Population structure can be defined as a difference in the frequencies of alleles among populations, and it is often caused by barriers to dispersal. I used mitochondrial DNA sequences to examine the population structure of two large, aquatic salamanders, Amphiuma means (the Two-Toed Amphiuma) and Siren lacertina (the Greater Siren), at two spatial scales in peninsular Florida. Both species appear to have similar life histories, including poor dry land dispersal capabilities, and I hypothesized that they would exhibit significant population structure at both broad and fine scales. Wetland loss and landscape fragmentation are certain to have caused decreases in abundance and even extirpation of local populations of both species. Understanding current levels of genetic diversity is important in conservation efforts, particularly if individuals must be translocated in the future. A portion of the cytochrome b gene was analyzed for 34 Amphiuma means and 21 Siren lacertina sequences. A neighbor-joining tree and haplotype network showed that A. means exhibited statistically significant population structure at the broad, but not the fine scale. The lack of structure at the fine scale was attributed to periodic flooding among drainage basins in the low-lying study area. The same analyses showed that S. lacertina did not exhibit statistically significant population structure at the broad scale (analyses were not conducted at the fine scale because of low sample size). The difference in broad-scale population structure between the two species is the result of a difference in gene flow, which in turn, can be the result of a difference in effective population size (Ne), female dispersal capability and/or behavior, chance of bait-bucket transfer, or biogeographic history. The best of these possible explanations seems to be a difference in biogeographic history. For the two sites from which both species were sampled, estimated population divergence date was 3.3-6.4 million years ago (mya) for A. means and 0.04-0.5 mya for S. lacertina. The large difference in estimated divergence dates suggests that S. lacertina colonized peninsular Florida from somewhere else following a glacial sea level rise or an interglacial sea level fall, at a time when A. means was already present in refugia within peninsular Florida. This is the first study to explicitly examine the population genetics of A. means and S. lacertina, and future studies should examine their population genetics range wide, to elucidate how gene flow and/or historical biogeography may have contributed to population structure elsewhere.

Population Genetics has led to countless numbers of fruitful studies of evolution, due to its abilities for prediction and description of the most important evolutionary processes such as mutation, genetic drift and selection. The field is still growing today, with new methods and models being developed to answer questions of evolutionary relevance and to lift the veil on the past of all life forms. In this thesis, I present a modest contribution to the growth of population genetics. I investigate different questions related to the dynamics of populations, with particular focus on studying human evolution. I derive an upper bound and a lower bound for FST, a classical measure of population differentiation, as functions of the homozygosity in each of the two studied populations, and apply the result to discuss observed differentiation levels between human populations. I introduce a new criterion, the Gain of Informativeness for Assignment, to help us decide whether two genetic markers should be combined into a haplotype marker and improve the assignment of individuals to a panel of reference populations. Applying the method on SNP data for French, German and Swiss individuals, I show how haplotypes can lead to better assignment results when they are supervised by GIA. I also derive the population size over time as a function of the densities of cumulative coalescent times, show the robustness of this result to the number of loci as well as the sample size, and together with a simple algorithm of gene-genealogy inference, apply the method on low recombining regions of the human genome for four worldwide populations. I recover previously observed population size shapes, as well as uncover an early divergence of the Yoruba population from the non-African populations, suggesting ancient population structure on the African continent prior to the Out-of-Africa event. Finally, I present a case study of human adaptation to an arsenic-rich environment.

