Central to the application of genomics to animal agriculture are DNA markers, especially microsatellites and single nucleotide polymorphisms. These markers are the resources necessary for constructing genetic maps and for determining how improved and unimproved animal breeds are related. Here, DNA markers were developed for two avian species, the turkey, Meleagris gallopavo, and the budgerigar (budgie), Melopsittacus undulatus. Genomic libraries enriched for simple sequence repeats were used to generate about 70 budgie sequences of a total length of 38 kb. From these sequences, 9 primer pairs were designed and used to screen for informativeness in a panel of DNA samples from unrelated budgie samples. All but one of the nine primers evaluated were polymorphic with the number of alleles ranging from two to four. Comparative analysis involving the use of these budgie primers showed moderate sequence similarity to turkey and chicken. The genomic libraries and the comparative sequences provide useful genomic reagents that could be used to construct a budgie genome map. In the turkey, ten previously described microsatellites and a gene-based single nucleotide polymorphism (SNP) were used to evaluate the relatedness of heritage varieties to a commercial strain. Estimates of Nei's genetic distance (D) and genetic differentiation (Rst) between populations using microsatellite markers showed that the commercial strain is genetically more closely related to the Bourbon Red and Narragansett and least related to the Royal palm and Spanish Black. Gene flow (Nm) level was highest between the commercial and Bourbon Red populations. The SNP analysis by PCR-RFLP revealed that the commercial strain was more closely related to the Spanish black and Narragansett and least related to the Bourbon red and Blue slate. Though results of the two marker systems, microsatellite and SNP, were inconsistent, they provide insights into using heritage turkeys to genetically improve commercial populations by introgression. The present thesis investigation showed that DNA markers provide a strong opportunity to develop genomic reagents needed to test hypotheses in little-studied agriculturally important and model avian species. / Master of Science

The elusive jaguar (Panthera onca) is extremely difficult to study due to its wide-ranging behavior, crepuscular activity peaks and its occurrence in low population densities in often dense forest habitats. Jaguars are also a species of concern, but our ability to provide for their survival is hampered by our inability to obtain reliable information on the status of their wild populations. This study combines innovative noninvasive research techniques such as scat detector dogs and molecular scatology to conduct the first genetic study on wild populations of Neotropical felids coexisting across fragmented forest habitats in Belize, Central America. Specifically, we analyzed multi-locus data in jaguars (Panthera onca), pumas (Puma concolor) and ocelots (Leopardus pardalis) collected from 1053 scat samples across their range in the country. First, we optimized 14 polymorphic microsatellite loci for jaguars (Panthera onca), pumas (Puma concolor), and ocelots (Leopardus pardalis), and assessed their utility for cross-species amplification. Additionally, we tested their reliability for species and individual identification using fecal DNA as he primary DNA source. All microsatellite loci examined successfully cross-amplified in the three target species, and were polymorphic. Second, to maximize PCR amplification success and genotyping accuracy rates, and to minimize genotyping error rates for fecal DNA samples, we evaluated the performance of two fecal DNA storage techniques (dimethyl sulfoxide saline solution/DET buffer, 95% EtOH) suitable for long-term preservation at remote tropical sites. Additionally, we tested fecal DNA samples collected from four different scat locations (top, side, bottom, inside). DET buffer was the superior fecal DNA preservation method and collecting fecal DNA from side and top locations of the scat resulted in the highest PCR success rates. For the main genetic study, we assessed the genetic conservation status of all three target species across the country of Belize. We examined levels of genetic diversity within different sites, (2) defined potential genetic clusters/populations, (3) and examined levels of gene flow and population structure for all three target species on a countrywide scale. Furthermore, we compared genetic diversity and gene flow levels among the three target species. Wild felids in Belize showed moderate levels of heterozygosity (HE = 0.60 - 0.70) with jaguars having the lowest genetic diversity with average expected heterozygosities of HE = 0.60 ± 0.05 and allelic richness (AR) of 4.94 ± 0.44 followed by pumas with HE = 0.65 ± 0.06 and AR of 7.52 ± 0.86 and ocelots with HE = 0.70 ± 0.05 and AR of 3.89 ± 0.23. We observed low to moderate levels of differentiation (FST = 0.00 - 0.15) and weak population structure using spatial Bayesian clustering techniques for all three target species. Although levels of genetic diversity and gene flow across the country are still fairly high, we did detect evidence of fragmentation indicating the risk of further habitat loss and fragmentation for wild felids. Felids were simultaneously monitored across all study sites by remote sensing camera traps, which allows for a comparison of density estimates obtained from two different noninvasive survey approaches. Furthermore, analytical methods for density estimation are advancing rapidly, making it difficult to choose the optimal technique. Thus, we compared a variety of density estimators including the conventional approach of estimating abundance ( ) in programs CAPTURE and MARK and dividing abundance by the effective trapping area (ETA), the recently developed spatially explicit capture-recapture (SECR) models, both the likelihood-based approach (ML-SECR) in program DENSITY and the Bayesian approach (B-SECR) in program SPACECAP, and finally the genetic-based mark-recapture one sampling occasion estimator in program CAPWIRE. Although different survey methods using various density estimators produced similar density estimates, confidence levels and coefficients of variation varied, with SECR methods resulting in the least precise estimates. Detection probabilities were generally higher for noninvasive genetic sampling than for camera trapping. Both techniques were shown to be reliable and highly efficient survey methods for density estimation of low-density Neotropical felids living in challenging environments such as the tropics. While less precise, SECR CMR models are probably a more realistic reflection of our uncertainty. They hold great promise for density estimation studies for wide-ranging and territorial carnivore species, especially if precision can be improved through study design or analysis advancements in the future. In conclusion, our results demonstrated that noninvasive sampling techniques such as molecular scatology and remote camera trapping are efficient research approaches to study multiple Neotropical felids in a multifaceted way and on a countrywide scale. We believe that the techniques and analyses developed in this study are widely applicable and relevant to the conservation and management of other elusive and difficult to study wild felids worldwide. / Ph. D.

