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Antarctic krill (Euphausia superba) is Earth’s most abundant wild animal, and its enormous biomass is vital to the Southern Ocean ecosystem. Here, we report a 48.01-Gb chromosome-level Antarctic krill genome, whose large genome size appears to have resulted from inter-genic transposable element expansions. Our assembly reveals the molecular architecture of the Antarctic krill circadian clock and uncovers expanded gene families associated with molting and energy metabolism, providing insights into adaptations to the cold and highly seasonal Antarctic environment. Population-level genome re-sequencing from four geographical sites around the Antarctic continent reveals no clear population structure but highlights natural selection associated with environmental variables. An apparent drastic reduction in krill population size 10 mya and a subsequent rebound 100 thousand years ago coincides with climate change events. Our findings uncover the genomic basis of Antarctic krill adaptations to the Southern Ocean and provide valuable resources for future Antarctic research., Antarctic krill (Euphausia superba) is Earth's most abundant wild animal, and its enormous biomass is vital to the Southern Ocean ecosystem. Here, we report a 48.01-Gb chromosome-level Antarctic krill genome, whose large genome size appears to have resulted from inter-genic transposable element expansions. Our assembly reveals the molecular architecture of the Antarctic krill circadian clock and uncovers expanded gene families associated with molting and energy metabolism, providing insights into adaptations to the cold and highly seasonal Antarctic environment. Population-level genome re-sequencing from four geographical sites around the Antarctic continent reveals no clear population structure but highlights natural selection associated with environmental variables. An apparent drastic reduction in krill population size 10 mya and a subsequent rebound 100 thousand years ago coincides with climate change events. Our findings uncover the genomic basis of Antarctic krill adaptations to the Southern Ocean and provide valuable resources for future Antarctic research.

Antarctic krill (Euphausia superba) is Earth’s most abundant wild animal, and its enormous biomass is vital to the Southern Ocean ecosystem. Here, we report a 48.01-Gb chromosome-level Antarctic krill genome, whose large genome size appears to have resulted from inter-genic transposable element expansions. Our assembly reveals the molecular architecture of the Antarctic krill circadian clock and uncovers expanded gene families associated with molting and energy metabolism, providing insights into adaptations to the cold and highly seasonal Antarctic environment. Population-level genome re-sequencing from four geographical sites around the Antarctic continent reveals no clear population structure but highlights natural selection associated with environmental variables. An apparent drastic reduction in krill population size 10 mya and a subsequent rebound 100 thousand years ago coincides with climate change events. Our findings uncover the genomic basis of Antarctic krill adaptations to the Southern Ocean and provide valuable resources for future Antarctic research., Antarctic krill (Euphausia superba) is Earth's most abundant wild animal, and its enormous biomass is vital to the Southern Ocean ecosystem. Here, we report a 48.01-Gb chromosome-level Antarctic krill genome, whose large genome size appears to have resulted from inter-genic transposable element expansions. Our assembly reveals the molecular architecture of the Antarctic krill circadian clock and uncovers expanded gene families associated with molting and energy metabolism, providing insights into adaptations to the cold and highly seasonal Antarctic environment. Population-level genome re-sequencing from four geographical sites around the Antarctic continent reveals no clear population structure but highlights natural selection associated with environmental variables. An apparent drastic reduction in krill population size 10 mya and a subsequent rebound 100 thousand years ago coincides with climate change events. Our findings uncover the genomic basis of Antarctic krill adaptations to the Southern Ocean and provide valuable resources for future Antarctic research.

For more than 100 years, house mice (Mus musculus) have been used as a key animal model in biomedical research. House mice are genetically diverse, yet their genetic background at the global level has not been fully understood. Previous studies have suggested that they originated in South Asia and diverged into three major subspecies, almost simultaneously, approximately 110,000-500,000 years ago; however, they have spread across the world with the migration of modern humans in prehistoric and historic times (similar to 10,000 years ago to the present day) and have undergone secondary contact, which has complicated the genetic landscape of wild house mice. In this study, we sequenced the whole-genome sequences of 98 wild house mice collected from Eurasia, particularly East Asia, Southeast Asia, and South Asia. Although wild house mice were found to consist of three major genetic groups corresponding to the three major subspecies, individuals representing admixtures between subspecies were more prevalent in East Asia than has been previously recognized. Furthermore, several samples exhibited an incongruent pattern of genealogies between mitochondrial and autosomal genomes. Using samples that likely retained the original genetic components of subspecies with the least admixture, we estimated the pattern and timing of divergence among the subspecies. The estimated divergence time of the three subspecies was 187,000-226,000 years ago. These results will help us to understand the genetic diversity of wild mice on a global scale, and the findings will be particularly useful in future biomedical and evolutionary studies involving laboratory mice established from such wild mice.

The bullhead Cottus gobio is a small-sized fish whose range extends over most of the European continent, and it is listed in Annex II of EU “Habitat” Directive for its great conservation interest. In the last decades, bullhead populations suffered local decline. Among the factors that negatively affect bullhead populations, major threats are pollution, habitat deterioration, and the massive introduction of salmonids. This study aims to better understand in which way the presence of the Salmo (trutta) trutta affects Cottus gobio populations. The investigation was carried out in two stretches of a stream located in the Orobic Alps (Italy). The downstream stretch hosts a fish assemblage constituted of both bullhead and brown trout, while in the upstream stretch only bullhead is present. An insurmountable barrier isolates the upstream population of C. gobio from trout, while the environmental conditions of the two stretches proved to be fully comparable. We evaluated population structure, habitat preference, and body shape of bullhead populations in both stretches: the results indicate that the presence of trout decreases the number of bullhead adults, reduces the average adult body size, and induces a bullhead suboptimal habitat occupation. However, both populations of C. gobio showed a well-structured population and good performance indexes, so trout do not seem to be a threat to the population survival.