Die Beziehung zwischen Genen und Verhalten ist in der Evolutionsbiologie von besonderem Interesse. Bestimmte Verhaltensweisen können die genetische Struktur natürlicher Populationen gestalten, dadurch deren genetische Diversität verändern und so ihr evolutives Schicksal beeinflussen. Abwanderung aus der Geburtsgruppe ist eine dieser Verhaltensweisen. Sie beeinflusst Genfluss, dessen Ausmaß die genetische Struktur von Populationen bestimmt. Paviane (Gattung Papio) sind ein besonders interessantes Forschungssystem um die Beziehung zwischen Verhalten und populationsgenetischer Struktur zu untersuchen. Die Evolution der Paviane wurde sowohl von historischem als auch gegenwärtigem Genfluss geprägt. Innerhalb dieser Gattung treten sowohl die überwiegende Abwanderung von Männchen als auch die überwiegende Abwanderung von Weibchen auf. Zudem wurde ihre gegenwärtige Verbreitung maßgeblich von Populationsausbreitung und –rückzug beeinflusst und es tritt häufig Genfluss zwischen verschiedenen Arten auf. In meiner Doktorarbeit untersuchte ich, wie verschiedene Abwanderungsmuster den Genfluss bei Pavianen beeinflussen. Damit hoffe ich zu einem besseren Ver-ständnis der Wechselbeziehung zwischen Verhaltensökologie und Genetik in natürlichen Populationen beizutragen. Ich fokussierte mich darauf, wie Unterschiede in den Sozialsystemen unterschiedlicher Pavianarten deren genetische Struktur beeinflussen. Die beobachteten Muster nutzte ich, um auf das geschlechtsspezifische Abwanderungsmuster bei Guineapavianen zu schließen, eine der am wenigsten untersuchten Pavianarten. Zudem untersuchte ich, wie sowohl historischer als auch gegenwärtiger Genfluss die genetische Struktur der Guineapaviane formten und ob es möglich ist von der Populationsausbreitung der Paviane Rückschlüsse auf die menschliche Evolutionsgeschichte zu ziehen. Um diese Fragen zu beantworten nutzte ich einen populationsgenetischen Ansatz, basierend auf im gesamten Verbreitungsgebiet gesammelten Kotproben, deren exakter geographischer Ursprung bekannt war. Ich analysierte sowohl autosomale Mikrosatelliten als auch Sequenzen der mitochondrialen Hypervariablen Region I. Meine Ergebnisse zeigen, dass die genetische Struktur der Guineapaviane am besten durch die überwiegende Abwanderung von Weibchen erklärt werden kann, sowohl in einem lokalen als auch im globalen Kontext. Weiblicher Genfluss führt zu einer hohen Diversität innerhalb von Populationen sowie einem Fehlen von genetisch-geographischer Struktur in mitochondrialer DNA. Nukleäre DNA hingegen zeigt eine starke globale geographische Struktur und Männchen sind im Vergleich zu Weibchen durch eine stärkere lokale Struktur gekennzeichnet. Dies entspricht den Vorhersagen für ein System, in welchem hauptsächlich Weibchen abwandern und Männchen in ihrer Geburtsgruppe verbleiben. Insgesamt scheint lokal begrenzte Abwanderung den wirksamen Genfluss auf eine Distanz unter 200 km zu beschränken, was zu einem starken Isolation-durch-Distanz Effekt und genetisch differenzierten Populationen führt. Anzeichen für Populationsausbreitung, die graduelle Struktur genetischer Variation, und mögliche Hinweise auf das “Allele-surfing” Phänomen, deuten auf eine historische westwärts gerichtete Ausbreitung von Guineapavianen hin. Introgressive Hybridisierung mit benachbarten Anubispavianen könnte genetische Muster im Bereich der Kontaktzone erklären, muss aber im Detail noch untersucht werden. Zusätzlich konnte ich zeigen, dass Mantelpaviane vermutlich im gleichen Zeitraum des Späten Pleistozäns von Afrika nach Arabien wanderten, wie Hypothesen für den modernen Menschen vorschlagen. Meine Studie ist die erste umfassende Analyse der genetischen Populationsstruktur der Guineapaviane und liefert Belege für die überwiegende Abwanderung von Weibchen in dieser Art. Dies untersützt die Ansicht, dass das Sozialsystem der Guineapaviane einige vergleichbare Merkmale zum System der Mantelpaviane aufweist und deutet somit darauf hin, dass während der Evolution dieser beiden Arten besondere evolutionäre Drücke gewirkt haben, die sie von allen anderen Pavianarten abgrenzen. In Kombination mit dem starken Einfluss von Populationsausbreitungen auf ihre Verbreitung und genetische Diversität, bekräftigt meine Arbeit Paviane als interssanten analogen Modellorganismus, der helfen kann, die Prozesse die während der Evolution des Menschen maßgeblich waren, aufzuklären.

