The phenomenon of repeated evolution runs counter to expectations about the role of contingency in adaptation. However, many examples of independently acquired similar traits show that evolution sometimes does follow the same path. Factors influencing the probability of such an event include selection, trait complexity and relatedness. Previous investigations of repeated adaptation have primarily focused on low-complexity traits subject to strong selection. Studies of systems with varying levels of trait complexity, selection, and relatedness are needed to evaluate the relative contributions of these factors. The series of studies reported here 1) establishes a system for inquiry into the role of parallel adaptation among hosts and parasites and 2) provides an assessment of the role of parallel genetic change in the evolution of a complex trait. In Chapter 2, I show that all-female broods in a line of Drosophila borealis are caused by infection with a male-killing strain of Wolbachia that is very closely-related to another male-killing strain infecting a geographically and evolutionarily distant species of Drosophila. This host-parasite system, together with two other known male-killing Wolbachia strains infecting Drosophila provides a framework for investigating the role of parallel evolution in the independent acquisition of the male-killing trait among Wolbachia, as well as in the adaptation of divergent hosts to similar male-killing parasites. In Chapters 3-5, I investigate the role of parallel genetic change in a complex trait in two species of Drosophila by searching for evidence of adaptation in the Drosophila americana homologs of genes thought to underlie adaptation to climate in Drosophila melanogaster. In Chapter 3, I investigate the D. americana homolog of Alcohol dehydrogenase (Adh). In contrast with D. melanogaster, which segregates functionally distinct variants in Adh that represent local adaptation to climate, D. americana segregates little variation. This is surprising, especially because Adh of D. americana is found near a polymorphic chromosomal rearrangement that does segregate geographically-structured alleles across the species' range. In Chapter 4, I report similarities at the Phosphoglucomutase (Pgm) locus in the two species, including a shared excess of nonsynonymous variants and the presence of clinal alleles. However, while variation at Pgm of D. melanogaster is proposed to underlie local adaptation, variation at Pgm of D. americana appears to be predominantly neutral. In Chapter 5, I investigate the role of positive selection in sequence evolution in the D. americana homologs of a group of genes thought to underlie local adaptation to climate in D. melanogaster. The two species share a large geographic range and exhibit levels of sequence variation that indicate a similar effective population size, but D. melanogaster appears to undergo more frequent fixation of advantageous alleles. Approximately half of all amino acid divergence in D. melanogaster is attributable to positive selection, but I find no signs of positive selection in the investigated genes in D. americana. Overall, the results reveal little or no parallel evolution at the single genes analyzed. This lack of parallel evolution is likely a result of the high complexity of adaptation to climate as well as contingency.

Evidence for the repeated, independent evolution of hot- and cool-season breeding populations across colonies of the Band-rumped Storm-petrel has garnered much interest from seabird ecologists and evolutionary biologists, alike. Sympatric seasonal populations have been shown to be each other’s closest relatives, implying that ecological divergence into two seasonal foraging types has taken place several times independently across the species’ range, each time in the absence of geographical barriers to gene flow. I present data on the molecular genetic characteristics of a unique year-round breeding population in the Cape Verde archipelago. Using mitochondrial control region sequence and five microsatellite loci, I characterized genetic relationships among 220 birds breeding in four different months (January, April, June and November) and tested for a relationship between temporal isolation and genetic differentiation. Birds breeding in April, June and November were genetically indistinguishable at microsatellite loci, but control region sequence suggested differentiation between January and other months (pairwise ΦST from 0.19 to 0.46, p≤0.05). No evidence for genetic isolation by time was found. A comparison of birds breeding in June and November revealed significant differences in a suite of morphological traits related to foraging strategy (tarsus length, bill length, bill depth, head length, wing length and tail shape), and even significant variation among birds breeding in the same month, despite evidence for gene flow between these groups. Interpreting these patterns in the context of Band-rumped Storm-petrel populations range-wide, I suggest that divergent selection on standing variation within ancestral populations may be an important mechanism explaining the repeated, independent evolution of conserved seasonal foraging types in this species. / Thesis (Master, Biology) -- Queen's University, 2011-02-28 12:02:44.256