For more than 100 years, house mice (Mus musculus) have been used as a key animal model in biomedical research. House mice are genetically diverse, yet their genetic background at the global level has not been fully understood. Previous studies have suggested that they originated in South Asia and diverged into three major subspecies, almost simultaneously, approximately 110,000-500,000 years ago; however, they have spread across the world with the migration of modern humans in prehistoric and historic times (similar to 10,000 years ago to the present day) and have undergone secondary contact, which has complicated the genetic landscape of wild house mice. In this study, we sequenced the whole-genome sequences of 98 wild house mice collected from Eurasia, particularly East Asia, Southeast Asia, and South Asia. Although wild house mice were found to consist of three major genetic groups corresponding to the three major subspecies, individuals representing admixtures between subspecies were more prevalent in East Asia than has been previously recognized. Furthermore, several samples exhibited an incongruent pattern of genealogies between mitochondrial and autosomal genomes. Using samples that likely retained the original genetic components of subspecies with the least admixture, we estimated the pattern and timing of divergence among the subspecies. The estimated divergence time of the three subspecies was 187,000-226,000 years ago. These results will help us to understand the genetic diversity of wild mice on a global scale, and the findings will be particularly useful in future biomedical and evolutionary studies involving laboratory mice established from such wild mice.

For more than 100 years, house mice (Mus musculus) have been used as a key animal model in biomedical research. House mice are genetically diverse, yet their genetic background at the global level has not been fully understood. Previous studies have suggested that they originated in South Asia and diverged into three major subspecies, almost simultaneously, approximately 110,000-500,000 years ago; however, they have spread across the world with the migration of modern humans in prehistoric and historic times (similar to 10,000 years ago to the present day) and have undergone secondary contact, which has complicated the genetic landscape of wild house mice. In this study, we sequenced the whole-genome sequences of 98 wild house mice collected from Eurasia, particularly East Asia, Southeast Asia, and South Asia. Although wild house mice were found to consist of three major genetic groups corresponding to the three major subspecies, individuals representing admixtures between subspecies were more prevalent in East Asia than has been previously recognized. Furthermore, several samples exhibited an incongruent pattern of genealogies between mitochondrial and autosomal genomes. Using samples that likely retained the original genetic components of subspecies with the least admixture, we estimated the pattern and timing of divergence among the subspecies. The estimated divergence time of the three subspecies was 187,000-226,000 years ago. These results will help us to understand the genetic diversity of wild mice on a global scale, and the findings will be particularly useful in future biomedical and evolutionary studies involving laboratory mice established from such wild mice.

Local declines of wild populations represent the most visible part of biodiversity loss, and their detection often relies on long-term surveys. An alternative to identify risk-prone populations is to use indicators informing on their general health (i.e., their general fitness and ability to cope with changing environment) based on simple and complementary parameters estimated from snapshot sampling. However, most studies on wildlife population health focus on one or only a few parameters, yielding potentially biased conclusions for conservation. Here, we developed a multifaceted index of population health by combining 3 complementary indicators, namely pathological, ecological, and genetic indicators, based on an integrative approach traditionally used to assess ecosystem multifunctionality. We investigated their complementarity and relevance for detecting brown trout (Salmo trutta) risk-prone populations at a large spatial scale, and the underlying environmental stressors. The multifaceted health index properly represented the individual indicators' complementary information. It identified a cluster of moderately risk-prone populations and raised the alarm for one population. Each indicator was individually associated with distinct environmental stressors relevant for brown trout requirements. The multifaceted health index highlighted surrounding agricultural land and oxygen concentration as the most impacting environmental factors for the general health and sustainability of brown trout populations. The implementation of such integrative index can be transferred to a wide range of species and contexts. This index therefore provides to environmental managers and conservationists a snapshot and easily operated tool to identify risk-prone populations and areas to restore or conserve.

For more than 100 years, house mice (Mus musculus) have been used as a key animal model in biomedical research. House mice are genetically diverse, yet their genetic background at the global level has not been fully understood. Previous studies have suggested that they originated in South Asia and diverged into three major subspecies, almost simultaneously, approximately 110,000-500,000 years ago; however, they have spread across the world with the migration of modern humans in prehistoric and historic times (similar to 10,000 years ago to the present day) and have undergone secondary contact, which has complicated the genetic landscape of wild house mice. In this study, we sequenced the whole-genome sequences of 98 wild house mice collected from Eurasia, particularly East Asia, Southeast Asia, and South Asia. Although wild house mice were found to consist of three major genetic groups corresponding to the three major subspecies, individuals representing admixtures between subspecies were more prevalent in East Asia than has been previously recognized. Furthermore, several samples exhibited an incongruent pattern of genealogies between mitochondrial and autosomal genomes. Using samples that likely retained the original genetic components of subspecies with the least admixture, we estimated the pattern and timing of divergence among the subspecies. The estimated divergence time of the three subspecies was 187,000-226,000 years ago. These results will help us to understand the genetic diversity of wild mice on a global scale, and the findings will be particularly useful in future biomedical and evolutionary studies involving laboratory mice established from such wild mice.