Broad whitefish, Coregonus nasus, is an important subsistence fish species in Arctic North America, yet virtually nothing is known regarding the genetic population structure of Nearctic populations of this species. In this thesis, microsatellite DNA variation was assayed among 1213 broad whitefish from 47 localities throughout North America, with emphasis on the Mackenzie River system, Northwest Territories. Specifically, I examined geographic variation in allele frequencies to assess how historical factors (Pleistocene glaciations) have shaped the current structuring of genetic variability and population differentiation. Microsatellite data was also used to resolve the relative contributions of broad whitefish populations to subsistence fisheries in the Mackenzie River system. Overall, broad whitefish exhibit relatively high intrapopulation microsatellite variation (average 12.29 alleles/locus, average HE = 0.58) and there were declines in these measures of genetic diversity with distance from putative refugia suggesting historical factors, namely post-glacial dispersal, have influenced current microsatellite variation. Interpopulation divergence was low (overall FST = 0.07), but the main regions assayed in this study (Russia, Alaska, Mackenzie River and Travaillant Lake systems) are genetically differentiated. Strong isolation-by-distance among samples was resolved when including only those populations occupying former Beringia, but not when assaying those at the periphery of the range in the Mackenzie River system, suggesting that broad whitefish in the Mackenzie system have not occupied the region long enough since their invasion post-glacially to have approached equilibrium between gene flow and drift. Mixture analysis indicated that most fish from the lower Mackenzie River subsistence fishery originated from the Peel River, highlighting the importance of this tributary. Additionally the mixture analysis provides evidence for a putative riverine life history form in the Mackenzie River. My results indicate that glaciation and post-glacial colonization have been important in shaping the current genetic population structure of North American broad whitefish. They also illustrate the utility of microsatellite DNA to delineate population structure and patterns of genetic diversity in recently founded populations in addition to resolving contributions to fisheries. My data also support the hypothesis that there are several designatable units of conservation among broad whitefish populations and that management strategies should be implemented accordingly.

Invaziniai augalai – tai sparčiai plintantys augalai. Jie įsikuria įvairiose buveinėse, jas smarkiai pakeičia arba net visai sunaikina. Vienas iš aplinkai pavojingų augalų laikomas gausialapis lubinas. Jis yra įtrauktas į Lietuvos augalų sąrašą, kuriuos reikia išnaikinti. Todėl šito augalo populiacijų tyrimai yra labai svarbus. Darbo tikslas – nustatyti gausialapio lubino (Lupinus polyphyllus) populiacijų demografinę sudėtį ir ištirti dauginimąsi skirtingomis ekologinėmis sąlygomis. Tyrimai atlikti 2008 ir 2010 metais. Kiekvienoje populiacijoje tyrimams 2008 metais buvo parinkta po du laukus. Tyrimams buvo rinkti gausialapio lubino individų šaknys ir įvertinti jų antžeminių dalių rodikliai. Laboratorijoje buvo atlikti šaknų kaklelio herbochronologiniai tyrimai. Tyrimams 2010 metais gausialapio lubino populiacijos buvo pasirinktos dvi vietos iš tų kurios buvo tirtos 2008 metais. Kiekvienoje populiacijoje buvo pasirinkta po 30 gausialapio lubino kerų, iš to kero pasirinkta po vieną žydinti stiebą. Tyrimo metu buvo įvertinti kiekvieno žiedyno parametrai. Tyrimo metu nustatyta, kad visos tirtos gausialapio lubino populiacijos nėra labai tankios. Pagal amžiaus grupes visos tirtos populiacijos turėjo ir generatyvinių, ir vegetatyvinių gausialapio lubino individų ir jų skaičius skirtingose populiacijose buvo įvairus. Pagal daugumą morfologinių generatyvinių ir vegetatyvinių individų požymių visos keturios populiacijos skiriasi nedaug. Pagal amžių tirtos populiacijos yra skirtingos... [toliau žr. visą tekstą] / Invasion plants are widely spread plants. They grow in different places, they are changed very much or even annihilated entirely. One of the most dangerous plants for environment is washington lupin. It is included in Lithuania plants list, which should be annihilated. Therefore investigations of this plant populiations are very important. The aim of the work is to determine demographic composition of populiations of washington lupin (Lupinus polyphyllus) and to investigate its reproduction in different ecological conditions. Investigations were made in 2008 and 2010 years. For each populiation of 2008 year investigations two fields were chosen. For investigations individuals roots of washington