Clark Spencer Larsen’s research while affiliated with The Ohio State University and other places

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Publications (192)


Figure 1: DNA preservation and organic preservation measured using FTIR spectra DNA in Çatalhöyük burials. A) Endogenous human DNA yield across libraries of 362 individuals. All libraries were produced using petrous bone samples. We used the raw human DNA proportion (before removing duplicates) and only libraries from petrous bones. B) Amide I (A1)/Phosphate (PV3) ratios of FTIR spectra measured from petrous bone samples in 202 individuals. The values plotted on the top show sample sizes. The r and p values are calculated using the Spearman correlation test. For a definition of age categories, see Supplementary Methods. The boxplots are plotted without outliers for visual clarity.
Figure S3: Endogenous human DNA across flexion levels among Çatalhöyük burials. Flexion levels did not show a significant association with endogenous DNA percentage (KW test p=0.12). The boxplots are plotted without outliers for visual clarity.
An age-specific burial practice reflected in ancient DNA preservation in Neolithic Çatalhöyük
  • Preprint
  • File available

December 2024

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Selective funerary practices can inform about social relationships in prehistoric societies but are often difficult to discern. Here we present evidence for an age-specific practice at the Neolithic site of Çatalhöyük in Anatolia, dating to the 7th millennium BCE. Among ancient DNA libraries produced from 362 petrous bone samples, those of subadults contained three times higher average human DNA than those of adults. This difference in organic preservation was also confirmed by FTIR analysis. Studying similar datasets from seven prehistoric and historical sites, we found a similar age-related difference in only one cemetery. We propose that the organic preservation difference with age was caused by the special treatment of chosen corpses before interment, such as defleshing or drying, which was more frequently applied to Çatalhöyük adults and promoted organic decay.

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Figure 1: Map of Aegean and Anatolian sites >6000 BCE with palaeogenomics data analysed in this study. Smaller fonts and symbols indicate sites where only published genomic data have been included, while bold fonts and large symbols indicate sites where new palaeogenomic data has been produced, with sample sizes shown in parentheses (see also Table 1, Figure S1, Tables S1-2). We also used published data of 453 individuals from U Mesopotamia, the Balkans, Zagros, Levant, Cyprus and from European sites in our analyses, not shown in this figure. To improve visualization, some of the locations were slightly shifted (the exact site coordinates can be found in Table S1-2).
Figure 4: The affinities of Epipalaeolithic Pınarbaşı, Girmeler and Aktopraklık genomes to C Anatolia versus W Anatolia/Greece analysed using f4-tests. The populations on the left side are C Anatolians post-7500 BCE (Çatalhöyük, Musular, Tepecik-Çiftlik) while those on the right side are Neolithic groups from W Anatolia or Greece. The boxplots show the distribution of the f4-statistics performed using groups of genomes per site; e.g. the top left comparison involves three comparisons of the form f4(Yoruba, Pınarbaşı/Girmeler/Aktopraklık; Çatalhöyük/Musular/Tepecik-Çiftlik, W Anatolia/Greece), one including Çatalhöyük, one Musular, and one Tepecik-Çiftlik. Colour coding indicates the proportion of nominally significant tests out of all comparisons (at |Z|>3). The "_HG" and "_N" suffixes indicate "hunter-gatherer" and "Neolithic"-related populations, respectively. The "CP" suffix stands for aDNA data produced using capture technologies (instead of shotgun).
Figure 5: IBD-sharing network across the Aegean showing distant genetic relatedness. The analysis was performed using imputed ancient genomes from the study region and includes ≥8 cM segments (the majority of these were 8-12 cM, and the only IBD-segments >16cM were found between Nea Nikeamedia-Revenia in Greece, and between Aktopraklık-Bahçelievler in NW Anatolia). The colours shown in the key indicate the strength of connections between pairs of genomes in any two sites. We calculate the strength given the number of comparisons and the maximum IBD sharing observed in the dataset. For example, if regions X and Y are represented by 3 and 5 genomes, if any two genomes share a maximum of 4 segments in the full dataset, and if across the 15 X-Y comparisons there are 7 segments in total shared, the X-Y connection strength is estimated as 7/(4x15) = 0.12 (see also Table S5 and Figure S22).
Figure 6: The influence of geographic proximity and genetic similarity on material culture similarities among 7 th millennium BCE sites across SW Asia and the Aegean. A: Presence/absence records of 58 material culture traits compiled from the literature for 16 SW Asian/Aegean sites covering 7000-5800 BCE and that have genetic data (see Table S6 for the full dataset). B-D: Correlations between pairwise distances among sites in material culture (Jaccard dissimilarity), geodesic distances (geographic shortest path estimates) and genetic distances (1-f3) across the 16 sites (Methods). E: Correlation between the residuals of sociocultural and genetic distances after each was regressed on geodesic distances using linear regression. The Spearman correlation coefficient and the Mantel test p-values are shown inside the panels. Partial Mantel tests between cultural and genetic distances controlling for the effect of geography were also non-significant (r=-0.03, p=0.56) (see also Figures S33-36).
Out-of-Anatolia: cultural and genetic interactions during the Neolithic expansion in the Aegean

