John R. Stewart

The identity of the extinct large crane Grus primigenia has been debated for over 150 years. Alternative interpretations suggest that such large crane remains represent extant cranes such as the sarus crane Antigone antigone, the Siberian white crane Leucogeranus leucogeranus or simply larger individuals of common crane Grus grus. Morphometrics has shown that the common crane is sexually dimorphic today with larger males and smaller females. We analysed cranes from the Late Pleistocene to Late Holocene and found that the lack of smaller female-sized craneremains suggests that G. grus may have reduced in size over time. In the present study, we successfully performed an ancient DNA analysis to assess the phylogenetic identity of 18 crane remains from the Late Pleistocene of Spain and France and the Late Holocene of Britain and Germany. All remains were identified as G. grus. These ancient cranes included individuals that were larger than modern G. grus and ones that conformed in size with common crane today. Ancient DNA-based sexing found that all the bones that were larger than those of modern males were male, while specimens the size of modern males included ancient females. This confirmed that the ancient cranes were sexually dimorphic G. grus that have become smaller since the Saxon times (884 yr BP).

Documenting past trophic relationships is crucial to understand deep time changes in the ecology and geographic distribution of large marine predators. Though bite marks on cetacean bones are a useful source of information to assess shark-whale predator-prey relationships, in many cases the identity of the prey and/or predator cannot be precisely determined. In this work, we investigate two cetacean specimens from the Kattendijk Formation (Lower Pliocene, north of Belgium): (i) the partial cranium of a small balaenid (right whale) that we describe and refer to Balaenella brachyrhynus and (ii) the previously described partial skeleton of a monodontid (family of beluga and narwhal), attributed here to the genus Casatia. Shark bite marks observed on the bones of the two specimens are described and the tip of a shark tooth found embedded in each cranium is visualized through micro-CT imaging. A comparison with shark species recorded in the Kattendijk Formation allows for the identification of the author of at least one bite for each cetacean: the bluntnose sixgill shark Hexanchus griseus for B. brachyrhynus and the large lamnid shark Carcharodon plicatilis for Casatia sp. Based on the position and topology of the marks, the H. griseus bite on B. brachyrhynus may have occurred on an upside down, floating carcass, a hypothesis that could indicate a scavenging event. Bite marks on the monodontid cranium suggest an attempt by C. plicatilis to sever the head from the rest of the body and point to the forehead region as a main targeted area. These new Early Pliocene records of shark-cetacean trophic relationships constitute a first step towards the exploration of the possible link between changes through time in the availability of prey in the southern North Sea and the local loss of large predatory sharks, which occurred in the Late Pliocene to Pleistocene time interval.

Ancient DNA studies revealed that, in Europe from 6500 to 4000 bce, descendants of western Anatolian farmers mixed with local hunter-gatherers resulting in 70–100% ancestry turnover¹, then steppe ancestry spread with the Corded Ware complex 3000–2500 bce². Here we document an exception in the wetland, riverine and coastal areas of the Netherlands, Belgium and western Germany, using genome-wide data from 112 people 8500–1700 bce. A distinctive population with high (approximately 50%) hunter-gatherer ancestry persisted 3,000 years later than in most European regions, reflecting incorporation of female individuals of Early European Farmer ancestry into local communities. In the western Netherlands, the arrival of the Corded Ware complex was also exceptional: lowland individuals from settlements adopting Corded Ware pottery had hardly any steppe ancestry, despite a Y-chromosome characteristic of people associated with the early Corded Ware complex. These distinctive patterns may reflect the specific ecology that they inhabited, which was not amenable to full adoption of the early Neolithic type of farming introduced with Linearbandkeramik³, and resulted in distinct communities where transfer of ideas was accompanied by little gene flow. This changed with the formation of Lower Rhine–Meuse Bell Beaker users by fusion of local people (13–18%) and Corded Ware associated migrants of both sexes. Their subsequent expansion then had a disruptive impact across a much wider part of northwestern Europe, especially in Great Britain where they were the main source of a 90–100% replacement of local Neolithic ancestry.

The Norwegian lemming ( Lemmus lemmus ) is a small rodent distributed across the Fennoscandian mountain tundra and the Kola Peninsula. The Norwegian lemming likely evolved during the Late Pleistocene and inhabited Fennoscandia shortly prior to the Last Glacial Maximum. However, the exact timing and origins of the species, and its phylogenetic position relative to the closely related Siberian lemming ( Lemmus sibiricus ) remain disputed. Moreover, the presence of ancient or contemporary gene flow between both species is largely untested. The Norwegian lemming displays characteristic phenotypic and behavioral adaptations (e.g., coat color, aggression) that are not present in other Lemmus species. We generated a de novo genome assembly for the Norwegian lemming and resequenced nine modern and two ancient Lemmus spp. genomes. We show that all Lemmus species form distinct monophyletic clades, with concordant topology between the mitochondrial and nuclear genome phylogenies. The Siberian lemming is divided into two distinct but paraphyletic clades, one in the east and one in the west, where the western clade represents a sister taxon to the Norwegian lemming. We estimate that the Norwegian and western Siberian lemming diverged shortly before the Last Glacial Maximum, making the Norwegian lemming one of the youngest known mammalian species. We did not find any indication of gene flow between L. lemmus and L. sibiricus , suggesting postglacial isolation of L. lemmus . Furthermore, we identify species-specific genomic differences in genes related to coat color and fat transport, which are likely associated with the distinctive coloration and overwintering behavior observed in the Norwegian lemming.