lupin were chosen and their overground parts readings were taken. Roots necks herbochronological investigations were made in laboratory. For 2010 year investigations of washington lupin populations, two places frons earlier investigated in 2008 year places, were chosen. In each population 30 bushes of washington lupin were chosen, from this bush one blooming stem was chosen. While investigating each floscule parameters were taken. While investigating it was ascertained that all investigated washington lupin populations were not very thick. As far as age group is concerned, all investigated populations ha generative and vegetative washington lupin individuals and their quantity in different populations were different. By majority of morphological generative and vegetative individuals... [to full text]

The cotton fleahopper, Pseudatomoscelis seriatus (Reuter) is a widely distributed insect across the United States. Although, it feeds on several native wild hosts, its agricultural importance lies as an economic pest of cotton in several states in the southern United States. No studies have addressed intraspecific genetic and phenotypic variation of this insect pest at a large geographic scale. I examined genetic variation among cotton fleahopper populations associated with cotton in different geographic locations across the southern United States (Chapter II). Using dominant, neutral, nuclear molecular markers (AFLP, amplified fragment length polymorphism) and mitochondrial DNA sequences, I found that overall genetic differentiation among different geographic populations, collected from cotton in eleven cotton growing states, was low but significant. AFLP revealed the presence of three regional groups representing western (Arizona), central (Texas, Oklahoma, Arkansas, Louisiana, Mississippi and Alabama), and eastern (Florida, Georgia, South Carolina and North Carolina) populations. I examined if there were distinct lineages of cotton fleahoppers associated with three of its host plant species: cotton (Gossypium hirsutum), horsemint (Monarda punctata) and woolly croton (Croton capitatus) in five different locations of Texas by using AFLP markers (Chapter III). I found two distinct host-associated lineages at three locations and local panmixia in the other two locations. I tested if host preference of cotton fleahoppers were affected by geographic variation and prior experience. Conducting choice tests with a Y-tube olfactometer, I found that host preference in cotton fleahoppers for horsemint (one of its native host plants) is conserved and unaffected by individual?s prior experience with cotton (Chapter IV). Finally, I explored the role of host-plant species in morphological differentiation of the cotton fleahopper in two locations that differ in presence of distinct host-associated lineages. Using a geometric-morphometric approach, I detected significant effect of host plant and geography on body morphology and wing shape of cotton fleahopper populations (Chapter V). Length of antenna and rostrum were two important traits associated with morphological divergence of cotton and horsemint associated insect populations. Cotton associated individuals had relatively longer antenna and rostrum compared to individuals associated with horsemint.

The goal of this study was to examine several aspects of the population genetics and population biology of the Nigeria-Cameroon chimpanzee at seven sampling locations in the south of Taraba State, Nigeria. Three of the sampling locations are within GGNP and two are situated just outside the southern boundary of GGNP. The final two sampling locations are found within Ngel Nyaki forest reserve, at each of the two forest fragments inside the reserve. Ngel Nyaki forest reserve was the focus of the study and the principal goal was to 16 determine if the community of chimpanzees at Ngel Nyaki forest reserve has become isolated from the chimpanzees at GGNP using microsatellite loci extracted from non-invasive sources of DNA. In Chapter two, the methods used to extract and amplify the DNA and the protocols used to confirm the genotypes are outlined. Chapter three examines the population structure of the chimpanzees among the regions sampled in this study, particularly addressing the question as to whether the chimpanzees at Ngel Nyaki forest reserve are isolated from the chimpanzees at GGNP. Chapter four investigates patterns of sex biased dispersal in the Nigeria-Cameroon chimpanzee. In Chapter five, population viability analysis is used to determine the fate of the chimpanzees at Ngel Nyaki forest reserve under a range of management scenarios. Chapter six summarizes the conclusions of the study and presents a conservation strategy to ensure the viability of the population of chimpanzees at Ngel Nyaki forest reserve.

