Vombatiformes: All vombatid species have 2n=14 chromosomes. The G-banded karyotype of




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Supplementary Material
a) Chromosome evolution in Diprotodontia

Vombatiformes: All vombatid species have 2n=14 chromosomes. The G-banded karyotype of Vombatus is identical to that seen in bandicoots (Rofe and Hayman, 1985), the microbiotherian Dromiciops gliroides (Spotorno et al. 1997), and some pygmy possums such as Cercartetus (Rofe and Hayman, 1985). As such it probably represents a retained plesiomorphic marsupial chromosome complement. The karyotype of Lasiorhinus latifrons differs from Vombatus in having a large pericentric inversion in its chromosome 1 (probably involving C1 and C6 sequences) and a small paracentric inversion towards the distal end of the long arm of its chromosome 2 in C9 (Rofe and Hayman, loc. cit.). In contrast, the 2n=16 karyotype of the koala, Phascolarctos cinereus, probably resulted from a simple centric fission in the equivalent of the submetacentric wombat second autosomal element thereby separating conserved elements C7+C8 from C9. The larger of the two resulting acrocentric chromosome pairs (C9) subsequently underwent an inversion event (Hayman, 1990).

Petauroidea: Petauroidea had probably diverged from Australoplagiaulacoida in the Eocene. Acrobatidae is the basal family and both of its constituent genera (Acrobates and Distoechurus) have only single living species which retain a 2n=14 chromosome complement superficially similar to that seen in wombats and burramyids. It is not, however, identical. Only the feather-tailed glider (Acrobates pygmeus) has so far been G-banded. A comparison with Vombatus G-banded chromosomes shows that some minor changes have occurred in the evolution of Acrobates’ karyotype including a small pericentric inversion in chromosome 2 (probably involving conserved segments C8 and C9), a small inversion in chromosomes 5 (breakpoints probably in C15 and C16) and another in chromosome 6 (probably involving breaks in C17 and C18) (Rofe and Hayman, 1985: Fig. 1). Unfortunately there is currently no G-band data for the closely related Distoechurus pennatus for comparison, though its chromosomes are morphologically similar to those of Acrobates (Westerman et al. 1984). Neither is there any cross-species chromosome painting information for acrobatids (or for any other petauroids) to confirm that the break points suggested above are correct.

The remaining petauroid families: Tarsipedidae, Petauridae and Pseudocheiridae are all ‘old’, having all originated in the later Eocene. All three show evidence of dramatic chromosomal reorganisation during their evolution; the monotypic family Tarsipedidae expanding from 2n=14 to 2n=24 chromosomes; the chromosome numbers of petaurid and pseudocheirid species ranging from 2n=10 to 2n=22 (see Figure 1). A consideration of the well resolved phylogenetic relationships within this superfamily in which only the relative placements of Gymnobelideus (sister to Petaurus in the Bayesian tree, albeit with little support, but weakly sister to Dactylopsila in the ML tree - only 64% bootstrap support) and of Pseudochirops (Petropseudes) dahli relative to the two other Pseudochirops species are not resolved, strongly suggests that a major reorganisation of the karyotype took place in the common ancestor of Tarsipedidae and of the Petauridae + Pseudocheiridae clade shown in Fig 1. We would note that addition of extra sequences and additional taxa (Meredith et al. in press) completely resolves Gymnobelideus as sister to Petaurus and P dahli is resolved as sister to Pseudocheirops corinnae, P. albertisii and P. cupreus.

Following the three small inversions retained in the basal acrobatid clade, a number of centric fissions occurred in some of these bi-armed ‘ancestral petauroid’ autosomes giving rise to the larger diploid chromosome numbers seen in the modern families Tarsipedidae, Petauridae and Pseudocheiridae. A detailed comparison consideration of the G-banded chromosomes of Tarsipes rostratus (2n=24) with those in Acrobates (Hayman, 1990) suggests that honey-possum chromosomes are readily derivable from an ancestral petauroid 2n=14 karyotype via three centric fissions (probably ancestral petauroid chromosome pairs 1, 3 and 4 which resulted in the uncoupling of C1-3 from C4-6, of C10 from C11+C12, and of C13 from C14). In addition, there was perhaps one further chromosomal change that involves segments of ancestral petauroid chromosome 3 (see fig. 1b of Hayman, 1990).