Phylogeographic studies have been conducted on many different mammal species in order to track their recent demographic histories. The climatic fluctuations associated with the Last Glacial Maximum (LGM) appear to have had a profound influence on the geographic patterning of genetic diversity in mammals. However, most phylogenetic studies have focused on single species. Few have used a holistic approach covering multiple taxa to explore common patterns. Here, we conducted meta-analyses of mitochondrial DNA control region sequences, identifying haplotype diversity and private allelic richness patterns in a geographic context. Four general patterns emerged among European mammals: an east–west decline in variation, a Western-Central belt of the highest diversity, southern richness, and homogeneity with no geographic pattern. These patterns likely reflect the refugial origins of modern populations. The east–west variation decline suggests species with eastern LGM refugia; the Western-Central belt of the highest diversity may harbor taxa with cryptic northern refugia, while southern richness may correspond to traditional southern refugia. Species with homogeneity and no geographic pattern may have been panmictic without a specific refugium or may reflect the occurrence of both southern and cryptic northern refugia. Surprisingly, the “no pattern” phenomenon is seldom discussed and may frequently have been discounted. Our study emphasizes the importance of considering multiple taxa, providing valuable insights into the responses of European mammals to past climatic changes.

The narrow-headed vole, collared lemming and common vole were the most abundant small mammal species across the Eurasian Late Pleistocene steppe-tundra environment. Previous ancient DNA studies of the collared lemming and common vole have revealed dynamic population histories shaped by climatic fluctuations. To investigate the extent to which species with similar adaptations share common evolutionary histories, we generated a dataset comprised the mitochondrial genomes of 139 ancient and 6 modern narrow-headed voles from several sites across Europe and northwestern Asia covering approximately the last 100 thousand years (kyr). We inferred Bayesian time-aware phylogenies using 11 radiocarbon-dated samples to calibrate the molecular clock. Divergence of the main mtDNA lineages across the three species occurred during marine isotope stages (MIS) 7 and MIS 5, suggesting a common response of species adapted to open habitat during interglacials. We identified several time-structured mtDNA lineages in European narrow-headed vole, suggesting lineage turnover. The timing of some of these turnovers was synchronous across the three species, allowing us to identify the main drivers of the Late Pleistocene dynamics of steppe- and cold-adapted species.

Late Pleistocene and Holocene pikas (Mammalia, Lagomorpha) from Europe and the validity of Ochotona spelaea: New insights based on mtDNA analysis

Aim: Many species experienced population turnover and local extinction during the Late Pleistocene. In the case of megafauna, it remains challenging to disentangle climate change and the activities of Palaeolithic hunter‐gatherers as the main cause. In contrast, the impact of humans on rodent populations is likely to be negligible. This study investigated which climatic and/or environmental factors affect the population dynamics of the common vole. This temperate rodent is widespread across Europe and was one of the most abundant small mammal species throughout the Late Pleistocene.Location: Europe.Taxon: Common vole (Microtus arvalis).Methods: We generated a dataset comprised of 4.2 kb long fragment of mitochondrial DNA (mtDNA) from 148 ancient and 51 modern specimens sampled from multiple localities across Europe and covering the last 60 thousand years (ka). We used Bayesian inference to reconstruct their phylogenetic relationships and to estimate the age of the specimens that were not directly dated.Results: We estimated the time to the most recent common ancestor of all last glacial and extant common vole lineages to be 90 ka ago and the divergence of the main mtDNA lineages present in extant populations to between 55 and 40 ka ago, which is earlier than most previous estimates. We detected several lineage turnovers in Europe during the period of high climate variability at the end of Marine Isotope Stage 3 (MIS 3; 57–29 ka ago) in addition to those found previously around the Pleistocene/Holocene transition. In contrast, data from the Western Carpathians suggest continuity throughout the Last Glacial Maximum (LGM) even at high latitudes.Main Conclusions: The main factor affecting the common vole populations during the last glacial period was the decrease in open habitat during the interstadials, whereas climate deterioration during the LGM had little impact on population dynamics. This suggests that the rapid environmental change rather than other factors was the major force shaping the histories of the Late Pleistocene faunas.

Aim: In this study, we conduct a quantitative meta‐analysis to investigate broad patterns of genetic variation throughout large geographical regions in order to elucidate concordant geographical patterns across species and identify common historical processes to better inform the “cryptic refugia” versus the traditional “southern refugia” hypothesis debate.Location: Europe.Time period: Late Pleistocene to present day.Major taxa studied: Small mammals (Rodentia, Eulipotyphla).Methods: A meta‐analysis was performed on large‐scale patterns of genetic diversity for 19 species from 59 papers. For each species, haplotype and nucleotide diversity were calculated using the mitochondrial D‐loop and compared to the species’ range.Results: No consistent patterns were observed between mitochondrial DNA (mtDNA) diversity indices (nucleotide and haplotype diversity) and any of the indicators of distribution examined [latitude and longitude (max, min, centre, range)]. The patterns of genetic diversity observed in all the 19 species studied appear to be species‐specific.Main conclusions: In contrast to the traditional southern refugial hypotheses, we found no evidence for a consistent south–north post‐glacial expansion. Instead individual species appear to respond to climate oscillations in niche‐specific ways. This individual nature of each species’ phylogeographical history indicates a complex web of post‐glacial recolonization dynamics across Europe.