Biology subjects

Gotherstrom, A.

Publications and source records attributed to Gotherstrom, A..

11 recordsLinked to original sources

bioRxiv2026

The Muskox Way: Humans, plants and animals in northeast Greenland through the Holocene

The Muskox Way hypothesis suggests that the first humans entering northeast Greenland from Arctic Canada followed and hunted muskox. Yet whether muskox arrived before people remains debated, as only two bones predate the Independence culture (4500-3900 cal BP). More broadly, the arrival of plants and animals, and how the three periods of human settlement related to ecosystem changes, remain poorly understood. We analysed sedimentary ancient DNA from lakes in Wandel Dal (Late Sommersoe and Midsommersoe) and Zackenberg, identifying 121 native plants and nine animal taxa. In Wandel Dal, the plant assemblage indicates a warmer climate than today about 8200-3900 years ago, followed by an abrupt change in flora and sedimentation rate at 3900 cal BP, especially at Midsommersoe. Muskox DNA is present continuously at Midsommersoe from 7400 cal BP, about three millennia before humans arrived. The Zackenberg record dates to 12,200 cal BP, with arctic forbs, grasses, ferns and crowberry in the earliest layers, willow from 8200 cal BP and birch from 7200 cal BP, but muskox only in the last 2500 years, the latter period coinciding with Greenlandic Dorset culture. The arrival of the Thule culture in 1400 CE coincides with a slight increase in plant richness at Wandel Dal and an increase in mammal detections. Reindeer occurred only in samples older than 6000 years, consistent with their absence from archaeological bone records. Overall, humans arrived long after the first megafauna and appear to have had limited impact on their populations, although cultural periods coincided with environmental changes.

ecology↗

bioRxiv2026

Of bone and ivory: Eastern Atlantic sources of the medieval European walrus ivory trade discovered by ancient mitochondrial and nuclear DNA

Previous molecular archaeological research has made the surprising discovery that almost all studied European walrus finds dating between the 11th and 14th centuries CE seemed to be traded from the Norse colony of Greenland. But why has almost no walrus ivory from the Barents Sea region been detected in medieval Europe, despite its closer proximity and being mentioned in historical accounts? Here, we show that the full spatial extent of medieval Atlantic walrus hunting has been underestimated in previous analyses that targeted modified walrus skulls (rostra) with which pairs of attached tusks were traded, because destructive sampling of ivory artefacts is not always practicable. By analysing workshop offcuts from medieval Sigtuna, Sweden, we directly compare the geographical sources of walrus ivory with rostra, and show that isolated tusks were traded in different ways. We first resolve the genome-wide trans-Atlantic walrus population structure, discovering significant genome-wide nuclear differentiation between western and eastern Atlantic walrus populations. By employing spatially diagnostic nuclear SNPs (n = 144,986), we then use low-coverage sequence data to classify historical walrus rostrum and tusk specimens to either western or eastern Atlantic origin, and thus overcome previous limitations when provenancing walruses based on mitochondrial DNA alone. We find that all medieval walrus rostra are assigned exclusively towards the western Atlantic. In contrast, half of the medieval ivory specimens from Sigtuna are assigned to eastern Atlantic sources including Iceland and the Barents Sea region. Moreover, the objects of eastern origin precede those from Norse Greenland in time, suggesting sequential exploitation. Our observations resolve a discrepancy between earlier molecular inference and historical evidence and imply a significantly broader extent and impact of medieval ecological globalisation in the Arctic.

evolutionary biology↗

bioRxiv2024

Ancient DNA analyses of two Early Chalcolithic Individuals from the West Mound

In this chapter, we investigate the genetics of two Early Chalcolithic Catalhoyuk individuals, U.18333 and U.16835, the only two burials yet recovered from the West Mound. These were two neonates buried within the same building. Using shotgun-sequenced partial genomes (0.06x and 0.02x coverage) we identify both as females. Despite being recovered from the same building, we find no close genetic kinship between them, in line with previously published kinship results from Catalhoyuk. We also find that the two West Mound neonates shared the same gene pool with Neolithic Catalhoyuk and other Central and West Anatolian Neolithic populations, and they did not carry the Caucasus-related "eastern" gene flow signature observed in later-coming Chalcolithic Anatolian genomes. This indicates no large-scale admixture between East and West Mound Catalhoyuk, and possibly that the post-Neolithic "eastern" gene flow event into Anatolia may have initiated only by the mid-6th millennium BCE.

genetics↗

bioRxiv2024

Out-of-Anatolia: cultural and genetic interactions during the Neolithic expansion in the Aegean

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, which reveals 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.

