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Highly polymorphic mitochondrial DNA and deceiving haplotypic differentiation: implications for assessing population genetic differentiation and connectivity
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Background Hyperdiverse mtDNA with more than 5% of variable synonymous nucleotide sites can lead to erroneous interpretations of population genetic differentiation patterns and parameters (φST, DEST). We illustrate this by using hyperdiverse mtDNA markers to infer population genetic differentiation and connectivity in Melarhaphe neritoides, a NE Atlantic (NEA) gastropod with a high dispersal potential. We also provide a recent literature example of how mtDNA hyperdiversity may have misguided the interpretation of genetic connectivity in the crab Opecarcinus hypostegus. Results mtDNA variation surveyed throughout the NEA showed that nearly all M. neritoides specimens had haplotypes private to populations, suggesting at first glance a lack of gene flow and thus a strong population genetic differentiation. Yet, the bush-like haplotype network, though visually misleading, showed no signs of phylogeographic or other haplotype structuring. Coalescent-based gene flow estimates were high throughout the NEA, irrespective of whether or not mtDNA hyperdiversity was reduced by removing hypervariable sites. Conclusions Melarhaphe neritoides seems to be panmictic over the entire NEA, which is consistent with its long-lived pelagic larval stage. With hyperdiverse mtDNA, the apparent lack of shared haplotypes among populations does not necessarily reflect a lack of gene flow and/or population genetic differentiation by fixation of alternative haplotypes (DEST ≈ 1 does not a fortiori imply φST ≈ 1), but may be due to (1) a too low sampling effort to detect shared haplotypes and/or (2) a very high mutation rate that may conceal the signal of gene flow. Hyperdiverse mtDNA can be used to assess connectivity by coalescent-based methods. Yet, the combined use of φST and DEST can provide a reasonable inference of connectivity patterns from hyperdiverse mtDNA, too.
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RBINS Staff Publications 2019
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Histological and stable isotope analysis of archeological bones from St. Rombout's cemetery (Mechelen, Belgium): Intrasite, intraindividual, and intrabone variability
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Abstract This study compares histological preservation in archeological bones from different burial types to unravel the histotaphonomy-to-funerary practices relationship. Αn intraskeletal approach is also adopted to explore intraindividual (inner ear part of the petrous bone vs. upper/lower limb long bones) and intrabone (proximal vs. distal diaphysis) variability in bone collagen preservation, δ13C, and δ15N. The aim is to (a) target bones that likely retain higher amounts of collagen, (b) better understand the inner ear bone collagen isotopic signature and remodeling, and (c) assess intrabone isotopic and histological homogeneity. For the histological analysis, the data have been collected from 61 specimens (20 individuals) from the medieval/postmedieval cemetery of St. Rombout, Belgium. Thin sections have been studied using optical and scanning electron microscopy. For the collagen and isotopic data, 101 samples have been collected from 21 individuals. Distinct histological patterns are observed only in bones from single coffin burials; however, bone histology can display intraindividual and intrabone variability, which are important to account for interpretations. Collagen wt.%, δ13C, and δ15N show significant intraindividual differences but insignificant intrabone variability. This study also confirms the extraordinary nature of the petrous bone, as the inner ear bone collagen δ13C and δ15N values reflect the dietary input of the first approximately 2–3 years of life.
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RBINS Staff Publications 2022
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Histology and growth pattern of the pachy-osteosclerotic premaxillae of the fossil beaked whale Aporotus recurvirostris (Mammalia, Cetacea, Odontoceti)
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Historical biogeography, systematics, and integrative taxonomy of the non‑Ethiopian speckled pelage brush‑furred rats (Lophuromys flavopunctatus group)
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RBINS Staff Publications 2021
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Historical management of equine resources in France from the Iron Age to the Modern Period
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Alongside horses, donkeys and their first-generation hybrids represent members of the Equidae family known for their social, economic and symbolic importance in protohistoric and historical France. However, their relative importance and their respective roles in different regions and time periods are difficult to assess based on textual, iconographic and archaeological evidence. This is both due to incomplete, partial and scattered historical sources and difficulties to accurately assign fragmentary archaeological remains at the proper taxonomic level. DNA- based methods, however, allow for a robust identification of the taxonomic status of ancient equine osseous material from minimal sequence data. Here, we leveraged shallow ancient DNA sequencing and the dedicated Zonkey computational pipeline to obtain the first baseline distribution for horses, mules and donkeys in France from the Iron Age to the Modern period. Our collection includes a total of 873 ancient specimens spanning 128 ubiquitous and the most dominant species identified, our dataset reveals the importance of mule breeding during Roman times, especially between the 1st and 3rd centuries CE (Common Era), where they represented between 20.0% and 34.2% of equine assemblages. In contrast, donkeys were almost absent from northern France as-semblages during the whole Roman period, but replaced mules in rural and urban commercial and economic centers from the early Middle Ages. Our work also identified donkeys of exceptional size during Late Antiquity, which calls for a deep reassessment of the true morphological space of past equine species. This study confirmed the general preference toward horses throughout all time periods investigated but revealed dynamic manage-ment strategies leveraging the whole breadth of equine resources in various social, geographic and temporal contexts.