Of the nine living species of Petauridae, chromosomes of only six are known; three Petaurus species, Gymnobelideus leadbeateri (all 2n=22), and two Dactylopsila species (both 2n=18) (Murray et al. 1990). Reconstruction of the ancestral karyotype of this family - and of Pseudocheiridae (see Figure 1), based mainly on G-banding studies, suggest that it probably comprised 22 chromosomes derived from a 2n=14 ‘ancestral petauroid’ karyotype via centric fissions and possibly followed by some centric shifts. The karyotypes seen in Gymnobelideus and Dactylopsila species subsequently underwent a number of chromosome fusions, translocations or inversions. Thus, for example, the chromosomes of Gymnobelideus are very different from those of Petaurus in having one large sub-metacentric chromosome pair with the rest of the chromosomes being more distinctly one-armed (centromeres being sub-terminally located) relative to Petaurus, probably as the result of multiple pericentric inversions (Murray et al. 1990).

The evolution of pseudocheirid karyotypes from an ancestral petauroid 2n=22 form seems to have been much more complex, though with only two species G-banded to date, a full understanding of chromosome evolution in this group is difficult. In marked contrast, the direction of chromosome evolution in the two gliders, Petauroides volans and Hemibelideus lemuroides, seems clear. The 2n=20 karyotype of Hemibelideus can be derived from an ancestral form (retained in Petauroides) by means of a simple centric fusion event (McQuade, 1984).

All species of Pseudocheirus retain a karyotype with 2n=20 chromosomes (Hayman, 1990), though there has been some re-patterning within this general form. Chromosome numbers in the genera Pseudochirulus (2n=12-18), Pseudochirops (2n=10-16), and Petropseudes (2n=16) are all lower - probably as the result of centric fusions from an ancestral petauroid karyotype of 22 chromosomes. As noted above, Pseudochirulus canescens has 2n=18 chromosomes per nucleus whilst Pseudochirulus herbertensis has only 12. Given that the most closely related species to P. herbertensis (Pseudochirulus cinereus) has 16 chromosomes, this suggests that the direction of karyotypic change in this genus has been via two autosomal fusions. The multiple sex chromosome systems seen in both of these Pseudochirulus species are, most likely, the result of X-autosome translocations that took place in their last common ancestor. Unfortunately our nuclear gene based phylogenetic tree currently contains information only for Pseudochirops (Petropseudes) dahli, P. archeri and P. corinnae (all 2n=16) and P. cupreus (2n=10), yet the known phylogenetic relationships of these taxa again point to an evolutionary reduction of chromosomes of the group - probably from 2n=22 to 2n=16 in the common ancestor of this clade and then a further reduction by centric fusions in P. cupreus. Once again, cross-species painting waits to be done to ascertain which particular chromosomes and conserved blocks were involved in these events.



Macropodiformes: Cytogenetically, this largest group of diprotodontians is very well known. Karyotypes are very diverse, and contain both the lowest and highest marsupial chromosome numbers recorded. Many species have been either G-banded and/or the subject of cross-species chromosome painting and many of the karyotypic interrelationships have been resolved (Rofe 1979, Hayman, 1990, Glas et al. 1999). It has been suggested that the karyotype of the common ancestor of all crown group Macropodiformes comprised 2n=22 acrocentric chromosomes made up of seven pairs of telocentrics, two pairs of acro-sub metacentrics and a single pair of small metacentric autosomes along with a pair of sex chromosomes (see Figure 2e). This “new” chromosome configuration, seen in the common ancestor of all macropodiforms (AMac), is retained today in genera such as Hypsiprymnodon, Bettongia, Thylogale, Petrogale and Dorcopsis, AMac chromosome 1 comprises conserved blocks C8+C9; AMac2 has C13+C14; AMac3 has C11+C12; Amac4 has C4-C6; Amac5 has C15+C16; AMac6 has C10; AMac7 has C7+C17, AMac8 has C2+C3; AMac9 has C18; and AMac10 comprises C1 (see Figure 3e). The X chromosome comprises C19. (Nomenclature of Rens et al 2003b).

Hysiprymnodontidae: This family, basal to the macropodiform radiation, comprises a single extant species - the musky rat-kangaroo Hypsiprymnodon moschatus. The species is characterised by a karyotype of 2n=22 chromosomes.

