Les processus d’hybridation et d’introgression occupent une place importante dans l’étude du mécanisme de spéciation, car ils permettent d’analyser les conséquences évolutives des échanges génétiques entre espèces partiellement isolées. Ici, nous nous sommes intéressés à la zone d’hybridation entre les soles S. senegalensis et S. aegyptiaca au niveau des côtes nord-tunisiennes, pour comprendre l’origine de leur diversification. Nous avons premièrement caractérisé les conséquences phénotypiques de l’hybridation sur la variabilité morphologique. Nos résultats montrent que si l’introgression provoque la convergence de certains caractères morphologiques, elle est en revanche à l’origine de transgressions et de distorsions morphologiques sur d’autres traits, pouvant refléter une condition plus faible des génotypes recombinants. Les phénomènes d’incompatibilité génétique associés à une éventuelle contre-sélection des hybrides sont supposés créer une perméabilité différentielle du génome face au flux génique entre espèces. Pour étudier cette semi-perméabilité à l’échelle du génome, nous avons établi un jeu de données de polymorphisme par la méthode RAD-seq. Ceci nous a permis de génotyper 200 individus pour 10 756 marqueurs SNP, qui nous ont permis de caractériser les flux géniques entre ces deux espèces à travers trois approches complémentaires. La première est basée sur une reconstitution démographique de l’histoire des échanges génétiques qui intègre les effets de la semi-perméabilité des génomes. La seconde approche se focalise sur l’évolution spatiale des fréquences alléliques à travers la zone d’hybridation. La dernière méthode, dite des clines génomiques, compare le comportement de chaque locus au patron d’introgression moyen attendu sous l’hypothèse de neutralité. Nos résultats indiquent que S. senegalensis et S. aegyptiaca ont subi une divergence ancienne en allopatrie suivie d’un contact secondaire récent. Seule une faible proportion du génome parvient à introgresser de manière asymétrique dans la zone hybride qui en résulte, selon une grande diversité de patrons d’introgression dont nous discutons les origines possibles. / Hybridisation and introgression processes have an important place in the study of speciation as they allow to analyse the evolutionary consequences of genetic exchanges between partially isolated species. Here we are interested in the hybrid zone resulting from the contact between the soles S. aegyptiaca and S. senegalensis along the North Tunisian coast. First, we studied the consequences of hybridisation on phenotypic variation. This allowed us to evidence that phenotypic convergence in hybrids was accompanied by phenotypic transgression and morphological distortions for certain traits that seem to reflect a reduced condition of hybrids. Possible genetic incompatibilities between species should be responsible for the differential permeability of the genome to gene flow, thereby creating a semi-permeable barrier. To study this barrier at the genome scale, we have produced a polymorphism dataset using the RAD-seq method. This allowed us to genotype 200 individuals at 10,756 SNP markers and to characterise genomic patterns of gene flow between the two species through three complementary approaches. The first is based on a reconstruction of the demographic history of the genetic and exchanges that incorporates the effects of the semi-permeability to gene flow. The second approach focuses on the spatial evolution of allele frequencies across the hybrid zone. The last method, called genomic clines, compares the behaviour of each locus to the average introgression pattern expected under the hypothesis of neutrality. Our results indicate that S. aegyptiaca and S. senegalensis underwent ancient divergence in allopatry followed by a recent secondary contact. Only a small proportion of the genome can asymmetrically introgress across the hybrid zone, resulting in a variety of introgression patterns of which we discuss the possible origins.