The bullhead Cottus gobio is a small-sized fish whose range extends over most of the European continent, and it is listed in Annex II of EU “Habitat” Directive for its great conservation interest. In the last decades, bullhead populations suffered local decline. Among the factors that negatively affect bullhead populations, major threats are pollution, habitat deterioration, and the massive introduction of salmonids. This study aims to better understand in which way the presence of the Salmo (trutta) trutta affects Cottus gobio populations. The investigation was carried out in two stretches of a stream located in the Orobic Alps (Italy). The downstream stretch hosts a fish assemblage constituted of both bullhead and brown trout, while in the upstream stretch only bullhead is present. An insurmountable barrier isolates the upstream population of C. gobio from trout, while the environmental conditions of the two stretches proved to be fully comparable. We evaluated population structure, habitat preference, and body shape of bullhead populations in both stretches: the results indicate that the presence of trout decreases the number of bullhead adults, reduces the average adult body size, and induces a bullhead suboptimal habitat occupation. However, both populations of C. gobio showed a well-structured population and good performance indexes, so trout do not seem to be a threat to the population survival.

Technological advances such as camera traps, and citizen science, coupled with advanced quantitative approaches, can help fill existing knowledge gaps and aid effective conservation. We combine citizen and camera trap observations to estimate survival of the Endangered lappet-faced vulture, assess the relative contribution of data from camera traps and citizens, as well as impact of loss of individual marks (wing tags), on survival estimates. We used data from 762 lappet-faced vultures wing tagged as nestlings during 2006–2017 in western Namibia. Observations of wing tagged individuals were provided by citizens or via camera traps. We formulated a multievent capture-mark-recapture model to estimate survival while accounting for probabilities of resighting by citizens and/or camera traps, recovery of dead individuals, and loss of the wing tag. Survival was relatively high for juveniles (0.79), and increased with age to 0.95. Citizen observations of live and dead birds were low in number. However, when combined with camera trap resightings of live individuals, citizen observations increased the precision of survival estimates of birds older than one year compared to using data from either sources separately. Wing tag loss was high after 5–6 years of tag age. If neglected, tag loss can result in severe underestimation of survival of the older age classes. Overall, we show that filling ecological knowledge gaps is possible through the efficient use of data provided by different sources, and by applying state-of the art approaches that minimise potential biases, such as those due to tag loss.

Technological advances such as camera traps, and citizen science, coupled with advanced quantitative approaches, can help fill existing knowledge gaps and aid effective conservation. We combine citizen and camera trap observations to estimate survival of the Endangered lappet-faced vulture, assess the relative contribution of data from camera traps and citizens, as well as impact of loss of individual marks (wing tags), on survival estimates. We used data from 762 lappet-faced vultures wing tagged as nestlings during 2006–2017 in western Namibia. Observations of wing tagged individuals were provided by citizens or via camera traps. We formulated a multievent capture-mark-recapture model to estimate survival while accounting for probabilities of resighting by citizens and/or camera traps, recovery of dead individuals, and loss of the wing tag. Survival was relatively high for juveniles (0.79), and increased with age to 0.95. Citizen observations of live and dead birds were low in number. However, when combined with camera trap resightings of live individuals, citizen observations increased the precision of survival estimates of birds older than one year compared to using data from either sources separately. Wing tag loss was high after 5–6 years of tag age. If neglected, tag loss can result in severe underestimation of survival of the older age classes. Overall, we show that filling ecological knowledge gaps is possible through the efficient use of data provided by different sources, and by applying state-of the art approaches that minimise potential biases, such as those due to tag loss.

Le lagopède des saules (Lagopus lagopus), au Québec, fait une irruption au sud de son aire de répartition de manière cyclique en général aux dix ans, comme ce fut le cas pour l’hiver 2010‒2011. Les informations sur la population qui effectue cette irruption, de même que sur l’espèce en général dans la province de Québec, sont très rares. La présente étude avait pour objectif principal de contribuer à l’avancement des connaissances sur la population de lagopèdes qui effectue une irruption dans les régions du Saguenay‒Lac-Saint-Jean et de Chibougamau. Avec la collaboration des chasseurs, un échantillon d’ailes de lagopèdes a été constitué afin de pouvoir étudier cette espèce. Les oiseaux ont été sexés par analyse génétique d’un morceau de tissu musculaire. Les adultes et les jeunes ont été différenciés grâce au patron de mue particulier de ces derniers qui conservent leurs primaires 9 et 10 juvéniles. Une observation fortuite a permis de confronter une nouvelle méthode de détermination de l’âge avec les méthodes déjà connues pour en valider l’efficacité. Il s’est avéré que l’observation des ailes sous la lumière UV amène une brillance différente des primaires 9 et 10 par rapport aux autres primaires chez les jeunes, alors que la brillance est la même chez les adultes. La différence de classification entre la méthode visuelle et la méthode UV était de l’ordre de 0,9% et une seconde observation a réduit ce résultat à 0,3%. De plus, la méthode UV a permis de déterminer l’âge de 10 individus qui n’auraient pu être utilisés pour la méthode visuelle en raison de la détérioration de leur plumage. Une fois l’âge et le sexe des individus identifiés, la structure de la population présente au nord de la région du Saguenay‒Lac-Saint-Jean et dans le secteur de Chibougamau a pu être déterminée à partir d’un échantillon de 416 individus pour l’hiver 2010‒2011 et 108 pour 2011‒2012, pour lesquels un lieu de capture était disponible. Ceci a permis de déterminer que les jeunes femelles

Headstarting is a conservation strategy that assumes raising hatchling turtles to larger body sizes increases their survivorship compared to wild non-headstarted turtles. This increased survivorship should increase population growth rate relative to wild recruitment. There are, however, few published results of long-term population recovery using headstarting. The lack of demographic assessment of population recovery has led to an overall lack of quantitative assessment of the effectiveness of headstarting as a conservation action. Headstarting needs to be efficient and effective as a poorly executed headstarting project can result in species extinction given it is often used with critically endangered species. We released 3 cohorts of headstarted Wood Turtles (Glyptemys insculpta) with varying degrees of headstarting to determine if headstarting increases survivorship. I showed that headstarting turtles to a larger body size confers a survival advantage, and this survival advantage should increase population growth rate relative to wild recruitment. I then quantitatively assessed the effectiveness of a 15-year Wood Turtle headstarting program by modeling population-specific demographic parameters to evaluate recovery efforts, and determine the next phase of recovery. I found some evidence of population recovery, but also identified challenges and make several management recommendations that should enhance the success of the headstarting program. Overall, I have provided support for headstarting as an effective conservation strategy, with the caveat that all headstarting projects must be paired with management plans that maintain high adult and juvenile survival.