The Nile tilapia Oreochromis niloticus is native to Africa and middle East, and is an important source of nutrition for many in sub-Saharan Africa. Understanding the genetic diversity within and differentiation among wild populations can help identify O. niloticus populations that are imperiled and require directed management, especially because of increasing threats to the species' long-term persistence in the wild, including habitat destruction, overfishing, climate change, and hybridization with farmed populations. Knowledge of the genetic variation among wild populations also can contribute to foundation and selection of genetically diverse populations for aquaculture. I assessed the genetic variation among tilapia populations using fin-clips collected between December 2014 and July 2017 from 14 farmed sources, mostly originating from cage farms on the Volta Lake, and 13 wild sources from nine river basins in Ghana. I also conducted a laboratory growth experiment in Ghana with two wild populations to evaluate the tolerance of different genotypes to high temperatures, to inform their development for aquaculture in West Africa. I found that pure O. niloticus populations persist in the wild but some have been extensively introgressed with the closely related species, O. aureus, which has not previously been documented in Ghana. Additionally, some wild populations appear to have recently declined significantly in numbers, likely due to overfishing and habitat modification, the latter primarily as a result of illegal alluvial mining ongoing in Ghana. Analysis of the farmed populations revealed that at least two farms were growing the unapproved genetically improved farmed tilapia (GIFT) and related strains, and that escaped individuals are admixed into some wild populations. The results of my laboratory experiment showed that O. niloticus populations occurring in northern Ghana already may be adapted to warmer temperatures and could be developed and used purposefully in aquaculture, taking advantage of their adaptation. To protect remnant pure O. niloticus populations in the wild, timely conservation decisions should be made and implemented. Protecting wild O. niloticus populations also would ensure that pure germplasms are available to develop aquaculture stocks from native populations. / Ph. D. / The Nile tilapia Oreochromis niloticus is an important food source for many people in Africa. However, many wild populations may be at risk of population decline and extinction because of increasing human activities such as overfishing and farming of non-native strains. Understanding the genetic differences among wild populations and comparing them with farmed strains can inform protection of wild populations and also help develop aquaculture strains using native populations as genetic resources. I assessed the genetic differences among tilapia populations using fin-clips I collected between December 2014 and July 2017 from 14 farmed sources, mostly originating from cage farms on the Volta Lake, and 13 wild sources from nine river basins in Ghana. I also conducted a laboratory study with two wild populations to test their tolerance to high water temperature. My research showed that pure O. niloticus populations still occur in Ghanaian rivers, but some have reproduced widely with a similar species, O. aureus, which is not known to occur in Ghanaian rivers. I also found that some wild populations may have reduced population sizes because of overfishing or because their environments have been impacted by illegal mining occurring in almost all Ghanaian rivers. My results indicated that at least two farms were growing the genetically improved farmed tilapia (GIFT) and related varieties, some of which have escaped the farms and mixed with wild populations. The results of my laboratory experiment showed that O. niloticus populations occurring in northern Ghana may be adapted to warmer water temperatures and could be selectively bred and used in aquaculture. The information generated from my research should help in making timely conservation decisions, which should help protect the remnant pure O. niloticus populations in the wild and contribute to developing aquaculture responsibly.

