At least since the Neolithic, humans have largely lived in networks of small, traditional communities. Often socially isolated, these groups evolved distinct languages and cultures over microgeographic scales of just tens of kilometers. Population genetic theory tells us that genetic drift should act quickly in such isolated groups, thus raising the question: do networks of small human communitiesmaintain levels of genetic diversity over microgeographic scales? This question can no longer be asked in most parts of the world, which have been heavily impacted by historical events that make traditional society structures the exception. However, such studies remain possible in parts of Island Southeast Asia and Oceania, where traditional ways of life are still practiced. We captured genome-wide genetic data, together with linguistic records, for a case-study system-eight villages distributed across Sumba, a small, remote island in eastern Indonesia. More than 4,000 years after these communities were established during the Neolithic period, most speak different languages and can be distinguished genetically. Yet their nuclear diversity is not reduced, instead being comparable to other, evenmuch larger, regional groups. Modeling reveals a separation of time scales: while languages and culture can evolve quickly, creating social barriers, sporadic migration averaged over many generations is sufficient to keep villages linked genetically. This loosely-connected network structure, once the global norm and still extant on Sumba today, provides a living proxy to explore fine-scale genome dynamics in the sort of small traditional communities within which the most recent episodes of human evolution occurred.

Speciation, the evolution of morphologically, behaviorally and/or ecologically distinct lineages from a common ancestor, is the fundamental process generating biodiversity. The rapidly developing field of speciation genomics is challenging traditional views of speciation as a gradual, genome-wide process, and highlighting the role of divergent natural selection in the speciation process. This study investigates morphological evolution and the genomic architecture of speciation in a clade of 12 "munias" in the genus Lonchura, one of the most extraordinary cases of recent and rapid diversification in birds. With a diversity of plumage patterns and replicate examples of closely related species living in sympatry, this group is ideally suited
for addressing fundamental questions about the genomics of speciation. In this study, I (1) test for evidence of character displacement between sympatric species using quantitative measurements of plumage coloration and morphology; (2) examine the structure of genome-wide variation using ddRAD-seq (double-digest Restriction Site Associated DNA sequencing); and (3) investigate the genomic structure of divergence using whole-genome sequencing. I find some evidence for character displacement, particularly in morphometrics and crown coloration. There is also a trend, however, for sympatric species to be more similar in coloration than allopatric species, particularly those that have come into contact more recently. Analysis of 7,043 ddRAD-seq loci reveals evidence of introgression among sympatric populations, with overall genomic variation corresponding more closely to geography than species identity. There is also substantial heterogeneity in genetic structure among mitochondrial, autosomal, and Z-linked markers. Finally, whole-genome sequencing reveals low overall genomic divergence while pinpointing "islands of differentiation" that exhibit elevated divergence between species. Two of these islands overlap genes known to be associated with coloration—Agouti signaling protein (ASIP) and Kit ligand (KITLG)—and allelic variation at these genes is associated with phenotypic traits. I also find evidence of a ~26 million base pair inversion on the Z chromosome, which groups the focal species differently than genome-wide variation. A strongly mosaic pattern of population structure among genomic regions supports a genic view of speciation, in which a small fraction of the genome is involved in the initial divergence of species.

京都大学 / 0048 / 新制・課程博士 / 博士(人間・環境学) / 甲第20459号 / 人博第809号 / 新制||人||194(附属図書館) / 28||人博||809(吉田南総合図書館) / 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