Made available in DSpace on 2014-08-20T13:25:43Z (GMT). No. of bitstreams: 1 Dissertacao_Gabriela_Fonseca.pdf: 1203937 bytes, checksum: 0779cafbd315bd99d44d8fbe5a6537c7 (MD5) Previous issue date: 2011-03-16 / The red rice (Oryza sativa) co-exists with the cultivated rice in commercial farmings, becoming one of the main limiting factors for the yield increase in this crop, since this weed competes for the same resources. The rice crop is one of the most important in the world, being the main nutritious source for more than half of the world´s population. Genes for resistance to herbicides have become the best option for the control of this weed. Herbicides that inhibit the ALS enzyme, such as those from the imidazolinone chemical group, are commonly used for weed control in many crops. These ALS inhibitors are currently used for the control of red rice, which is known as Clearfield® technology. This work aimed to study the morphological features that can assist in identifying Only® herbicide tolerance in hydroponic bioassays, and introgression of ALS inhibitor herbicide tolerance genes in cultivars through artificial hybridizations. The rice cultivars used were BRS Sinuelo CL and Puitá INTA CL as imidazolinone herbicide tolerant, and the BRS Pampa, BRS Querência, BRS Atalanta and BRS Fronteira, as sensitive. The variable insertion of the first leaf can be considered an appropriate candidate for study because it discriminates more effectively the responses of different genetic constitutions. Taking in account the doses and periods of development, it can be recommended for use as a morphological marker. The concentration of herbicide that allows better discrimination between tolerant and sensitive genotypes is 25μg L-1 as described in the methodology for this bioassay. The results of this study show that F2 hybrids resulting from crosses between cultivars carrying the allele for herbicide tolerance to the imidazolinone class and conventional rice cultivars, are feasible, enabling the establishment of populations with desirable agronomic characteristics of herbicidetolerant rice, with higher ability to fight the red rice. / O arroz vermelho (Oryza sativa) co-existe com o arroz cultivado em lavouras comerciais, sendo esse um dos principais entraves para o aumento da produtividade dessa cultura, já que essa invasora compete pelos mesmos recursos que as cultivares necessitam. A cultura do arroz é uma das mais importantes no mundo, considerada a principal fonte nutritiva para mais da metade da população mundial. Genes para resistência a herbicidas têm se tornado uma das opções mais utilizadas no mundo para o controle de invasoras, sendo que os herbicidas inibidores da enzima ALS, classe das imidazolinonas, são amplamente utilizados para o controle de plantas daninhas em diversas culturas. Esses inibidores de ALS são atualmente utilizados para o controle do arroz vermelho, sendo esta tecnologia denominada Clearfield®. Este trabalho objetivou o estudo de características morfológicas capazes de auxiliar na identificação de tolerância ao herbicida Only®, em bioensaio em condições hidropônicas, e a introgressão de genes de tolerância ao herbicida inibidor de ALS em cultivares, através de hibridações controladas. Foram utilizados as cultivares de arroz BRS Sinuelo CL e Puitá INTA CL como padrão tolerante aos herbicidas imidazolinonas, e as cultivares BRS Pampa, BRS Querência, BRS Fronteira e BRS Atalanta, como padrão sensível. A variável inserção da primeira folha pode ser considerada uma variável apropriada para estudos, pois discrimina de maneira mais eficiente as diferentes respostas das constituições genéticas frente às doses utilizadas e aos períodos de desenvolvimento, podendo ser indicada para ser utilizada como marcador morfológico. A concentração de herbicida que possibilita melhor discriminação entre genótipos tolerantes e sensíveis é 25μg L-1, conforme metodologia descrita para esse bioensaio. Os resultados desse estudo mostram que os híbridos F2, resultantes de cruzamentos entre cultivares portadores do alelo de tolerância ao herbicida da classe das imidazolinonas e cultivares de arroz irrigado convencionais, são viáveis, possibilitando o estabelecimento de populações de arroz irrigado tolerantes ao herbicida, com maior capacidade de combater o arroz vermelho e com características de interesse agronômico.

Advancements in molecular sequencing have revealed unexpected cryptic genetic diversity and contrasting evolutionary histories within genes and between genomes of many organisms; often in disagreement with recognized taxonomy. Incongruent patterns between the mitochondrial and nuclear evolutionary history can have several plausible explanations, but widespread systematic conflict inevitably challenges our conceptions of species boundaries when there is discordance between coevolving and coinherited genomes. It is unknown to what degree mitonuclear conflict drives the process of divergence, or how ubiquitous these patterns are across the tree of life. To understand the evolutionary relevance of intergenomic discordance we must identify the conflicting patterns that exist in natural systems by generating robust estimates of the underlying species history, quantify support for alternative hypotheses of lineage formation, and describe patterns of genetic variation present in robust nuclear genomic datasets. Empirically testing correlations between mitonuclear genomic conflict and reduced gene flow at the organism level will contribute toward a better understanding of lineage boundaries and how intergenomic interactions shape the process of divergence. Mitochondrial introgression has been inferred in many salamander systems with limited perspective from nuclear sequence data. Within dusky salamanders (Desmognathus), these patterns have been observed between morphologically and geographically disparate populations. I sequenced regions throughout the nuclear genome to reconstruct species trees, performed population-level analyses testing concordance between the mitochondrial, nuclear datasets, and nuclear genes with mitochondrial functions with the expectation that coevolutionary interactions among genomes are more likely to manifest in these regions. I also estimated migration rates between populations that may have experienced historical mitochondrial introgression to evaluate phylogeographic patterns. Using these data we definitively reject species models in which genetic boundaries are based solely on mitochondrial data, favoring geographic models instead. Furthermore, analyses soundly reject current taxonomic models based on morphological characteristics, suggesting there is greater lineage diversity than is currently recognized. I also used empirical assays of pre-zygotic reproductive mating behavior within and among populations containing diverse mitochondrial lineages to test metrics of reproductive isolation, and to determine if introgression shapes the evolution of complex traits directly influencing rates of divergence. These results may explain incongruent patterns observed between the mitochondrial and nuclear data as a function of inheritance and population dynamics rather than directly functioning to suppress nuclear gene flow. This research builds upon recent studies suggesting that speciation is a highly complex and often non-bifurcating process in which introgression can have a profound and lasting signature on the nuclear evolutionary history. Mechanisms responsible for divergence with gene flow challenge evolutionary biologists to reevaluate our notions and definitions of species boundaries to accommodate seemingly conflicted genomic patterns within and between genomes.