Plant-herbivore interactions are among the most common of ecological interactions. It is therefore not surprising that plants have evolved multiple mechanisms to defend themselves, using both constitutive chemical and physical barriers and by induced responses which are only expressed after herbivory has occurred. Herbivores, on the other hand, respond to these plant defenses by evolving counter-adaptations which makes defenses less effective or even useless. Adaptation can occur at different geographical scales, with varying coevolutionary interactions across a spatially heterogenous landscape. By looking at the underlying genes responsible for these defensive traits and herbivore related phenotypic traits, it is possible to investigate the coevolutionary history of these plant- herbivore interactions. Here I use molecular population genetic tools to investigate the evolutionary history of several inducible defense genes in European Aspen (Populus tremula) in Sweden. Two genes, belonging to the Polyphenol oxidase gene-family (PPO1 and PPO2), show skews in their site frequency spectrum together with patterns of diversity and divergence from an outgroup which correspond to signatures of adaptive evolution (Paper II). 71 single nucleotide polymorphisms (SNPs) from seven inducible defense genes (PPO1-PPO3, TI2-TI5) show elevated levels of population differentiation compared to control genes (genes not involved in plant defense), and 10 of these defense SNPs show strong signatures of natural selection (Paper III). These 71 defense SNPs also divides a sample of Swedish P. tremula trees into three distinct geographical groups, corresponding to a Southern, Central and Northern cluster, a patterns that is not present in control SNPs (Paper III). The same geographical pattern, with a distinct Northern cluster, is also observed in several phenotypic traits related to herbivory in our common garden in Sävar (Paper IV). These phenotypic traits show patterns of apparent local maladaptation of the herbivore community to the host population which could indicate the presence of “information coevolution” between plants and herbivores (Paper IV). 15 unique defense SNPs also show significant associations to eight phenotypic traits but the causal effects of these SNP associations may be confounded by the geographic structure found in both the underlying genes and in the phenotypic traits. The co-occurrence of population structure in both defense genes and herbivore community traits may be the result from historical events during the post-glacial recolonization of Sweden. / Interaktioner mellan växter och herbivorer är bland de vanligaste ekologiska interaktionerna och det är därför inte förvånande att växter har utvecklat flera olika mekanismer för att försvara sig. Dessa försvarsmekanismer består både av konstitutiva kemiska och fysiska barriärer så väl som inducerade försvar som bara är uttryckta efter att en växt har blivit skadad genom betning. Herbivorerna å sin sida svarar på dessa försvar genom att utveckla motanpassningar som gör växternas försvar mindre effektiva eller till och med verkningslösa. Dessa anpassningar kan ske över olika geografiska skalor beroende på om de samevolutionära interaktionerna varierar i ett rumsligt heterogent landskap. Genom att studera de underliggande gener som kontrollerar dessa försvarsegenskaper tillsammans med herbivorrelaterade fenotypiska egenskaper är det möjligt att undersöka den samevolutionära historien av interaktionerna mellan växter och herbivorer. Här använder jag mig av molekylärpopulationsgenetiska verktyg för att undersöka den evolutionära historien i flera inducerade försvarsgener hos asp (Populus tremula) i Sverige. Två gener, som tillhör genfamiljen Polyphenol-oxidaser (PPO1 och PPO2), uppvisar ett frekvensmönster som man förväntar sig vid positiv selektion. Detta mönster kan också ses i dessa geners diversitet samt i divergens från en utgrupp (Uppsats II). 