Tuesday 13 December 2022

Successful genotyping of two end-Pleistocene, Palaeolithic, individuals from Britain.

The warming period after the Last Glacial Maximum saw radical shifts in the distribution of Animals and Plants in Europe, and with it an expansion of both Human populations and their cultural diversity. However, while the importance of this interval is well understood, we have relatively little evidence from this time.

Improvements in genotyping ancient remains have enabled scientists to study ever older populations in recent years, with the ability now including individuals from the Late Pleistocene of Europe. Such studied have exposed shifts in genetic patterns within populations, exposing Human migrations that were not clear from the conventional archaeological record. One of the more notable of these newly discovered population shifts occurred between the Last Glacial Maximum, approximately 23 000 years ago, and the onset of the Holocene Epoch, which is placed at 11 700 years before the present. During this shift, populations belonging the 'Goyet Q2' ancestry group, named after the 15 090-year-old Goyet Q2 individual from Belgium were replaced with populations belonging to the 'Villabruna' ancestry group, named after the approximately 14 010-year-old Villabruna individual from Italy. 

The Goyet Q2 ancestry group has been shown to include the roughly 18 700-year-old El Mirón individual from Spain, as well as other individuals associated with the ancient Magdalenian Culture, which is found at archaeological sites dated to between about 20 500 years ago and about 14 000 years ago across Europe. It has been suggested that this group represents individuals descended from a population from a southwest European glacial refugia, which spread across Europe as the glaciers covering the continent retreated.

The Villabruna ancestry group, also known as the Western Hunter Gatherers, includes a range of individuals found across Europe, dating to between about 14 000 and about 7000 years ago. This genotype group has been associated with individuals from archaeological sites associated with Epigravettian, Azilian/Federmesser, Epipalaeolithic and Mesolithic cultures. While this ancestry group is considered to be entirely European in distribution, all of the individuals assigned to it also show genetic affinities to modern Near Eastern populations. The expansion of this population has been linked to the onset of the rapid warming phase known as the Late Glacial Interstadial, about 14 650 years ago, as well as the cultural transition that saw the Magdalenian/Late Upper Palaeolithic culture replaced by the Azilian/Federmesser-Gruppen/Final Palaeolithic culture, and has been suggested to have been linked to a new group of people migrating into Europe during this warming phase.

Curiously, individuals of mixed Goyet Q2/Villabruna ancestry are also known from southern Europe, first appearing about 18 700 years ago, with the El Mirón individual. This has led to the suggestion that European Humans were confined to a few isolated refugia in the southern part of the continent during the Last Glacial Maximum, but that there was some genetic and cultural exchange between these refugia. However, the fact that people with unadmixed Goyet Q2 genotypes were living in Europe as late as 14 000 years ago suggests that this interchange was very limited, and that high levels of isolation persisted through the Last Glacial Maximum and into the Late Glacial. 

There is also evidence of people living north of the Alps during the Last Glacial Maximum, migrating from east to west, and remaining in ice-marginal environments. These people have been linked to the Magdalenian culture, which would fit with the model of the Goyet Q2 ancestry group being Magdalenian hunter gatherers, who retreated into northern Europe as the climate warmed, possibly following herds of Reindeer or Horses. South of the Alps, species such as Red Deer persisted throughout the Last Glacial Maximum and Late Glacial, creating a wider range of ecological opportunities for Human hunter gatherers, and thereby allowing greater population admixture in this region. 

The northwesternmost limit of this post-glacial expansion reached Britain, of which two thirds were covered with ice during the Last Glacial Maximum. Britain deglaciated rapidly, leading to accelerated ecological and environmental changes. By 19 000 years ago the ice sheet which had covered much of Britain and Ireland was melting rapidly, with England and Wales being free of ice by about 16 000 years ago. Reindeer are known to have been present in southwest England by 17 000 years ago, living in a landscape dominated by open steppe–tundra vegetation. The earliest evidence for Human occupation in post-glacial Britain comes from about 15 500 years ago, with populations probably established in several areas by the onset of the Late Glacial Interstadial, 14 650 years ago. Current dating suggests that Britain was repopulated after the nearby Paris Basin and the Belgian Ardennes, possibly by people expanding from those regions. The Magdalenian toolset used by these earliest colonisers was similar to that used in the northern Netherlands and the lowlands of northern Germany and Poland. Nevertheless, the amount of archaeological material we have from Britain during this period is extremely limited, restricting the the inferences that can be made about this population.

Genetic analysis techniques have been applied to Mesolithic, Neolithic, and Bronze Age individuals from Britain, but not, to date, to individuals from the Palaeolithic. This is, at least in part, due to the extremely limited nature of the Palaeolithic skeletal record, with such material only having been recovered from only six sites across Britain. The position of this population, at the extreme fringe of the post-Late Glacial Maximum European expansion, means that they can potentially tell us a great deal about the movement of Human populations during this time. All Mesolithic British individuals genotyped to date have belonged to the Villabrauna population, suggesting that this group had reached the northwesternment fringe of Europe by about 10 500 years ago. It is not clear, however, just when these people arrived in Britain, or what the genetic affinities of the Palaeolithic populations of Britain were. The apparent link between the Goyet 2 ancestry group and the Magdalenian culture leads to the hypothesis that these earliest settlers in Britain belonged to that group, but this has not, to date, been tested.