Genetic composition of hybrid zones often reflects geographical and ecological gradients. Hybrid zone of Arabidopsis lyrata and A. arenosa in Central Europe can be convenient model system for testing such hypothesis. These are well circumscribed but still interfertile, and their offspring is fully fertile. Besides repeated hybridisation events, the current state is complicated by the autopolyploidisation events of one of the parents, namely A. lyrata, which is present in the area studied both as diploid and tetraploid. This hybrid zone was already described in previous publications, which showed certain gradient of introgression. Moreover, the area of the hybrid zone represents a transition between Alpine and Pannonian climate along an altitudinal gradient leading from the Prealps to the lowland Wienerwald. The current thesis is the as yet most detailed study of this hybrid zone both in respect of number of studied populations and the amount of data acquired using the methods of RAD Sequencing, multivariate morphometrics and flow cytometry. The analysis of genetic data showed a gradient of introgression, where parental populations are placed at opposite ends, whereas genetically intermediate hybrids are placed in its centre. Analysis of the genome size showed an additional gradient, where hybrids...

6 Summary Wetland plants share several common characters, such as clonality, wind pollination and self-compatibility that facilitate hybridization, especially in complexes of closely related taxa. In this thesis, a Sparganium erectum complex of four subspecies and 14 species of the genus Bolboschoenus were investigated to detect hybridization and verify the origins of putative hybrids. The first part of the thesis is dedicated to an introduction to hybridization, a process of great evolutionary impact, and its several general consequences, which are broadly discussed with numerous examples. In addition, an introduction to the studied taxa is provided as well as the main results of three papers that are presented and discussed herein. The second part of the thesis consists of three papers on hybridization within the Sparganium erectum aggregate (Paper I) and in the genus Bolboschoenus (Paper II, central European species; Paper III all 14 species worldwide). AFLP molecular marker analysis, sequencing of nuclear and chloroplast DNA, and genome size and morphometric analyses were applied to elucidate the genetic relationships among taxa and to confirm the suitability of morphometric characters for taxa and hybrid delimitation. The results clearly present the differentiation of individual taxa and their stable...

6 ABSTRACT Bird song is a sexually selected trait that is crucial for mate choice and for maintenance of pre-mating reproductive barriers. Secondary contact of closely related and partially reproductively isolated song bird species may result in changes in their songs; these can either diverge and strengthen the reproductive barrier between the two species, or converge and contribute to mixing of their gene pools. The Thrush Nightingale (Luscinia luscinia) and its congener Common Nightingale (L. megarhynchos) may serve as model species suitable for studying these phenomena. In their secondary contact zone, an interspecific hybridization has been documented, as well as convergence of songs of Thrush Nightingales caused by copying of heterospecific songs. Such copying may be a result of erroneous learning of species- specific songs or by genetic introgression. We tested these hypotheses by simultaneous analyses of DNA and song recordings of both species from allopatry (Czech Republic and northeastern Poland) and sympatry (central Poland). Comparisons between our recordings and a catalogue of songs recorded in a Common Nightingale population from allopatry (Germany) confirmed that most of Thrush Nightingale males from the sympatric region were 'mixed singers' that use Common Nightingale phrases in their...