Headstarting is a conservation strategy that assumes raising hatchling turtles to larger body sizes increases their survivorship compared to wild non-headstarted turtles. This increased survivorship should increase population growth rate relative to wild recruitment. There are, however, few published results of long-term population recovery using headstarting. The lack of demographic assessment of population recovery has led to an overall lack of quantitative assessment of the effectiveness of headstarting as a conservation action. Headstarting needs to be efficient and effective as a poorly executed headstarting project can result in species extinction given it is often used with critically endangered species. We released 3 cohorts of headstarted Wood Turtles (Glyptemys insculpta) with varying degrees of headstarting to determine if headstarting increases survivorship. I showed that headstarting turtles to a larger body size confers a survival advantage, and this survival advantage should increase population growth rate relative to wild recruitment. I then quantitatively assessed the effectiveness of a 15-year Wood Turtle headstarting program by modeling population-specific demographic parameters to evaluate recovery efforts, and determine the next phase of recovery. I found some evidence of population recovery, but also identified challenges and make several management recommendations that should enhance the success of the headstarting program. Overall, I have provided support for headstarting as an effective conservation strategy, with the caveat that all headstarting projects must be paired with management plans that maintain high adult and juvenile survival.

The study of ancient genomics of pre-historic human remains has in recent years offered unprecedented knowledge regarding pre-historic migration and population structure on the European continent which has fundamentally altered the current views in the archaeological community. However, the merging of the two fields, archaeology and genetics, is still in its infancy and much work is still needed in order for these fields to integrate. In this thesis I explore how genetic analyses, in combination with contextual radiocarbon dating and isotopic analyses for diet and mobility can be used to investigate demographic events on a local and regional level. This is done through the investigation of people buried in five previously excavated megalithic tombs on the Island of Gotland dated to the Neolithic period. I present the genomic population structure and archaeological background for the pre-historic European reference data and show how this is used to investigate population continuity, demographic shifts, cultural duality, and admixture for local and regional contexts. I present new data and explore the Strontium-baseline for the Gotland biosphere which is used for the mobility analyses. I show that mitochondrial haplogroup data is especially useful in combination with isotopic data, and radiocarbon dating for investigation of demographic shifts on a larger scale. I also show that genomic data gives unique insights into the individuals’ life history which, together with the established demographic background allows for fine scale investigation of population demographic events within and between different archaeological contexts. Finally I show that the different Neolithic contexts on Gotland to a large extent involves immigration of new groups to the island, and that the contextual breaks seen in the archaeological record during the Neolithic period are connected with cultural and population demographic shifts. This dissertation demonstrates that genomic analyses, in co, The ATLAS of Ancient Human Genomes project

The study of ancient genomics of pre-historic human remains has in recent years offered unprecedented knowledge regarding pre-historic migration and population structure on the European continent which has fundamentally altered the current views in the archaeological community. However, the merging of the two fields, archaeology and genetics, is still in its infancy and much work is still needed in order for these fields to integrate. In this thesis I explore how genetic analyses, in combination with contextual radiocarbon dating and isotopic analyses for diet and mobility can be used to investigate demographic events on a local and regional level. This is done through the investigation of people buried in five previously excavated megalithic tombs on the Island of Gotland dated to the Neolithic period. I present the genomic population structure and archaeological background for the pre-historic European reference data and show how this is used to investigate population continuity, demographic shifts, cultural duality, and admixture for local and regional contexts. I present new data and explore the Strontium-baseline for the Gotland biosphere which is used for the mobility analyses. I show that mitochondrial haplogroup data is especially useful in combination with isotopic data, and radiocarbon dating for investigation of demographic shifts on a larger scale. I also show that genomic data gives unique insights into the individuals’ life history which, together with the established demographic background allows for fine scale investigation of population demographic events within and between different archaeological contexts. Finally I show that the different Neolithic contexts on Gotland to a large extent involves immigration of new groups to the island, and that the contextual breaks seen in the archaeological record during the Neolithic period are connected with cultural and population demographic shifts. This dissertation demonstrates that genomic analyses, in co, The ATLAS of Ancient Human Genomes project

The study of ancient genomics of pre-historic human remains has in recent years offered unprecedented knowledge regarding pre-historic migration and population structure on the European continent which has fundamentally altered the current views in the archaeological community. However, the merging of the two fields, archaeology and genetics, is still in its infancy and much work is still needed in order for these fields to integrate. In this thesis I explore how genetic analyses, in combination with contextual radiocarbon dating and isotopic analyses for diet and mobility can be used to investigate demographic events on a local and regional level. This is done through the investigation of people buried in five previously excavated megalithic tombs on the Island of Gotland dated to the Neolithic period. I present the genomic population structure and archaeological background for the pre-historic European reference data and show how this is used to investigate population continuity, demographic shifts, cultural duality, and admixture for local and regional contexts. I present new data and explore the Strontium-baseline for the Gotland biosphere which is used for the mobility analyses. I show that mitochondrial haplogroup data is especially useful in combination with isotopic data, and radiocarbon dating for investigation of demographic shifts on a larger scale. I also show that genomic data gives unique insights into the individuals’ life history which, together with the established demographic background allows for fine scale investigation of population demographic events within and between different archaeological contexts. Finally I show that the different Neolithic contexts on Gotland to a large extent involves immigration of new groups to the island, and that the contextual breaks seen in the archaeological record during the Neolithic period are connected with cultural and population demographic shifts. This dissertation demonstrates that genomic analyses, in co, The ATLAS of Ancient Human Genomes project

