Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival

While sequencing ancient DNA (aDNA) from archaeological material is now commonplace, very few attempts to sequence ancient transcriptomes have been made, even from typically stable deposition environments such as permafrost. This is presumably due to assumptions that RNA completely degrades relatively quickly, particularly when dealing with autolytic, nuclease-rich mammalian tissues. However, given the recent successes in sequencing ancient RNA (aRNA) from various sources including plants and animals, we suspect that these assumptions may be incorrect or exaggerated. To challenge the underlying dogma, we generated shotgun RNA data from sources that might normally be dismissed for such study. Here, we present aRNA data generated from two historical wolf skins, and permafrost-preserved liver tissue of a 14,300-year-old Pleistocene canid. Not only is the latter the oldest RNA ever to be sequenced, but it also shows evidence of biologically relevant tissue specificity and close similarity to equivalent data derived from modern-day control tissue. Other hallmarks of RNA sequencing (RNA-seq) data such as exon-exon junction presence and high endogenous ribosomal RNA (rRNA) content confirms our data's authenticity. By performing independent technical library replicates using two high-throughput sequencing platforms, we show not only that aRNA can survive for extended periods in mammalian tissues but also that it has potential for tissue identification. aRNA also has possible further potential, such as identifying in vivo genome activity and adaptation, when sequenced using this technology

Defining management units for cetaceans by combining genetics, morphology, acoustics and satellite tracking

Managing animal units is essential in biological conservation and requires spatial and temporal identification of such units. Since even neighbouring populations often have different conservation status and face different levels of anthropogenic pressure, detailed knowledge of population structure, seasonal range and overlap with animals from neighbouring populations is required to manage each unit separately. Previous studies on genetic structure and morphologic separation suggests three distinct populations of harbour porpoises with limited geographic overlap in the North Sea (NS), the Belt Sea (BS) and the Baltic Proper (BP) region. In this study, we aim to identify a management unit for the BS population of harbour porpoises. We use Argos satellite data and genetics from biopsies of tagged harbour porpoises as well as acoustic data from 40 passive acoustic data loggers to determine management areas with the least overlap between populations and thus the least error when abundance and population status is estimated. Discriminant analysis of the satellite tracking data from the BS and NS populations showed that the best fit of the management unit border during the summer months was an east–west line from Denmark to Sweden at latitude 56.95°N. For the border between BS and BP, satellite tracking data indicate a sharp decline in population density at 13.5°E, with 90% of the locations being west of this line. This was supported by the acoustic data with the average daily detection rate being 27.5 times higher west of 13.5°E as compared to east of 13.5°E. By using this novel multidisciplinary approach, we defined a management unit for the BS harbour porpoise population. We recommend that these boundaries are used for future monitoring efforts of this population under the EU directives. The boundaries may also be used for conservation efforts during the summer months, while seasonal movements of harbour porpoises should be considered during winter

Archives of human-dog relationships: Genetic and stable isotope analysis of Arctic fur clothing

Among Indigenous populations of the Circumpolar North, domestic dogs (Canis familiaris) were social actors aiding in traction and subsistence activities. Less commonly, dogs fulfilled a fur-bearing role in both the North American and Siberian Arctic. Examples of garments featuring dog skins were collected during the 19th-20th centuries and are now curated by the National Museum of Denmark. We sequenced the mitochondrial genomes of macroscopically identified dog skin garments. We conducted stable carbon and nitrogen isotope ratio analysis of the dog furs and of fur samples from contemporaneous pelts of Arctic (C. lupus arctos) and grey (C. lupus) wolves. Despite the presence of biocides used to protect the fur clothing during storage, we extracted well-preserved DNA using a minimally-invasive sampling protocol. Unexpectedly, the mtDNA genomes of one-third of the samples were consistent with wild taxa, rather than domestic dogs. The strong marine component in the diets of North American dogs distinguished them from Greenland and Canadian wolves, but Siberian dogs consumed diets that were isotopically similar to wild species. We found that dog provisioning practices were variable across the Arctic, but in all cases, involved considerable human labor

Global dispersal and adaptive evolution of domestic cattle: a genomic perspective

