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Article Reference Ancient DNA suggests modern wolves trace their origin to a Late Pleistocene expansion from Beringia
Located in Library / RBINS Staff Publications 2019
Article Reference Ancient DNA suggests modern wolves trace their origin to a Late Pleistocene expansion from Beringia
Grey wolves (Canis lupus) are one of the few large terrestrial carnivores that have maintained a wide geographical distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the Late Pleistocene and early Holocene, and that extant wolves trace their ancestry to a single Late Pleistocene population. Both the geographical origin of this ancestral population and how it became widespread remain unknown. Here, we used a spatially and temporally explicit modelling framework to analyse a data set of 90 modern and 45 ancient mitochondrial wolf genomes from across the Northern Hemisphere, spanning the last 50,000 years. Our results suggest that contemporary wolf populations trace their ancestry to an expansion from Beringia at the end of the Last Glacial Maximum, and that this process was most likely driven by Late Pleistocene ecological fluctuations that occurred across the Northern Hemisphere. This study provides direct ancient genetic evidence that long‐range migration has played an important role in the population history of a large carnivore, and provides insight into how wolves survived the wave of megafaunal extinctions at the end of the last glaciation. Moreover, because Late Pleistocene grey wolves were the likely source from which all modern dogs trace their origins, the demographic history described in this study has fundamental implications for understanding the geographical origin of the dog.
Located in Library / RBINS Staff Publications 2020
Article Reference Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe.
Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4\% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process.
Located in Library / RBINS Staff Publications 2019
Article Reference 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.
Located in Library / RBINS Staff Publications 2019
Article Reference Ancient West African foragers in the context of African population history
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.
Located in Library / RBINS Staff Publications 2020
Article Reference Ancient whales did not filter feed with their teeth
Located in Library / RBINS Staff Publications 2017
Article Reference Ancyrocephalidae (Monogenea) of Lake Tanganyika: does the Cichlidogyrus parasite fauna of Interochromis loocki (Teleostei, Cichlidae) reflect its host’s phylogenetic affinities?
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.
Located in Library / No RBINS Staff publications
Article Reference Ancyrocephalidae (Monogenea) of Lake Tanganyika: IV: Cichlidogyrus parasitizing species of Bathybatini (Teleostei, Cichlidae): reduced host-specificity in the deepwater realm?
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.
Located in Library / No RBINS Staff publications
Article Reference Animal remains from predynastic sites in the Nagada region, Middle Egypt
Faunal samples from excavations between 1974 and 1981 in predynastic sites and a late predynastic/early dynastic cemetery in the Nagada region are inventoried. The faunal spectra compare well with those of other neolithic and predynastic sites of Nilotic Egypt. They point to agrarian communities relying mainly on fishing and livestock, as also suggested by most other known sites of the same neolithic and predynastic contexts. The neolithisation of the Nile Valley is an earlier event, perhaps coeval with and related to the origin and development of the complex pastoralist Late Neolithic of Nabta and the Western Desert.
Located in Library / RBINS Staff Publications
Article Reference Annelids in Extreme Aquatic Environments: Diversity, Adaptations and Evolution
Located in Library / RBINS Staff Publications 2021