Marine bivalves are a group of species composed of clams, mussels and oysters. Bivalves are keystone species in coastal ecosystems and represent an increasingly important segment of the global aquaculture industry. Domestication of shellfish species is in the early stages, with few organized breeding programmes and a heavy reliance on wild seed. Consequently, the development and use of genomic markers may significantly assist shellfish aquaculture breeding and production. However, molecular genetic markers typically exhibit unusual patterns of segregation in bivalve species, which result in deviations from Mendelian expectations, and could potentially limit their use in parental assignment, mapping of quantitative trait loci and genomic prediction. Previous studies have suggested that segregation distortions originate at the larval stage, as a result of the linkage of markers to deleterious mutations. This high genetic load has been associated with the high fecundity of bivalve species. However, no direct evidence of a high incidence of de novo mutations has been provided. The aim of this thesis is to gain further insight into segregation distortions in bivalve species by studying the phenomenon at a genome-wide scale, using modern high-throughput sequencing technology. The studies presented in this thesis derive from experiments involving genotyping of parents and offspring from pair-crosses of three different bivalve species (the Pacific oyster Crassostrea gigas, the Blue mussel Mytilus edulis, and the GreenshellTM mussel Perna canaliculus) using high throughput sequencing and SNP arrays. The parent and offspring genotype data were used to characterize patterns of segregation distortion at a genome-wide level, followed by exploratory analyses to test hypotheses related to possible causes of this distortion. Three main findings resulted from the genome-wide analysis of segregation patterns. First, by using Restriction site Associated DNA sequencing (RAD-Seq) we observe that technical artefacts are more widespread than previously considered, contributing to apparent distortions via unreliable genotype calls. By analysing read depth data from RAD-Seq, we suggest that apparent homozygous genotype calls may actually be hemizygous, suggesting a very high frequency of null alleles which contribute to distorted segregation patterns. Bioinformatic pipelines to improve RAD-Seq locus assembly and marker genotyping for bivalve species are presented. Second, by using a high-density SNP array and RAD-Seq in pair crosses of Pacific oyster and aligning to the reference genome assembly, we find that segregation distortions cover extensive regions of the genome, and that certain genomic regions are consistently distorted in different families. Finally, following previous suggestions that the reproductive strategies of bivalve species may favour a high mutation rate, we provide preliminary evidence of a high incidence of de novo mutations that appear spontaneously (i) during male and female gamete formation and (ii) post-zygotically, during larval development. This putative high de novo mutation rate is likely to also contribute to deviations from Mendelian inheritance patterns in these species. New genomic technologies have allowed us to gain substantial insight into the intriguing yet poorly understood phenomena related to inheritance in bivalve species. The results have both fundamental and practical implications for genetic analysis interpretation and selective breeding for aquaculture in this large and highly diverse group of species.

Indiana University-Purdue University Indianapolis (IUPUI) / Modern DNA profiling techniques have increased in sensitivity allowing for higher success in producing a DNA profile from limited evidence sources. However, this can lead to the amplification of more DNA profiles that do not get a hit on a suspect or DNA database and more mixture profiles. The work here aims to address or improve these consequences of current DNA profiling techniques. Based on allele-specific PCR and quantitative color measurements, a 24-SNP forensic phenotypic profile (FPP) assay was designed to simultaneously predict eye color, hair color, skin color, and ancestry, with the potential for age marker incorporation. Bayesian Networks (BNs) were built for model predictions based on a U.S sample population of 200 individuals. For discrete pigmentation traits using an ancestry influenced pigmentation prediction model, AUC values were greater than 0.65 for the eye, hair, and skin color categories considered. For ancestry using an all SNPs prediction model, AUC values were greater than 0.88 for the 5 continental ancestry categories considered. Quantitative pigmentation models were also built with prediction output as RGB values; the average amount of error was approximately 7% for eye color, 12% for hair color, and 8% for skin color. A novel sequencing method, methyl-RADseq, was developed to aid in the discovery of candidate age-informative CpG sites to incorporate into the FPP assay. There were 491 candidate CpG sites found that either increased or decreased with age in three forensically relevant xii fluids with greater than 70% correlation: blood, semen, and saliva. The effects of exogenous microbial DNA on human DNA profiles were analyzed by spiking human DNA with differing amounts of microbial DNA using the Promega PowerPlex® 16 HS kit. Although there were no significant effects to human DNA quantitation, two microbial species, B. subtilis and M. smegmatis, amplified an allelic artifact that mimics a true allele (‘5’) at the TPOX locus in all samples tested, interfering with the interpretation of the human profile. Lastly, the number of contributors of theoretically generated 2-, 3-, 4-, 5-, and 6-person mixtures were evaluated via allele counting with the Promega PowerPlex® Fusion 6C system, an amplification kit with the newly expanded core STR loci. Maximum allele count in the number of contributors for 2- and 3-person mixtures was correct in 99.99% of mixtures. It was less accurate in the 4-, 5-, and 6-person mixtures at approximately 90%, 57%, and 8%, respectively. This work provides guidance in addressing some of the limitations of current DNA technologies.