Potoroidae: Relationships within Potoroidae are well resolved at the genus level. Aepyprymnus is sister to Bettongia and these two taxa (Bettongini) are divergent from Potorous (Potoroini). It is estimated that these two tribes had diverged from one another by the middle Miocene (Meredith et al. 2009) and further radiations within the two tribes occurred in the later Miocene and Plio-Pleistocene periods. The phylogenetic relationships of the extinct desert rat kangaroo Caloprymnus seem to lie with Potorous based on limited mitochondrial data from this extinct species (Westerman et al. 2004). Relationships between species within both Bettongia and Potorous await more detailed study with more extensive datasets, but P. longipes diverged from other P. tridactylus, at least 10 million years ago (Meredith et al. 2008b).Although the AMac 2n=22 karyotype is apparently retained in all four species of Bettongia, no living potoroine species shows it. Within Bettongia there have been some pericentric inversions/centric shifts making some chromosomes more metacentric as suggested by G-banding (Sharman et al. 1980). The two other extant potoroid genera, Aepyprymnus and Potorous, are characterised by dramatic karyotypic changes. Aepyprymnus, a member of the Bettongini, has undergone a further series of centric fissions to generate the highest number of chromosomes known for any marsupial (2n=32), whilst Potorous longipes (Potoroini) shows what appears to be a single additional centric fission to increase its chromosome number from 22 to 24 (see below). In contrast, both P. tridactylus and P. gilberti, the only other potoroo species for which we have chromosome data, have undergone a number of fusion and/or translocation events involving both autosomal and sex chromosomal elements, as well as possible centric shifts to generate distinct karyotypes with 2n=12XX♀/13XY1Y2♂ multiple sex chromosome systems. The strong similarities between these two karyotypes suggest that the initial changes took place in a common ancestor of the two species but given the inter-species relationships of the genus Potorous suggested by the mitochondrial DNA sequences (Sinclair and Westerman, 1997, Westerman et al. 2004) only G-banding and cross-species chromosome painting with P. gilberti will clarify this. G-banding of P. longipes and P. tridactylus (Johnston et al. 1984) and Aepyprymnus rufescens (Rens et al., 2003a) as well as cross-species chromosome painting involving the latter two species have clearly demonstrated which particular chromosomes (and conserved segments) were involved in these chromosomal reorganisations (Hayman, 1990, Rens et al. 2003a). Knowledge of the G-band pattern of P. longipes (Johnston et al. 1984) suggests that its 2n=24 karyotype is the result of a centric fission in the AMac 4 which separates conserved block C4 from C5+C6 to give two new linkage groups. This latter chromosome is the element that later fused with the X chromosome in P. tridactylus (and P. gilberti?) whilst that comprising C4 fused with AMac 1 (C8+C9) and AMac 10 (C1) to give rise to the new P. tridactylus chromosome 1 (Rens et al. 2003: Figure 4).

Macropodidae: Phylogenetic relationships between extant genera and species of kangaroos and their relatives are also well known. (Fig 1 and see Meredith et al. 2009). All molecular studies suggest that one of the first macropodid lineages to diverge (~16-23Mya) was that represented today by the banded hare wallaby, Lagostrophus fasciatus, which may possibly be the last surviving species of an otherwise extinct group (Sthenurinae) (Westerman et al. 2002). Only a single species, L. fasciatus, survives today. It is characterised by having 24 chromosomes, suggesting the occurrence of an additional centromeric fission in one of the bi-armed chromosome pairs of the ancestral macropodid 2n=22 karyotype. Which particular chromosome (and conserved blocks) was involved awaits chromosome painting studies in this species.