genomics↗

bioRxiv2024

High-resolution genomic ancestry reveals mobility in early medieval Europe

Ancient DNA has unlocked new genetic histories and shed light on archaeological and historical questions, but many known and unknown historical events have remained below detection thresholds because subtle ancestry changes are challenging to reconstruct. Methods based on sharing of haplotypes1,2 and rare variants3,4 can improve power, but are not explicitly temporal and have not been adopted in unbiased ancestry models. Here, we develop Twigstats, a new approach of time-stratified ancestry analysis that can improve statistical power by an order of magnitude by focusing on coalescences in recent times, while remaining unbiased by population-specific drift. We apply this framework to 1,151 available ancient genomes, focussing on northern and central Europe in the historical period, and show that it allows modelling of individual-level ancestry using preceding genomes and provides previously unavailable resolution to detect broader ancestry transformations. In the first half of the first millennium [~]1-500 CE (Common Era), we observe an expansion of Scandinavian-related ancestry across western, central, and southern Europe. However, in the second half of the millennium [~]500-1000 CE, ancestry patterns suggest the regional disappearance or substantial admixture of these ancestries in multiple regions. Within Scandinavia itself, we document a major ancestry influx by [~]800 CE, when a large proportion of Viking Age individuals carried ancestry from groups related to continental Europe. This primarily affected southern Scandinavia, and was differentially represented in the western and eastern directions of the wider Viking world. We infer detailed ancestry portraits integrated with historical, archaeological, and stable isotope evidence, documenting mobility at an individual level. Overall, our results are consistent with substantial mobility in Europe in the early historical period, and suggest that time-stratified ancestry analysis can provide a new lens for genetic history.

evolutionary biology↗

bioRxiv2024

Unravelling the ancient fungal DNA from the Iceman's gut

Here, we explore the possible ancient fungal species in the gut of Otzi, the Iceman, a naturally mummified human found in the Tyrolean Alps (border between Italy and Austria). While ancient DNA (aDNA) has been extensively used to study human, animal, and plant evolution, this research focuses on ancient microbial diversity, specifically fungi. Fungal DNA is often underestimated in metagenomic samples, however here we hypothesise the possibility of retrieving ancient fungal sequences from Otzis gut. A robust bioinformatic pipeline has been developed to detect and authenticate fungal aDNA from stomach, small intestine, and large intestine samples. We revealed the presence of Pseudogymnoascus genus, with P. destructans and P. verrucosus as possible species, that were particularly abundant in the stomach and small intestine. We suggest that Otzi may have consumed these fungi accidentally, likely in association with other elements of his diet, and they thrived in his gut after his death due to their adaptability to harsh and cold environments. This research provides insight into the coexistence of ancient humans with specific fungal species and proposes and validates a conservative bioinformatic approach for detecting fungal aDNA in historical metagenomic samples. Significance statementDespite their essential interactions with all kingdoms of life, limited molecular studies have focused on ancient fungi. Here, we developed a thorough bioinformatic pipeline that allowed us to detect the presence of ancient DNA likely belonging to Pseudogymnoascus destructans and P. verrucosus in the gut of Otzi, a human naturally mummified over 3,000 years ago in the Tyrolean Alps. Both species can survive harsh environmental conditions, and P. destructans is known for its pathogenicity, suggesting that Otzi may have accidentally ingested them and providing valuable insights into how ancient humans coexisted with specific fungal species. We propose a highly reliable methodology for detecting ancient fungal DNA in metagenomic studies of historical samples that can have broader applications to understand ancient ecosystems and their interactions.

microbiology↗

bioRxiv2022

aMeta: an accurate and memory-efficient ancient Metagenomic profiling workflow

Analysis of microbial data from archaeological samples is a rapidly growing field with a great potential for understanding ancient environments, lifestyles and disease spread in the past. However, high error rates have been a long-standing challenge in ancient metagenomics analysis. This is also complicated by a limited choice of ancient microbiome specific computational frameworks that meet the growing computational demands of the field. Here, we propose aMeta, an accurate ancient Metagenomic profiling workflow designed primarily to minimize the amount of false discoveries and computer memory requirements. Using simulated ancient metagenomic samples, we benchmark aMeta against a current state-of-the-art workflow, and demonstrate its superior sensitivity and specificity in both microbial detection and authentication, as well as substantially lower usage of computer memory. aMeta is implemented as a Snakemake workflow to facilitate use and reproducibility.

bioinformatics↗

bioRxiv2022

A genomic snapshot of demographic and cultural dynamism in Upper Mesopotamia during the Neolithic Transition