L’Océan austral est l’un des pivot des écosystèmes et du climat de notre planète, qui concentre plus de 20% de la productivité primaire marine mondiale. La complexité de ses réseaux trophiques et son inaccessibilité rendent plus encore qu’ailleurs nécessaire l’utilisation d’espèces bio-indicatrices. Plusieurs espèces de manchots (comme le Manchot Royal et le Manchot Empereur) sont ainsi l’objet de programmes de suivi à long terme. Dans cette étude, nous utilisons les données offertes par la génomique des populations (« RAD-sequencing » couvrant le génome de centaines d'individus issus couvrant la distribution de ces deux espèces) et les représentations numériques du climat de l’IPCC-CMIP5 pour calibrer dans le temps long les analyses démographique plus précises réalisées à l'échelle de quelques générations dans le cadre de suivis démographiques, et mieux comprendre la réponse des manchots au changement climatique. Au-delà de ses conséquences immédiates pour l’étude des Manchots en tant que sentinelles de l’Océan Austral, cette étude montre l’intérêt d’une plus forte intégration de la génomique des populations dans les études démographiques et comportementales. / The Southern Ocean plays a central role in the regulation of the Earth’s climate and ecosystems, and accounts for more than 20% of the world’s marine productivity. The complexity of its trohpic networks and its sheer inaccessibility make the use of bioindicator species more necessary there than anywhere else. Several penguin species (such as the King and the Emperor penguin) are therefore the focus of long-term monitoring programs.In this study, we use the information from population genomics (« RAD-sequencing » data covering the genome of hundreds of individuals from the two species’ full distribution) and from IPCC-CMIP5 numerical climate models to calibrate in the long time the more precise demographic analyses realised in the framework of field surveys, and understand penguin responses to cliamte change. Beyond its implications for the study of penguins as sentinels of the Southern Ocean, our work demonstrates the interest of a stronger integration of population genomics in demographic and behavioural investigation.