The study of ancient genomics of pre-historic human remains has in recent years offered unprecedented knowledge regarding pre-historic migration and population structure on the European continent which has fundamentally altered the current views in the archaeological community. However, the merging of the two fields, archaeology and genetics, is still in its infancy and much work is still needed in order for these fields to integrate. In this thesis I explore how genetic analyses, in combination with contextual radiocarbon dating and isotopic analyses for diet and mobility can be used to investigate demographic events on a local and regional level. This is done through the investigation of people buried in five previously excavated megalithic tombs on the Island of Gotland dated to the Neolithic period. I present the genomic population structure and archaeological background for the pre-historic European reference data and show how this is used to investigate population continuity, demographic shifts, cultural duality, and admixture for local and regional contexts. I present new data and explore the Strontium-baseline for the Gotland biosphere which is used for the mobility analyses. I show that mitochondrial haplogroup data is especially useful in combination with isotopic data, and radiocarbon dating for investigation of demographic shifts on a larger scale. I also show that genomic data gives unique insights into the individuals’ life history which, together with the established demographic background allows for fine scale investigation of population demographic events within and between different archaeological contexts. Finally I show that the different Neolithic contexts on Gotland to a large extent involves immigration of new groups to the island, and that the contextual breaks seen in the archaeological record during the Neolithic period are connected with cultural and population demographic shifts. This dissertation demonstrates that genomic analyses, in co, The ATLAS of Ancient Human Genomes project

The study of ancient genomics of pre-historic human remains has in recent years offered unprecedented knowledge regarding pre-historic migration and population structure on the European continent which has fundamentally altered the current views in the archaeological community. However, the merging of the two fields, archaeology and genetics, is still in its infancy and much work is still needed in order for these fields to integrate. In this thesis I explore how genetic analyses, in combination with contextual radiocarbon dating and isotopic analyses for diet and mobility can be used to investigate demographic events on a local and regional level. This is done through the investigation of people buried in five previously excavated megalithic tombs on the Island of Gotland dated to the Neolithic period. I present the genomic population structure and archaeological background for the pre-historic European reference data and show how this is used to investigate population continuity, demographic shifts, cultural duality, and admixture for local and regional contexts. I present new data and explore the Strontium-baseline for the Gotland biosphere which is used for the mobility analyses. I show that mitochondrial haplogroup data is especially useful in combination with isotopic data, and radiocarbon dating for investigation of demographic shifts on a larger scale. I also show that genomic data gives unique insights into the individuals’ life history which, together with the established demographic background allows for fine scale investigation of population demographic events within and between different archaeological contexts. Finally I show that the different Neolithic contexts on Gotland to a large extent involves immigration of new groups to the island, and that the contextual breaks seen in the archaeological record during the Neolithic period are connected with cultural and population demographic shifts. This dissertation demonstrates that genomic analyses, in co, The ATLAS of Ancient Human Genomes project

Continental islands provide opportunities for testing the effects of isolation and migration on genetic variation in plant populations. In characteristic of continental islands is that the geographic connections between these islands, which are currently distinguished by seaways, have experienced fluctuations caused by sea-level changes due to climate oscillations during the Quaternary. Plant populations on the islands have migrated between these islands via the exposed seafloors or been isolated. Here, we examined the demographic history of a temperate shrub, Rhododendron weyrichii, which is distributed in the southwestern parts of the Japanese archipelago and on an island of South Korea, using statistical phylogeographic approaches based on the DNA sequences of two chloroplast and eight nuclear loci in samples analyzed from 18 populations on eight continental islands, and palaeodistribution modeling. Time estimates for four island populations indicate that the durations of vicariance history are different between these populations, and these events have continued since the last glacial or may have predated the last glacial. The constancy or expansion of population sizes on the Japanese islands, and in contrast a bottleneck in population size on the Korean island Jeju, suggests that these islands may have provided different conditions for sustaining populations. The result of palaeodistribution modeling indicates that the longitudinal range of the species as a whole has not changed greatly since the last glacial maximum. These results indicate that exposed seafloors during the glacial period formed both effective and ineffective migration corridors. These findings may shed light on the effects of seafloor exposure on the migration of plants distributed across continental islands.

The evolution of male traits that inflict direct harm on females during mating interactions can result in a so-called tragedy of the commons, where selfish male strategies depress population viability. This tragedy of the commons can be magnified by intralocus sexual conflict (IaSC) whenever alleles that reduce fecundity when expressed in females spread in the population because of their benefits in males. We evaluated this prediction by detailed phenotyping of 73 isofemale lines of the seed beetle Callosobruchus maculatus. We quantified genetic variation in life history andmorphology, as well as associated covariance in male and female adult reproductive success. In parallel, we created replicated artificial populations of each line and measured their productivity. Genetic constraints limited independent trait expression in the sexes, and we identified several instances of sexually antagonistic covariance between traits and fitness, signifying IaSC. Population productivity was strongly positively correlated to female adult reproductive success but uncorrelated with male reproductive success. Moreover, male (female) phenotypic optima for several traits under sexually antagonistic selection were exhibited by the genotypes with the lowest (highest) population productivity. Our study forms a direct link between individuallevel sex-specific selection and population demography and places lifehistory traits at the epicenter of these dynamics.

