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When Genomics Is Not Enough: Experimental Evidence for a Decrease in LINE-1 Activity During the Evolution of Australian Marsupials.

ABSTRACT: The autonomous transposable element LINE-1 is a highly abundant element that makes up between 15% and 20% of therian mammal genomes. Since their origin before the divergence of marsupials and placental mammals, LINE-1 elements have contributed actively to the genome landscape. A previous in silico screen of the Tasmanian devil genome revealed a lack of functional coding LINE-1 sequences. In this study we present the results of an in vitro analysis from a partial LINE-1 reverse transcriptase coding sequence in five marsupial species. Our experimental screen supports the in silico findings of the genome-wide degradation of LINE-1 sequences in the Tasmanian devil, and identifies a high frequency of degraded LINE-1 sequences in other Australian marsupials. The comparison between the experimentally obtained LINE-1 sequences and reference genome assemblies suggests that conclusions from in silico analyses of retrotransposition activity can be influenced by incomplete genome assemblies from short reads.

SUBMITTER: Gallus S

PROVIDER: S-EPMC5010896 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature

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When Genomics Is Not Enough: Experimental Evidence for a Decrease in LINE-1 Activity During the Evolution of Australian Marsupials.

Gallus Susanne S Lammers Fritjof F Nilsson Maria Anna MA

Genome biology and evolution 20160825 8

The autonomous transposable element LINE-1 is a highly abundant element that makes up between 15% and 20% of therian mammal genomes. Since their origin before the divergence of marsupials and placental mammals, LINE-1 elements have contributed actively to the genome landscape. A previous in silico screen of the Tasmanian devil genome revealed a lack of functional coding LINE-1 sequences. In this study we present the results of an in vitro analysis from a partial LINE-1 reverse transcriptase codi ...[more]

PMID: 27389686

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Project description:BackgroundThe order Dasyuromorphia is a diverse radiation of faunivorous marsupials, comprising >80 modern species in Australia and New Guinea. It includes dasyurids, the numbat (the myrmecobiid Myrmecobius fasciatus) and the recently extinct thylacine (the thylacinid Thylacinus cyncocephalus). There is also a diverse fossil record of dasyuromorphians and "dasyuromorphian-like" taxa known from Australia. We present the first total evidence phylogenetic analyses of the order, based on combined morphological and molecular data (including a novel set of 115 postcranial characters), to resolve relationships and calculate divergence dates. We use this information to analyse the diversification dynamics of modern dasyuromorphians.ResultsOur morphology-only analyses are poorly resolved, but our molecular and total evidence analyses confidently resolve most relationships within the order, and are strongly congruent with recent molecular studies. Thylacinidae is the first family to diverge within the order, and there is strong support for four tribes within Dasyuridae (Dasyurini, Phascogalini, Planigalini and Sminthopsini). Among fossil taxa, Ankotarinja and Keeuna do not appear to be members of Dasyuromorphia, whilst Barinya and Mutpuracinus are of uncertain relationships within the order. Divergence dates calculated using total evidence tip-and-node dating are younger than both molecular node-dating and total evidence tip-dating, but appear more congruent with the fossil record and are relatively insensitive to calibration strategy. The tip-and-node divergence dates indicate that Dasyurini, Phascogalini and Sminthopsini began to radiate almost simultaneously during the middle-to-late Miocene (11.5-13.1 MYA; composite 95% HPD: 9.5-15.9 MYA); the median estimates for these divergences are shortly after a drop in global temperatures (the middle Miocene Climatic Transition), and coincide with a faunal turnover event in the mammalian fossil record of Australia. Planigalini radiated much later, during the latest Miocene to earliest Pliocene (6.5 MYA; composite 95% HPD: 4.4-8.9 MYA); the median estimates for these divergences coincide with an increase in grass pollen in the Australian palynological record that suggests the development of more open habitats, which are preferred by modern planigale species.ConclusionsOur results provide a phylogenetic and temporal framework for interpreting the evolution of modern and fossil dasyuromorphians, but future progress will require a much improved fossil record.

Project description:The 2019-2020 Australian bushfire season had a devastating impact on native wildlife. It was estimated that 3 billion native animals were impacted by the fires, yet there are few estimates of the number of animals that were rescued and rehabilitated post-fire. Focusing on the state of New South Wales (NSW) and Kangaroo Island, South Australia, we used a case study approach to determine the number of marsupials that were reported rescued due to the 2019-2020 bushfires in these areas and analysed species-specific trends in rescue and release success. In NSW, we found 889 reports of fire-affected marsupials in 2019-2020, mostly comprising kangaroos and wallabies (macropods; n = 458), koalas (n = 204), and possums (n = 162), with a smaller number of wombats (n = 43) and other marsupial species. Most reports of fire-affected marsupials occurred 6-8 weeks after fire ignition, and there was no difference in temporal frequency of rescues between marsupial groups. For the three main groups, the probability of survival and subsequent release differed, with macropods having the lowest probability of release after rescue (0.15 ± 0.04) compared to koalas (0.47 ± 0.04) and possums (0.55 ± 0.10). The type of injury was the main predictor of survival during rehabilitation for all three marsupial groups, with those malnourished/moribund or with traumatic injuries less likely to survive rehabilitation. Death or euthanasia occurred on the day of rescue for 77% of macropods, 48% of possums and 15% of koalas. Koalas most often died during rehabilitation rather than on the day of rescue, with 73% either dying or being euthanised between day 1 and 30 post-rescue, representing a potential welfare concern. On Kangaroo Island, koalas were the most frequently rescued marsupial species; most euthanasia cases and deaths occurred in a hospital, whereas other marsupials were mostly euthanised at triage. In both jurisdictions, koalas were over-represented while possums were under-represented relative to baseline population densities and wildlife rescue trends in the years before the 2019-2020 bushfires. These species differences in presentation post-fire warrant further investigation, as do the differences in triage, survival and release outcomes. It is hypothesised that the high intensity and large scale of the 2019-2020 fires impeded marsupial fire evasion tactics, as evidenced by the small number of animals found for rescue, and the differing rates of presentation relative to underlying population densities for the main marsupial groups. Based on our findings, there is a need for detailed record keeping and data sharing, development of consistent and evidence-based triage, treatment and euthanasia guidelines and deployment of trained wildlife emergency rescue teams with advanced search techniques to minimise animal suffering where safe to do so.

Dataset Information

When Genomics Is Not Enough: Experimental Evidence for a Decrease in LINE-1 Activity During the Evolution of Australian Marsupials.

Publications

When Genomics Is Not Enough: Experimental Evidence for a Decrease in LINE-1 Activity During the Evolution of Australian Marsupials.

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