The genomic landscape of contemporary western Remote Oceanians

The Vanuatu archipelago served as a gateway to Remote Oceania during one of the most extensive human migrations to uninhabited lands around 3,200 years ago. Ancient DNA studies suggest an initial settlement by East Asian-related peoples that was quickly followed by the arrival of Papuan-related populations, leading to a major population turnover. Yet, there is uncertainty over the population processes and the sociocultural factors that have shaped the genomic diversity of ni-Vanuatu, who present nowadays among the world's highest linguistic and cultural diversity. Here, we report genome-wide data for 1,433 contemporary ni-Vanuatu from 29 different islands, including 287 couples. We find that ni-Vanuatu derive their East Asian- and Papuan-related ancestry from the same source populations and descend from relatively synchronous admixture events that occurred around 1,700-2,300 years ago, indicating a peopling history common to all the archipelago. However, our analyses reveal that the Papuan population turnover was geographically uneven, and that the genetic contribution of Papuan-related peoples was male-biased. Furthermore, we detect Polynesian ancestry arriving around 600-1,000 years ago to South Vanuatu, and map its distribution to both Polynesian- and non-Polynesian-speaking islands. Lastly, we provide evidence for a tendency of spouses to carry similar genetic ancestry, when accounting for relatedness avoidance. The signal is not driven by strong genetic effects of specific loci or trait-associated variants, suggesting that it results instead from social assortative mating. Altogether, our findings provide insight into both the genetic history of ni-Vanuatu populations and how sociocultural processes have shaped the diversity of their genomes.

Development of a Genomics-Based Approach To Identify Putative Hypervirulent Nontyphoidal Salmonella Isolates: Salmonella enterica Serovar Saintpaul as a Model

Not all Salmonella isolates are equally likely to cause human disease, and Salmonella control strategies may unintentionally focus on serovars and subtypes with high prevalence in source populations but are rarely associated with human clinical illness. We describe a framework leveraging WGS data in the NCBI PD database to identify Salmonella subtypes over- and underrepresented among human clinical cases.

Genetic signature of immigrants and their effect on genetic diversity in the recently established Scandinavian wolf population

Transboundary connectivity is a key component when conserving and managing animal species that require large areas to maintain viable population sizes. Wolves Canis lupus recolonized the Scandinavian Peninsula in the early 1980s. The population is geographically isolated and relies on immigration to not lose genetic diversity and to maintain long term viability. In this study we address (1) to what extent the genetic diversity among Scandinavian wolves has recovered during 30 years since its foundation in relation to the source populations in Finland and Russia, (2) if immigration has occurred from both Finland and Russia, two countries with very different wolf management and legislative obligations to ensure long term viability of wolves, and (3) if immigrants can be assumed to be unrelated. Using 26 microsatellite loci we found that although the genetic diversity increased among Scandinavian wolves (n = 143), it has not reached the same levels found in Finland (n = 25) or in Russia (n = 19). Low genetic differentiation between Finnish and Russian wolves, complicated our ability to determine the origin of immigrant wolves (n = 20) with respect to nationality. Nevertheless, based on differences in allelic richness and private allelic richness between the two countries, results supported the occurrence of immigration from both countries. A priori assumptions that immigrants are unrelated is non-advisable, since 5.8% of the pair-wise analyzed immigrants were closely related. To maintain long term viability of wolves in Northern Europe, this study highlights the potential and need for management actions that facilitate transboundary dispersal.

Putting the “Beaver” Back in Beverley Brook: Rapid Shifts in Community Composition Following the Restoration of a Degraded Urban River

Widespread habitat degradation has caused dramatic declines in aquatic biodiversity. Reconfiguring channels and adding physical structures to rivers has become common practice in order to reinstate natural processes and restore biodiversity. However, the effectiveness of such measures is often questioned, especially in urban settings where overriding factors (e.g., water quality) might constrain biotic responses to increased habitat heterogeneity. We monitored invertebrate and fish communities before and up to five years after extensive restoration of Beverley Brook, a small, urban river flowing through a Royal Park in London, UK. Total invertebrate density was 5–148% higher with restoration across the monitoring period, and there was an increase in evenness but not invertebrate richness. Riverflies (Ephmemeroptera and Trichoptera) and crustaceans (Amphipoda, Asellidae) showed marked increases in density with restoration, suggesting improved flow, enhanced water quality, and greater quantity of basal resources. Fish biomass increased by 282% with restoration as did fish richness and the average body mass of three common fish species. Our results provide evidence for the effectiveness of common restoration methods in increasing standing stocks across trophic levels, from basal resources to apex predators. However, we primarily observed changes in the density of existing taxa rather than the development of novel assemblages, suggesting that large-scale factors, such as water quality and the lack of adequate source populations, might be important for understanding changes in biodiversity following river restoration.

