The past hidden in our genes : Combining archaeological and genetic methodology : Prehistoric population bottlenecks in Finland

This doctoral dissertation combines archaeological and genetic methodology to find evidence of prehistoric population bottleneck(s) in Finland. This was performed by applying forward-time population genetic simulations with archaeologically justified development of population size. We ran different simulation scenarios to evaluate genetic effects of past demographic events and the results were compared with the known population genetic features of the current gene pool. In this thesis the focus in the simulations was on uniparental markers, the mitochondrion and the Y chromosome. The simulations were carried out in the forward time population genetic simulation environment simuPOP. The prehistoric Finnish population has not been previously simulated to this extent with population genetic simulations. In addition to genetic simulations, we performed analyses of the Stone and Ceramic Artefact Database as well as the radiocarbon date database to find out temporal differences in the intensity of the archaeological signal. We found similar evidence for a marked increase in the archaeological signal 4000-3500 cal BC followed by a distinct weakening. Previously, the Stone Artefact Database has been used to study singular artefacts and a few artefact types exclusively. This is the first time the Database including thousands of objects belonging to several Mesolithic and Neolithic time periods has been data mined to a large extent. Furthermore, we carried out a Bayesian spatial analysis of radiocarbon datings and archaeological finds from Finland and ceded Karelia, to better understand the overall geographical distribution of human activity through time. The analyses were carried out within the framework of Bayesian spatial modelling, using the Besag-York-Mollie (BYM) model to build spatial distributions of various archaeological datasets in Finland. This model is based on image analysis and assumes similarity of neighbouring areas in geospatial applications. The methodology presented here is one of the first efforts of applying Bayesian spatial analysis with different types of archaeological data in Finland. The main results of the study are: Archaeological and genetic evidence, together with the Stone Artefact Analysis, indicate that there has been at least one Neolithic bottleneck in Finland. Moreover, we show that immigration from neighbouring populations, even if very limited but constant over prolonged time periods, can have drastic effects on a population s genetic composition. Furthermore, our simulations showed that a tight prehistoric bottleneck can still have an effect on genetic diversity, even after thousands of years. With this kind of approach, we can evaluate the evidence in a more detailed fashion compared to solely an archeological or genetic approach.Tässä väitöskirjassa yhdistetään arkeologisia ja geneettisiä menetelmiä Suomen esihistoriallisten populaatiopullonkaulojen todentamiseen. Yhdistimme geneettisiä simulaatioita ja arkeologiseen todistusaineistoon perustuvia väestömäärän arvioita. Kokeilimme erilaisia simulaatioskenaarioita arvioidaksemme demografisten tapahtumien geneettisisiä vaikutuksia ja vertasimme tuloksia nykyisen geenipoolimme tunnettujen geneettisten piirteiden kanssa. Tässä väitöskirjassa keskityimme mitokondriaaliseen ja Y-kromosomaaliseen tutkimukseen. Simulaatiot tehtiin simuPOP -nimisessä eteenpäin ajassa kulkevassa populaatiosimulaatioympäristössä. Suomen esihistoriallista väestöä ei ole aikaisemmin näin laajasti simuloitu geneettisin simulaatiomenetelmin. Geneettisten simulaatioiden lisäksi analysoimme kivi- ja keramiikkatietokantaa sekä radiohiiliajoitusten tietokantaa selvittääksemme arkeologisen signaalin vahvuutta eri aikoina. Löysimme todistusaineistoa arkeologisen signaalin voimistumisesta 4000-3500 cal BC jota seurasi signaalin selvä heikentyminen. Kiviesinetietokantaa on aikaisemmin käytetty ainoastaan yksittäisten esineiden ja harvojen esinetyyppien tutkimiseen. Tämä on ensimmäinen kerta kun tuhansia mesoliittiselle ja neoliittiselle kivikaudelle kuuluvia esineitä sisältävää tietokantaa on tutkittu laajemmassa mittakaavassa. Teimme bayesilaisen spatiaalisen analyysin radiohiiliajoituksista sekä arkeologisista löydöistä, jotka on löydetty Suomesta ja luovutetusta Karjalasta ymmärtääksemme paremmin ihmisaktiviteetin maantieteellistä jakaumaa eri aikoina. Analyysit tehtiin bayesilaisen spatiaalisen mallin viitekehyksessä käyttäen Besag-York-Mollie (BYM) -mallia jolla analysoitiin erilaisten arkeologisten aineistojen jakautumista Suomessa. Tämä malli perustuu kuva-analyysiin ja olettaa naapurialueiden muistuttavan toisiaan maantieteellis-spatiaalisesti. Bayesilaista spatiaalista analyysiä käytetään tässä tutkimuksessa ensimmäisiä kertoja erilaisten arkeologisten aineistojen tutkimiseen Suomessa. Tutkimuksen päätulokset ovat: arkeologinen ja geneettinen todistusaineisto yhdessä kiviesinetietokanta-analyysin kanssa viittaa siihen, että Suomessa on ollut ainakin yksi neoliittinen populaatiopullonkaula. Tutkimuksemme mukaan naapuripopulaatioista tullut migraatio, vaikkakin rajallinen mutta pitkäaikainen, voi merkittävästi vaikuttaa populaation geneettiseen rakenteeseen. Simulaatiomme osoittivat, että ahdas esihistoriallinen pullonkaula voi vieläkin vaikuttaa geneettiseen diversiteettiin, jopa tuhansien vuosien päähän. Tällä lähestymistavalla on mahdollista arvioida tuloksia perusteellisemmin kuin yksinomaan arkeologisella tai geneettisellä lähestymistavalla

