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- Dehasque, Marianne, 1993-
(author)
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Palaeogenomic reconstruction of woolly mammoth evolutionary history and extinction dynamics
- 2023
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Doctoral thesis (other academic/artistic)abstract
- Biodiversity is declining globally. Yet, the biological and genetic processes associated with these declines on a longer timescale are still poorly understood. Ancient DNA is a powerful tool to study evolution in real-time. Despite advances in the field, there is further need for refinement of laboratory and computational techniques. In this thesis, I used mitochondrial and nuclear genomes, as well as radiocarbon data, to study the evolutionary history and extinction dynamics of the woolly mammoth (Mammuthus primigenius). In Chapter I, I developed and optimized a silica column-based extraction protocol for ancient DNA. Based on systematic tests, I advise against routine use of pretreatment methods, like bleach wash and/or predigestion, for well-preserved permafrost samples. Furthermore, I suggest that USER enzyme, which removes uracil from damaged DNA molecules, is effective at half the concentration compared to an established control protocol. Finally, I did not find a significant difference between different silica columns for the clean-up steps, or concentrator columns with different DNA retention sizes. In Chapter II, I used five high coverage Siberian mammoth genomes to develop a method based on differences in read depth to identify indels, insertions and deletions, in the mammoth genome. The results show that indels are enriched in intergenic regions, suggesting strong selection against structural variants affecting gene function. Nevertheless, 87 genes were identified that were severely affected. These genes are related to various functions like body-fat distribution, fur growth and hair shape, body temperature, and body size, and most likely represent important adaptations to the cold steppe-tundra. In Chapter III, I studied the population and extinction dynamics of the woolly mammoths in Siberia by combining Bayesian age models from radiocarbon data with inferences from complete mitogenomes. The results show that the woolly mammoth’s extinction was a complex process with consecutive extirpations, but also partial recolonizations, occurring in different Siberian localities. I hypothesize that Wrangel Island, one of the last refugia of the woolly mammoth, was colonized by mammoths from, or closely related to, a population from central or western Siberia. Mammoths reappeared on the island around 10 ky ago, where they became isolated due to rising sea levels, and went extinct around 4 ky ago. To investigate the genetic consequences of the founder bottleneck event of Wrangel Island and long-term survival at small population size, I analyzed time-series data of 21 woolly mammoth genomes in Chapter IV. Changes in heterozygosity and inbreeding show that while the initial bottleneck was dramatic, the population recovered fast and remained remarkably stable. Analysis of mutation load shows that mammoths purged highly deleterious mutations over time, but also accumulated slightly deleterious mutations, indicating reduced efficacy of selection. Nevertheless, there were no clear signs of a mutational meltdown, and it remains a mystery why mammoths went extinct on the island. In conclusion, this thesis presents methodological advances for DNA extraction and detecting structural variants (i.e., deletions) in ancient genomes. Furthermore, I demonstrate that extinctions are a complex process. Finally, I show that ancient DNA is a powerful tool to study evolutionary processes over long timescales.
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| 2. |
- Handlin, Linda
(author)
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Human-Human and Human-Animal Interaction : Some Common Physiological and Psychological Effects
- 2010
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Doctoral thesis (other academic/artistic)abstract
- The aim of the present thesis was to investigate hormonal and physiological effects in mothers during a breastfeeding session and in dogs and their owners in response to short-term interaction. In study one, sixty-six mothers receiving either exogenous oxytocin infusion and/or epidural analgesia (EDA) during labor or intramuscular oxytocin injection post partum were studied. Oxytocin, prolactin, adrenocorticotrophic hormone (ACTH) and cortisol levels, as well as blood pressure were measured during a breastfeeding session two days after birth. In response to breastfeeding two days after birth, the mothers displayed a pulsatile release of oxytocin and increasing prolactin levels. In addition, the activity in the HPA-axis was reduced and maternal blood pressure decreased. The results also show that EDA administration in combination with oxytocin during labor resulted insignificantly lower oxytocin levels and higher cortisol levels, as well as higher bloodpressure in response to breastfeeding two days after birth, compared to EDA administration alone. In addition, oxytocin infusions dose-dependently lowered the mothers’ endogenous oxytocin levels two days after birth. In study two, ten female dog owners and their male Labrador dogs participated, together with ten controls. Their levels of oxytocin, cortisol and insulin, as well as their heart rate, were measured. The connection between the quality of the dogowner relationship and hormone levels was also explored. Short-term interaction between dogs and their owners resulted in oxytocin release in both species and their cortisol levels and heart rate were also affected. Oxytocin levels and positive attitudes regarding the dog-owner relationship were positively correlated. In conclusion, both human-human and human-animal interactions induce oxytocin release and promote oxytocin mediated effects, such as decreasing cortisol levels and blood pressure. In addition, social interaction and oxytocin levels arepositively related.
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