71 ”single nucleotide polymorphisms” (SNPar) från 7 inducerade försvarsgener (PPO1-PPO3, TI2-TI5) visar förhöjda nivåer av populationsdifferentiering jämfört med kontrollgener (gener som inte är involverade i trädens försvar), och 10 av dessa försvars-SNPar visar även tecken på naturlig selektion (Uppsats III). Dessa 71 försvars-SNPar delar in ett urval av svenska aspar i tre distinkta geografiska grupper som beskriver ett sydligt, centralt och nordligt kluster som inte förekommer hos kontroll-SNPar (Uppsats III). Samma geografiska mönster, med ett distinkt nordligt kluster, återfinns däremot i ett antal fenotypiska egenskaper som är relaterade till herbivori i ett odlingsförsök utanför Sävar (Uppsats IV). Dessa fenotypiska egenskaper visar tecken på lokal felanpassning hos herbivorsamhället till den lokala värdpopulationen, vilket kan indikera förekomsten av ett ”samevolutionärt informationsutbyte” mellan växter och herbivorer (Uppsats IV). 15 unika försvars-SNPar påvisar också signifikanta associationer med 8 olika fenotypiska egenskaper, men om dessa har en verklig effekt eller inte är svårt att säga på grund av den geografiska strukturen som förekommer både hos de underliggande generna och hos de fenotypiska egenskaperna. Att denna populationsstruktur förekommer hos både försvarsgener och egenskaper som är förknippade med herbivorsamhället kan däremot vara ett resultat av historiska händelser som skett under aspens post-glaciala återkolonisation av Sverige.

The study of genetic variation in populations is of great interest for the study of the evolutionary history of humans and other species. Improvement in sequencing technology has resulted in the availability of many large datasets of genetic data. Computational methods have therefore become quite important in analyzing these data. Two important problems that have been studied using genetic data are population stratification (modeling individual ancestry with respect to ancestral populations) and genetic association (finding genetic polymorphisms that affect a trait). In this thesis, we develop methods to improve our understanding of these two problems. For the population stratification problem, we develop hierarchical Bayesian models that incorporate the evolutionary processes that are known to affect genetic variation. By developing mStruct, we show that modeling more evolutionary processes improves the accuracy of the recovered population structure. We demonstrate how nonparametric Bayesian processes can be used to address the question of choosing the optimal number of ancestral populations that describe the genetic diversity of a given sample of individuals. We also examine how sampling bias in genotyping study design can affect results of population structure analysis and propose a probabilistic framework for modeling and correcting sample selection bias. Genome-wide association studies (GWAS) have vastly improved our understanding of many diseases. However, such studies have failed to uncover much of the variation responsible for a number of common multi-factorial diseases and complex traits. We show how artificial selection experiments on model organisms can be used to better understand the nature of genetic associations. We demonstrate using simulations that using data from artificial selection experiments improves the performance of conventional methods of performing association. We also validate our approach using semi-simulated data from an artificial selection experiment on Drosophila Melanogaster.

Wind-pollinated plants often have little genetic structure owing to high gene flow. However, sex chromosomes evolution promotes divergence, potentially leading to population subdivision. Rumex hastatulus (Polygonaceae) is a wind-pollinated, dioecious coloniser of open disturbed land with two sex chromosome races (SCRs), which occupy different parts of the species’ range in the southern USA. My thesis investigated phenotypic and genetic differentiation between the SCRs, based on a study of 28 populations sampled throughout the range. A glasshouse experiment demonstrated significant differentiation between the SCRs in several life-history traits, several of which exhibited clinal variation. Analysis of population genetic structure, based on 13 nuclear loci, revealed two distinct clusters corresponding to the two SCRs, with an estimated origin of the North Carolina SCR from the Texas SCR between ~5000–15000 generations ago. My results indicate that the SCRs have developed a moderate degree of phenotypic and genetic differentiation despite ongoing gene flow.