In a paper published in the journal Nature Ecology and Evolution on 24 October 2022, a team of scientists led by Sophy Charlton of the School of Archaeology at the University of Oxford and the Natural History MuseumSelina Brace, also of the Natural History Museum, and Mateja Hajdinjak of the Ancient Genomics Laboratory a the Francis Crick Institute, present the results of analysis of the DNA of two individuals from the Late Palaeolithic of England and Wales, and discuss the implications of their results. 

The first individual included in the study came from Kendrick’s Cave, which is located on Great Orme’s Head, a limestone massif in Llandudno, North Wales. This cave yielded four individuals, three adults and a child, which have been radiocarbon dated to between 11 990 and 11 905 years before the present. As well as the Human remains, the site yielded a range of artefacts which have been linked to the Magdalenian culture, including the proximal portion of a broken blade with en éperon butt preparation, a cut-marked Bovine bone dated to about 14 500 years before the present, a decorated Horse mandible dated to about 12 900 years before the present, and beads made from the teeth of Brown Bear,  Aurochs and Red Deer. 

The first molar from the mandible of the one individual (Kendricks_074, the skeleton dated to 11 905 years before the present) from Kendrick's Cave was subjected to DNA analysis. In addition, samples a were taken from all four Kendrick's Cave skeletons for  carbon and nitrogen isotope analysis. This isotopic analysis provided insight into the diet of the individuals, which suggested a diet rich resources obtained from marine or freshwater sources. This is known to have an impact on radiocarbon dating, leading to a revised date for Kendricks_074 of 13 770 to 13 390 years before the present, and a revised occupancy period for the cave, starting between 16 410 and 14 070 years before the present, and ending between 13 730 and 13 140 years ago. 

The second individual included in the study comes from Gough’s Cave, part of a large cave system situated in Cheddar Gorge in Somerset, southwest England. Gough's Cave is one of the best known Palaeolithic sites in Britain, with a large assemblage of both stone tools and Animal remains. Occupancy at the site is thought to have begun at the beginning of the Late Glacial Interstadial, as temperatures in the region began to rise rapidly. The technology present comprises a mixture of late Magdalenian and early Federmesser-Gruppen tools. At least six Palaeolithic Humans were buried here (one child, two adolescents, and three adults), as well as a later, Mesolithic individual (famous as 'Cheddar Man'). Two of the Palaeolithic Humans have been directly radiocarbon dated, and all show signs of considerable postmortem modification, interpreted as signs of cannibalism, and the modification of skulls to manufacture drinking cups. Based upon the radiocarbon dates obtained and the technologies present in the cave, the Palaeolithic occupation of Gough's Cave is thought to have lasted from about 14 840 to about 14 680 years ago - less than 200 years.

One of the human skulls carefully shaped into a cup or bowl by the people who lived at Gough's Cave 14,700 years ago. Natural History Museum.

Charlton et al. obtained sample DNA from a Human temporal bone (PVM 96544) from Gough's Cave, as well as carrying out new radiocarbon dating on this and other material from the site. The new radiocarbon data was used to obtain a revised occupation period for the cave, starting between 15 070 and 14 850 years ago, and ending between 14 960 and 14 610 years ago. This new dating suggests that occupation began before the onset of the Late Glacial Interstadial warming.

None of the Human material from Gough's and Kendrick's caves shows overlapping dates. However, the modified Bovid bone from Kendrick's Cave does overlap chronologically with the Human remains from Gough's Cave, suggesting that both sites were occupied simultaneously for at least some of the period. The two individuals included in the study were separated in time by at least 600 years (assuming no seafood was consumed in either party's diet), but this could potentially be as high as 840-1200 years.

Charlton et al. recovered 15 497 unique fragments of mitochondrial DNA and 30 587 614 unique fragments of nuclear DNA from the Gough's Cave individual, representing about 23% of the total genome. From the Kendrick's Cave individual they recovered 9702 unique fragments of mitochondrial DNA, and 29 326 159 unique fragments of nuclear DNA, representing about 18% of the total genome. 

ecause mitochondrial DNA is found in the mitochondria, organelles outside the cell nucleus, it is passed directly from mother to child without being sexually recombined each generation, enabling precise estimations of when individuals shared common ancestors, at least through the female line, forming a mitochondrial haplogroup. It is also possible to trace direct ancestry through the male line, using DNA from the Y chromosome, which is passed directly from father to son without sexual recombination, forming a Y-chromosome haplogroup.

The mitochondrial DNA recovered was sufficient to assign both individuals to mitochondrial haplogroups. The Gough's Cave individual belongs to the U8a haplogroup, while the Kendrick's Cave individual belongs to the U5a2 haplogroup. The U8a haplogroup has not been previously recorded in Britain, but is the haplogroup to which the Goyet Q2 individual belongs, as well as individuals associated with Magdalenian artefacts at several archaeological sites, including those at Hohle Fels and Brillenhöhle in Germany. The U5 haplogroup has been recorded at several Mesolithic sites in Britain, including one from Kent's Cavern who shares the U5a2 haplogroup variant. 