The evolution of male traits that inflict direct harm on females during mating interactions can result in a so-called tragedy of the commons, where selfish male strategies depress population viability. This tragedy of the commons can be magnified by intralocus sexual conflict (IaSC) whenever alleles that reduce fecundity when expressed in females spread in the population because of their benefits in males. We evaluated this prediction by detailed phenotyping of 73 isofemale lines of the seed beetle Callosobruchus maculatus. We quantified genetic variation in life history andmorphology, as well as associated covariance in male and female adult reproductive success. In parallel, we created replicated artificial populations of each line and measured their productivity. Genetic constraints limited independent trait expression in the sexes, and we identified several instances of sexually antagonistic covariance between traits and fitness, signifying IaSC. Population productivity was strongly positively correlated to female adult reproductive success but uncorrelated with male reproductive success. Moreover, male (female) phenotypic optima for several traits under sexually antagonistic selection were exhibited by the genotypes with the lowest (highest) population productivity. Our study forms a direct link between individuallevel sex-specific selection and population demography and places lifehistory traits at the epicenter of these dynamics.

The evolution of male traits that inflict direct harm on females during mating interactions can result in a so-called tragedy of the commons, where selfish male strategies depress population viability. This tragedy of the commons can be magnified by intralocus sexual conflict (IaSC) whenever alleles that reduce fecundity when expressed in females spread in the population because of their benefits in males. We evaluated this prediction by detailed phenotyping of 73 isofemale lines of the seed beetle Callosobruchus maculatus. We quantified genetic variation in life history andmorphology, as well as associated covariance in male and female adult reproductive success. In parallel, we created replicated artificial populations of each line and measured their productivity. Genetic constraints limited independent trait expression in the sexes, and we identified several instances of sexually antagonistic covariance between traits and fitness, signifying IaSC. Population productivity was strongly positively correlated to female adult reproductive success but uncorrelated with male reproductive success. Moreover, male (female) phenotypic optima for several traits under sexually antagonistic selection were exhibited by the genotypes with the lowest (highest) population productivity. Our study forms a direct link between individuallevel sex-specific selection and population demography and places lifehistory traits at the epicenter of these dynamics.

Author Posting. © The Author(s), 2015. This is the author's version of the work. It is posted here by permission of The Royal Society for personal use, not for redistribution. The definitive version was published in Proceedings of the Royal Society B: Biological Sciences, 282 (2015): 20151311, doi:10.1098/rspb.2015.1311., Determining the conditions under which populations may persist requires accurate estimates of demographic parameters, including immigration, local reproductive success, and mortality rates. In marine populations, empirical estimates of these parameters are rare, due at least in part to the pelagic dispersal stage common to most marine organisms. Here, we evaluate population persistence and turnover for a population of orange clownfish, Amphiprion percula, at Kimbe Island in Papua New Guinea. All fish in the population were sampled and genotyped on five occasions at 2-year intervals spanning eight years. The genetic data enabled estimates of reproductive success retained in the same population (reproductive success to self-recruitment), reproductive success exported to other subpopulations (reproductive success to local connectivity), and immigration and mortality rates of sub-adults and adults. Approximately 50% of the recruits were assigned to parents from the Kimbe Island population and this was stable through the sampling period. Stability in the proportion of local and immigrant settlers is likely due to: low annual mortality rates and stable egg production rates, and the short larval stages and sensory capacities of reef fish larvae. Biannual mortality rates ranged from 0.09 to 0.55 and varied significantly spatially. We used these data to parameterize a model that estimated the probability of the Kimbe Island population persisting in the absence of immigration. The Kimbe Island population was found to persist without significant immigration. Model results suggest the island population persists because the largest of the subpopulations are maintained due to having low mortality and high self-recruitment rates. Our results enable managers to appropriately target and scale actions to maximize persistence likelihood as disturbance frequencies increase., This research was supported by LABEX Corail, ERC, CRISP, the GEF CRTR Connectivity Working Group, NSF, the ARC CoE Coral Reef Studies, TNC, Total Foundation, JCU, KAUST, and WHOI., 2016-11-18

Author Posting. © The Author(s), 2015. This is the author's version of the work. It is posted here by permission of The Royal Society for personal use, not for redistribution. The definitive version was published in Proceedings of the Royal Society B: Biological Sciences, 282 (2015): 20151311, doi:10.1098/rspb.2015.1311., Determining the conditions under which populations may persist requires accurate estimates of demographic parameters, including immigration, local reproductive success, and mortality rates. In marine populations, empirical estimates of these parameters are rare, due at least in part to the pelagic dispersal stage common to most marine organisms. Here, we evaluate population persistence and turnover for a population of orange clownfish, Amphiprion percula, at Kimbe Island in Papua New Guinea. All fish in the population were sampled and genotyped on five occasions at 2-year intervals spanning eight years. The genetic data enabled estimates of reproductive success retained in the same population (reproductive success to self-recruitment), reproductive success exported to other subpopulations (reproductive success to local connectivity), and immigration and mortality rates of sub-adults and adults. Approximately 50% of the recruits were assigned to parents from the Kimbe Island population and this was stable through the sampling period. Stability in the proportion of local and immigrant settlers is likely due to: low annual mortality rates and stable egg production rates, and the short larval stages and sensory capacities of reef fish larvae. Biannual mortality rates ranged from 0.09 to 0.55 and varied significantly spatially. We used these data to parameterize a model that estimated the probability of the Kimbe Island population persisting in the absence of immigration. The Kimbe Island population was found to persist without significant immigration. Model results suggest the island population persists because the largest of the subpopulations are maintained due to having low mortality and high self-recruitment rates. Our results enable managers to appropriately target and scale actions to maximize persistence likelihood as disturbance frequencies increase., This research was supported by LABEX Corail, ERC, CRISP, the GEF CRTR Connectivity Working Group, NSF, the ARC CoE Coral Reef Studies, TNC, Total Foundation, JCU, KAUST, and WHOI., 2016-11-18

