Maria A. Nilsson; Gennady Churakov; Mirjam Sommer; Ngoc Van Tran; Anja Zemann; Jürgen Brosius; Jürgen Schmitz

“ All ten are absent in other mammals, significantly confirming the monophyly of marsupials (p = 2.0×10−5; [10 0 0] [15] ) .
The other 43 phylogenetically informative retroposon markers provide significant support for most of the basal splits within marsupials. The earliest marsupial divergence was previously impossible to resolve based on sequence data, which could not distinguish between Paucituberculata and Didelphimorphia as the sister group to Australidelphia [14] , [16] – [17] . ”

“ Thus, the current findings support a simple paleobiogeographic hypothesis, indicating only a single effective migration from South America to Australia, which is remarkable given that South America, Antarctica, and Australia were connected in the South Gondwanan continent for a considerable time.
The search for diagnostic South American or Australidelphian marsupial morphological characters has been so far confounded by the lack of a resolved marsupial phylogeny [19] , [20] , [28] . ”

“ Abstract Genome-wide comparisons of shared retroposon insertion patterns resolve the phylogeny of marsupials, clearly distinguishing South American and Australian species and lending support to Didelphimorphia as the basal split.==Abstract== The Australasian and South American marsupial mammals, such as kangaroos and opossums, are the closest living relatives to placental mammals, having shared a common ancestor around 130 million years ago. ”

“ Several retroposon families were active around and after the split of Australasian [31] and South American marsupials and potentially encrypt information about their phylogeny. For successful and focused experimental retroposon screening it is invaluable to have, a priori, a map of the ancestral retroposon activities. ”

“ No other sequenced mammalian genome has shown as high a percentage of discernible retroposed elements as marsupials (52%) [5] , an extremely large number of possible informative markers.
In addition, because young retroposed elements can insert into older elements, but older, inactive elements are not capable of inserting into younger ones, nested retroposon insertion patterns provide invaluable information about the relative times during which given retroposon families integrated into genomes. ”

“ On the other hand, we also did not find any loci with MIR3_Mars elements present in opossum plus Paucituberculata but absent in kangaroo, which would have supported the alternative of a close relationship between Didelphimorphia and Paucituberculata. We then screened for markers that would support the alternative hypothesis of Paucituberculata being the sister to all marsupials by performing an exhaustive in silico pre-screening for orthologous MIR3_Mars elements present in short introns of opossum and kangaroo. ”

“ The outstanding advantage of using retroposon presence/absence data for phylogenetic reconstructions is the low probability of insertion homoplasy. Independent parallel insertions of identical elements or exact deletions are extremely rare [9] , but nevertheless not completely negligible, especially after genome-wide in silico screening of rare informative loci. LINE1-mobilized elements, in particular, show a slight preference for a TTAAAA consensus insertion motif [26] , but on the other hand, such elements are rare in the deep phylogenetic branches of marsupials (Figure 1; Figure S1) . ”

“ These three groups of elements were then used as a basis to screen for phylogenetically informative markers present in (1) the opossum lineage, (2) the branches leading to kangaroo, and (3) to find marsupial monophyly markers.
Transposition in transposition (TinT) pattern of selected marsupial SINEs.In genomes there is an intricate association between SINE elements and the much longer long interspersed elements (LINEs) , as the replication of SINEs ultimately depends on the enzymatic machinery of LINEs. ”

“ The extended presence of diverse SINE transposition systems found in marsupial genomes is unique in mammals. Twenty-four SINE subfamilies were extracted from genomic data of M. domestica and M. eugenii to screen for nested insertions, revealing information about their relative activity periods. Elements shown in black denote L3-, those in blue L2-, those in green RTE-, and those in red L1-mobilized SINEs. Ovals represent the 50% probability of the activity distribution and horizontal lines indicate the 90% probability of the activity distribution. ”

“ Didelphimorphia, Virginia opossum; Paucituberculata, shrew opossum; Microbiotheria, monito del monte; Notoryctemorphia, marsupial mole; Dasyuromorphia, Tasmanian devil; Peramelemorphia, bilby; Diprotodontia, kangaroo. Phylogenetically informative retroposon insertions are shown as circles. Gray lines denote South American species distribution, and black lines Australasian marsupials. The cohort Australidelphia is indicated as well as the new name proposed for the four “true” Australasian orders (Euaustralidelphia) . Table 1 "Presence-absence table of the marsupial markers. ”

“ Kuritzin, A & Mayr, G (2007) , Waves of genomic hitchhikers shed light on the evolution of gamebirds (Aves: Galliformes) ., vol. 7, p. 190, 17925025, pmid:17925025 ↑ Lou, Z; Ji, Q; Wible, J. R & Yuan, C-X (2003) , An early Cretaceous tribosphenic mammal and metatherian evolution., vol. ”