June 2024

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811 Reads

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2 Citations

Western Anatolia has been a crucial yet elusive element in the Neolithic expansion from the Fertile Crescent to Europe. Using 30 new palaeogenomes from Anatolia c.8000-6000 BCE we describe the early Holocene genetic landscape of Western Anatolia, suggesting population continuity since the late Upper Pleistocene. Our findings indicate that the Neolithisation of Western Anatolia in the 7th millennium BCE was a multifaceted process, characterised by the assimilation of Neolithic practices by indigenous groups and the influx of populations from the east, their admixed descendants eventually laying the foundations of Neolithic Southeast Europe. Intriguingly, the observed diversity in material culture among Aegean Early Neolithic communities correlates with their geographical distances but not their genetic differences, signifying a decoupling between cultural developments and genetic admixture processes.


Figure 2: Characterising the Çatalhöyük East Mound gene pool and temporal change. A) 221 Multidimensional scaling (MDS) plot summarising outgroup f 3 -based genetic distances 222 among late Upper Pleistocene and early Holocene genomes from Southwest Asia, including 223 67 unrelated Çatalhöyük genomes. B) qpAdm modelling of ancestry sources (shown in 224 colours) 8th and 7th millennium Neolithic Anatolian genomes from Çatalhöyük (three 225 periods), Tepecik-Çiftlik, Musular, and Barcın. Each column indicates a feasible model, with 226 the y-axis showing admixture proportions. C) f 4 -statistics between groups of genomes from 227 the three Çatalhöyük periods. D) IBD-sharing with genetically sampled PPN and PN 228 settlements from Anatolia. The colour represents the relative strength of IBD-sharing 229 between two settlements, calculated as the total number of segments shared between all 230 pairwise comparisons divided by the total number of comparisons and the maximum sharing 231 between any pairs in the full sample. E) Mitochondrial DNA and Y chromosome haplogroup 232 diversity in Çatalhöyük and French Neolithic Gurgy (8), the latter representing a gene pool 233 shaped by patrilocal practices. The numbers of total pairs in each category is indicated on 234 the bars. The difference in chrY diversities between Gurgy and Çatalhöyük is significant as 235 measured by a random subsampling experiment (Figure S7). F) Comparison of the F ROH 236 values, the inbreeding coefficient estimated using runs of homozygosity (ROH) >4cM, 237 among different Neolithic sites in Anatolia. G) The distribution of mean F (inbreeding 238 coefficient) values in a sample of 16 individuals estimated using genealogy simulations 239
Figure 3: A network of genetic kin across Çatalhöyük buildings and the changing frequency 368 of genetic ties among co-burials. A) The figure shows genetic relatedness among intramural 369 burials with common SNPs >3000, shown as dots. The lines show close to more distant 370 relationships from dark to light colours. The coloured blocks show buildings, with building 371 numbers assigned by the excavation team indicated adjacent to the blocks. The height of the 372 blocks is proportional to the number of genetically represented burials in that building. North 373 and South refer to the two main excavation areas on the mound separated by ~200m. B) 374 The proportion of genetic kin (up to third-degree) identified between individuals buried in 375 different buildings in the three Çatalhöyük periods. C) The proportion of genetic kin (up to 376 third-degree) identified in co-burials within the same building, separated into three 377 Çatalhöyük periods. See also Figure S9 for the same proportion calculated for different sets 378 of relatives and age groups. The analysis involves 23 buildings. Percentages indicated on 379 the horizontal bars show the percentage of Monte Carlo simulations where the null 380 hypothesis of no difference between a pair of periods was rejected (p<0.05) out of 24 381 scenarios involving various assumptions/conditions. The overall rate of rejection among all 382 108 comparisons was 69% (see Figure S12 for details). D) The proportion of genetic kin 383 within co-burials in 15 buildings (only including buildings with a minimum of 2 burials). The 384 inset shows the Spearman correlation coefficient (p=0.03). 385 386 Co-burial of genetically unrelated individuals increases over time 387 388 Interestingly, we noticed a temporal change in the density of genetic connections among 389 burials in the same building. Specifically, co-buried pairs inside Early-period buildings were 390 frequently third-degree (e.g., cousin) or closer genetic kin (63%) (Figure 3), a pattern similar 391 to those of PPN Anatolian settlements such as Aşıklı, Boncuklu, and Çayönü(31, 42). In 392 contrast, genetic kin among co-buried pairs was only at 30% and 22% frequencies in the 393 Middle and Late periods, respectively (Figure 3, Figure S12). We also calculated the 394 correlation between co-burial genetic kin frequencies per building and the building ages and 395
Female lineages and changing kinship patterns in Neolithic Çatalhöyük