The evolution of male traits that inflict direct harm on females during mating interactions can result in a so-called tragedy of the commons, where selfish male strategies depress population viability. This tragedy of the commons can be magnified by intralocus sexual conflict (IaSC) whenever alleles that reduce fecundity when expressed in females spread in the population because of their benefits in males. We evaluated this prediction by detailed phenotyping of 73 isofemale lines of the seed beetle Callosobruchus maculatus. We quantified genetic variation in life history andmorphology, as well as associated covariance in male and female adult reproductive success. In parallel, we created replicated artificial populations of each line and measured their productivity. Genetic constraints limited independent trait expression in the sexes, and we identified several instances of sexually antagonistic covariance between traits and fitness, signifying IaSC. Population productivity was strongly positively correlated to female adult reproductive success but uncorrelated with male reproductive success. Moreover, male (female) phenotypic optima for several traits under sexually antagonistic selection were exhibited by the genotypes with the lowest (highest) population productivity. Our study forms a direct link between individuallevel sex-specific selection and population demography and places lifehistory traits at the epicenter of these dynamics.

The evolution of male traits that inflict direct harm on females during mating interactions can result in a so-called tragedy of the commons, where selfish male strategies depress population viability. This tragedy of the commons can be magnified by intralocus sexual conflict (IaSC) whenever alleles that reduce fecundity when expressed in females spread in the population because of their benefits in males. We evaluated this prediction by detailed phenotyping of 73 isofemale lines of the seed beetle Callosobruchus maculatus. We quantified genetic variation in life history andmorphology, as well as associated covariance in male and female adult reproductive success. In parallel, we created replicated artificial populations of each line and measured their productivity. Genetic constraints limited independent trait expression in the sexes, and we identified several instances of sexually antagonistic covariance between traits and fitness, signifying IaSC. Population productivity was strongly positively correlated to female adult reproductive success but uncorrelated with male reproductive success. Moreover, male (female) phenotypic optima for several traits under sexually antagonistic selection were exhibited by the genotypes with the lowest (highest) population productivity. Our study forms a direct link between individuallevel sex-specific selection and population demography and places lifehistory traits at the epicenter of these dynamics.

1.If not actively managed, small and isolated populations lose their genetic variability and the inbreeding rate increases. Combined, these factors limit the ability of populations to adapt to environmental changes, increasing their risk of extinction. The effective population size (Ne) is proportional to the loss of genetic diversity and therefore of considerable conservation relevance. However, estimators of Ne that account for demographic parameters in species with overlapping generations require sampling of populations across generations, which is often not feasible in long-lived species.2.We created an individual-based model that allows calculation of Ne based on demographic parameters that can be obtained in a time period much shorter than a generation. It can be adapted to every life-history parameter combination. The model is freely available as an R-package NEff.3.The model was first used in a simulation experiment observing changes in Ne in response to different degrees of generational overlap. Results showed that increased generational overlap slowed annual rates of heterozygosity loss, resulting in higher annual effective sizes (Ny) but decreased Ne per generation. Adding the effect of different recruitment rates only affected Ne for populations with low generational overlap.4.The model was further tested using real population data of the Australian arboreal gecko Gehyra variegata. Simulation results were compared to genetic analyses and matched estimates of the real population very well.5.Unlike other estimation methods of Ne, NEff neither requires long time series of population monitoring nor genetic analyses of changes in gene frequencies. Thus, it seems to be the first method for calculating Ne within short time periods and comparably low costs facilitating the use of Ne in applied conservation and management.

It is becoming routine to obtain data sets on DNA sequence variation across several thousands of chromosomes, providing unprecedented opportunity to infer the underlying biological and demographic forces. Such data make it vital to study summary statistics that offer enough compression to be tractable, while preserving a great deal of information. One well-studied summary is the site frequency spectrum-the empirical distribution, across segregating sites, of the sample frequency of the derived allele. However, most previous theoretical work has assumed that each site has experienced at most one mutation event in its genealogical history, which becomes less tenable for very large sample sizes. In this work we obtain, in closed form, the predicted frequency spectrum of a site that has experienced at most two mutation events, under very general assumptions about the distribution of branch lengths in the underlying coalescent tree. Among other applications, we obtain the frequency spectrum of a triallelic site in a model of historically varying population size. We demonstrate the utility of our formulas in two settings: First, we show that triallelic sites are more sensitive to the parameters of a population that has experienced historical growth, suggesting that they will have use if they can be incorporated into demographic inference. Second, we investigate a recently proposed alternative mechanism of mutation in which the two derived alleles of a triallelic site are created simultaneously within a single individual, and we develop a test to determine whether it is responsible for the excess of triallelic sites in the human genome.