Phylogenetics is transitioning from a history of deep-time analyses with few genes to a future of full-genome data that allows species-level resolutions at deep and shallow time scales. Accompanying this transition is a new focus on demographic parameters like ancestral population sizes and gene flow events in addition to the bifurcating trees that are the cornerstone of the field. As access to more data has highlighted some shortcomings of traditional phylogenetic methods that do not account for the processes of recombination, selection, population size changes, and inter-species gene flow, the field is exploring new theory and methods to catch up with the data. My thesis focuses on signals of demographic processes in genomic data. In exploring these processes, we attempt to avoid biases involved in simply extending old phylogenetic methods -- which have typically been applied to just a handful of genes -- to genomic datasets. Chapter 1 introduces a tool, ipcoal, for simulating genomic data on phylogenetic trees within a framework that includes recombination and the ability to specify effective population sizes, gene flow events, recombination maps, and differences in generation times. This tool enables, to varying degrees, all further chapters. Chapter 2 studies the effects of species tree demographic parameters on the resulting linkage among nearby local genealogies, including implications for gene tree and species tree inference. Chapter 3 examines turnover in local histories along the genome using a theoretical framework, the MS-SMC, which links topological heterogeneity along the genome to species tree model. Chapter 4 introduces simcat, a machine-learning method that uses genome-wide SNP data to infer admixture events on a phylogeny without relying on gene tree inference. This is an important step toward decreasing gene tree estimation error over deep evolutionary time scales. Behind the scenes, simcat uses ipcoal to train a machine learning model to map patterns in SNP data to the demographic scenarios that produced them. These chapters demonstrate new phylogenetic theory and methods for refining our ability to infer historical processes at phylogenetic scales, while also illuminating the importance of population-scale processes like gene flow and recombination for shaping genomes sampled in the present day.

No description available.

Despite a number of recent studies focused on the issue, patterns of stream insect dispersal in temperate streams of North America remain poorly understood. Movement of benthic invertebrates is notoriously difficult to measure directly using traditional means; however, genetic markers provide an ideal method for estimating stream insect dispersal. In this study, the control region of mitochondrial DNA was used to study gene flow and dispersal among populations of the stonefly <i>Peltoperla tarteri</i> in the Southern Appalachians. The control region of <i>P. tarteri</i> is approximately 1270 base pairs (bp) in length, 81% AT-rich, and contains variable numbers of a 74 bp tandem repeat containing the sequence motif "5'-GGGGGC-3". Many stream insects have long life cycles that result in the simultaneous existence of multiple cohorts throughout the larval development period. If larval development is fixed, genetic isolation among cohorts may confound genetic estimates of dispersal. Although larval head width data indicated that <i>P. tarteri</i> is semivoltine in southwestern Virginia, low levels of genetic differentiation among cohorts suggested that larval development of <i>P. tarteri</i> is not fixed and that some individuals complete development in one or three years rather than two. This 'cohort splitting' would result in individuals from distinct cohorts maturing at the same time and mating with one another. Such developmental plasticity may allow some individuals to avoid adverse environmental conditions. The extent and likely mechanism of dispersal was determined by comparing levels of population genetic differentiation within drainages to that among drainages. While there was no consistent relationship between genetic and geographic distance, genetic differentiation was generally high within and among drainages. Nested clade analysis indicates that historical fragmentation and range expansion coupled with contemporary gene flow explain the present day pattern of genetic variation in <i>P. tarteri.</i> In order for these historical patterns to have such a strong influence on present day genetic structure, both larval and adult dispersal must be restricted. However, the genetic data suggest that larval dispersal is more frequent than adult dispersal. / Ph. D.

From the agent-based, correlated random walk model presented, we observe the effects of varying the parameter values of maximum insect turning area, 𝛿max, density of trees, ω, maximum pollen carryover, 𝜅max, and probability of fertilization, P𝜅, on the distribution of pollen within a population of Cornus florida (flowering dogwood). We see that varying 𝛿max and 𝜅max changes the dispersal distance of pollen, which greatly affects many measures of connectivity. The clustering coefficient of fathers is maximized when 𝛿max is between 60° and 90°. Varying ω does not have a major effect on the clustering coefficient of fathers, but it does have a greater effect on other measures of genetic diversity. Lastly, we compare our simulations with randomly-placed trees with that of actual tree placement of C. florida at the VCU Rice Center, concluding that in order to truly understand how pollen is distributed within a specific ecosystem, specificity in describing tree locations is necessary.

The understanding of gene movement in plant species is critical to the management of both plant and animal species reliant on that plant. Pollen is the mechanism by which plants pass their genetic material from one generation to the next. Pollen dispersal studies have focused primarily on purely random diffusion processes, while this may be a good assumption for species pollinated mainly by abiotic means, such as wind, it is most likely an over simplification for species that are pollinated by biotic means, such as insects [3]. Correlated random walk (CRW) models are a model of animal movement [10] and have been successfully used to explore the movement of animals in varying ecological contexts [1]. An agent-based model (ABM) is developed to describe pollen movement via insects as a correlated random walk (CRW). This model is used to explore how insect path lengths and pollen distribution are affected by the varying turning angle and plant density.