June 2024

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727 Reads

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3 Citations

Arguments have long suggested that the advent of early farming in the Near East and Anatolia was linked to a ‘Mother Goddess’ cult. However, evidence for a dominant female role in these societies has been scarce. We studied social organisation, mobility patterns and gendered practices in Neolithic Southwest Asia using 131 paleogenomes from Çatalhöyük East Mound (7100-5950 BCE), a major settlement in Central Anatolia with an uninterrupted occupation and an apparent egalitarian structure. In contrast to widespread genetic evidence for patrilocality in Neolithic Europe, the Çatalhöyük individuals revealed no indication of patrilocal mobility. Analysing genetic kin ties among individuals buried in the same house (co-burials) across 35 Çatalhöyük buildings, we identified close ties concentrated within buildings and among neighbours in Çatalhöyük’s Early period, akin to those in the preceding Pre-Pottery Neolithic in Southwest Asia. This pattern weakened over time: by the late 7th millennium BCE, subadults buried in the same building were rarely closely genetically related, despite sharing similar diets. Still, throughout the site’s occupation, genetic connections within Çatalhöyük buildings were much more frequently connected via the maternal than the paternal line. We also identified differential funerary treatment of female subadults compared to those of males, with a higher frequency of grave goods associated with females. Our results reveal how kinship practices changed while key female roles persisted over one thousand years in a large Neolithic community in western Eurasia.


Bioarchaeology: Transformations in Lifestyle, Morbidity, and Mortality

March 2023

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104 Reads

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2 Citations

Bioarchaeology, a highly contextualized study of human remains embedded in their cultural and natural settings, is a multidisciplinary study of past human biological variation that draws upon allied fields in the natural, social, and medical sciences, as well as the humanities. This chapter focuses on how human remains enhance their knowledge about the lives of past people, and hence provides a deep temporal context for a better understanding of the world as it exists today. Bioarchaeologists direct most of their attention to human remains from the Holocene. Case reports of single, or perhaps a few, skeletons have always been an important part of bioarchaeology. This is especially true of paleopathology, where the identification of specific diseases, such as tuberculosis, has long been of interest. Patterning in age‐at‐death in large and well‐characterized skeletal samples provides perspectives on population structure and change that cannot be obtained from other sources.


Fig. 1. The Konya paleolake basin detailing the geological area in which the sites are situated. After Roberts and Rosen (13) and de Meester (14).
Fig. 2. Sr and O isotope values for Boncuklu (n = 18) and Pınarbas¸ı (n = 4). Paleolake basin and terrace Sr value constraints follow Bogaard et al. (39). For raw data see SI Appendix, Table S3. British Geological Survey data # UKRI 2022.
Fig. 3. Strontium and oxygen isotope values from C¸atalh€ oy€ uk (n = 77) plotted according to site, sex, and occupation period. Paleolake basin and terrace Sr value constraints follow Bogaard et al. (39). For raw data see SI Appendix, Table S3. British Geological Survey data # UKRI 2022.
Fig. 4. A box and whisker plot of strontium isotope values for C¸atalh€ oy€ uk sheep (n = 7), humans (n = 77), and plants (n = 7) [sheep and plant data from Bogaard et al. (39)]. British Geological Survey data # UKRI 2022.
Mobility and kinship in the world's first village societies