Chromosome evolution in Macropodidae is probably the best understood of all marsupial groups, having been studied in detail with both G-banding and cross species chromosome painting techniques. Indeed our current ideas on modes of chromosome evolution within the group, and of conserved marsupial genomic blocks, stem largely from the studies by Rofe, Rens, Eldridge and their co-workers (Eldridge and Close, 1993, O’Neill et al. 1999, Glas et al. 1999, Hayman, 1990; Rens et al. 1999, 2001, 2003a, b; Rofe, 1978). Our well resolved phylogenetic tree for the superfamily (see Fig 1 and Meredith 2008b) illustrates clearly just which of the 19 conserved blocks were involved in particular fusions, and other changes, as well informing us as to when many of these chromosomal rearrangements occurred. Our tree-based approach, based as it is on a well substantiated multi nuclear gene dataset, allows us to correct some of the previously postulated pathways for chromosome evolution in macropodids which were based on much less substantial datasets. Figure 1 and Supplementary Figure 1 show that the genus Macropus is paraphyletic since it includes the swamp wallaby (Wallabia bicolor). It is also clear that two of the three constituent subgenera - Notamacropus and Osphranter, are clearly distinct from the other - Macropus. The swamp wallaby seems to be most closely related to the Notamacropus clade (though without strong bootstrap support - see Meredith et al. 2009 and Supplementary Fig 1) and the red kangaroo is sister to the two wallaroos. M. rufus is clearly a member of Osphranter and not sister to all Macropus species as suggested by Bulazel et al. (2007). Since the swamp wallaby is, phylogenetically, more closely related to M. agilis, M. eugenii and other members of the Notamacropus clade, then the 2n=10♀, 11♂ chromosomes of M. (Wallabia) bicolor could not have been derived from those of a common ancestor with M. giganteus as suggested by Bulazel et al. (2007: Fig 3a), but rather from a 2n=20 common ancestor with M. rufus, M. robustus and Notamacropus species (see below). Inferences on the direction of chromosome change in the evolution of any group of organisms can only be correctly drawn if the phylogenetic tree underpinning them is well resolved.

The centric fusions/Robertsonian translocations linking ancestral macropodiform (AMac) chromosomes 5 and 8 (5^8), and chromosomes 6 and 9 (6^9) in species of subgenus Notamacropus must have occurred after the divergence of these taxa from a common ancestor with the subgenus Osphranter, since both subgenera share the same AMac 1^10 fusion. Indeed this is the only centric fusion seen in M. (Osphranter) rufus. Macropus robustus (and probably M. antilopinus) have further fusions linking AMac chromosomes 5 with 6 (5^6) and 8 with 9 (8^9). Although the chromosome number of the black wallaroo, M. bernardus, is known to be 2n=18, its chromosomes have so far not been either G-banded or subject to cross-species chromosome painting. Thus, which particular members of its karyotype have been involved in the second fusion that reduced its diploid number from 20 to 18 is unknown. However, we may make predictions based on the phylogenetic relationships of this species as determined by DNA sequence analysis. Limited mitochondrial DNA sequences for M. bernardus have been obtained and analysis (not shown) places it as part of the Osphranter clade and more specifically as sister to M. antilopinus + M. robustus -i.e. (M. rufus, (M. bernardus, (M. antilopinus, M. robustus))). This would suggest that one of the two chromosome fusions seen in M. bernardus will prove to be between AMac 1 and 10, the other to have involved either AMac5 and 6, or AMac chromosomes 8 and 9.

Given the relationship of M. (Wallabia) bicolor to Notamacropus and Osphranter seen in our phylogenetic tree (and in Meredith et al. 2008b), the derivation of the swamp wallaby karyotype can also be readily understood. The first chromosomal change in this group of kangaroos and wallabies was the AMac1^10 fusion, the only fusion seen in M. rufus and common to Notamacropus and Osphranter species. The swamp wallaby karyotype can then be derived via a subsequent translocation between the 1^10 and 6^9 fused chromosomes of a Notamacropus-type arrangement giving rise to a new 1^9 combination and a 6^10 element which subsequently interacted with the initially separate AMac 4 to link three macropodiform ancestral chromosomal elements together into a single new linkage group (6^10^4). At the same time there would have been a complex translocation involving chromosomes 2, 7 and the X to give the complex swamp wallaby sex-chromosome system. M. (Notamacropus) irma also had some subsequent changes to its chromosomes involving a unique pericentric inversion in its chromosome 3.