From STRs to SNPs via ddRAD-seq: geographic assignment of confiscated tortoises at reduced costs

Assigning individuals to their source populations is crucial for conservation research, especially for endangered species threatened by illegal trade and translocations. Genetic assignment can be achieved with different types of molecular markers, but technical advantages and cost saving are recently promoting the shift from short tandem repeats (STRs) to single nucleotide polymorphisms (SNPs). Here, we designed, developed, and tested a small panel of SNPs for cost-effective geographic assignment of individuals with unknown origin of the endangered Mediterranean tortoise Testudo hermanni. We started by performing a ddRAD-seq experiment on 70 wild individuals of T. hermanni from 38 locations. Results obtained using 3,182 SNPs are comparable to those previously obtained using STR markers in terms of genetic structure and power to identify the macro-area of origin. However, our SNPs revealed further insights into the substructure in Western populations, especially in Southern Italy. A small panel of highly informative SNPs was then selected and tested by genotyping 190 individuals using the KASP genotyping chemistry. All the samples from wild populations of known geographic origin were genetically re-assigned with high accuracy to the original population. This reduced SNPs panel represents an efficient molecular tool that enables individuals to be genotyped at low cost (less than €15 per sample) for geographical assignment and identification of hybrids. This information is crucial for the management in-situ of confiscated animals and their possible re-allocation in the wild. Our methodological pipeline can easily be extended to other species.

Disentangling signatures of selection before and after European colonization in Latin Americans

Throughout human evolutionary history, large-scale migrations have led to intermixing (i.e., admixture) between previously separated human groups. While classical and recent work have shown that studying admixture can yield novel historical insights, the extent to which this process contributed to adaptation remains underexplored. Here, we introduce a novel statistical model, specific to admixed populations, that identifies loci under selection while determining whether the selection likely occurred post-admixture or prior to admixture in one of the ancestral source populations. Through extensive simulations we show that this method is able to detect selection, even in recently formed admixed populations, and to accurately differentiate between selection occurring in the ancestral or admixed population. We apply this method to genome-wide SNP data of ~4,000 individuals in five admixed Latin American cohorts from Brazil, Chile, Colombia, Mexico and Peru. Our approach replicates previous reports of selection in the HLA region that are consistent with selection post-admixture. We also report novel signals of selection in genomic regions spanning 47 genes, reinforcing many of these signals with an alternative, commonly-used local-ancestry-inference approach. These signals include several genes involved in immunity, which may reflect responses to endemic pathogens of the Americas and to the challenge of infectious disease brought by European contact. In addition, some of the strongest signals inferred to be under selection in the Native American ancestral groups of modern Latin Americans overlap with genes implicated in energy metabolism phenotypes, plausibly reflecting adaptations to novel dietary sources available in the Americas.

Development and Application of Otolith-Based Methods to Infer Demographic Connections in a Marine Metapopulation

<p>Connectivity between local populations is critical if these are to function as a metapopulation and sustain locally open sink populations. Assessing whether such connections between local populations exist is thus an important step towards understanding coastal metapopulation dynamics as well as assessing the efficacy of spatial management tools such as marine reserve networks. For this thesis, I investigate population connectivity of the common triplefin (Forsterygion lapillum) in Cook Strait, New Zealand, using chemical signatures contained within fish otoliths (ear stones). I concentrate on likely connections between three local marine reserves: Kapiti Island (Kapiti coast), Long Island (Marlborough Sounds) and Taputeranga Marine Reserve (Wellington south coast). To this end I develop and implement new statistical methods to enable stronger inferences from otolith chemistry based approaches. In chapter 2, I evaluate otolith core chemistry as a potential tool (i.e. an environmental fingerprint) for identification of natal source populations of the common triplefin. I sampled otolith chemistry from hatchling fish across a range of hierarchical scales: obtained from individual egg masses within a site; sites within different regions; and regions distributed on the two main islands of New Zealand (North and South Island). This sampling enabled me to construct an “atlas” (or baseline) of otolith core chemistry. I developed and applied a set of novel statistical approaches to examine the characteristics of this natal atlas and optimize its spatial resolution. These analyses allowed me to assess the utility of otolith chemistry as a potential tool to infer patterns of population connectivity in the vicinity of Cook Strait. Chapter 3 develops a new Bayesian approach to facilitate improved clustering and classification of dispersing fish to putative natal populations based on their otolith chemistry. Otolith-based approaches used to infer natal origins of fishes routinely suffer from the (unrealized) requirement to sample all potential natal source populations. An incomplete baseline atlas has greatly limited the application of otolith chemistry as a tool for assessments of connectivity in the marine environment. In this chapter, I develop, evaluate, and implement statistical solutions to this problem. Specifically, I present a clustering model, based on infinite mixtures, which does not require the specification of a potential number of sources. In a second step, I embed this clustering model in a large-scale classification model that allows for classification on scales encompassing a number of potential sources, where recruits are clustered with observations from the baseline or a separate cluster within these regions. This opens the potential for fish that came from an identifiable source other than those sampled to not be assigned to a sampled source. I evaluate the strength of this approach using the well-known weakfish (Cynoscion regalis) dataset. In chapter 4, I apply the statistical methods developed in chapter 3 to the common triplefin. I sampled recent recruits of the common triplefin within each of three marine reserves (Kapiti, Long Island, and Taputeranga) and used otolith chemistry to infer probable natal origins. I then compare these inferred patterns of connectivity with those predicted by a set of hydrodynamic simulations. This comparison enabled me to (qualitatively) assess the likelihood of connectivity (as predicted by otolith chemistry) given local hydrodynamic conditions. For chapter 5, I extend the Bayesian modelling approaches developed in previous chapters to incorporate otolith chemistry data sampled from throughout the life-history of dispersers. As in chapter 3, I develop and evaluate the utility of this approach using a previously published data set (Chinook salmon), and I apply the approach to the common triplefin in a subsequent chapter. Specifically, I propose flexible formulations based on latent state models, and compare these in a series of illustrative simulations and an application to Chinook salmon contingent analysis. In chapter 6, I apply the Bayesian framework (developed in chapter 5) to the common triplefin data set. Specifically, I formulate a model based on putative chemical distinctions between inshore and offshore water-masses. This model allows me to compare dispersal histories among recruits to a set of reserves (evaluated initially in chapter 4), and the approach reveals patterns that appear to be common to all successful recruits. I examine these findings in the light of results obtained in chapter 4 as well as local hydrodynamic conditions. Finally, I conclude my thesis in chapter 7 by discussing the relevance of my findings for the functioning of networks of sub-populations, both in a metapopulation and a reserve network context.</p>