In the future, food security will face significant challenges due to climate change and a growing world population. One approach to make agriculture more sustainable is to preserve biodiversity by utilizing crop wild relatives as a source of genetic material. These crop wild relatives are closely related to today’s cultivated crops and can be an important asset to combat food insecurity. Gaining more knowledge about a species’ genetic diversity through microsatellite analysis is an important step for future conservation and potential utilization in crop improvement. However, before these studies can take place the microsatellite markers have to be optimized for PCR. In this study, eleven microsatellite markers were optimized for bilberry individuals. Optimized annealing temperatures were found for all markers and most of them had amplification in three or more of the individuals tested from Sweden, Finland and Iceland. Ten out of the eleven tested markers were regarded suitable for future genetic diversity analyses. The eleventh, VCB-C00694, was considered unsuitable due to formation of primer dimers and not amplifying in several individuals. By assessing the genetic diversity of bilberry, Vaccinium myrtillus, it opens up the possibility to enrich their domesticated relative the American blueberry, Vaccinium corymbosum, by introducing new genetic variety. In relation to this, the increased knowledge about genetic diversity among bilberries in the Nordic can lead to better understanding of their need for conservation.

Noninvasive methods for monitoring wildlife species have revolutionized the way population parameters, such as population density and survival and recruitment rates, are estimated while accounting for imperfect detection using capture-recapture models. Reliable estimates of these parameters are vital information required for making sound conservation decisions; however to date, noninvasive sampling methods have been of limited use for a vast number of species which are difficult to identify to the individual level–a general requirement of capture-recapture models. Capture-recapture models that utilize partial identity information have only recently been introduced and have not been extended to most types of noninvasive sampling scenarios in a manner that uses the spatial location where noninvasive samples were collected to further inform complete identity (i.e. spatial partial identity models). Herein, I extend the recently introduced spatial partial identity models to the noninvasive methods of remote cameras for species that are difficult to identify from photographs and DNA from hair or scat samples. The ability of these novel models to improve parameter estimation and extend study design options are investigated and the methods are made accessible to applied ecologists via statistical software. This research has the potential to greatly improve wildlife conservation decisions by improving our knowledge of parameters related to population structure and dynamics that inform those decisions. Unfortunately, many species of conservation concern (e.g., Florida panthers, Andean bears) are managed without having the necessary information on population status or trends, largely a result of the cost and difficulty of studying species in decline and because of the difficulty of applying statistical models to sparse data, which can produce imprecise and biased estimates of population parameters. By leveraging partial identity information in noninvasive samples, the models I developed will improve these parameter estimates and allow noninvasive methods to be used for more species, leading to more informed conservation decisions, and a more efficient allocation of conservation resources across species and populations. / Ph. D. / Noninvasive methods for monitoring wildlife species have revolutionized the way population parameters, such as population density and survival and recruitment rates, are estimated while accounting for imperfect detection using capture-recapture models. Reliable estimates of these parameters are vital information required for making sound conservation decisions; however to date, noninvasive sampling methods have been of limited use for a vast number of species which are difficult to identify to the individual levela general requirement of capture-recapture models. Capture-recapture models that utilize partial identity information have only recently been introduced and have not been extended to most types of noninvasive sampling scenarios in a manner that uses the spatial location where noninvasive samples were collected to further inform complete identity (i.e. spatial partial identity models). Herein, I extend the recently introduced spatial partial identity models to the noninvasive methods of remote cameras for species that are difficult to identify from photographs and DNA from hair or scat samples. The ability of these novel models to improve parameter estimation and extend study design options are investigated and the methods are made accessible to applied ecologists via statistical software. This research has the potential to greatly improve wildlife conservation decisions by improving our knowledge of parameters related to population structure and dynamics that inform those decisions. Unfortunately, many species of conservation concern (e.g., Florida panthers, Andean bears) are managed without having the necessary information on population status or trends, largely a result of the cost and difficulty of studying species in decline and because of the difficulty of applying statistical models to sparse data, which can produce imprecise and biased estimates of population parameters. By leveraging partial identity information in noninvasive samples, the models I developed will improve these parameter estimates and allow noninvasive methods to be used for more species, leading to more informed conservation decisions, and a more efficient allocation of conservation resources across species and populations.

