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  • Thylacine Sequencing Project at PSU
    Wemmer Figure 1 A 1902 painting by Joseph Gleeson depicts a thylacine mother with three cubs including one in the pouch as they appeared on arrival at the National Zoo photo courtesy of Smithsonian Archives Our study sampled hairs from the mother and one of the cubs This particular thylacine family has loomed large in the study of the species both in life and death The longer surviving offspring subjects of one of the most famous photographs of the species Fig 2 provided a very rare example of thylacine young surviving to maturity in a zoo When the zoo obtained another adult male thylacine from Tasmania in 1904 the surviving daughter was the subject of one of few attempts at captive breeding ultimately unsuccessful All of these thylacines are today preserved as specimens in the United States National Museum of Natural History USNM Smithsonian Institution where they have been studied by several generations of comparative morphologists The mother on display at USNM as a taxidermy mount since 1904 can still be viewed in the museum s public galleries where it has been seen by tens of millions of visitors Notably the accompanying skeleton of this specimen has been the subject of previous efforts to obtain thylacine molecular sequence data using ancient DNA protocols and the USNM thylacines provide a partial focus for our study as well Figure 2 Among the highest quality of known thylacine photographs this portrait apparently depicts the two surviving offspring see Fig 1 two to three years after their arrival at the National Zoo One of these animals most likely the one in front is USNM 125345 a specimen sequenced for this study photo courtesy of Smithsonian Archives High resolution version 778 355 bytes The first Smithsonian specimen we investigated was the mother USNM 124662 skin

    Original URL path: http://thylacine.psu.edu/history.html (2016-02-12)
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  • Thylacine Sequencing Project at PSU
    the Swedish Museum that was collected in 1870 NRM 592206 but were unsuccessful Photo Staffan Waerndt copyright Swedish Museum of Natural History Anders Götherström and Love Dalén Copenhagen had been working with Stephan Schuster and Webb Miller on previous projects and were aware of the potential of the method that was being developed at Penn State As they were discussing the evolution of the Tasmanian tiger they remembered the specimen kept in ethanol at the Swedish Museum of Natural History This is really a beautiful piece of museum collection says Anders When looking at it you have the feeling that it is about to jump out of the jar and run away They contacted Stephan and Webb to investigate the possibility of sequencing a large portion of its DNA With the results from the previous mammoth studies we were hoping to be able to retrieve a complete mitochondrial sequence and to be able to better resolve the species phylogenetic position says Love Anders and Love collected material from the Swedish specimen and after initial successful screening partly supported by Spain s Juan Luis Arsuaga who also takes an interest in the evolution of the Tasmanian tiger full sampling on several

    Original URL path: http://thylacine.psu.edu/thyla2.html (2016-02-12)
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  • Thylacine Sequencing Project at PSU
    thylacine skin the average was 87 5 and for the ethanol stored specimen it was only 67 In addition to the problems that stemmed from working with shorter sequences analysis of the thylacine data was complicated by the lack of a genome sequence from a close relative to use as a reference point With mammoth we could use the sequence from the African savanna elephant which is the same as

    Original URL path: http://thylacine.psu.edu/techniques.html (2016-02-12)
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  • Thylacine Mitochondrial DNA
    The New Marsupial Mitochondrial Genomes the first thylacine specimen the second thylacine specimen the numbat

    Original URL path: http://thylacine.psu.edu/data.html (2016-02-12)
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  • Thylacine Sequencing Project at PSU
    with conservation plans for endangered species One approach would be to sample large percentages of global museum holdings for all recently extinct mammals for which adequate numbers of individuals across a reasonable timeframe multiple decades at least are available Note that approaching diversity through time with museum collections is especially powerful because samples are usually dated to the nearest year and commonly to the exact date and month Species meeting these criteria include approximately five Australian marsupials the Caribbean monk seal Japanese sea lion perhaps Steller s sea cow two bat species possibly the Falkland Islands wolf and a handful of rodents Pre extinction patterns of diversity can be compared across unrelated mammals that have suffered global extinction For example is there any overwhelming shared signature of mtDNA diversity that precedes global extinction in a predictable manner across taxa Or is this different for every species based on the unique conditions of its particular decline Documenting the spread of disease from invasive to native species Dates of local e g insular or global extinction are known for many mammal species and populations with reasonable accuracy as are dates of exotic introduction invasion of certain species into novel landscapes In some cases it is suspected that extinctions of native species have followed causally from introductions of certain invasive species especially on islands and that disease may be involved in some of these cases but these types of claims generally remain anecdotal The timing of the global decline of certain endemic insular rodent and potentially other small mammal lineages and the global spread of commensal rats offer many iterative analogous cases for studying the spread of disease from invasive rats with enormous global population sizes and greater exposure to a vast array of pathogens across time and geography to comparatively naive and