Genomic evidence uncovers inbreeding and supports translocations in rescuing the genetic diversity of a landlocked seal population

Peer reviewe

Vestiges of an Ancient Border in the Contemporary Genetic Diversity of North-Eastern Europe

It has previously been demonstrated that the advance of the Neolithic Revolution from the Near East through Europe was decelerated in the northernmost confines of the continent, possibly as a result of space and resource competition with lingering Mesolithic populations. Finland was among the last domains to adopt a farming lifestyle, and is characterized by substructuring in the form of a distinct genetic border dividing the northeastern and southwestern regions of the country. To explore the origins of this divergence, the geographical patterns of mitochondrial and Y-chromosomal haplogroups of Neolithic and Mesolithic ancestry were assessed in Finnish populations. The distribution of these uniparental markers revealed a northeastern bias for hunter-gatherer haplogroups, while haplogroups associated with the farming lifestyle clustered in the southwest. In addition, a correlation could be observed between more ancient mitochondrial haplogroup age and eastern concentration. These results coupled with prior archeological evidence suggest the genetic northeast/southwest division observed in contemporary Finland represents an ancient vestigial border between Mesolithic and Neolithic populations undetectable in most other regions of Europe.Peer reviewe

Buried in water, burdened by nature-Resilience carried the Iron Age people through Fimbulvinter

Levanluhta is a unique archaeological site with the remains of nearly a hundred Iron Age individuals found from a water burial in Ostrobothnia, Finland. The strongest climatic downturn of the Common Era, resembling the great Fimbulvinter in Norse mythology, hit these people during the 6th century AD. This study establishes chronological, dietary, and livelihood synthesis on this population based on stable carbon and nitrogen isotopic and radiocarbon analyses on human remains, supported by multidisciplinary evidence. Extraordinarily broad stable isotopic distribution is observed, indicating three subgroups with distinct dietary habits spanning four centuries. This emphasizes the versatile livelihoods practiced at this boundary of marine, freshwater, and terrestrial ecosystems. While the impact of the prolonged cold darkness of the 6th century was devastating for European communities relying on cultivation, the broad range of livelihoods provided resilience for the Levanluhta people to overcome the abrupt climatic decline.Peer reviewe

Buried in water, burdened by nature – Resilience carried the Iron Age people through Fimbulvinter

Levänluhta is a unique archaeological site with the remains of nearly a hundred Iron Age individuals found from a water burial in Ostrobothnia, Finland. The strongest climatic downturn of the Common Era, resembling the great Fimbulvinter in Norse mythology, hit these people during the 6th century AD. This study establishes chronological, dietary, and livelihood synthesis on this population based on stable carbon and nitrogen isotopic and radiocarbon analyses on human remains, supported by multidisciplinary evidence. Extraordinarily broad stable isotopic distribution is observed, indicating three subgroups with distinct dietary habits spanning four centuries. This emphasizes the versatile livelihoods practiced at this boundary of marine, freshwater, and terrestrial ecosystems. While the impact of the prolonged cold darkness of the 6th century was devastating for European communities relying on cultivation, the broad range of livelihoods provided resilience for the Levänluhta people to overcome the abrupt climatic decline

Improved chromosome-level genome assembly of the Glanville fritillary butterfly (Melitaea cinxia) integrating Pacific Biosciences long reads and a high-density linkage map

Background The Glanville fritillary (Melitaea cinxia) butterfly is a model system for metapopulation dynamics research in fragmented landscapes. Here, we provide a chromosome-level assembly of the butterfly's genome produced from Pacific Biosciences sequencing of a pool of males, combined with a linkage map from population crosses. Results The final assembly size of 484 Mb is an increase of 94 Mb on the previously published genome. Estimation of the completeness of the genome with BUSCO indicates that the genome contains 92-94% of the BUSCO genes in complete and single copies. We predicted 14,810 genes using the MAKER pipeline and manually curated 1,232 of these gene models. Conclusions The genome and its annotated gene models are a valuable resource for future comparative genomics, molecular biology, transcriptome, and genetics studies on this species.Peer reviewe

The population history of northeastern Siberia since the Pleistocene.

Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of 'Ancient North Siberians' who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to 'Ancient Palaeo-Siberians' who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name 'Neo-Siberians', and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas

Sattuma on muovannut Suomen esihistoriallisen väestön geenejä

Suomalaista väestöhistoriaa tutkimalla voidaan selvittää sitä, miten väestön määrä on vaihdellut esihistorian aikana. Populaation koko ja erityisesti sen vaihtelut vaikuttavat oleellisesti geneettisen variaation määrään. Varsinkin ahtaan populaation pullonkaulan merkitys on suuri, sillä sellainen voi eliminoida aiemmin olemassa olleesta geneettisestä vaihtelusta jopa valtaosan. Yhdistämällä arkeologista ja geneettistä tietämystä voidaan rakentaa tarkempaa kuvaa esihistoriallisen väestön vaiheista