Weedy rice is a persistent weed of cultivated rice (Oryza sativa) fields worldwide, which competes with the crop and drastically reduces yields. Within the US, two main populations of genetically differentiated weedy rice exist, the straw-hulled (SH) group and the black-hulled awned (BHA) group. Current research suggests that both groups are derived from Asian cultivated rice. However, the weeds differ from the cultivated groups in various morphological traits. My research focus is on the genetic basis of two such traits: seed shattering ability and differences in flowering time. The persistence of weedy rice has been partly attributed to its ability to shatter (disperse) seed prior to crop harvesting. I have investigated the shattering phenotype in a collection of US weedy rice accessions and find that all US weedy rice groups shatter seeds easily. Additionally, I characterized the morphology of the abscission layer at the site where seed release occurs and find that weeds begin to degrade their abscission layers at least five days prior to wild plants. I also assessed allelic identity and diversity at the major shattering locus, sh4, in weedy rice and find that all cultivated and weedy rice share similar haplotypes at sh4. These haplotypes contain a single derived mutation associated with decreased seed shattering during domestication. The combination of a shared cultivar sh4 allele and a highly shattering phenotype suggests that US weedy rice have re-acquired the shattering trait after divergence from their crop progenitors through alternative genetic mechanisms. Additionally, my investigation into flowering time in weedy rice shows that weed populations differ in their flowering times. I also assessed allelic identity and diversity at two genes involved in the transition to flowering, Hd1 and Hd3a, and again found haplotype sharing between weeds and cultivars with Hd1 only accounting for some of the flowering time differences between weeds. In order to locate genomic regions containing additional candidate genes I conducted a QTL mapping study on two F2 populations derived from crosses of weedy rice with cultivated rice. My results show sharing of QTL for flowering time between populations, yet lack of sharing of QTL for shattering.

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第20208号 / 理博第4293号 / 新制||理||1616(附属図書館) / 京都大学大学院理学研究科生物科学専攻 / (主査)准教授 渡辺 勝敏, 教授 沼田 英治, 教授 曽田 貞滋 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

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Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal

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Yes / A crucial step in the transition from outcrossing to self-fertilization is the loss of genetic self-incompatibility (SI). In the Brassicaceae, SI involves the interaction of female and male speci-ficity components, encoded by the genesSRKandSCRat the self-incompatibility locus (S-lo-cus). Theory predicts thatS-linked mutations, and especially dominant mutations inSCR, arelikely to contribute to loss of SI. However, few studies have investigated the contribution ofdominant mutations to loss of SI in wild plant species. Here, we investigate the genetic basis of loss of SI in the self-fertilizing crucifer speciesCapsella orientalis, by combining genetic mapping, long-read sequencing of completeS-hap-lotypes, gene expression analyses and controlled crosses. We show that loss of SI inC. orientalisoccurred<2.6 Mya and maps as a dominant trait totheS-locus. We identify a fixed frameshift deletion in the male specificity geneSCRand con-firm loss of male SI specificity. We further identify anS-linked small RNA that is predicted tocause dominance of self-compatibility. Our results agree with predictions on the contribution of dominantS-linked mutations toloss of SI, and thus provide new insights into the molecular basis of mating system transitions. / Work at Uppsala Genome Center is funded by 550 RFI / VR and Science for Life Laboratory, Sweden. The SNP&SEQ Platform is supported by 551 the Swedish Research Council and the Knut and Alice Wallenberg Foundation. V.C. 552 acknowledges support by a grant from the European Research Council (NOVEL project, 553 grant #648321). The authors thank the French Ministère de l’Enseignement Supérieur et de la 554 Recherche, the Hauts de France Region and the European Funds for Regional Economical 555 Development for their financial support to this project. This work was supported by a grant 556 from the Swedish Research Council (grant #D0432001) and by a grant from the Science for 557 Life Laboratory, Swedish Biodiversity Program to T.S. The Swedish Biodiversity Program is 558 supported by the Knut and Alice Wallenberg Foundation.

