced by the mother and, in egg-laying species, are often mediated via egg resources. There is currently great interest among behavioural ecologists in maternally allocated yolk androgens, especially their relationship with offspring sex and development. Such studies need embryonic tissue for sexing, however, requiring eggs to be incubated (usually for 3 days). Therefore, there are concerns about whether the androgen concentrations assayed reflect those allocated by the mother. In addition, studies showing sex biases in maternal allocation of androgens could be confounded if male and female embryos uptake or metabolise androgens at different rates. We ran a series of experiments using zebra finch (Taeniopygia guttata) eggs to address these potential confounding factors. First we showed, using eggs naturally incubated for up to 5 days, that eggs containing embryos had lower yolk androgen concentrations than eggs that had failed to form embryos. We then tested various hypotheses for this difference using controlled incubation treatments. Our results suggested that (a) embryo development causes the yolk to become progressively more diluted with albumin; and (b) between 3 and 5 days of incubation embryos start uptaking or metabolising androgens. Crucially, we found no decline in yolk androgen concentration at 3 days incubation, and no evidence for sex-specific rates of uptake or metabolism of androgens. This strongly suggests that yolk androgen levels up to 3 days incubation do reflect those allocated by the mother, and that studies of sex biased maternal allocation of yolk androgens are not confounded by sex differences in embryo development.

Sex determination in platypus and echidna: autosomal location of SOX3 confirms the absence of SRY from monotremes.

In eutherian ('placental') mammals, sex is determined by the presence or absence of the Y chromosome-borne gene SRY, which triggers testis determination. Marsupials also have a Y-borne SRY gene, implying that this mechanism is ancestral to therians, the SRY gene having diverged from its X-borne homologue SOX3 at least 180 million years ago. The rare exceptions have clearly lost and replaced the SRY mechanism recently. Other vertebrate classes have a variety of sex-determining mechanisms, but none shares the therian SRY-driven XX female:XY male system. In monotreme mammals (platypus and echidna), which branched from the therian lineage 210 million years ago, no orthologue of SRY has been found. In this study we show that its partner SOX3 is autosomal in platypus and echidna, mapping among human X chromosome orthologues to platypus chromosome 6, and to the homologous chromosome 16 in echidna. The autosomal localization of SOX3 in monotreme mammals, as well as non-mammal vertebrates, implies that SRY is absent in Prototheria and evolved later in the therian lineage 210-180 million years ago. Sex determination in platypus and echidna must therefore depend on another male-determining gene(s) on the Y chromosomes, or on the different dosage of a gene(s) on the X chromosomes.

Marsupial WT1 has a novel isoform and is expressed in both somatic and germ cells in the developing ovary and testis.

The Wilms' tumour 1 gene is essential for the formation of the mouse and human urogenital systems. We characterised this gene and examined its expression throughout gonadal development in a marsupial, the tammar wallaby. WT1 protein was detected in the Sertoli and granulosa cells of the developing testis and ovary, respectively. There was also strong immunostaining in the germ cells of both males and females at all stages of gonadal development. In the adult gonads WT1 appears to be dynamically regulated during spermatogenesis and oogenesis. Tammar WT1 has a novel isoform in which a portion of exon 1 is removed, partially deleting the RNA recognition motif (RRM). Despite its removal, WT1 still localised to RNA rich regions of the oocyte including speckled bodies within the nucleus, in the nucleolus and the perinucleolar compartment. This suggests that the RRM is not required for WT1 co-localisation with RNA. This is also the first report of WT1 in association with the perinucleolar compartment, important for RNA metabolism. Our data suggest that WT1 has a conserved function in both the somatic and germ cell lineages of the gonads of marsupials.

Characterization of two whey protein genes in the Australian dasyurid marsupial, the stripe-faced dunnart (Sminthopsis macroura).

We report the first isolation and sequencing of genomic BAC clones containing the marsupial milk protein genes Whey Acidic Protein (WAP) and Early Lactation Protein (ELP). The stripe-faced dunnart WAPgene sequence contained five exons, the middle three of which code for the WAPmotifs and four disulphide core domains which characterize WAP. The dunnart ELPgene sequence contained three exons encoding a protein with a Kunitz motif common to serine protease inhibitors. Fluorescence in situ hybridization located the WAPgene to chromosome 1p in the stripe-faced dunnart, and the ELPgene to 2q. Northern blot analysis of lactating mammary tissue of the closely related fat-tailed dunnart has shown asynchronous expression of these milk protein genes. ELPwas expressed at only the earlier phase of lactation and WAPonly at the later phase of lactation, in contrast to beta-lactoglobulin (BLG) and alpha-lactalbumin (ALA) genes, which were expressed in both phases of lactation. This asynchronous expression during the lactation cycle in the fat-tailed dunnart is similar to other marsupials and it probably represents a pattern that is ancestral to Australian marsupials.

Construction of a highly enriched marsupial Y chromosome-specific BAC sub-library using isolated Y chromosomes.

The Y chromosome is perhaps the most interesting element of the mammalian genome but comparative analysis of the Y chromosome has been impeded by the difficulty of assembling a shotgun sequence of the Y. BAC-based sequencing has been successful for the human and chimpanzee Y but is difficult to do efficiently for an atypical mammalian model species (Skaletsky et al. 2003, Kuroki et al. 2006). We show how Y-specific sub-libraries can be efficiently constructed using DNA amplified from microdissected or flow-sorted Y chromosomes. A Bacterial Artificial Chromosome (BAC) library was constructed from the model marsupial, the tammar wallaby (Macropus eugenii). We screened this library for Y chromosome-derived BAC clones using DNA from both a microdissected Y chromosome and a flow-sorted Y chromosome in order to create a Y chromosome-specific sub-library. We expected that the tammar wallaby Y chromosome should detect approximately 100 clones from the 2.2 times redundant library. The microdissected Y DNA detected 85 clones, 82% of which mapped to the Y chromosome and the flow-sorted Y DNA detected 71 clones, 48% of which mapped to the Y chromosome. Overall, this represented a approximately 330-fold enrichment for Y chromosome clones. This presents an ideal method for the creation of highly enriched chromosome-specific sub-libraries suitable for BAC-based sequencing of the Y chromosome of any mammalian species.