La propagation de bactéries intracellulaires invasives peut entrainer celle des génomes mitochondriaux qui leur sont liés génétiquement au sein du cytoplasme. Cette sélection par autostop peut conduire à une réduction de la taille efficace (Ne) pour le génome mitochondrial. Elle peut également favoriser l'introgression d'une mitochondrie introduite dans une espèce suite à une hybridation. Le principal objectif de ma thèse est de quantifier ces différents effets, de manière globale, au moyen d'un large échantillonnage d'Arthropodes de Polynésie française. Les événements d'introgressions mitochondriales sont à l'origine de discordances entre les histoires évolutives des génomes mitochondriaux et nucléaires. Afin de rechercher de telles discordances, nous avons développé des marqueurs génomiques nucléaires de type RADseq, permettant de reconstruire l'histoire des populations étudiées. J'ai pu montrer au moyen de simulations que ce type de données pouvait être utilisé pour inférer des relations phylogénétiques entre espèces (Cariou et al. 2013). Des améliorations du protocole RADseq nous ont également permis de démontrer l'applicabilité de cette méthode à de nombreux spécimens au sein de librairies hautement multiplexées (Henri et al. 2015). A partir d'analyses in silico, j'ai par ailleurs évalué l'importance de différents biais liés à l'utilisation de marqueurs RADseq pour estimer les diversités génétiques et proposé une méthode permettant de corriger certains d'entre eux. A partir de ces développements, j'ai pu démontrer que sur 30 espèces de Diptères et de Lépidoptères testées à ce jour, la proximité génétique mitochondriale est systématiquement confirmée par les marqueurs nucléaires, rejetant ainsi l'hypothèse d'une introgression mitochondriale récente. Sur un plus large échantillon, nous avons en revanche mis en évidence une réduction significative du Ne mitochondrial dans les lignées infectées par Wolbachia, suffisante pour réduire le polymorphisme, mais insuffisante pour générer une réduction notable de l'efficacité de la sélection naturelle / The spread of endosymbiotic bacteria can drive that of the linked mitochondrial genomes within the cytoplasm. This hitchhiking selection can lead to a reduction of the effective population size of the mitochondrial genomes (Ne). 1t can also facilitate mitochondrial introgression, following the introduction of exogenous mitochondria in a species by hybridization. The main objective of my thesis is to quantify these different effects, on a global scale, using a large sample of Arthropods. Mitochondrial introgressions can lead to discrepancies between the evolutionary histories of mitochondrial and nuclear genomes. To investigate such patterns, we used RADseq genomic markers, that allow reconstructing population histories, and developed improvements for the library preparation and data analysis. Using in silico experiments, 1 showed that RADseq data is suitable for phylogenetic inferences (Cariou et al. 2013). Adjustments in the RADseq protocol also allowed us to demonstrate the applicability of this method for highly multiplexed libraries (Henri et al. 2015). The impact of various biases related the estimation of population genetic diversity using RADseq was also investigated in silico, which lead me to propose an ABC method to correct some of them. Following these developments, 1 showed on 30 species of Diptera and Lepidoptera that nuclear markers always confirmed the mitochondrial genetic relatedness, ruling out the hypothesis of recent mitochondrial introgressions. On a larger sample, we detected a reduction of the mitochondrial Ne in Wolbachia infected lineages. This reduction caused a significant decrease in the polymorphism of infected populations, but appeared insufficient to reduce the efficacy of natural selection

No description available.

La génomique des populations rend possible la mise en évidence de traces de sélection dans le génome. Les travaux effectués considèrent en général une échelle de temps longue (~ 10³ générations). En comparaison, peu d’intérêt a été porté aux études expérimentales de court terme (~ 10 générations). De telles expériences sont pourtant susceptibles de nous renseigner sur la base génétique de caractères complexes. Nous proposons une méthode de vraisemblance basée sur un modèle de Wright-Fisher pour détecter la sélection à partir d’échantillons génétiques temporels acquis sur une période de dix générations. Nous montrons par simulation que notre méthode permet de différencier les signaux dus à la combinaison de la sélection et de la dérive génétique de ceux dus à la dérive seule. Nous montrons également par simulation qu’il est possible d’estimer le coefficient de sélection appliqué à un locus testé. De plus, nous illustrons l’intérêt de notre méthode pour la détection de marqueurs candidats à la sélection au travers de deux études génomiques sur données réelles, chez le diable de Tasmanie (Sarcophilus harrisii) et chez la truite arc-en-ciel (Oncorhynchus mykiss). Ces applications mettent en évidence des régions génomiques candidates pour des phénotypes complexes dans des contextes différents. Dans l’ensemble, nos résultats montrent qu’il est possible de détecter des gènes sujets à une sélection directionnelle intense à partir d’échantillons génétiques temporels, même si la sélection est de courte durée et si les populations examinées ont un faible effectif. / Population genomics makes it possible to detect traces of selection in the genome. Studies in this field have mainly focused on long time scale (~ 10³ generations). In comparison, short-term experimental studies (~ 10 generations) have attracted much less interest. Such experiments are, however, likely to inform us about the genetic basis of complex characters. We propose a likelihood method based on a Wright-Fisher model to detect selection from genetic temporal samples collected over ten generations. We show through simulation that our method can disentangle signals due to the combination of genetic drift and selection to those due to drift alone. We also show through simulation that it is possible to estimate the selection coefficient applied to a tested locus. In addition, we illustrate the interest of our method for the detection of candidate markers for selection through two genome scans performed on real data, in the Tasmanian devil (Sarcophilus harrisii) and in the rainbow trout (Oncorhynchus mykiss). These practical applications highlight candidate genomic regions for complex phenotypes in different contexts. Collectively, our results show the possibility of detecting genes submitted to strong directional selection from genetic time-series, even if selection is applied on a short time period and if the examined populations are small.