A caracterização fenotípica representa uma temática clássica na biologia evolutiva e o modo como diferentes caracteres respondem aos processos evolutivos tem sido problemática frequente em estudos envolvendo as mais diversas espécies. O presente trabalho visou investigar justamente como determinado fenótipo se comporta mediante o fluxo gênico. Primeiramente, explorou-se a possibilidade de se identificar e distinguir a partir de análises de traços craniométricos indivíduos anteriormente separados quanto a cor em três grupos: brancos, negros e pardos. Em um segundo momento, testou-se se a morfologia craniana expressa por indivíduos classificados como pardos seria intermediária em comparação com a expressa por brancos e negros. As análises estatísticas uni e multivariadas empregadas sobre os diferentes bancos de dados (dados brutos, dados das parcelas masculina e feminina separadamente, dados corrigidos para tamanho e também corrigidos para normalidade) apontaram ser possível discriminar os indivíduos previamente classificados de acordo com a cor em brancos, negros e pardos. Estes últimos, por sua vez, apresentam morfologia intermediária entre os grupos considerados parentais. Tais resultados permitem inferir que traços craniométricos, além de bons marcadores para a compreensão das relações histórico-biológicas populacionais, também seguiram o esperado como resposta ao fluxo gênico para um modelo de genética aditiva clássica segundo o qual a população híbrida apresenta frequências médias entre as populações parentais. Apesar de cor da pele e morfologia craniana representarem fenótipos com diferentes histórias evolutivas, observou-se correlação entre os dois caracteres para esta amostra, evidenciando-se que ambos representaram bons marcadores de mistura entre populações / Phenotypic characterization is a classic theme in evolutionary biology. The way different characters respond to evolutionary processes has been a frequent issue in studies involving a diverse number of species. This study aimed to investigate how a particular phenotype behaves by gene flow. First, it was explored the possibility to use analysis of craniometric traits to identify and distinguish individuals previously sorted by color into three groups: white, black and brown. Secondly, it was tested whether the cranial morphology expressed by individuals classified as brown would be intermediate compared to that expressed by whites and blacks. The univariate and multivariate statistical analysis used for the different databases (raw databases, data from male and female portions separately, data ajusted regarding size factor and normality) pointed out to be possible to discriminate individuals previously classified as white, black and brown, the latter being presented as an intermediate morphology between the considered parental groups. These results indicate that craniometric traits, besides being good markers for understanding the historical-biological population relationships, also followed as expected in response to gene flow for a classic additive genetic model, in which the hybrid population has medium frequencies between parental populations. Although skin color and cranial morphology represent phenotypes with different evolutionary histories, it was observed a correlation between the two characters for this sample, indicating that both represent good markers for mixture between populations