Development and Application of Otolith-Based Methods to Infer Demographic Connections in a Marine Metapopulation

<p>Connectivity between local populations is critical if these are to function as a metapopulation and sustain locally open sink populations. Assessing whether such connections between local populations exist is thus an important step towards understanding coastal metapopulation dynamics as well as assessing the efficacy of spatial management tools such as marine reserve networks. For this thesis, I investigate population connectivity of the common triplefin (Forsterygion lapillum) in Cook Strait, New Zealand, using chemical signatures contained within fish otoliths (ear stones). I concentrate on likely connections between three local marine reserves: Kapiti Island (Kapiti coast), Long Island (Marlborough Sounds) and Taputeranga Marine Reserve (Wellington south coast). To this end I develop and implement new statistical methods to enable stronger inferences from otolith chemistry based approaches. In chapter 2, I evaluate otolith core chemistry as a potential tool (i.e. an environmental fingerprint) for identification of natal source populations of the common triplefin. I sampled otolith chemistry from hatchling fish across a range of hierarchical scales: obtained from individual egg masses within a site; sites within different regions; and regions distributed on the two main islands of New Zealand (North and South Island). This sampling enabled me to construct an “atlas” (or baseline) of otolith core chemistry. I developed and applied a set of novel statistical approaches to examine the characteristics of this natal atlas and optimize its spatial resolution. These analyses allowed me to assess the utility of otolith chemistry as a potential tool to infer patterns of population connectivity in the vicinity of Cook Strait. Chapter 3 develops a new Bayesian approach to facilitate improved clustering and classification of dispersing fish to putative natal populations based on their otolith chemistry. Otolith-based approaches used to infer natal origins of fishes routinely suffer from the (unrealized) requirement to sample all potential natal source populations. An incomplete baseline atlas has greatly limited the application of otolith chemistry as a tool for assessments of connectivity in the marine environment. In this chapter, I develop, evaluate, and implement statistical solutions to this problem. Specifically, I present a clustering model, based on infinite mixtures, which does not require the specification of a potential number of sources. In a second step, I embed this clustering model in a large-scale classification model that allows for classification on scales encompassing a number of potential sources, where recruits are clustered with observations from the baseline or a separate cluster within these regions. This opens the potential for fish that came from an identifiable source other than those sampled to not be assigned to a sampled source. I evaluate the strength of this approach using the well-known weakfish (Cynoscion regalis) dataset. In chapter 4, I apply the statistical methods developed in chapter 3 to the common triplefin. I sampled recent recruits of the common triplefin within each of three marine reserves (Kapiti, Long Island, and Taputeranga) and used otolith chemistry to infer probable natal origins. I then compare these inferred patterns of connectivity with those predicted by a set of hydrodynamic simulations. This comparison enabled me to (qualitatively) assess the likelihood of connectivity (as predicted by otolith chemistry) given local hydrodynamic conditions. For chapter 5, I extend the Bayesian modelling approaches developed in previous chapters to incorporate otolith chemistry data sampled from throughout the life-history of dispersers. As in chapter 3, I develop and evaluate the utility of this approach using a previously published data set (Chinook salmon), and I apply the approach to the common triplefin in a subsequent chapter. Specifically, I propose flexible formulations based on latent state models, and compare these in a series of illustrative simulations and an application to Chinook salmon contingent analysis. In chapter 6, I apply the Bayesian framework (developed in chapter 5) to the common triplefin data set. Specifically, I formulate a model based on putative chemical distinctions between inshore and offshore water-masses. This model allows me to compare dispersal histories among recruits to a set of reserves (evaluated initially in chapter 4), and the approach reveals patterns that appear to be common to all successful recruits. I examine these findings in the light of results obtained in chapter 4 as well as local hydrodynamic conditions. Finally, I conclude my thesis in chapter 7 by discussing the relevance of my findings for the functioning of networks of sub-populations, both in a metapopulation and a reserve network context.</p>