Karyotypic restructuring in other kangaroo lineages also become clearer when one uses a tree-based approach. These changes include the pericentric inversions/centric shifts in Setonix that make its chromosomes 1 and 2 submetacentric; the fusions seen in D. vanheurni to give a 2n=18 karyotype; those in Onychogalea (2n=20 and 18); those in Petrogale species (giving karyotypes with 2n=16, 18, and 20 chromosomes) as well as the complex of fusions and translocations seen in the hare wallabies (Lagorchestes) (see Hayman, 1990: Fig 2). In L. conspicillatus, AMac 3 and AMac 8 seem to have separately fused with the two arms of the AMac Y chromosome, and the other AMac 3 has fused with the AMac X to give the complex sex-chromosome system seen in this species. At the same time AMac chromosomes 6, 10 and 7 fused to give a single chromosome (6^10^7) (Hayman, 1990; Hayman and Sharp, 1981) thereby reducing the nuclear chromosome number to 15♂ 16♀. Although the number of chromosomes of the closely related species L. hirsutus were initially reported by Sharman (1961) as 2n=22 along with a supporting camera lucida drawing. Without any real comment, Sharman subsequently changed the number to 2n=20 and suggested that the reduction was due to a centric fusion of chromosomes 2 and 6, although no karyotype was ever been published to substantiate this change and assertion. Further observations of karyotypes of L. hirsutus animals from Dorre and Bernier Islands in Western Australia also proved to be 2n=20 (Eldridge, pers comm.). Since no G-banding or cross species chromosome painting has yet been done on this species, we cannot be certain as to which chromosomes were involved in the presumed fusion event. However, given what we know of the apparent non-random involvement of macropodiform chromosomes in karyotypic change and of the postulated changes in the closely related L. conspicillatus, it would be of interest to confirm that the single fusion in L. hirsutus involved AMac chromosomes 6 and 10.

In describing the sex chromosomes of O. unguifera, Sharman (1961) noted that they were ‘somewhat different from those of other marsupials… the Y is larger than the smallest autosome … giving a bivalent different in shape, and larger than the XY bivalent in other marsupials’. This size difference could be due to the incorporation of autosomal material into the sex chromosomes. If this were so, then the 2n=20 karyotype of O. unguifera could actually represent a Neo XY system following fusions between the AMac X and one ancestral autosomal element along with fusion of the AMac Y chromosome with the other ancestral autosomal homologue, rather than being due to a ‘simple’ autosome-autosome fusion event. G-banding and/or chromosome painting would confirm this suggestion as well as identifying the ancestral autosome involved.

Tree kangaroos (genus Dendrolagus) are generally viewed as being secondarily derived from a ground dwelling ancestor, most likely from a rock wallaby-like common ancestor (Flannery et al. 1996). Within tree kangaroos, two distinct groups are recognised, the long footed forms (D. inustus, D. lumholtzi and D. bennettianus) and the short -footed forms (other species) but little is known of either the relationships between or within these groups. Although we only included two species of tree kangaroos in our current study (both were short-footed forms), the phylogenetic relationships shown in Figure 1 clearly shows that tree kangaroos belong to a well defined clade comprising Thylogale, Petrogale and Dendrolagus (with the latter two genera as sisters). This group of genera is consistently linked with the forest wallabies Dorcopsis and Dorcopsulus though only weakly supported. Since all genera in this clade, apart from Dendrolagus (and Dorcopsulus 2n=18), retain the ancestral macropodiform karyotype of 22 chromosomes, then the low chromosome numbers seen in extant members of the genus Dendrolagus (12 and 14) must represent a highly derived state and not be a simple retention of the plesiomorphic marsupial karyotype as originally suggested by Rofe and Hayman (1985). The derived nature of tree kangaroo karyotypes is supported by consideration of both G-banding (Rofe, 1978, Hayman, 1990) and the chromosome painting studies of deLeo et al. (1999). Postulated fusions include those between AMac 5 and 10 (5^10), 1^7, 3^6, 8^9 and probably 4^X. Many of these same chromosomes are involved in fusions in Petrogale species (see Eldridge et al. 1988, Eldridge and Close, 1992, Sharman et al. 1990). Since all tree kangaroos karyotyped so far have 2n=12 or 14 chromosomes, this points to the occurrence of a number of centric fusions having occurred in an ancestral tree kangaroo at the time of origin of this group - which may have been as early as the Pliocene (see Flannery et al. 1996). Since neither the precise phylogenetic interrelationships of living tree kangaroos (Bowyer et al. 2003, Meredith unpublished data) nor chromosome numbers of all species are known at present, considerations of either the process or precise direction of chromosomal evolution in this group must remain speculative. Using our current knowledge of the phylogenetic relationships of Dendrolagus species and of their chromosome numbers, the fact that 2n=12 and 2n=14 karyotypes are found in both long-footed and short-footed lineages (see Table 1, Hayman 1990), then we might predict that many, if not all, of those species still chromosomally undescribed will have 2n=14 chromosomes as this karyotype must have arisen very early in the evolution of tree kangaroos.

