Genom att utvinna och analysera genetiskt material från subfossila lämningar av olika djurarter kan man undersöka en mängd aspekter av deras evolutionära historia. Den här avhandlingen undersöker dynamik, släktskap och ekologi hos olika populationer av tre stora rovdjur; grottlejon (Panthera spelaea), varg (Canis lupus) och brunbjörn (Ursus arctos). Resultaten är främst baserade på mitokondrie-DNA, men även på nukleärt DNA och stabila isotoper från insamlat benmaterial. Åldern på lämningarna har mer specifikt kunnat bestämmas med hjälp av 14C-datering och tidsskalan sträcker sig ända till den bortre gränsen för denna metod – ca 50,000 år tillbaka i tiden. Denna senkvartära tidsrymd innefattar både den Holocena, samt senare delen av den Pleistocena tidsepoken, en tid som utmärktes av dramatiska klimatförändringar med låga medeltemperaturer. Genom att använda analyser som jämför lämningarnas geografiska ursprung, den genetiska diversiteten vid olika tidpunkter samt information om samtida ekologiska förhållanden, har avsikten varit att hitta mönster som kan visa på kopplingar mellan populationernas dynamik och förändringar i deras miljö. Även interaktioner mellan arter samt mänsklig påverkan har tagits upp för att uppskatta om/hur dessa faktorer inverkat. I en del fall har vi utgått från tidigare studier, som antytt förändringar i vissa geografiska områden (Paper I) eller slagit fast att en flaskhals inträffat (Paper V). I andra har vi mer förutsättningslöst undersökt genetisk diversitet på en global (Paper II) eller temporal skala (Papers III & IV).
Korta mitokondrie-sekvenser från daterade prover av grottlejon från hela Eurasien analyserades i Paper I. En tydlig förlust av genetisk diversitet som kunde tolkas som orsakad av en flaskhals testades genom simuleringar av olika populationsmodeller, där resultaten stödde ett scenario med en långvarig flaskhals mellan ca 47-18,000 år sedan i Beringia. Tidsintervallet tillsammans med samtida nedgångar hos andra stora däggdjur antyder att djupgående klimatförändringar kan ha legat bakom. I Paper II undersöktes temporal diversitet hos vargar utifrån mitokondrie-DNA. Moderna prover från hela utbredningsområdet samt två lämningar från Sibirien analyserades. Resultaten visade lite geografisk struktur utöver två grupperingar, där den ena innehöll alla vargar från sen Pleistocen tid. Vidare påvisade simuleringar stöd för att en flaskhals inträffat i slutet av Pleistocen hos nordamerikanska vargar. En av varglämningarna från Sibirien analyserades utifrån både mitokondrie- och nukleärt DNA i Paper III. Jämförelser av det nukleära DNA:t med motsvarande data från moderna hundar och vargar stödde ett scenario där den sibiriska vargen tillhört en population som troligen utgjordes av de gemensamma föregångarna till de två moderna grupperna. Utifrån den uppskattade mutationshastigheten skilde sig de två sistnämnda genetiska linjerna förmodligen så tidigt som för minst ca 27,000 år sedan. I Paper IV sekvenserades mitokondrie-DNA från lämningar av europeisk brunbjörn. Flera demografiska förändringar kunde avslöjas med hjälp av 14C-dateringar och provernas fastställda haplotyper. En minskning av diversitet kunde iakttas i samband med den senaste istiden (LGM), samt en kraftigt minskande populationsstorlek efter mitten av Holocen. Den geografiska
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utbredningen i västra Europa under LGM motsäger tidigare hypoteser om att brunbjörnens utbredning skulle ha varit begränsad till enbart södra Europa under denna tid. I Paper V fokuserade vi på den skandinaviska björnpopulationen, för att undersöka genetiska effekter av den flaskhals som inträffade under sent 1800-tal, orsakad av intensiv och okontrollerad jakt. Jämförelser av mitokondrie-DNA och nukleära mikrosatelliter från museimaterial respektive moderna björnar påvisade en signifikant minskning av diversitet, framför allt i södra Skandinavien. Simuleringar gav vidare stöd för en modell där en flaskhals påverkat alla skandinaviska björnar.
Acknowledgements
I would first of all like to thank my supervisor Professor Love Dalén for taking me on and supporting me during the work on these and all other projects. I have also received much support from colleagues and fellow PhD students at the departments of zoology and archaeology, but especially in the ancient DNA group; Vendela, Elle, Edson, Patricia, Jean-Luc, George, Johanna, Matti and David - I am very grateful for all your help and your company over the years. For valuable assistance at the Department of Bioinformatics and Genetics and in the DNA-lab I am most grateful to; Fredrik Ronquist, Pia Eldenäs, Jane Parker, Anna-Lena Löfberg, Martin Irestedt, Bodil Cronholm, Veronica Nyström Edmark, Rodrigo Esparza-Salas and Keyvan Mirbakhsh. All other colleagues at NRM are acknowledged, especially Daniella Kalthoff, Peter Mortensen and Peter Nilsson for helping out with the bear samples from the museum.
For work on the simulations I am in much gratitude to Ludovic Orlando, Edson Sandoval-Castellanos, Jean-Luc Tison and Yvonne Chan. I am also grateful to Pontus Skoglund, in whose hands the data from the Taimyr-wolf turned into a great paper. For inviting me to work on the dataset gathered from modern wolves I would like to thank Peter Savolainen at the Royal Institute of Technology (KTH) and Cornelya Klütsch at Trent University. I would further like to express my gratitude to everyone that have helped with and facilitated the contribution of samples for all projects, as well as all the co-authors (more thoroughly acknowledged in the papers/manuscripts). Tom Gilbert and Mikkel Sinding-Larsen are especially acknowledged for sharing their data on the wolf samples from Greenland.
Additionally, I would like to express my gratitude to Tom Higham and Katerina Douka at the Research Laboratory for Archaeology and the History of Art in Oxford for all their help and for a real good time. The group working under Michael Hofreiter in Potsdam is acknowledged, especially Axel Barlow, Johanna Paijmans and Mick Westbury, and so are Beth Shapiro and her group for hosting me at UCSC in Santa Cruz, US. I am grateful for financial support from Tullbergs stiftelse and Föreningen Riksmusei Vänner. I would also like to thank my co-supervisor Kerstin Lidén and the other members of my evaluation committee; Karl Gotthard and Lars Werdelin.
Last but not least, I want to thank family and friends for their support, especially Hani for supporting and sticking with me ♥.
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Contributions
Paper I
I took part in the design of the study. All laboratory work was performed by me and I helped with the data analyses. The paper was written by me, with input from the co-authors.
Paper II
I helped to design the study and performed laboratory analyses on the two Late Pleistocene wolf samples. I also conducted all data analyses, except for the coalescent simulations, which were done together with Yvonne Chan. I wrote the manuscript with help from the other authors.
Paper III
This study was based on the DNA extractions I did for paper II. I further helped building the Illumina libraries. The analyses of the mitochondrial genome were performed by me, and I also participated in writing the paper.
Paper IV
For this manuscript I helped to design the study and to formulate hypotheses. I collected samples from museum collections around Europe, on which I did all DNA extractions, amplifications and sequencing. I also conducted all the computational analyses on the data, interpreted the results and wrote the manuscript with input from the co-authors.
Paper V
I helped to design the study and to formulate hypotheses. I collected all the historical samples, and conducted laboratory and data analyses together with George Xenikoudakis. I also took part in the work on the Bayesian simulations as well as in interpreting the results and writing the paper.
32
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