January 2023

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1,302 Reads

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9 Citations

Proceedings of the National Academy of Sciences

Around 10,000 y ago in southwest Asia, the cessation of a mobile lifestyle and the emer-gence of the first village communities during the Neolithic marked a fundamental change in human history. The first communities were small (tens to hundreds of individuals) but remained semisedentary. So-called megasites appeared soon after, occupied by thousands of more sedentary inhabitants. Accompanying this shift, the material culture and ancient ecological data indicate profound changes in economic and social behavior. A shift from residential to logistical mobility and increasing population size are clear and can be explained by either changes in fertility and/or aggregation of local groups. However, as sedentism increased, small early communities likely risked inbreeding without maintaining or establishing exogamous relationships typical of hunter-gatherers. Megasites, where large populations would have made endogamy sustainable, could have avoided this risk. To examine the role of kinship practices in the rise of megasites, we measured strontium and oxygen isotopes in tooth enamel from 99 individuals buried at Pınarbası, Boncuklu, and Catalh€oy€uk (Turkey) over 7,000 y. These sites aregeographically proximate and, critically, span both early sedentary behaviors (Pınarbas ̧ıand Boncuklu) and the rise of a local megasite (Catalh€oy€uk). Our data are consistent with the presence of only local individuals at Pınarbası and Boncuklu, whereas at Catalh€oy€uk, several nonlocals are present. The Catalh€oy€uk data stand in contrast to other megasites where bioarchaeological evidence has pointed to strict endogamy. These different kinship behaviors suggest that megasites may have arisen by employing unique, community-specific kinship practices.


Fig. 1. Bioarchaeological evidence of IPCC Predicted Health Impacts.
Fig. 2. Diverse pathways to resilience relevant to the UN Sustainable Development Goals.
Climate change, human health, and challenges to resilience in the holocene

January 2023

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733 Reads

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56 Citations

Proceedings of the National Academy of Sciences

Climate change is a significant threat to human health, especially for societies already confronted with rising social inequality, political and economic uncertainty, and a cascade of concurrent environmental challenges. Archaeological data about climate and environmental change provide a source of evidence about the potential challenges we face and the long-term outcomes of different short-term adaptive strategies employed in the past. Bioarchaeologists and paleopathologists study human health in the Holocene using evidence from archaeological human skeletons and mummified remains. Our research provides a basis for understanding the health impacts of past climate and environmental change within an evolutionary and biocultural framework. Here we provide bioarchaeological case studies from the published literature and discuss their relevance to research priorities outlined in the United Nations Sustainable Development Goals. We discuss the impact of environmental marginalization, famine and nutritional insufficiency, infectious disease, violence, and migration in the past. Although the magnitude and the pace of current global warming exceed the parameters of climate change experienced by past societies, bioarchaeology provides valuable insights into how variation in human historical and socio-cultural circumstances shaped epidemiological patterns across the millennia. It also provides clarity on the constraints of modernity, including limits to mobility and increasingly high levels of structural inequality. By demonstrating how past human societies perceived and experimented with solutions to climate and environmental challenges, bioarchaeology contributes to current prediction, planning, and policy-making efforts for a more equitable and sustainable future.






Citations (61)


... Bioarchaeologists have equated repeated observations of relatively shorter average adult statures in the Neolithic to a likely general health decline for individuals during this cultural period (13,14,16,34,55,87). Combinations of reduced nutritional diversity, unpredictable food availability (e.g., crop failure, storage loss), and increased infectious disease burden may have negatively impacted childhood health and growth (18,88,89). Understandably, those prior studies did not account for the contribution of interindividual variation in the contribution of heritable genetic factors to adult stature. ...

Reference:

An integrative skeletal and paleogenomic analysis of stature variation suggests relatively reduced health for early European farmers
Foraging to Farming Transition: Global Health Impacts, Trends, and Variation
  • Citing Chapter
  • October 2020

... We had previously reported a trend towards higher aDNA preservation in juvenile temporal bones versus adult temporal bones at Çatalhöyük (Yaka et al. 2021), raising the question of whether aDNA preservation levels may be related to age-specific burial treatments. We recently generated a larger aDNA dataset comprising the skeletal remains of 395 individuals as part of an investigation into the social structure of Çatalhöyük, the results of which may be found in an accompanying study (Yüncü et al. 2024). Here, we present findings from this dataset on age-related differences in organic preservation in Çatalhöyük human remains and in other archaeological sites with published aDNA datasets. ...

Female lineages and changing kinship patterns in Neolithic Çatalhöyük

... Bioarchaeological analysis of human skeletal remains recovered from carefully excavated archaeological contexts reveals important elements of the life histories represented. Coupled with archaeological interpretations, skeletal data provide unique sources of information regarding health conditions and the factors that affected them (Milner and Larsen 2023). In comparative contexts, such studies offer an opportunity to evaluate the quality of life through time and space and understand the complex influences of geography, diet, population size and density and related cultural issues (Steckel and Rose 2002). ...