b) Chromosomal evolution and Interstitial telomeric sequences in didelphoids

Phylogenetic relationships of didelphid marsupials based a combined non-molecular and concatenated nuclear gene dataset of Voss and Jansa (2009) are shown in Supplementary Figure 2. The phylogenetic placement of Glironia venusta is still unresolved (see Voss and Jansa, 2009: Fig 36). Plotting chromosome numbers of various didelphids onto this phylogenetic tree shows that, as with australidelphian marsupials, the ancestral karyotype probably comprised 2n=14 chromosomes with twelve autosomal and two sex chromosome elements.. G-banding studies suggest that this ancestral karyotype, retained for example in Caluromyinae, differed from that seen in wombats, pygmy possums bandicoots and Dromiciops by a number of small pericentric inversions involving chromosomes 1, 3, 5 and 6 (Rofe and Hayman, 1985). This ancestral didelphoid karyotype is retained in most living species including all members of Caluromyinae and many clades within Didelphinae but is changed by means of centric fissions to the higher chromosome numbers in two major groups, viz Monodelphis species (Didelphinae, Marmosini 2n=18) and Didelphis, Chironectes, Philander and Lutreolinus (Didelphinae, Didelphini, 2n=22). Centric fissions also seem to have occurred, probably independently, in Tlacuatzin (2n=22) and Glironia venusta (2n=18). The chromosomal status of Hyladelphinae is currently unknown. Thus the cytogenetic evidence favours an evolutionary increase in chromosome number in didelphids, as is true for australidelphids, though there seem to be no examples of the subsequent chromosomal reductions from the high chromosome numbers as seen in tree kangaroos and macropodids.

It has often been suggested (Svartman and Vianna-Morgante, 1998, Svartman, 2009) that presence of interstitial telomeric sequences (ITS) in the centric heterochromatin of the bi-armed chromosomes of didelphoid species with 2n=14 karyotypes is evidence of evolutionary fusions involving those chromosomes. Whilst this suggestion is possible, other explanations may be necessary, especially where the number of ITS vary in samples of Micoureus demerarae taken from different localities in the species range (Pagnozzi et al, 2000). Also, Ruiz-Herrera et al. (2002) have identified two different kinds of ITS: one comprising large stretches of telomere-like DNA located mainly at centromeres and another with short stretches of telomere repeats located interstitially in chromosomes. These two kinds of ITS probably have different origins and properties as the former seem to be intrinsically prone to breakage and may represent sites of ancient fusions/rearrangements but the latter may be inserted at the sites of double-strand DNA breaks which were repaired using systems including telomerase and thus not indicate sites of centric fusions.

Considering the presence or absence of ITS on the didelphoid species shown in Supplementary Figure 2 raises interesting questions. Thus, although no ITS have been identified on the 2n=22 chromosomes of Chironectes minimus, Didelphis albiventris D. marsupialis or Lutrelina crassicaudata, they are present on the largest four pairs of autosomes of the 2n=14 species Marmosops parvidens - in line with expectations based on their marking sites of past fusion events. It was noted by Svartman (2009) that whereas a single ITS was detected on the large chromosome 1s of three Monodelphis species with 2n=18 chromosomes (including M. domestica), none were present on the metacentric chromosome 2s. Similarly, only some of the four largest bi-armed chromosomes of Marmosops incanus carried ITS, only the largest of the six pairs of autosomes of Gracilianus microtarsus had ITS on them, and none of the larger bi-armed autosomes of Caluromys philander, Metachirus nudicaudatus, and Gracilianus emiliae had detectable ITS. IF, fluorescence-detected ITS really do relate to or mark past evolutionary chromosome fusion events, then why are they conspicuously absent in so many species?


Supplementary References

Bowyer JC, Newell GR, Metcalfe CJ, Eldridge MBD, 2003 Tree kangaroos Dendrolagus, in Australia: Are D. lumholtzi and D. bennettianus sister taxa? Aust Zool. 32: 207-213.

DeLeo AA, Guedelha N, Toder R, Voullaire L, Ferguson-Smith MA, O’Brien PCM, Graves JAM, 1999. Comparative chromosome painting between marsupial orders: relationships with a 2n=14 ancestral marsupial karyotype. Chromosome Res. 7: 509-517.

Eldridge MDB, Dollin AE, Johnston PG, Close RL, Murray JD, 1988 Chromosomal rearrangements in rock wallabies, Petrogale (Marsupialia, Macropodidae) I. The Petrogale assimilis species complex: G-banding and synaptonemal complex analysis. Cytogenet Cell Genet. 48: 228-232.