We gathered mitochondrial DNA sequences (557 bp from the control region in 935 specimens and 668 bp of the cytochrome b gene in 139 specimens) of Pacific herring collected from 20 nearshore localities spanning the species' extensive range along the North Pacific coastlines of Asia and North America. Haplotype diversity and nucleotide diversity were high, and three major phylogeographic lineages (sequence divergences ca. 1.5%) were detected. Using a variety of phylogenetic methods, coalescent reasoning, and molecular dating interpreted in conjunction with paleoclimatic and physiographic evidence, we infer that the genetic make-up of extant populations of C. pallasii was shaped by Pleistocene environmental impacts on the historical demography of this species. A deep genealogical split that cleanly distinguishes populations in the western vs. eastern North Pacific probably originated as a vicariant separation associated with a glacial cycle that drove the species southward and isolated two ancestral populations in Asia and North America. Another deep genealogical split may have involved either a vicariant isolation of a third herring lineage (perhaps originally in the Gulf of California) or it may have resulted simply from the long coalescent times that are possible in large populations. Coalescent analyses showed that all the three evolutionary lineages of C. pallasii experienced major expansions in their most recent histories after having remained more stable in the preceding periods. Independent of the molecular calibration chosen, populations of C. pallasii appear to have remained stable or grown throughout the periods that covered at least two major glaciations, and probably more.

We gathered mitochondrial DNA sequences (557 bp from the control region in 935 specimens and 668 bp of the cytochrome b gene in 139 specimens) of Pacific herring collected from 20 nearshore localities spanning the species' extensive range along the North Pacific coastlines of Asia and North America. Haplotype diversity and nucleotide diversity were high, and three major phylogeographic lineages (sequence divergences ca. 1.5%) were detected. Using a variety of phylogenetic methods, coalescent reasoning, and molecular dating interpreted in conjunction with paleoclimatic and physiographic evidence, we infer that the genetic make-up of extant populations of C. pallasii was shaped by Pleistocene environmental impacts on the historical demography of this species. A deep genealogical split that cleanly distinguishes populations in the western vs. eastern North Pacific probably originated as a vicariant separation associated with a glacial cycle that drove the species southward and isolated two ancestral populations in Asia and North America. Another deep genealogical split may have involved either a vicariant isolation of a third herring lineage (perhaps originally in the Gulf of California) or it may have resulted simply from the long coalescent times that are possible in large populations. Coalescent analyses showed that all the three evolutionary lineages of C. pallasii experienced major expansions in their most recent histories after having remained more stable in the preceding periods. Independent of the molecular calibration chosen, populations of C. pallasii appear to have remained stable or grown throughout the periods that covered at least two major glaciations, and probably more.

Genetic variation was examined in two endangered mussel species, Epioblasma brevidens and E. capsaeformis, and a common species Lampsilis fasciola, in the Clinch River, TN, by screening mitochondrial DNA (mtDNA) sequences and nuclear DNA microsatellites. These species use fish hosts with varying dispersal capabilities, ranging from low, moderate, and high, respectively. Patterns of mtDNA polymorphism exhibited different trends for long-term population sizes for each species during the Holocene (~10,000 ya to present); namely, E. brevidens has declined over time, E. capsaeformis has remained stable, and L. fasciola has expanded. Long-term effective population size (Ne) was smallest in E. brevidens, intermediate in E. capsaeformis, and highest in L. fasciola. Moderately diverged mtDNA lineages, perhaps indicative of secondary contact, were observed in E. brevidens and E. capsaeformis. High levels of gene flow (Nm) were estimated among demes of L. fasciola using traditional F-statistics and likelihood estimates of Nm, whereas such metrics were lower in E. brevidens and E. capsaeformis. Data are consistent with population dynamics and life history traits of each species and their fish hosts. Age, shell growth, and population demography of Epioblasma brevidens, E. capsaeformis, and Lampsilis fasciola were studied from 2004-2007 in a 32-km reach of the Clinch River, TN. Observed maximum age and length of E. brevidens was 28 y and 71.5 mm for males and 11 y and 56.6 mm for females; of E. capsaeformis, 12 y and 54.6 mm for males and 9 y and 48.6 mm for females; and of L. fasciola, 45 y and 91.3 mm for males and 13 y and 62.6 mm for females. For all three species, observed maximum age and length was greater among males than females. Estimated population size in this river reach was approximately 43,000 individuals for E. brevidens, 579,000 individuals for E. capsaeformis, and 30,000 individuals for L. fasciola. Mean recruitment y-1 of 1 y-old E. brevidens ranged from 7.1% to

Prediction capacity of three main shoot population dynamics methods (age structure, net shoot recruitment per plagiotropic rhizome and shoot census) have been tested for a period of four years (2002–2006) on a Posidonia oceanica meadow. Accuracy of each method was checked by comparing measured and predicted densities at the end of the study period. Predicted densities came from the evolution of initial densities (measured in 2002) by a basic exponential model of population growth. The exponential model used the different net shoot recruitment rate estimates by each population dynamics method on three depths (upper, medium and lower limit) and three localities at each depth. Predictions performed by shoot census and net shoot recruitment per plagiotropic rhizome methods matched with measured densities at the end of the study period. Conversely, age structure method underestimated shoot densities at each depth, indicating an unreal decrease of shoot population in the meadow.

Prediction capacity of three main shoot population dynamics methods (age structure, net shoot recruitment per plagiotropic rhizome and shoot census) have been tested for a period of four years (2002–2006) on a Posidonia oceanica meadow. Accuracy of each method was checked by comparing measured and predicted densities at the end of the study period. Predicted densities came from the evolution of initial densities (measured in 2002) by a basic exponential model of population growth. The exponential model used the different net shoot recruitment rate estimates by each population dynamics method on three depths (upper, medium and lower limit) and three localities at each depth. Predictions performed by shoot census and net shoot recruitment per plagiotropic rhizome methods matched with measured densities at the end of the study period. Conversely, age structure method underestimated shoot densities at each depth, indicating an unreal decrease of shoot population in the meadow.