These studies compare neurotransmitter localization and the behavioral functions of homologous neurons in nudibranch molluscs to determine the types of changes that might underlie the evolution of species-specific behaviors. Serotonin (5-HT) immunohistochemistry in eleven nudibranch species indicated that certain groups of 5 HT-immunoreactive neurons, such as the Cerebral Serotonergic Posterior (CeSP) cluster, are present in all species. However, the locations and numbers of many other 5 HT-immunoreactive neurons were variable. Thus, particular parts of the serotonergic system have changed during the evolution of nudibranchs. To test whether the functions of homologous neurons are phylogenetically variable, comparisons were made in species with divergent behaviors. In Tritonia diomedea, which crawls and also swims via dorsal-ventral body flexions, the CeSP cluster includes the Dorsal Swim Interneurons (DSIs). It was previously shown that the DSIs are members of the swim central pattern generator (CPG); they are rhythmically active during swimming and, along with their neurotransmitter 5-HT, are necessary and sufficient for swimming. It was also known that the DSIs excite efferent neurons used in crawling. DSI homologues, the CeSP-A neurons, were identified in six species that do not exhibit dorsal-ventral swimming. Many physiological characteristics, including excitation of putative crawling neurons were conserved, but the CeSP A neurons were not rhythmically active in any of the six species. In the lateral flexion swimmer, Melibe leonina, the CeSP-A neurons and 5-HT, were sufficient, but not necessary, for swimming. Thus, homologous neurons, and their neurotransmitter, have functionally diverged in species with different behaviors. Homologous neurons in species with similar behaviors also exhibited functional divergence. Like Melibe, Dendronotus iris is a lateral flexion swimmer. Swim interneuron 1 (Si1) is in the Melibe swim CPG. However, its putative homologue in Dendronotus, the Cerebral Posterior ipsilateral Pedal (CPiP) neuron, was not rhythmically active during swim-like motor patterns, but could initiate such a motor pattern. Together, these studies suggest that neurons have changed their functional relationships to neural circuits during the evolution of species-specific behaviors and have functionally diverged even in species that exhibit similar behaviors.

The concept of biodiversity – the phenotypic and genotypic variation among organisms – is central to conservation biology. There is growing recognition that biodiversity does not exist in isolation, but rather is intrinsically and evolutionarily linked to cultural diversity and indigenous knowledge systems. In Canada, caribou (Rangifer tarandus) occupy a central place in the livelihoods and identities of indigenous people and display substantial variation across their distribution. However, quantifying caribou intraspecific variation has proven challenging. Interdisciplinary approaches are necessary to produce effective species characterizations and conservation strategies that acknowledge the interdependent relationships between people and nature in complex social-ecological systems. In this dissertation I use multiple disciplinary traditions to develop comprehensive and united representations of caribou variation through an exploration of population genetics, phylogenetics, traditional knowledge, language, and visual approaches in the Sahtú region of the Northwest Territories, Canada. First, I examine caribou variation through analysis of population genetics and the relationships Dene and Métis people establish with animals within bioculturally diverse systems. Next, I focus on how the Pleistocene glacial-interglacial cycles have shaped the current patterns of caribou phylogeographic lineage diversification. Finally, I explore how art can be used to facilitate cross-cultural collaboration and externalize the unique heterogeneity of biocultural diversity. The results demonstrate a broad scale understanding of the distribution, spatial organization, and the degree of differentiation of caribou populations in the region. I found evidence for caribou population differentiation that corresponds to the caribou types recognized by Dene people: tǫdzı “boreal woodland caribou,” ɂekwę́ “barren-ground caribou,” and shúhta ɂepę́ “mountain caribou.” Phylogenetic results reveal that in their northern margin the boreal ecotype of woodland caribou evolved independently from the northern Beringian lineage in contrast with southern boreal caribou which belong to the sub-Laurentide refugia lineage. In addition, I demonstrate how art can be used improve communication, participation, and knowledge production among interdisciplinary research collaborations and across language and knowledge systems. A collaborative process of research that facilitates łeghágots'enetę “learning together” has the potential to produce sustainable conservation solutions, develop efficient and effective wildlife management policies, and ensure caribou remain an important part of the landscape. / February 2017