Flannery TF, Martin R, Szalay A, 1996. Tree Kangaroos: A curious Natural History. Reed Books, Melbourne.

Hayman DL, Sharp PJ, 1981. Verification of the structure of the complex sex chromosome system in Lagorchestes conspicillatus Gould (Marsupialia: Mammalia). Chromosoma. 83: 249-262.

Johnston PG, Davey RJ, Seebeck JH, 1984. Chromosome homologies in Potorous tridactylus and P. longipes (marsupialia: Macropodidae) based on G-banding. Aust J Zool. 32: 319-324.

MacQuade, LR, 1984. Taxonomic relationship of the greater glider, Petauroides volans, and the lemur-like possum, Hemibelideus lemuroides. In Smith AP, and Hume ID, editors. Possums and Gliders. Mammal Society of Australia, Sydney. p303-310.

Meredith RW, Mendoza M, Roberts KK, Westerman M, Springer MS, 2010. A phylogeny and timescale for Pseudocheirid (Marsupialia: Diprotodontia) evolution in Australia and New Guinea. J Mammal Evol. 17: (in press)

Murray JD, Donnellan S, McKay GM, Rofe RH, Baverstock PR, Hayman DL, Gelder M, 1990. The chromosomes of four genera of possums from the family Petauridae (Marsupialia: Diprotodonta). Aust J Zool. 38: 33-39.

Rofe RH, Hayman D, 1985. G-banding evidence for a conserved complement in the Marsupialia. Cytogenet Cell Genet. 39: 40-50.

Ruiz-Herrera A, Nergadze SG, Santagostino M, Giulotto E, 2008. Telomeric repeats far from the ends: mechanism of origin and role in evolution. Cytogenet Genome Res. 122: 219-228.

Sharman GB, Murtagh CE, Johnson PM, Weaver CM, 1980. The Chromosomes of a Rat-kangaroo attributable to Bettongia tropica (Marsupialia : Macropodidae). Aust J Zool. 28: 59-63.

Sinclair EA, Westerman M, 1997. Phylogenetic relationships within the genus Potorous (Marsupialia: Potoroidae) based on allozyme electrophoresis and sequence analysis of the cytochrome b gene. J Mammal Evol. 4: 147-161.

Svartman M, 2009. American marsupials: why study them? Genet Mol. Biol. 32: 675-687.

Svartman M, Vianna-Morgante AM, 1998. Karyotype evolution of marsupials: from higher to lower diploid numbers. Cytogenet Cell Genet. 82: 263-266.

Voss RS, Jansa SA, 2009. Phylogenetic relationships and classification of didelphid marsupials, an extant radiation of New World metatherian mammals. Bull Am Mus Nat Hist. 322: 1-177.

Westerman M, Loke S, Springer MS, 2004. Molecular phylogenetic relationships of two extinct potoroid marsupials Potorous platyops and Caloprymnus campestris (Potoroinae: Marsupialia). Mol Phylogenet Evol. 31: 476-485.


Supplementary Table S1. Genbank accession numbers for new diprotodontian species used in this study.


Species

BRCA1

IRBP

APOB

RAG1

vWF

Petrogale lateralis

GU566716

GU566719

GU566713

GU566722

GU566725

Thylogale brunii

GU566717

GU566720

GU566714

GU566723

GU566726

Cercartetus concinnus

GU566715

GU566718

GU566712

GU566721

GU566724

Supplementary Figure Legends


Supplementary Figure S1. Bayesian tree for marsupials based on sequences for five nuclear genes (APOB, BRCA1, IRBP, RAG1, VWF). Placental outgroups are not shown. Mean Bayesian posterior probabilities expressed as percentages and based on two independent runs less than 100% are shown above line);. Similar values corresponding to maximum likelihood bootstrap estimates are below the line. Did = Didelphimorphia; V = Vombatiformes; Das = Dasyuromorphia; Per = Peramelemorphia; N = Notoryctemorphia; M = Microbiotheria; P = Paucituberculata.
Supplementary Figure S2. Phylogenetic relationships of ameridelphian marsupials after Voss and Jansa, (2009). Chromosome numbers for each species, where known, are indicated as follows: green - 2n=14, brown - 2n=18, red 2n=22, black - unknown.. Probable chromosome numbers of ancestors are indicated at each node.


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