<p>The capacity of marine organisms to adapt to natural and anthropogenic stressors is an integral component of ocean health. Harmful algal blooms (HABs), which are one of many growing threats in coastal marine ecosystems, represent a historically present natural stressor that has recently intensified and expanded in geographic distribution partially due to anthropogenic activities. In the Gulf of Mexico, HABs of <italic>Karenia brevis</italic> occur almost annually and produce neurotoxic brevetoxins that have been associated with large-scale mortality events of many marine species, including the common bottlenose dolphin (<italic>Tursiops truncatus</italic>). The factors resulting in large-scale dolphin mortality associated with HABs are not well understood, particularly in regards to the seemingly different impacts of HABs in geographically disjunct dolphin populations. My dissertation investigates a genetic basis for resistance to HABs in bottlenose dolphins in central-west Florida and the Florida Panhandle. I used both genome-wide and candidate gene approaches to analyze genetic variation in dolphins that died putatively due to brevetoxicosis and live dolphins from the same geographic areas that survived HAB events. Using restriction site-associated DNA sequencing, I identified genetic variation that suggested both a common genetic basis for resistance to HABs in bottlenose dolphins across the Gulf coast of Florida and regionally specific resistance. Many candidate genes involved in the immune, nervous, and detoxification systems were found in close genomic proximity to survival-associated polymorphisms throughout the bottlenose dolphin genome. I further investigated two groups of candidate genes, nine voltage-gated sodium channel genes selected because of their putative role in brevetoxin binding and four major histocompatibility complex (MHC) loci selected because of their genomic proximity to a polymorphism exhibiting a strong association with survival. I found little variation in the sodium channel genes and conclude that bottlenose dolphins have not evolved resistance to HABs via mutations in the toxin binding site. The immunologically relevant MHC loci were highly variable and exhibited patterns of genetic differentiation among geographic regions that differed from neutral loci; however, genetic variation at the MHC also could not fully explain variation in survival of bottlenose dolphins exposed to HABs. In my final chapter, I consider the advantages and drawbacks of the genome-wide approach in comparison to a candidate gene approach and, as laid out in my dissertation, I recommend using both complementary approaches in future investigations of adaptation in genome-enabled non-model organisms.</p> / Dissertation

The tilapias are a group of African and Middle Eastern cichlid fish that are widely cultured in developed and developing countries. With many different species and sub-species, and extensive use of interspecies hybrids, identification of tilapia species is of importance in aquaculture and in wild populations where introductions occur. This research set out to distinguish between tilapia species and sub-species by retrieving species-specific nuclear DNA markers (SNPs) using two approaches: (i) sequencing of the coding regions of the ADA gene; and (ii) next-generation sequencing, both standard RADseq and double-digest RADseq (ddRADseq). The mitochondrial DNA (mtDNA) marker cytochrome c oxidase subunit I (COI) was used to verify tilapia species status. ADA gene sequence analysis was partially successful, generating SNP markers that distinguished some species pairs. Most species could also be discriminated using the COI sequence. Reference based analysis (RBA: using only markers found in the O. niloticus genome sequence) of standard RADseq data identified 1,613 SNPs in 1,002 shared RAD loci among seven species. De novo based analysis (DBA: based on the entire data set) identified 1,358 SNPs in 825 loci and RBA detected 938 SNPs in 571 shared RAD loci from ddRADseq among 10 species. Phylogenetic trees based on shared SNP markers indicated similar patterns to most prior phylogenies based on other characteristics. The standard RADseq detected 677 species-specific SNP markers from the entire data set (seven species), while the ddRADseq retrieved 38 (among ten species). Furthermore, 37 such SNP markers were identified from ddRADseq data from a subset of four economically important species which are often involved in hybridization in aquaculture, and larger numbers of SNP markers distinguished between species pairs in this group. In summary, these SNPs are a valuable resource in further investigating hybridization and introgression in a range of captive and wild stocks of tilapias.

No description available.