Bioarchaeology: Transformations in Lifestyle, Morbidity, and Mortality
  • Citing Chapter
  • March 2023

... Holocene might be viewed as a good starting point to appreciate the different behavioural pathways undertaken by humans. For example, on the one hand, this geological epoch saw a drastic change in humans' subsistence patterns, thus prompting a sequence of unpredictable deleterious effects that have pervaded our biosocial condition (Larsen, 2023;Lewis et al., 2023); this mode of relation with the environment has thus shaped the current patterns of sedentism, population growth, hostpathogen dynamics, and socio-economic and health disparities. On the other, evidence suggests that, throughout the Holocene climate change events, some small-scale societies coped and thrived of complex hierarchies during the Neolithic Revolution. ...

The past 12,000 years of behavior, adaptation, population, and evolution shaped who we are today

Proceedings of the National Academy of Sciences

... Mobility in urban and rural spaces refers to the movement and exchange of human and nonhuman elements. 23 Throughout history, the reasons for mobility in traditional villages have included market transactions, social interactions, disaster avoidance and business activities. The mobility of traditional villages has undergone significant changes in the context of modern adaptation. ...

Mobility and kinship in the world's first village societies

Proceedings of the National Academy of Sciences

... Sociocultural food practices profoundly influence the choices of resources and food production systems 17 . Western preferences tend towards baked goods such as bread, cookies and doughnuts, whereas Asian nations, including China, predominantly consume wheat in the form of steamed bread, stuffed buns, noodles and dumplings. ...

The Oxford Handbook of the Archaeology of Diet

... Human societies are complex systems characterized by multiple patterns, structures, and properties that determine their demographic processes [63]. Therefore, deterministic narratives that suggest climate inevitably causes migration, violence, or ill health should be avoided [64]. Thus, climate should be conceived as one of several factors influencing decision-making in the face of potential challenges facing humans [65], and not as a delimiting factor. ...

Climate change, human health, and challenges to resilience in the holocene

Proceedings of the National Academy of Sciences

... Paleogenetic data can also provide a means for expanding beyond focusing on a single disease at a time and on those diseases with pathognomonic skeletal pathologies to consider also parasite burdens and other coinfections that are not visible skeletally or in archaeological contexts. This may allow for the discernment of otherwise hidden heterogeneity in frailty, as described by Wood and colleagues (87), as well as enable bioarchaeological examination of syndemics [the co-occurrence of multiple conditions that produce outcomes worse than their individual effects (88,89)]. For example, recent studies, although not focused on the transition to agriculture, demonstrate the rich potential for paleogenetic data (combined with or independent of skeletal signs of infection or other health burdens) to reveal comorbidities or coinfections in past populations that might have shaped health outcomes beyond the individual effects of each etiology. ...

Paleosyndemics: A Bioarchaeological and Biosocial Approach to Study Infectious Diseases in the Past

Centaurus

... Based on self-identified ethnic and race information, the membership of the AABA in 2022 was 87% white, 1.6% Indigenous, and less than 1% African American (Sumner et al. 2022). As our association strives to become more diverse, it also becomes clear that there is a need for deeper commitment to understanding the ethical dimensions of our practices, including the engagement with the origin, collection practices (including the social-historical contexts), and curation of human remains we use for teaching and research (Buikstra et al. 2022). It is not enough to attract membership from diverse groups (although that is an important priority) but people from underrepresented backgrounds often do not feel included in a way that they find respectful (Kaplan 2020;Morris and Washington, 2018) and those who are from these groups often have an overbearing amount of community service roles. ...

Twenty‐first century bioarchaeology: Taking stock and moving forward

American Journal of Biological Anthropology

... The settlement is known for its dense housing, wall paintings, striking imagery and figurines (Ian Hodder and Cessford 2004;Ian Hodder 2021;I Hodder 2007). About 700 human skeletal remains, either as complete individuals in their original location (primary burials), or as burials moved to another location (secondary) or loose skeletal elements (tertiary) have been excavated to date; these are mostly individual burials, with roughly even numbers of subadults and adults, and also similar numbers of females and males (Larsen et al. 2019;Knüsel et al. 2021;Haddow et al. 2021). These burials revealed a number of funerary patterns. ...

Bioarchaeology at neolithic Çatalhöyük: Indicators of health, well-being and lifeway in their social context