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Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival
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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.
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RBINS Staff Publications 2019
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Ancient West African foragers in the context of African population history
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Our knowledge of ancient human population structure in sub-Saharan Africa, particularly prior to the advent of food production, remains limited. Here we report genome-wide DNA data from four children—two of whom were buried approximately 8,000 years ago and two 3,000 years ago—from Shum Laka (Cameroon), one of the earliest known archaeological sites within the probable homeland of the Bantu language group1–11. One individual carried the deeply divergent Y chromosome haplogroup A00, which today is found almost exclusively in the same region12,13. However, the genome-wide ancestry profiles of all four individuals are most similar to those of present-day hunter-gatherers from western Central Africa, which implies that populations in western Cameroon today—as well as speakers of Bantu languages from across the continent—are not descended substantially from the population represented by these four people. We infer an Africa-wide phylogeny that features widespread admixture and three prominent radiations, including one that gave rise to at least four major lineages deep in the history of modern humans.
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RBINS Staff Publications 2020
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Ancyrocephalidae (Monogenea) of Lake Tanganyika: does the Cichlidogyrus parasite fauna of Interochromis loocki (Teleostei, Cichlidae) reflect its host’s phylogenetic affinities?
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The faunal diversity of Lake Tanganyika, with its fish species flocks and its importance as a cradle and reservoir of ancient fish lineages seeding other radiations, has generated a considerable scientific interest in the fields of evolution and biodiversity. The Tropheini, an endemic Tanganyikan cichlid tribe, fills a peculiar phylogenetic position, being closely related to the haplochromine radiations of Lakes Malawi and Victoria. Several problems remain regarding their genus-level classification. For example, the monotypic genus Interochromis is phylogenetically nested within Petrochromis; its only representative, I. loocki, has often been reclassified. As monogenean flatworms are useful markers for fish phylogeny and taxonomy, the monogenean fauna of Interochromis loocki was examined and compared to that of other tropheine cichlids. Three new monogenean species belonging to Cichlidogyrus are described from Interochromis loocki: Cichlidogyrus buescheri Pariselle and Vanhove, sp. nov., Cichlidogyrus schreyenbrichardorum Pariselle and Vanhove, sp. nov. and Cichlidogyrus vealli Pariselle and Vanhove, sp. nov. Their haptoral anchors remind more of congeners infecting species of Petrochromis than of all Cichlidogyrus spp. hitherto described from other tropheine cichlids. Attachment organ morphology has been proven to mirror the phylogenetic affinities of Cichlidogyrus lineages. Therefore the monogenean parasite fauna of I. loocki reflects this host’s position within Petrochromis. Moreover, I. loocki differs in habitat choice from Petrochromis spp. This study hence confirms that host range and host-specificity in Cichlidogyrus spp. parasitizing tropheines is determined by the host’s phylogenetic position, rather than by a shared ecological niche.
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Ancyrocephalidae (Monogenea) of Lake Tanganyika: IV: Cichlidogyrus parasitizing species of Bathybatini (Teleostei, Cichlidae): reduced host-specificity in the deepwater realm?
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Lake Tanganyika’s biodiversity and endemicity sparked considerable scientific interest. Its monogeneans, minute parasitic flatworms, have received renewed attention. Their host-specificity and simple life cycle render them ideal for parasite speciation research. Because of the wide ecological and phylogenetic range of its cichlids, Lake Tanganyika is a "natural experiment" to contrast factors influencing monogenean speciation. Three representatives of Bathybatini (Bathybates minor, B. fasciatus, B. vittatus), endemic predatory non-littoral cichlids, host a single dactylogyridean monogenean species. It is new to science and described as Cichlidogyrus casuarinus sp. nov. This species and C. nshomboi and C. centesimus, from which it differs by the distal end of the accessory piece of the male apparatus and the length of its heel, are the only Cichlidogyrus species with spirally coiled thickening of the penis wall. In Cichlidogyrus, this feature was only found in parasites of endemic Tanganyika tribes. The seemingly species poor Cichlidogyrus community of Bathybatini may be attributed to meagre host isolation in open water. The new species infects cichlids that substantially differ phylogenetically and ecologically. This may be an adaptation to low host availability. Cichlidogyrus species infecting African Great Lake cichlids are summarized and proposed as model for the influence of host ecology on disease transmission.
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No RBINS Staff publications
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Animal burials and food offerings at the Elite Cemetery HK6 of Hierakonpolis
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RBINS Staff Publications
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Animal dung from arid environments and archaeobotanical methodologies for its analysis: An example from animal burials of the Predynastic elite cemetery HK6 at Hierakonpolis, Egypt
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Bioarchaeological studies of animal dung from arid environments provide valuable information on various aspects of life in ancient societies relating to land use and environmental change, and from the Neolithic onwards to the animal husbandry and the use of animals as markers of status and wealth. In this study we present the archaeobotanical analysis of animal gut contents from burials in the elite Predynastic cemetery HK6 at Hierakonpolis, Upper Egypt. The study involved analysis of plant macrofossils, phytoliths and pollen applied on samples from two elephants, a hartebeest, an aurochs and five domestic cattle. The study showed that most probably the elephants were given fodder containing emmer spikelets (dehusking by-products) before the animals death. Most of the other animals were also foddered with cereal chaff, but were mainly allowed to browse and graze in the settlement area and near the Nile. The diet of some contained only wild growing plants. The variety of plant remains identified in the stomach contents indicates that the food plants for the animals were obtained from three possible habitats near the site: the river banks, the low desert and the cultivated/anthropogenically modified areas.
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RBINS Staff Publications
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Animal exploitation at ed-Dur (Umm al-Qaiwain, United Arab Emirates)
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Faunal remains are described from a series of contexts excavated in the coastal site of ed-Dur, dated between the second and fourth century AD. The more than 19,000 identified animal bones allowed a diachronic and spatial analysis. Subsistence relied heavily on domestic animals, in particular sheep and goat, and on fishing. Whereas the exploitation of terrestrial resources seems to have been quite constant throughout the period considered, the aquatic fauna shows changes through time. A shift, possibly linked to overexploitation, is seen both in the proportions of the targeted fish species and in their sizes. The deposition of some of the mammals encountered in burials is also dealt with; dog and ovicaprid can probably be added to the list of mammals used in ritual context in the region. Spatial analysis did not reveal particular concentrations or activity areas. In general the finds fit nicely in the archaeozoological record of the wider region.
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RBINS Staff Publications 2017
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Animal exploitation during the Iron Age at Tepe Düzen (SW Turkey): preliminary results
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RBINS Staff Publications 2017
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Animal remains and human-animal-environment relationships at Early Neolithic Bestansur and Shimshara
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RBINS Staff Publications 2020
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Animal remains from Mahal Teglinos (Kassala, Sudan) and the arrival of pastoralism in the Southern Atbai
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Faunal remains from Mahal Teglinos span the period from about 3000 to 1000 BC. They indicate that the arrival of cattle, sheep and goat in the region predates the occupation of the site, but the evidence available from other and older sites near Khashm-el-Girba does not suffice to document precisely the development of pastoralism and its consequences in the Southern Atbai. Among the limited mammalian game, the many gazelles and dikdiks point to steppe conditions, while the equally numerous buffalo remains suggest that this large bovid thrived in the seasonally inundated land along the Gash River.
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RBINS Staff Publications