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RBINS Staff Publications 2021
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Holarctic genetic structure and range dynamics in the woolly mammoth
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Ancient DNA analyses have provided enhanced resolution of population histories in many Pleistocene taxa. However, most studies are spatially restricted, making inference of species-level biogeographic histories difficult. Here, we analyse mitochondrial DNA (mtDNA) variation in the woolly mammoth from across its Holarctic range to reconstruct its history over the last 200 thousand years (kyr).We identify a previously undocumented major mtDNA lineage in Europe, which was replaced by another major mtDNA lineage 32–34 kyr before present (BP). Coalescent simulations provide support for demographic expansions at approximately 121 kyr BP, suggesting that the previous interglacial was an important driver for demography and intraspecific genetic divergence. Furthermore, our results suggest an expansion into Eurasia fromAmerica around 66 kyr BP, coinciding with the first exposure of the Bering Land Bridge during the Late Pleistocene. Bayesian inference indicates Late Pleistocene demographic stability until 20–15 kyr BP, when a severe population size decline occurred.
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Holocene Excursion of the Northwest European Geoid.
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RBINS Staff Publications
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Holocene history of Lac des Lauzons (2180 m a.s.l.), reconstructed from multiproxy analyses of Coleoptera, plant macro-remains and pollen (Hautes-Alpes, France)
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Holocene palaeoecology and human environmental interactions at the coastal Black Sea Lake Durankulak, northeastern Bulgaria
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The environmental changes (vegetation history, human impact and land use, influence of the Black Sea) in the area of Lake Durankulak, northeastern Bulgaria, were reconstructed and synthesized for the last ca. 8000 years. The palaeoecological information derived from various proxies (pollen, plant macrofossils, molluscs, sediments) was compared on a regional scale with the evidence from the nearby coastal lakes ShablaeEzeretz and Bolata. The Early Holocene xerothermic steppe vegetation, dominated by Chenopodiaceae, Artemisia and Poaceae species, and accompanied by stands of trees in moister habitats, was transformed after 6000 cal. BP into a forest-steppe, comprising oak woods with Carpinus betulus, Ulmus, Tilia, Acer. This vegetation pattern has been periodically modified, depleted and replaced by arable land or xerothermic herbaceous communities enriched with anthropophytes and ruderals, particularly after the intensification of human activities since 3300 cal. BP. The archaeobotanical evidence from the region has provided valuable information about the occupation phases and subsistence strategy of the local people since the Late Neolithic (5300 cal. BC/7250 cal. BP). Periods with cultivation of cereals (Triticum, Hordeum) and/or stock-breeding activity were interrupted by abandonment of the settlements and the arable land due to unfavourable environmental changes. The periodical connection/isolation of Lake Durankulak with the Black Sea and the periods of marine influence were recorded by changes in the composition of the fossil molluscan fauna and the lithology of the sediments, and chronologically confirmed by radiocarbon dates. The development of the coastal lakes throughout the largest part of the Holocene has been also considerably influenced by the fluctuations of the Black Sea level.
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RBINS Staff Publications
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Holocene palaeoecology and human–environmental interactions at the coastal Black Sea Lake Durankulak, northeastern Bulgaria
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Abstract The environmental changes (vegetation history, human impact and land use, influence of the Black Sea) in the area of Lake Durankulak, northeastern Bulgaria, were reconstructed and synthesized for the last ca. 8000 years. The palaeoecological information derived from various proxies (pollen, plant macrofossils, molluscs, sediments) was compared on a regional scale with the evidence from the nearby coastal lakes Shabla–Ezeretz and Bolata. The Early Holocene xerothermic steppe vegetation, dominated by Chenopodiaceae, Artemisia and Poaceae species, and accompanied by stands of trees in moister habitats, was transformed after 6000 cal. BP into a forest-steppe, comprising oak woods with Carpinus betulus, Ulmus, Tilia, Acer. This vegetation pattern has been periodically modified, depleted and replaced by arable land or xerothermic herbaceous communities enriched with anthropophytes and ruderals, particularly after the intensification of human activities since 3300 cal. BP. The archaeobotanical evidence from the region has provided valuable information about the occupation phases and subsistence strategy of the local people since the Late Neolithic (5300 cal. BC/7250 cal. BP). Periods with cultivation of cereals (Triticum, Hordeum) and/or stock-breeding activity were interrupted by abandonment of the settlements and the arable land due to unfavourable environmental changes. The periodical connection/isolation of Lake Durankulak with the Black Sea and the periods of marine influence were recorded by changes in the composition of the fossil molluscan fauna and the lithology of the sediments, and chronologically confirmed by radiocarbon dates. The development of the coastal lakes throughout the largest part of the Holocene has been also considerably influenced by the fluctuations of the Black Sea level.
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RBINS Staff Publications