    Original URL path: http://thylacine.psu.edu/museomics.html (2016-02-12)
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  • Thylacine Sequencing Project at PSU
    include sequences from the nuclear genome which contains essentially all of the functional genetic information plus sequences from micro organisms found in the sample and perhaps coming from the living animal Data like ours can potentially answer fascinating questions about the thylacine s extinction Here is one example On pages 202 203 the book by Robert Paddle discusses an epidemic that hit thylacines in the years around 1900 It was described as resembling distemper or mange resulting in a loss of hair and producing scabs on the body It took the disease about six years to spread from the east coast of Tasmania to the west coast Among captive animals the disease could be fatal during 1900 1903 the Melbourne Zoo lost 16 of their 17 thylacines The disease may have persisted in the thylacines up to the very end the book by Guiler p 64 describes an animal that died in the Hobart Zoo in 1935 and thus was one of the very last to exist as follows its skin was in such poor shape as to be useless Currently the extent to which the epidemic contributed to the thylacines extinction is not known It is possible that the

    Original URL path: http://thylacine.psu.edu/understand.html (2016-02-12)
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  • Thylacine Sequencing Project at PSU
    project had been picked up by another group The sticking point for resurrecting the thylacine is likely to be the absence of a sufficiently close living relative to supply eggs and act as a surrogate If however it were somehow possible to boot up the thylacine genome in a living cell then things would be looking up The interesting thing about marsupials as opposed to other mammals is that pregnancy

    Original URL path: http://thylacine.psu.edu/restore.html (2016-02-12)
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  • Thylacine Sequencing Project at PSU
    is more closely related to kangaroos and koalas than to dogs or tigers The last known specimen died in a Tasmanian zoo in 1936 Thylacines have played a central role in discussions about the possibility of bringing extinct species back to life but despite the availability of many bones and other remains previous attempts to read thylacine DNA had been unsuccessful Miller Schuster and their colleagues were the first to report the genome wide sequence of an extinct animal the woolly mammoth in November 2008 They next collaborated with Anders Goetherstroem at Uppsala University in Sweden to target the Tasmanian Tiger because like the mammoth it was a coveted goal of ancient DNA researchers who considered its sequencing unfeasable due to the inadequate quality of the DNA available from specimens The speculation was that the only reason we were able to extract DNA from mammoth hair is that the mammoths had remained frozen in the Arctic permafrost but our success with the Tasmanian Tiger shows that hair can protect DNA for long periods under a variety of environmental conditions Schuster said In their new paper in Genome Research Miller Schuster and their colleagues describe the completion of the mitochondrial genome sequences of two Tasmanian Tigers one on display at the Smithsonian Museum and the other at the Swedish Museum of Natural History One specimen was prepared by a taxidermist as a skin and the other one was submerged in ethanol The team extracted DNA from small amounts of the hair of both specimens then used their methods to sequence independent copies of each region of the DNA molecule from many different fragments of DNA in the hairs The scientists assured the high fidelity of their results by independently determining each position in the sequences an average of 50 times The scientists sequenced all the DNA in the hair samples from the two Tasmanian Tigers including mitochondrial DNA which is the focus of the Genome Research paper and nuclear DNA which the team plans to analyze in future work This study in which we sequenced the complete mitochondrial genome of the thylacine species also shows that it is feasible to sequence its complete nuclear genome Schuster said The new gene sequences permitted the team to accurately determine how the Tasmanian Tiger is related to other marsupials They compared the sequences to a mitochondrial genome sequence they determined from a living reference species a marsupial called a numbat The two thylacine sequences were extremely similar to each other with only 5 differences in 15 492 nucleotides Miller reports The researchers say this similarity suggests that as the species neared extinction there was too little genetic diversity to resist bacterial and other environmental stresses Low genetic diversity is appearing as a common theme in the extinct species being studied by our team Schuster said The research also revealed that two previous sequences in public databases both labeled as Tasmanian Tiger mitochondrial genes were incorrect Our Smithsonian specimen was the male offspring of the

    Original URL path: http://thylacine.psu.edu/press_release.html (2016-02-12)
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