Upper Mesopotamia played a key role in the Neolithic Transition in Southwest Asia through marked innovations in symbolism, technology, and foodways. We present thirteen ancient genomes (c.8500-7500 calBCE) from Pre-Pottery Neolithic Cayonu in the Tigris basin together with bioarchaeological and material culture data. Our findings reveal that Cayonu was a genetically diverse population, carrying a mixed ancestry from western and eastern Fertile Crescent, and that the community received immigrants. Our results further suggest that the community was organised along biological family lines. We document bodily interventions such as head-shaping and cauterization among the individuals examined, reflecting Cayonus cultural ingenuity. Finally, we identify Upper Mesopotamia as the likely source of eastern gene flow into Neolithic Anatolia, in line with material culture evidence. We hypothesise that Upper Mesopotamias cultural dynamism during the Neolithic Transition was the product not only of its fertile lands but also of its interregional demographic connections.

genetics↗

bioRxiv2022

Whole genome analysis sheds light on the genetic origin of Huns, Avars and conquering Hungarians

Huns, Avars and conquering Hungarians were Migration Period nomadic groups which arrived in three successive waves in the Carpathian Basin between the 5th and 9th centuries. Based on historical data each of these groups are thought to have arrived from Asia, although their exact origin and relation to other ancient and modern populations has been debated. In this study we have sequenced 9 Hun, 143 Avar and 113 Hungarian conquest period samples, and identified three core populations, representing immigrants from each period, with no recent European ancestry. Our results suggest that this "immigrant core" of both Huns and Avars originated in present day Mongolia, and their origin can be traced back to Xiongnus. On the other hand, the "immigrant core" of the conquering Hungarians derived from an earlier admixture of Mansis, early Sarmatians and descendants of late Xiongnus. In addition, we detected shared Hun-related ancestry in numerous Avar and Hungarian conquest period genetic outliers indicating a genetic link between these successive nomadic groups. Aside from the immigrant core groups we identified that the majority of the individuals from each period were local residents, harboring "native European" ancestry.

genetics↗

bioRxiv2020

Human inbreeding has decreased in time through the Holocene

The history of human inbreeding is controversial. The development of sedentary agricultural societies may have had opposite influences on inbreeding levels. On the one hand, agriculture and food surplus may have diminished inbreeding by increasing population sizes and lowering endogamy, i.e. inbreeding due to population isolation. On the other hand, increased sedentism, as well as the advent of private property may have promoted inbreeding through the emergence of consanguineous marriage customs or via ethnic and caste endogamy. The net impact is unknown, and to date, no systematic study on the temporal frequency of inbreeding in human societies has been conducted. Here we present a new approach for reliable estimation of runs of homozygosity (ROH) in genomes with [≥]3x mean coverage across >1 million SNPs, and apply this to 440 ancient Eurasian genomes from the last 15,000 years. We show that the frequency of inbreeding, as measured by ROH, has decreased over time. The strongest effect is associated with the Neolithic transition, but the trend has since continued, indicating a population size effect on inbreeding prevalence. We further show that most inbreeding in our historical sample can be attributed to endogamy, although singular cases of high consanguinity can also be found in the archaeogenomic record. HighlightsA study of 440 ancient genomes shows inbreeding decreased over time. The decrease appears linked with population size increase due to farming. Extreme consanguineous matings did occur among farmers, but rarely.

genomics↗

bioRxiv2018

Early Pleistocene enamel proteome sequences from Dmanisi resolve Stephanorhinus phylogeny.

Ancient DNA (aDNA) sequencing has enabled unprecedented reconstruction of speciation, migration, and admixture events for extinct taxa1. Outside the permafrost, however, irreversible aDNA post-mortem degradation2 has so far limited aDNA recovery within the {small tilde}0.5 million years (Ma) time range3. Tandem mass spectrometry (MS)-based collagen type I (COL1) sequencing provides direct access to older biomolecular information4, though with limited phylogenetic use. In the absence of molecular evidence, the speciation of several Early and Middle Pleistocene extinct species remain contentious. In this study, we address the phylogenetic relationships of the Eurasian Pleistocene Rhinocerotidae5-7 using {small tilde}1.77 million years (Ma) old dental enamel proteome sequences of a Stephanorhinus specimen from the Dmanisi archaeological site in Georgia (South Caucasus)8. Molecular phylogenetic analyses place the Dmanisi Stephanorhinus as a sister group to the woolly (Coelodonta antiquitatis) and Mercks rhinoceros (S. kirchbergensis) clade. We show that Coelodonta evolved from an early Stephanorhinus lineage and that this genus includes at least two distinct evolutionary lines. As such, the genus Stephanorhinus is currently paraphyletic and its systematic revision is therefore needed. We demonstrate that Early Pleistocene dental enamel proteome sequencing overcomes the limits of ancient collagen- and aDNA-based phylogenetic inference, and also provides additional information about the sex and taxonomic assignment of the specimens analysed. Dental enamel, the hardest tissue in vertebrates, is highly abundant in the fossil record. Our findings reveal that palaeoproteomic investigation of this material can push biomolecular investigation further back into the Early Pleistocene.

evolutionary biology↗