Domestic cattle have spread across the globe and inhabit variable and unpredictable environments. They have been exposed to a plethora of selective pressures and have adapted to a variety of local ecological and management conditions, including UV exposure, diseases, and stall-feeding systems. These selective pressures have resulted in unique and important phenotypic and genetic differences among modern cattle breeds/populations. Ongoing efforts to sequence the genomes of local and commercial cattle breeds/populations, along with the growing availability of ancient bovid DNA data, have significantly advanced our understanding of the genomic architecture, recent evolution of complex traits, common diseases, and local adaptation in cattle. Here, we review the origin and spread of domestic cattle and illustrate the environmental adaptations of local cattle breeds/populations

Complete Inactivation of Sebum-Producing Genes Parallels the Loss of Sebaceous Glands in Cetacea

Publisher's version (útgefin grein)Genomes are dynamic biological units, with processes of gene duplication and loss triggering evolutionary novelty. The mammalian skin provides a remarkable case study on the occurrence of adaptive morphological innovations. Skin sebaceous glands (SGs), for instance, emerged in the ancestor of mammals serving pivotal roles, such as lubrication, waterproofing, immunity, and thermoregulation, through the secretion of sebum, a complex mixture of various neutral lipids such as triacylglycerol, free fatty acids, wax esters, cholesterol, and squalene. Remarkably, SGs are absent in a few mammalian lineages, including the iconic Cetacea. We investigated the evolution of the key molecular components responsible for skin sebum production: Dgat2l6, Awat1, Awat2, Elovl3, Mogat3, and Fabp9. We show that all analyzed genes have been rendered nonfunctional in Cetacea species (toothed and baleen whales). Transcriptomic analysis, including a novel skin transcriptome from blue whale, supports gene inactivation. The conserved mutational pattern found in most analyzed genes, indicates that pseudogenization events took place prior to the diversification of modern Cetacea lineages. Genome and skin transcriptome analysis of the common hippopotamus highlighted the convergent loss of a subset of sebum-producing genes, notably Awat1 and Mogat3. Partial loss profiles were also detected in non-Cetacea aquatic mammals, such as the Florida manatee, and in terrestrial mammals displaying specialized skin phenotypes such as the African elephant, white rhinoceros and pig. Our findings reveal a unique landscape of “gene vestiges” in the Cetacea sebum-producing compartment, with limited gene loss observed in other mammalian lineages: suggestive of specific adaptations or specializations of skin lipids.This work was supported by Project No. 031342 cofinanced by COMPETE 2020, Portugal 2020 and the European Union through the ERDF, and by Fundac¸a~o para a Cie^ncia e a Tecnologia through national funds. R.R.F. thanks the Danish National Research Foundation for its support of the Center for Macroecology, Evolution, and Climate (grant DNRF96). We acknowledge the various Cetacea genome consortiums for genome sequencing and assemblies. We also thank Gısli Vikingsson at the Marine and Freshwater Research Institute in Iceland for lending us the Larsen gun and to North Sailing whale watching for the use of their zodiac.Peer Reviewe

Genomic insights into the conservation status of the world’s last remaining Sumatran rhinoceros populations

Highly endangered species like the Sumatran rhinoceros are at risk from inbreeding. Five historical and 16 modern genomes from across the species range show mutational load, but little evidence for local adaptation, suggesting that future inbreeding depression could be mitigated by assisted gene flow among populations. Small populations are often exposed to high inbreeding and mutational load that can increase the risk of extinction. The Sumatran rhinoceros was widespread in Southeast Asia, but is now restricted to small and isolated populations on Sumatra and Borneo, and most likely extinct on the Malay Peninsula. Here, we analyse 5 historical and 16 modern genomes from these populations to investigate the genomic consequences of the recent decline, such as increased inbreeding and mutational load. We find that the Malay Peninsula population experienced increased inbreeding shortly before extirpation, which possibly was accompanied by purging. The populations on Sumatra and Borneo instead show low inbreeding, but high mutational load. The currently small population sizes may thus in the near future lead to inbreeding depression. Moreover, we find little evidence for differences in local adaptation among populations, suggesting that future inbreeding depression could potentially be mitigated by assisted gene flow among populations