Phylogenetics is crucial in the study of evolutionary processes and the determination of appropriate conservation units, and often these efforts are complicated by hybridization and introgression. Aliciella subsection Subnuda consists of seven species of herbaceous plants occurring in Utah and the Four Corners region of North America. Previous molecular and morphological work left relationships in the subsection unresolved. Here, we use comparative DNA sequencing of ITS and cpDNA regions and RAD-seq data to clarify phylogenetic relationships and examine the role of hybridization in the subsection. We construct haplotype and nucleotype networks from the cpDNA and ITS sequence matrices and compare nuclear and chloroplast phylogenies to identify multiple putative chloroplast capture events. The RAD-seq maximum likelihood phylogeny robustly resolves relationships between six clades, supportive of merging of two species. We employ STRUCTURE and HyDe on the RAD-seq data to evaluate the influence of hybridization within the subsection. The HyDe results provide evidence of hybridization among and between all species in the subsection. Our study robustly resolves relationships in Aliciella subsection Subnuda and provides a framework for discussing its speciation despite a history of hybridization and introgression.

The ability to recover ancient DNA from skeletal material has completely transformed the field of evolutionary anthropology, making it possible to sequence the genomes of individuals who lived thousands of years ago. In addition to solving the long-standing question of admixture between neanderthals and modern humans and uncovering evidence of dramatic migration events throughout human history, ancient DNA has become an important resource for understanding many facets of natural selection, which is often challenging using today's genetic variation alone. Chapter 1 examines the dynamics of negative selection acting against Neanderthal ancestry in modern humans and establishes its limits over long evolutionary timescales. It shows that the previously reported monotonic decline in Neanderthal ancestry over the last fifty-thousand years, thought to be a result of negative selection, is a statistical artifact caused by incorrect assumptions about modern human demographic history, in particular the gene flow between Africa and West Eurasia. Re-estimation of the Neanderthal ancestry proportions over time using a more robust statistic no longer infers a significant decline in Neanderthal ancestry, which is proven to be consistent with simulations of negative selection across a wide range of selection parameters. Chapter 2 describes the first comprehensive analysis of the Y chromosomes of neanderthals and Denisovans. Although Neanderthals and Denisovans form a sister group to modern humans at the autosomal level, Neanderthal Y chromosomes are more similar to modern humans than Denisovan Y chromosomes. In fact, the Y chromosomes of late neanderthals represent a lineage introgressed from an early modern human population. This introgression, which occurred hundreds of thousands of years, completely replaced the Y chromosomes of early neanderthals, reflecting the observations made from mitochondrial DNA. Population genetic simulations of selection and introgression show that although a complete replacement of both mitochondrial DNA and Y chromosomes is unlikely under neutrality, higher deleterious burden of neanderthals predicts a rapid replacement of both loci by their modern human counterparts. Finally, Chapter 3 presents an R package admixer, designed to facilitate the programming of automated, fully reproducible population genetic analyses using ADMIXTOOLS, a suite of programs widely used in ancient DNA research.

京都大学 / 0048 / 新制・課程博士 / 博士(人間・環境学) / 甲第19086号 / 人博第739号 / 新制||人||177(附属図書館) / 26||人博||739(吉田南総合図書館) / 32037 / 京都大学大学院人間・環境学研究科相関環境学専攻 / (主査)教授 瀬戸口 浩彰, 教授 加藤 眞, 教授 市岡 孝朗 / 学位規則第4条第1項該当 / Doctor of Human and Environmental Studies / Kyoto University / DGAM

Once thought to be an evolutionary dead-end, hybridization is now being detected in genomes across kingdoms, perhaps even playing an integral role in evolution. In chapter 1, I investigated the potential influences of hybridization on the evolution of a group of vagrant, asexual species in the Rhizoplaca melanophthalma species group. I sequenced the mitochondrial and nuclear genomes of 55 specimens and found well-supported nuclear phylogenies of both datasets. There were, however, multiple instances of discordance between the mitochondrial and nuclear trees, which can be caused by hybridization. PhyloNet and ABBA-BABA also detected widespread hybridization among this group. In chapter 2, I shifted to the Holarctic clade of lichen-forming fungi in Xanthoparmelia to characterize gene tree conflict and investigate the potential for hybrization. Here, I used three different tests for hybridization that account for incomplete lineage sorting "ABBA-BABA, PhyloNet, and SplitsTree" as well as PhyParts to characterize gene tree conflict. Like the Rhizoplaca species group, widespread hybridization was detected in the Holarctic clade despite robust phylogenies. My research underscores the value of investigating hybridization when studying species boundaries and evolutionary history.