Submitted by (ana.araujo@ufrpe.br) on 2017-02-21T16:20:25Z No. of bitstreams: 1 Romero de Lima Sousa.pdf: 670144 bytes, checksum: d35f2bc03e9baddbb24bad3b4dfd477e (MD5) / Made available in DSpace on 2017-02-21T16:20:25Z (GMT). No. of bitstreams: 1 Romero de Lima Sousa.pdf: 670144 bytes, checksum: d35f2bc03e9baddbb24bad3b4dfd477e (MD5) Previous issue date: 2010-02-22 / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / The Brazilian Northeast is the center of origin of cotton Gossypium mustelinum (Miers) Watt. This cotton has not been improved or exploited commercially, but there is evidence of their introgression into the genome of varieties of upland cotton G. hirsutum L. variety marie galante Hutch. When considering the loss of variability can be said that G. mustelinum, G. barbadense L. and G. hirsutum L. var. marie galante Hutch of extinction are very high, high and medium, respectively, requiring immediate efforts for their preservation. This study aims to determine whether there is competition between pollen G. mustelinum and herbaceous in relation to fertilization of wild species, as well as whether there are differences of competition in different proportions of pollen of these species. For both crossings were performed between the two species used the G. mustelinum mother as having been fertilized by pollen from: i) mixture of 50% G. mustelinum and 50% herbaceous ii) a mixture of 75% herbaceous and 25% G. mustelinum iii) a mixture of 25% herbaceous and 75% G. mustelinum iv) herbaceous v) G. mustelinum. The latter two were used as controls to determine the expression pattern of alleles in polyacrylamide gels and validate the crosses with mixed pollen. We obtained seeds from each cross. The molecular analysis determined the proportion of seeds from crosses inter-and intra-specific by genotyping with SSR markers of the type. The frequency of offspring in each proportion of pollen used in crosses were compared using statistical test, chi-square (x²), with expected frequencies of 50% of hybrid seeds and 50% of seeds derived from selfing, 75% of seeds hybrid and 25% of the seeds of self-fertilization, 25% seed and 75% hybrid seed selfing. Were pollinated between 10:42 Flowers in the crosses with mixed pollen. The average number of seeds obtained ranged between nine and 11. Comparing these values with the average number of seeds from the intersection with 100% of pollen of the respective species, it was found that there was little variation. There were no differences in fertility or crossability between the genotypes of G. mustelinum. The only male parent in crosses that did not get the seeds was C27, and this was possibly caused by physiological conditions unfavorable. Through the data can be seen that the higher the percentage of pollen from G. hirsutum, the greater tendency of hybrids between two species. Therefore the higher the percentage of pollen from G. mustelinum, the lower the amount of hybrids. After analyzing the results, the chi-square (x²), a 1% probability it was established that there was competition between pollen from wild species and cultivated at all levels studied. / O Nordeste brasileiro é o centro de origem do algodão Gossypium mustelinum (Miers) Watt. Esta espécie ainda não foi melhorado ou explorado comercialmente, entretanto há evidências de sua introgressão no genoma das variedades de algodoeiro herbáceo G. hirsutum L. variedade marie galante Hutch. Ao considerar a perda de variabilidade pode-se afirmar que G. mustelinum, G. barbadense L. e G. hirsutum L. variedade marie galante Hutch estão com risco de extinção muito alto, alto e médio, respectivamente, necessitando de esforços imediatos para sua preservação. Este trabalho tem por finalidade verificar se há competição de pólen entre G. mustelinum e herbáceo em relação à fertilização da espécie silvestre, bem como se há diferença de competição em diferentes proporções de polens das referidas espécies. Para tanto, foram realizados cruzamentos entre as duas espécies, utilizado o G. mustelinum como genitor feminino tendo sido fecundado por pólen de: i) mistura de 50% herbáceo e 50% de G. mustelinum; ii) mistura de 75% herbáceo e 25% de G. mustelinum; iii) mistura de 25% herbáceo e 75% de G. mustelinum; iv) herbáceo e v) G. mustelinum. Estes dois últimos foram utilizados como controle para saber o padrão da expressão dos alelos nos géis de poliacrilamida e validar os cruzamentos com misturas de pólen. Foram obtidas sementes provenientes de cada cruzamento. Na análise molecular foi determinada a proporção de sementes provenientes de cruzamentos inter e intraespecíficos por meio da genotipagem com marcadores do tipo SSR. A frequência de descendentes em cada proporção de pólen usada no cruzamento foi comparada por meio de teste estatístico do qui-quadrado (x²), com frequência esperada de: 50% de sementes híbridas e 50% de sementes oriundas de autofecundação; 75% de sementes hibridas e 25% de sementes de autofecundação; 25% de sementes hibridas e 75% de sementes de autofecundação. Foram polinizadas entre dez e 42 flores nos cruzamentos com mistura de pólen. O número médio de sementes obtidas variou entre nove e 11. Comparando-se tais valores com o número médio de sementes provenientes do cruzamento com 100% de pólen das respectivas espécies, verificou-se que houve pouca variação. Não foi verificada diferenças de fertilidade ou de cruzabilidade entre os genótipos de G. mustelinum. Os únicos genitores masculinos nos cruzamentos que não obtiveram sementes foram o C27 e Mac 01, fato este ocasionado possivelmente por condições fisiológicas desfavoráveis. Por intermédio dos dados pode-se constatar que quanto maior a porcentagem de pólen de G. hirsutum, maior tendência de híbridos entre as duas espécies. Consequentemente, quanto maior a porcentagem de pólen de G. mustelinum, menor a quantidade de híbridos. Após análise dos resultados obtidos pelo teste de qui-quadrado (x²), a 1% de probabilidade, foi possível constatar que houve competição entre pólen da espécie silvestre e cultivada em todos os níveis estudados.