Neotoma bryanti bunkeri - Bunker's woodrat †.Neotoma bryanti anthonyi - Anthony's woodrat †.Neotoma angustapalata - Tamaulipan woodrat.Neotoma albigula varia - Turner Island woodrat.Neotoma albigula - white-throated woodrat.Pack rats are noticeably larger than deer mice, harvest mice, and grasshopper mice, and are usually somewhat larger than cotton rats. Pack rats have a rat-like appearance, with long tails, large ears, and large, black eyes. "Further investigation into the taxonomic composition of middens could refine our understanding of the timeline of past climate change, species migration, and extinction, and this will better inform the study of the effects of current and future climate change.A pack rat or packrat, also called a woodrat or trade rat, are any species in the North and Central American rodent genus Neotoma. "As the costs of DNA sequencing continue to decrease and computational power increases, the prospects for using this technique will greatly improve," Harbert said. Because of this, and DNA degradation, the researchers say that they were only able to definitively match the DNA fragments to the family level and were unable to match it to genus or species groupings. If the data for that organism do not exist, scientists only get the closest match, or no match at all. Since shotgun sequences random fragments of DNA, it requires researchers to have a strong database they can use to match the sequences to an organism. Viruses were also present in small quantities.Īlthough this study underscores the promise of deep DNA sequencing to illuminate previous ecosystems, a great deal of progress is required to make the work more accurate. As expected, a large portion of this DNA is bacterial, but between 20-40 percent is classified as belonging to eukaryotic organisms - those whose cells have a nucleus - including plants like grasses, pines, junipers, daisies, and roses, as well as a small number of vertebrates, including insects and fungi. They decided to focus on the shotgun technique for this study, finding that packrat middens up to 32,000 years old contain recoverable DNA that is consistent with fossils found in these deposits. The researchers explored the use of two next-generation sequencing techniques to compare the DNA: amplicon, during which the same gene is sequenced from every sample, and shotgun, which randomly selects DNA fragments to sequence. These two sites span the range of current climatic conditions across which North American packrat middens are preserved and have been studied. The samples come from two locations: City of Rocks National Reserve in south-central Idaho, and Guadalupe Canyon in Northern Baja California, Mexico. The researchers analyzed ancient DNA from 25 packrat midden samples between 300 and 48,000 years old from the North American Packrat Midden Collection at the University of Arizona's Tree Ring Laboratory. Because of their dense distribution, fossil middens in the Americas offer the chance to genetically profile entire communities through time and space, but first, we need to improve the way we analyze data from these deposits - the principal aim of this study." "They have been used to identify an extinct ground sloth preserved in southern Argentina, tell us about the history of bighorn sheep in California, and provided evidence of papillomavirus infection in packrats over the last 27,000 years. "Midden contents are so well preserved that fragments of ancient DNA can be extracted and analyzed across millennia," said Rob Harbert, an assistant professor at Stonehill College who conceived of this study when he was a postdoc at the Museum. Since 1960, more than 2,000 ancient packrat middens from western North America have been analyzed for fossil contents and archived. Because the foraging range of these small rodents is limited, the contents of packrat middens represent the local environment at the time the material was gathered, providing clues about past climates and environments. These plant-rich deposits - called middens, which also can contain insects, bones, and other materials the packrats habitually collect - are found in arid parts of North America. Their sticky, viscous urine helps the nests to bind together into a solid mass, capable of being preserved for tens of thousands of years - some nests even date to beyond the last ice age. Packrats (Neotoma spp.) are long-tailed nocturnal rodents that create nests out of plant materials in dry caves and crevices. "We wanted to see how we could take this invaluable resource and expand its use to give us a big-picture view of what life in the Americas was like 1,000, 10,000, or even 30,000 years ago, and measure how it has changed in the time since then." "Rodent middens are powerful tools in paleoecology," said Michael Tessler, a postdoctoral fellow at the American Museum of Natural History.
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