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal.

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal.

La gorgone rouge, Paramuricea clavata (Cnidaire, Octocoralliaire), est une espèce sessile, longévive à faible croissance dont les populations présentent une lente dynamique. Cette espèce est caractérisée par une phase larvaire pélagique qui représente l’unique phase de dispersion potentielle au cours du cycle de vie de cette espèce. P. clavata est une espèce clé des assemblages à coralligène de Méditerranée, qui subit les effets combinés des activités de plongée sous-marine et du changement climatique. Dans ce contexte, il était donc fondamental d’approfondir les connaissances sur les traits d’histoire de vie, la biologie et l’écologie de cette espèce. L’objectif de ce travail était d’étudier, à l’aide d’une approche génétique, les facteurs biologiques et écologiques clés qui devraient être importants pour la réponse de l’espèce aux changements environnementaux. Parmi ces facteurs, la dispersion larvaire joue un rôle fondamental dans la dynamique et la connectivité des populations marines. Dans le contexte actuel des fortes pressions anthropiques, la compréhension des degrés de connectivité entre les populations est primordiale pour évaluer le devenir des populations, face au changement climatique, et pour mettre en place des plans de conservation et des réseaux d’aires marines protégées. / The red gorgonian, Paramuricea clavata (Cnidaria, Octocorallia), is a sessile, long-lived and slow growing species which displays slow population dynamics. This species is characterized by a pelagic larval phase that represents the sole potential phase of dispersal during the life cycle of this species. P. clavata is a key species of coralligenous assemblages of the Mediterranean Sea which undergoes the combined effects of diving activities and climate change. In this context, extending the knowledge about life history traits, biology and ecology of the red gorgonian was of fundamental importance. Using a genetic approach, the goal of this work was to study some key biological and ecological factors which should be important for the response of this species to environmental changes. Among these factors, larval dispersal plays a major role in driving marine population dynamics and connectivity. In the current context of strong anthropic pressures, understanding the level of population connectivity is primordial to evaluate population outcome, facing climate change, and to develop conservation plans as well as to design marine reservenetworks.