It was also possible to determine the sex of both individuals, with the Gough's Cave individual being female, and the Kendrick's Cave individual being male. Interestingly, the Kendrick's Cave individual had been recorded as 'male' in the original description of the skeleton, although no reason was ever given for this.

The nuclear genome of the Gough's Cave individual is close to that of the Goyet Q2 individual, placing that individual within the Goyet Q2 ancestry group. The Kendrick's Cave individual clusters with individuals from the Villabrauna ancestry group, including Mesolithic individuals from Britain; to date all Mesolithic individuals from Britain have belonged exclusively to the Villabrauna ancestry group, with the exception of 'Cheddar Man' (who was also recovered from Gough's Cave), who's ancestry was 84.6% Villabrauna and 15.4% Goyet Q2.

Location, genetic ancestry and Accelerator Mass Spectrometry date of End Palaeolithic European individuals. (a) Map indicating the location of Pleistocene sites and the genetic ancestry of individuals analysed from them. (b) North Greenland Ice Core Project ice core δ¹⁸O values and event stratigraphy, genetic ancestry and date  of individuals (95% confidence interval of calibrated radiocarbon dates for directly dated Humans). The Gough’s Cave and Höhle Fels specimens are not directly dated and therefore for Höhle Fels specimen the age range shown is the 95% confidence interval of calibrated radiocarbon dates from bones recovered from the same area/context. For the Gough’s Cave specimen, the age range shown is the Bayesian modelled site occupation start and end dates based on Accelerator Mass Spectrometry dating of the Human remains and Human modified faunal remains. Charlton et al. (2022).

The genetic and radiocarbon dating evidence obtained by Charlton et al. indicates that two genetically distinct populations of Humans were present in Britain during the Late Glacial period. The individual sampled from Gough's Cave showed clear affinity to the Goyet Q2 ancestry group, while the Kendrick's Cave individual clearly grouped with the Villabrauna group. Neither individual showed any genetic admixture, although the Gough's Cave tool assemblage does appear to be of mixed origins, containing both late Magdalenian and early Federmesser-Gruppen technologies. Furthermore, the only lithic tool from Kendrick's Cave clearly fits with the Magdalenian technology, while the individual sampled from the same location belonged to the Villabrauna ancestry group, typically associated with the Epigravettian and Azilian/Federmesser technologies. However, the decorative objects from Kendrick's Cave are similar to items from Federmesser-Gruppen sites in Europe. This may indicate that the boundaries between cultures were not so rigid at this time as generally assumed, or even that the populations at both sites contained a mixture of Humans from both cultures, but this has not been captured by sampling only one individual from each group. What the study does clearly demonstrate is that the Villabrauna ancestry group had clearly reached Britain by the Late Glacial, though whether there is a continuity with Holocene populations belonging to the same group, or whether they represent a subsequent second migration to the island after the Younger Dryas cooling event (between 12 900 and 11 700 years ago) is unclear.

The Younger Dryas represents a significant interlude between the temperate climate of the Late Glacial and that of the Holocene. During this interval ice sheets spread southward from Scotland, and Reindeer become the most common Animal remains found in caves in southwest Britain. At the moment, there are no Human remains from Britain which can be assigned to the Younger Dryas interval by radiocarbon dating, though it is unclear if this represents a lack of (discovered) preserved material or an actual absence of Humans. If there really were no Humans present in Britain during this period, then the subsequent Villabrauna populations must represent a second migration of that group into Britain. Furthermore, whilst the Villabrauna ancestry group appears to be dominant in Britain during the Mesolithic, at least one individual is known to be of mixed heritage, possibly suggesting that the cultural changes that led to the Mesolithic involved a degree of blending between groups.

Britain is not the only area where both Late Palaeolithic European populations are present, the same has been observed in Iberia, where individuals with mixed heritage are present at El Mirón in Spain from about 18 770 years ago. However, while both populations have been detected in Britain, no trace of genetic admixture has (yet) been discovered in the Palaeolithic, which may indicate a more dramatic population turnover.

These two Late Palaeolithic populations from Britain lived somewhere between 600 and 12 000 years apart, and, as well as being genetically different, appear to have had different diets, based upon stable isotope analysis of skeletal material from the two sites. They also appear to have had quite different approaches to the handling of the dead, with modification of remains and possible cannibalism present at Gough's Cave but not at Kendrick's Cave. This does suggest that a considerable degree of cultural, as well as genetic, turnover was occurring during a time of known climatic and ecological shifts, again, something seen elsewhere in Europe.

The very limited supply of skeletal material from the Late Pleistocene of Britain, along with the rate at which DNA degrades in deceased individuals, means that there will never be a very clear picture of the genetic make-up of these populations. However, a limited amount of information is not zero, and Charlton et al. have demonstrated that useful studies can be done on Late Pleistocene genetics in Britain, raising the potential that we yet learn more about this subject.

See also...

Follow Sciency Thoughts on Facebook.

Follow Sciency Thoughts on Twitter.