En plus des facteurs environnementaux et démographiques, les propriétés génétiques des populations sont devenues une préoccupation majeure pour préserver les populations en déclin de l'extinction. Afin d’acquérir des informations pertinentes pour la planification et la mise en œuvre des stratégies de conservation, les biologistes de la conservation ont réalisé le besoin d’avoir des connaissances en génétique des populations. Grace à l'acquisition de plus en plus rapide et de moins en moins chère d'une large gamme de marqueurs moléculaires, le recours a l’usage de l’outil moléculaire se répand de plus en plus. Ainsi, la génétique de la conservation se confirme comme une discipline à part entière qui est donc l’utilisation de la génétique dans la préservation des espèces comme entités dynamiques capables d'évoluer pour faire face aux changements environnementaux et afin de minimiser leur risque d'extinction. Par le biais de l’utilisation d’un large panel de marqueurs moléculaires (gènes mitochondriaux et nucléaires, microsatellites et SNPs), nous nous sommes intéresse à l’histoire évolutive à différentes échelles spatio-temporelles de la sous-espèce ouest méditerranéenne Testudo. hermanni hermanni (THH), qui présente une distribution insulaire et continentale très fragmentée. Le but de ce travail consiste à 1) comprendre les processus qui expliqueraient la distribution actuelle de la diversité génétique des populations et leur structure, 2) identifier l'origine des populations introduites (à Minorque et au Delta de l’Ebre), et 3) dater l’origine de la sous espèce THH. A l’échelle des populations, il s’agit d’identifier le nombre de groupes génétiques homogènes chez la tortue d’Hermann et le degré de différentiation génétique entre ces groupes afin de définir des unités de conservation évolutivement significatives (ESU) et des unités de gestion (MU). Enfin, nous nous sommes intéresses à l’étude des derniers noyaux de populations de THH dans le Var par des approches de génétique du paysage. Nos résultats ont révélé qu’une divergence par vicariance est à l’ origine de l’apparition de la sous-espèce T.h. hermanni. Ce scenario biogéographique s’expliquerait par les successions d’évènements glaciaires et interglaciaires qu’a connu le Pléistocène depuis plus de 2 MA provoquant un mouvement de retrait de l’espèce vers des zones refuges sur la frange côtière nord-méditerranéenne. Par ailleurs, le patron de différentiation mitochondriale Ile-continent observe et confirme par les microsatellites est très original par rapport à ce qui est connu chez d’autres espèces de reptiles partageant la même aire de distribution. Au vue de l’analyse phylogénétique confirmée par les microsatellites, on peut affirmer que la tortue d’Hermann n’est pas native sur Minorque et qu’elle a une double origine : la première, résultant d’une introduction à partir d’une seule source, probablement d’une population continentale génétiquement proche des Albères. La seconde d'origine insulaire, serait le résultat d’apports multiples, à partir de la Corse, de la Sardaigne ou de la Sicile. Enfin, l’isolement des populations de THH au sein de chaque région géographique reflète une structure génétique très forte. Par conséquent, six unités de gestion (MUs) sont proposées comme unités de conservation et de suivi sur le terrain. / In addition to environmental and demographic factors, the study of genetic properties of populations became inevitable issues in the conservation of declining populations. To acquire relevant information for conservation planning and implementing conservation strategies, conservationists have realized the need of population genetics tools. Moreover, this discipline has become more efficient with the development of a wide range of effective and relatively cheap methods for the characterization of a huge number of molecular markers. This led to define the conservation genetics as a separate discipline, which is the use of genetics in species preservation as dynamic entities evolving to cope with environmental changes and to minimize their extinction risk. Using a broad panel of molecular markers (mitochondrial and nuclear genes, microsatellites and SNPs), we interested in the evolutionary history at different spatial and temporal scales of the Mediterranean western subspecies Testudo hermanni hermanni (THH), which presents a very fragmented insular and continental distribution. The aim of this study is to 1) understand the processes that explain the current distribution of the structure and genetic diversity of populations, 2) identify the origin of introduced populations (Menorca and Ebro Delta) and 3) Dating the origin of the subspecies THH. At the population level, our study aimed to identify the number of homogeneous genetic groups of THH tortoise and the degree of genetic differentiation between these groups in order to identify evolutionarily significant units (ESU) and management units (MU). Finally, we were interested in the study of the last core populations of THH in the Var by landscape genetics approach. Our results revealed that a divergence by vicariance pattern explains the origin of the appearance of the subspecies THH. This biogeographic scenario is explained by the succession of glacial and interglacial events of the Pleistocene causing a withdrawal of the species toward refugia on the northern Mediterranean fringe. Moreover, the observed differentiation pattern (island vs continent) is very original compared to the reported diversity patterns of other reptiles sharing the same distribution range. According to our results, we may conclude that the Hermann’s tortoise is not native in Menorca and has a double origin: the first, is an introduction resulting from a unique source, probably from a continental lineage genetically close to Albera. The second, from an island origin, is the result of multiple contributions, from Corsica, Sardinia or Sicily. Lastly,the isolation of THH populations within each geographic region reflects a very strong genetic structure, therefor the six most relevant management units forconservation purposes are proposed on the basis that they represent a significant part of the evolutionary legacy of the species.

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal