Molecular genetic investigation of the Neolithic population history in the western Carpathian Basin

Der Fokus dieser Dissertation ist die populationsgenetische Analyse der neolithischen Bevölkerungswechsel in den 6.-5. Jahrtausende vor Christus, die im westlichen Karpatenbecken stattfanden. Die Zielsetzung der Studie war, mittels der Analyse von mitochondrialer und Y-chromosomaler aDNA, den Genpool der sechs neolithischen und kupferzeitlichen Populationen zu untersuchen und die daraus resultierenden Ergebnisse mit anderen prähistorischen und modernen genetischen Daten zu vergleichen.rnInsgesamt wurden 323 Individuen aus 32 ungarischen, kroatischen und slowakischen Fundplätzen beprobt und bearbeitet in den archäogenetischen Laboren der Johannes Gutenberg-Universität in Mainz. Die DNA Ergebnisse wurden mit verschiedenen populationsgenetischen Methoden ausgewertet. Vergleichsdaten von prähistorischen und modernen eurasiatischen Populationen wurden dazu gesammelt.rnDie HVS-I Region der mitochondrialen DNA konnten bei 256 Individuen reproduziert und authentifiziert werden (mit einer Erfolgsrate von 85.9%). Die Typisierung der HVS-II Region war in 80 Fällen erfolgreich. Testend alle gut erhaltene Proben, die Y-chromosomale Haplogruppe konnte in 33 männlichen Individuen typisiert werden.rnDie neolithischen, mitochondrialen Haplogruppen deuten auf eine hohe Variabilität des maternalen Genpools hin. Sowohl die mitochondrialen als auch die Y-chromosomalen Daten lassen Rückschlüsse auf eine nah-östliche bzw. südwestasiatische Herkunft der frühen Bauern zu. Die Starčevo- und linearbandkermaischen-Populationen in westlichem Karpatenbecken (letztere abgekürzt als LBKT) und die linearbandkermaischen-Population in Mitteleuropa (LBK) haben so starke genetische Ähnlichkeit, dass die Verbreitung der LBK nach Mitteleuropa mit vorangegangenen Wanderungsereignissen zu erklären ist. Die Transdanubische aDNA Daten zeigen hohe Affinität zu den publizierten prähistorischen aDNA Datensätzen von Mitteleuropa aus den 6.-4. Jahrtausende vor Chr. Die maternal-genetische Variabilität der Starčevo-Population konnte auch innerhalb der nachfolgenden Populationen Transdanubiens festgestellt werden. Nur kleinere Infiltrationen und Immigrationsereignissen konnten während der Vinča-, LBKT-, Sopot- und Balaton-Lasinja-Kultur in Transdanubien identifiziert werden. Zwischen den transdanubischen Regionen konnten mögliche genetische Unterschiede nur in der LBKT und in der Lengyel-Periode beobachtet werden, als sich die nördlichen Gruppen von den südlichen Populationen trennten. rnDie festgestellte Heterogenität der mtDNA in Zusammenhang mit der Y-chromosomalen Homogenität in den Starčevo- und LBK-Populationen, weisen auf patrilokale Residenzregeln und patrilineare Abstammungsregeln in den ersten Bauergemeinschaften hin. rnObwohl die hier präsentierten Daten einen großen Fortschritt in der Forschung von aDNA und Neolithikum des Karpatenbeckens und Mitteleuropas bedeuten, werfen sie auch mehrere Fragen auf, deren Beantwortung durch zukünftige Genomforschungen erbracht werden könnte.

Phylogeography and population genetics of north European Atlantic salmon (Salmo salar L.)

Although abundant in the number of individuals, the Atlantic salmon may be considered as a threatened species in many areas of its native distribution range. Human activities such as building of power plant dams, offshore overfishing, pollution, clearing of riverbeds for timber floating and badly designed stocking regimes have diminished the distribution of Atlantic salmon. As a result of this, many of the historical populations both in Europe and northern America have gone extinct or are severely depressed. In fact, only 1% of Atlantic salmon existing today are of natural origin, the rest being farmed salmon. All of this has lead to a vast amount of research and many restoration programmes aiming to bring Atlantic salmon back to rivers from where it has vanished. However, many of the restoration programmes conducted thus far have been unsuccessful due to inadequate scientific research or lack of its implementation, highlighting the fact that more research is needed to fully understand the biology of this complex species. The White and Barents Seas in northwest Russia are among the last regions in Europe where Atlantic salmon populations are still stable, thus forming an important source of biodiversity for the entire European region. Salmon stocks from this area are also of immense economic and social importance for the local people in the form of fishing tourism. The main aim of this thesis was to elucidate the post-glacial history and population genetic structure of north European and particularly northwest Russian Atlantic salmon, both of which are aspects of great importance for the management and conservation of the species. Throughout the whole thesis, these populations were studied by utilizing microsatellites as the main molecular tool. One of the most important discoveries of the thesis was the division of Atlantic salmon from the White and Barents Seas into four separate clusters, which has not been observed in previous studies employing nuclear markers although is supported by mtDNA studies. Populations from the western Barents Sea clustered together with the northeast Atlantic populations into a clearly distinguishable group while populations from the White Sea and eastern Barents Sea were separated into three additional groups. This has important conservation implications as this thesis clearly indicates that conservation of populations from all of the observed clusters is warranted in order to conserve as much of the genetic diversity as possible in this area. The thesis also demonstrates how differences in population life histories within a species, migratory behaviour in this case, and in their phylogeographic origin affect the genetic characteristics of populations, namely diversity and divergence levels. The anadromous populations from the Atlantic Ocean, White Sea and Barents Sea possessed higher levels of genetic diversity than the anadromous populations form the Baltic Sea basin. Among the non-anadromous populations the result was the opposite: the Baltic freshwater populations were more variable. This emphasises the importance of taking the life history of a population into consideration when developing conservation strategies: due to the limited possibilities for new genetic diversity to be generated via gene flow, it is expected that freshwater Atlantic salmon populations would be more vulnerable to extinction following a population crash and thus deserve a high conservation status. In the last chapter of this thesis immune relevant marker loci were developed and screened for signatures of natural selection along with loci linked to genes with other functions or no function at all. Also, a novel landscape genomics method, which combines environmental information with molecular data, was employed to investigate whether immune relevant markers displayed significant correlations to various environmental variables more frequently than other loci. Indications of stronger selection pressure among immune-relevant loci compared to non-immune relevant EST-linked loci was found but further studies are needed to evaluate whether it is a common phenomenon in Atlantic salmon.

Pyruvate kinase and glucose-6-phosphate dehydrogenase deficies and their association with malaria - population genetics and proteomic studies

A malária é reconhecida como uma das principais forças selectivas a actuar na história recente no genoma humano. Inúmeros polimorfismos genéticos têm sido descritos como protectores contra a gravidade da malária, como o alelo HbS (designado de traço falciforme) e o alelo G6PD A- (associado à deficiência de G6PD). Mais recentemente, também a deficiência de PK foi associada com a protecção contra a malária. Evidências desta associação foram obtidas em estudos com modelos de roedor e estudos in vitro utilizando GV humanos deficientes em PK. Até à data, não foram obtidos dados em populações humanas que revelem esta associação: ainda não foi identificada uma variante de PK com uma prevalência elevada em regiões endémicas de malária e não foram identificadas marcas de selecção na região do gene que codifica para a PK (gene PKLR). Além disso, os mecanismos subjacentes à protecção contra a malária por deficiências enzimáticas dos GV não estão bem esclarecidos. Assim, os objectivos do presente estudo foram: investigar os polimorfismos genéticos humanos com associação com a malária em Cabo Verde; pesquisar marcas de selecção da malária na região do gene PKLR em populações Africanas; determinar a frequência da deficiência em PK e identificar uma eventual variante da enzima que possa estar sob selecção positiva em regiões endémicas de malária; avaliar o efeito das duas deficiências enzimáticas (PK e G6PD) na invasão e maturação do parasita em culturas in vitro de Plasmodium usando GV normais e deficientes; e analisar o perfil proteómico de GV infectados e não infectados, normais e com deficiência (em PK e G6PD), bem como de parasitas isolados de GV tanto deficientes como normais. Em Cabo Verde (área epidémica), não foram identificadas marcas de selecção pela malária, através da análise dos vários polimorfismos. No entanto, quando a análise foi realizada em dois países endémicos (Angola e Moçambique), foram detectadas várias marcas de selecção: a genotipagem de microssatélites (STRs) e polimorfismos de base única (SNPs) localizados na vizinhança do gene PKLR revelou uma diferenciação consideravelmente maior entre as populações Africana e Europeia (Portuguesa), do que a diferenciação determinada aquando da utilização de marcadores genéticos neutros. Além disso, uma região genómica de maior amplitude apresentou um Desequilíbrio de Ligação (LD) significativo no grupo de malária não grave (e não no grupo de malária grave), sugerindo que a malária poderá estar a exercer pressão selectiva sobre a região do genoma humano que envolve o gene PKLR. No estudo que incidiu na determinação da prevalência da deficiência de PK no continente Africano (realizado em Moçambique), esta revelou-se elevada - 4,1% - sendo o valor mais elevado descrito até ao momento a nível mundial para esta enzimopatia. Na pesquisa de mutações que pudessem estar na causa deste fenótipo (baixa actividade de PK), foi identificada uma mutação não sinónima 829G>A (277Glu>Lys), significativamente associada à baixa actividade enzimática. Esta mutação foi também identificada em Angola, São Tomé e Príncipe e Guiné Equatorial, onde a frequência de portadores heterozigóticos foi entre 2,6 e 6,7% (valores que se encontram entre os mais elevados descritos globalmente para mutações associadas à deficiência em PK). Não foi possível concluir acerca da associação entre a deficiência de PK e o grau de severidade da malária e da associação entre o alelo 829A e a mesma, devido ao baixo número de amostras. Os resultados dos ensaios de invasão/maturação do parasita sugeriram que, nos GV com deficiência de PK ou G6PD, a invasão (onde está envolvida a membrana do GV hospedeiro e o complexo apical do parasita) é mais relevante para a eventual protecção contra a malária do que a maturação. Os resultados da análise proteómica revelaram respostas diferentes por parte do parasita nas duas condições de crescimento (GV com deficiência de PK e GV com deficiência de G6PD). Esta resposta parece ser proporcional à gravidade da deficiência enzimática. Nos parasitas que cresceram em GV deficientes em G6PD (provenientes de um indivíduo assintomático), a principal alteração observada (relativamente às condições normais) foi o aumento do número de proteínas de choque térmico e chaperones, mostrando que os parasitas responderam às condições de stress oxidativo, aumentando a expressão de moléculas de protecção. Nos parasitas que cresceram em condições de deficit de PK (GV de indivíduo com crises hemolíticas regulares, dependente de transfusões sanguíneas), houve alteração da expressão de um maior número de proteínas (relativamente ao observado em condições normais), em que a maioria apresentou uma repressão da expressão. Os processos biológicos mais representados nesta resposta do parasita foram a digestão da hemoglobina e a troca de proteínas entre hospedeiro e parasita/remodelação da superfície do GV. Além disso, uma elevada percentagem destas proteínas com expressão alterada está relacionada com as fendas de Maurer, que desempenham um papel importante na patologia da infecção malárica. É colocada a hipótese de que a protecção contra a malária em GV deficientes em PK está relacionada com o processo de remodelação da membrana dos GV pelo parasita, o que pode condicionar a invasão por novos parasitas e a própria virulência da malária. Os resultados da análise do proteoma dos GV contribuirão para confirmar esta hipótese.

Molecular estimation of dispersal for ecology and population genetics

The dispersal process, by which individuals or other dispersing agents such as gametes or seeds move from birthplace to a new settlement locality, has important consequences for the dynamics of genes, individuals, and species. Many of the questions addressed by ecology and evolutionary biology require a good understanding of species' dispersal patterns. Much effort has thus been devoted to overcoming the difficulties associated with dispersal measurement. In this context, genetic tools have long been the focus of intensive research, providing a great variety of potential solutions to measuring dispersal. This methodological diversity is reviewed here to help (molecular) ecologists find their way toward dispersal inference and interpretation and to stimulate further developments.

The effect of host social system on parasite population genetic structure: comparative population genetics of two ectoparasitic mites and their bat hosts.

BACKGROUND: The population genetic structure of a parasite, and consequently its ability to adapt to a given host, is strongly linked to its own life history as well as the life history of its host. While the effects of parasite life history on their population genetic structure have received some attention, the effect of host social system has remained largely unstudied. In this study, we investigated the population genetic structure of two closely related parasitic mite species (Spinturnix myoti and Spinturnix bechsteini) with very similar life histories. Their respective hosts, the greater mouse-eared bat (Myotis myotis) and the Bechstein's bat (Myotis bechsteinii) have social systems that differ in several substantial features, such as group size, mating system and dispersal patterns. RESULTS: We found that the two mite species have strongly differing population genetic structures. In S. myoti we found high levels of genetic diversity and very little pairwise differentiation, whereas in S. bechsteini we observed much less diversity, strongly differentiated populations and strong temporal turnover. These differences are likely to be the result of the differences in genetic drift and dispersal opportunities afforded to the two parasites by the different social systems of their hosts. CONCLUSIONS: Our results suggest that host social system can strongly influence parasite population structure. As a result, the evolutionary potential of these two parasites with very similar life histories also differs, thereby affecting the risk and evolutionary pressure exerted by each parasite on its host.

THE USE OF SIMULATIONS IN EVOLUTIONARY POPULATION GENETICS: APPLICATIONS ON HUMANS, OWLS AND VIRTUAL ORGANISMS

Summary (in English) Computer simulations provide a practical way to address scientific questions that would be otherwise intractable. In evolutionary biology, and in population genetics in particular, the investigation of evolutionary processes frequently involves the implementation of complex models, making simulations a particularly valuable tool in the area. In this thesis work, I explored three questions involving the geographical range expansion of populations, taking advantage of spatially explicit simulations coupled with approximate Bayesian computation. First, the neutral evolutionary history of the human spread around the world was investigated, leading to a surprisingly simple model: A straightforward diffusion process of migrations from east Africa throughout a world map with homogeneous landmasses replicated to very large extent the complex patterns observed in real human populations, suggesting a more continuous (as opposed to structured) view of the distribution of modern human genetic diversity, which may play a better role as a base model for further studies. Second, the postglacial evolution of the European barn owl, with the formation of a remarkable coat-color cline, was inspected with two rounds of simulations: (i) determine the demographic background history and (ii) test the probability of a phenotypic cline, like the one observed in the natural populations, to appear without natural selection. We verified that the modern barn owl population originated from a single Iberian refugium and that they formed their color cline, not due to neutral evolution, but with the necessary participation of selection. The third and last part of this thesis refers to a simulation-only study inspired by the barn owl case above. In this chapter, we showed that selection is, indeed, effective during range expansions and that it leaves a distinguished signature, which can then be used to detect and measure natural selection in range-expanding populations. Résumé (en français) Les simulations fournissent un moyen pratique pour répondre à des questions scientifiques qui seraient inabordable autrement. En génétique des populations, l'étude des processus évolutifs implique souvent la mise en oeuvre de modèles complexes, et les simulations sont un outil particulièrement précieux dans ce domaine. Dans cette thèse, j'ai exploré trois questions en utilisant des simulations spatialement explicites dans un cadre de calculs Bayésiens approximés (approximate Bayesian computation : ABC). Tout d'abord, l'histoire de la colonisation humaine mondiale et de l'évolution de parties neutres du génome a été étudiée grâce à un modèle étonnement simple. Un processus de diffusion des migrants de l'Afrique orientale à travers un monde avec des masses terrestres homogènes a reproduit, dans une très large mesure, les signatures génétiques complexes observées dans les populations humaines réelles. Un tel modèle continu (opposé à un modèle structuré en populations) pourrait être très utile comme modèle de base dans l'étude de génétique humaine à l'avenir. Deuxièmement, l'évolution postglaciaire d'un gradient de couleur chez l'Effraie des clocher (Tyto alba) Européenne, a été examiné avec deux séries de simulations pour : (i) déterminer l'histoire démographique de base et (ii) tester la probabilité qu'un gradient phénotypique, tel qu'observé dans les populations naturelles puisse apparaître sans sélection naturelle. Nous avons montré que la population actuelle des chouettes est sortie d'un unique refuge ibérique et que le gradient de couleur ne peux pas s'être formé de manière neutre (sans l'action de la sélection naturelle). La troisième partie de cette thèse se réfère à une étude par simulations inspirée par l'étude de l'Effraie. Dans ce dernier chapitre, nous avons montré que la sélection est, en effet, aussi efficace dans les cas d'expansion d'aire de distribution et qu'elle laisse une signature unique, qui peut être utilisée pour la détecter et estimer sa force.

A population genetics study of Anopheles darlingi (Diptera: Culicidae) from Colombia based on random amplified polymorphic DNA-polymerase chain reaction and amplified fragment lenght polymorphism markers

The genetic variation and population structure of three populations of Anopheles darlingi from Colombia were studied using random amplified polymorphic markers (RAPDs) and amplified fragment length polymorphism markers (AFLPs). Six RAPD primers produced 46 polymorphic fragments, while two AFLP primer combinations produced 197 polymorphic fragments from 71 DNA samples. Both of the evaluated genetic markers showed the presence of gene flow, suggesting that Colombian An. darlingi populations are in panmixia. Average genetic diversity, estimated from observed heterozygosity, was 0.374 (RAPD) and 0.309 (AFLP). RAPD and AFLP markers showed little evidence of geographic separation between eastern and western populations; however, the F ST values showed high gene flow between the two western populations (RAPD: F ST = 0.029; Nm: 8.5; AFLP: F ST = 0.051; Nm: 4.7). According to molecular variance analysis (AMOVA), the genetic distance between populations was significant (RAPD:phiST = 0.084; AFLP:phiST = 0.229, P < 0.001). The F ST distances and AMOVAs using AFLP loci support the differentiation of the Guyana biogeographic province population from those of the Chocó-Magdalena. In this last region, Chocó and Córdoba populations showed the highest genetic flow.

A preliminary analysis of the population genetics and molecular phylogenetics of Onchocerca volvulus (Nematoda: Filarioidea) using nuclear ribosomal second internal transcribed spacer sequences

Nuclear internal transcribed spacer 2 (ITS2) rDNA sequences were used for a molecular phylogenetics analysis of five Onchocerca species. The sister species of the human parasite O. volvulus was found to be the cattle parasite O. ochengi and not O. gibsoni, contrary to chromosomal evidence. The genetic differentiation of two African populations (representing the two African strains) and a Brazilian population of O. volvulus was also studied. Phylogenetic and network reconstruction did not show any clustering of ITS2 alleles on geographic or strain grounds. Furthermore, population genetics tests showed no indication of population differentiation but suggested gene flow among the three populations.

On the use of principal components in contemporany population genetics: a case study

In human Population Genetics, routine applications of principal component techniques are oftenrequired. Population biologists make widespread use of certain discrete classifications of humansamples into haplotypes, the monophyletic units of phylogenetic trees constructed from severalsingle nucleotide bimorphisms hierarchically ordered. Compositional frequencies of the haplotypesare recorded within the different samples. Principal component techniques are then required as adimension-reducing strategy to bring the dimension of the problem to a manageable level, say two,to allow for graphical analysis.Population biologists at large are not aware of the special features of compositional data and normally make use of the crude covariance of compositional relative frequencies to construct principalcomponents. In this short note we present our experience with using traditional linear principalcomponents or compositional principal components based on logratios, with reference to a specificdataset

Impact of social structure variation on population genetics, social conflicts and life histories in ants

Summary The evolution of social structures and breeding systems in animals is a complex process that combines ecological, genetical and social factors. This thesis sheds light on important changes in population genetics, life-history and social behavior that are associated with variation in social structure in ants. The socially polymorphic ant Formica selysi was chosen as the model organism because single- and multiple-queen colonies occur in close proximity within a single large population. The shift from single- to multiple-queen colonies is generally associated with profound changes in dispersal behavior and mode of colony founding. In chapter 1, we examine the genetic consequences of variation in social structure at both the colony and population levels. A detailed microsatellite analysis reveals that both colony types have similar mating systems, with few or no queen turnover. Furthermore, the complete lack of genetic differentiation observed between single- and multiple-queen colonies provides no support to the hypothesis that change in queen number leads to restricted gene flow between social forms. Besides changes in the genetic composition of the colony, the variation in the number of queens per colony is associated with changes in a network of behavioral and life-history traits that have been described as forming a "polygyny syndrome". In chapter 2, we demonstrate that multiple-queen colonies profoundly differ from single-queen ones in terms of size, nest density and lifespan of colonies, in weight of queens produced, as well as in allocation to reproductive individuals relative to workers. These multifaceted changes in life-history traits can provide various fitness benefits to members of multiple-queen colonies. Increasing the number of queens in a colony usually results in a decreased level of aggression towards non-nestmates. The phenotype matching hypothesis predicts that, compared to single-queen colonies, multiple-queen colonies have more diverse genetically-derived cues used for recognition, resulting in a lower ability to discriminate non-nestmates. In sharp contrast to this hypothesis, we show in chapter 3 that single- and multiple-queen colonies exhibit on average similar levels of aggression. Moreover, stronger aggression is recorded between colonies of different social structure than between colonies of the same social structure. Several hypotheses propose that the evolution of multiple-queen colonies is at least partly due to benefits resulting from an increase in colony genetic diversity. The task-efficiency hypothesis holds that genetic variation improves task performance due to a more complete or more sensitive expression of the genetically-based division of labor. In .chapter 4, we evaluate if higher colony genetic diversity increases worker size polymorphism and thus may improve division of labor. We show that despite the fact that worker size has a heritable component, higher levels of genetic diversity do not result in more polymorphic workers. The smaller size and lower polymorphism levels of workers of multiple-queen colonies compared to single-queen ones further indicate that an increase in colony genetic diversity does not increase worker size polymorphism but might improve colony homeostasis. In chapter 5, we provide clear evidence for an ongoing conflict between queens and workers on sex allocation, as predicted by kin selection theory. Our data show that queens of F. selysi strongly influence colony sex allocation by biasing the sex ratio of their eggs. However, there is also evidence that workers eliminated some male brood, resulting in a population sex-investment ratio that is between the queens' and workers' equilibria. Résumé L'évolution des structures sociales et systèmes d'accouplement chez les animaux est un processus complexe combinant à la fois des facteurs écologiques, génétiques et sociaux. Cette thèse met en lumière des changements importants dans la génétique des populations, les traits d'histoire de vie et les comportements sociaux qui sont associés à des variations de structure sociale chez les fourmis. Durant ce travail, nous avons étudié une population de Formica selysi composée à la fois de colonies à une reine et de colonies à plusieurs reines. La transition de colonie à une reine à colonie à plusieurs reines est généralement associée à des changements profonds dans le comportement de dispersion ainsi que le mode de fondation des sociétés. Dans le chapitre 1, nous examinons les conséquences génétiques de la variation de structure sociale tant au niveau de la colonie qu'au niveau de la population. Une analyse détaillée à l'aide de marqueurs microsatellites nous révèle que les deux types de colonies ont des systèmes d'accouplements similaires avec peu ou pas de renouvellement de reines. L'absence totale de différenciation génétique entre les colonies à une et à plusieurs reines n'apporte aucun support à l'hypothèse selon laquelle un changement dans le nombre de reines conduit à un flux de gènes restreint entre les deux formes sociales. A côté de changements dans la composition génétique de la colonie, la variation du nombre de reines dans une colonie est associée à une multitude de changements comportementaux et de traits d'histoire de vie qui ont été décrits comme formant un "syndrome polygyne". Dans le chapitre 2, nous démontrons que les colonies à plusieurs reines diffèrent profondément des colonies à une reine en terme de taille, densité de nids, longévité des colonies, poids des nouvelles reines produites ainsi que dans l'allocation entre les individus reproducteurs et les ouvrières. Ces changements multiples dans les traits d'histoire de vie peuvent apporter des bénéfices variés en terme de fitness aux colonies à plusieurs reines. L'augmentation du nombre de reines dans une colonie est généralement associée à une baisse du degré d'agressivité envers les fourmis étrangères au nid. L'hypothèse "phénotype matching" prédit que les colonies à plusieurs reines ont une plus grande diversité dans les facteurs d'origine génétique utilisés pour la reconnaissance, résultant en une capacité diminuée à discriminer une fourmi étrangère au nid. Contrairement à cette hypothèse, nous montrons dans le chapitre 3 que les colonies à une et à plusieurs reines ont des niveaux d'agressivité similaires. De plus, une agressivité accrue est observée entre colonies de structures sociales différentes comparée à des colonies de même structure sociale. Plusieurs hypothèses ont proposé que l'évolution de colonies ä plusieurs reines soit en partie due aux bénéfices résultant d'une augmentation de la diversité génétique dans la colonie. L'hypothèse "task efficiency" prédit que la diversité génétique améliore l'efficacité à effectuer certaines tâches grâce à une expression plus complète et plus souple d'une division du travail génétiquement déterminée. Nous évaluons dans le chapitre 4 si un accroissement de la diversité génétique augmente le polymorphisme de taille des ouvrières, d'où peut ainsi découler une meilleure division du travail. Nous montrons qu'en dépit du fait que la taille des ouvrières soit un caractère héritable, une forte diversité génétique ne se traduit pas par un plus fort polymorphisme chez les ouvrières. Les ouvrières de colonies à plusieurs reines sont plus petites et moins polymorphes que celles des colonies à une seule reine. Dans le chapitre 5, nous démontrons l'existence d'un conflit ouvert entre reines et ouvrières à propos de l'allocation dans les sexes, comme le prédit la théorie de la sélection de parentèle. Nos données révèlent que les reines de F. selysi influencent fortement l'allocation dans les sexes en biaisant la sexe ratio des oeufs. Cependant, certains indices indiquent que les ouvrières éliminent une partie du couvain mâle, ce qui a pour effet d'avoir un investissement dans les sexes au niveau de la population intermédiaire entre les intérêts des reines et des ouvrières.

The population genetics of clonal and partially clonal diploids.

The consequences of variable rates of clonal reproduction on the population genetics of neutral markers are explored in diploid organisms within a subdivided population (island model). We use both analytical and stochastic simulation approaches. High rates of clonal reproduction will positively affect heterozygosity. As a consequence, nearly twice as many alleles per locus can be maintained and population differentiation estimated as F(ST) value is strongly decreased in purely clonal populations as compared to purely sexual ones. With increasing clonal reproduction, effective population size first slowly increases and then points toward extreme values when the reproductive system tends toward strict clonality. This reflects the fact that polymorphism is protected within individuals due to fixed heterozygosity. Contrarily, genotypic diversity smoothly decreases with increasing rates of clonal reproduction. Asexual populations thus maintain higher genetic diversity at each single locus but a lower number of different genotypes. Mixed clonal/sexual reproduction is nearly indistinguishable from strict sexual reproduction as long as the proportion of clonal reproduction is not strongly predominant for all quantities investigated, except for genotypic diversities (both at individual loci and over multiple loci).

Going the distance: human population genetics in a clinal world.

Global human genetic variation is greatly influenced by geography, with genetic differentiation between populations increasing with geographic distance and within-population diversity decreasing with distance from Africa. In fact, these 'clines' can explain most of the variation in human populations. Despite this, population genetics inferences often rely on models that do not take geography into account, which could result in misleading conclusions when working at global geographic scales. Geographically explicit approaches have great potential for the study of human population genetics. Here, we discuss the most promising avenues of research in the context of human settlement history and the detection of genomic elements under natural selection. We also review recent technical advances and address the challenges of integrating geography and genetics.

Uncovering the genetic basis of adaptive change: on the intersection of landscape genomics and theoretical population genetics

A workshop recently held at the Ecole Polytechnique Federale de Lausanne (EPFL, Switzerland) was dedicated to understanding the genetic basis of adaptive change, taking stock of the different approaches developed in theoretical population genetics and landscape genomics and bringing together knowledge accumulated in both research fields. Indeed, an important challenge in theoretical population genetics is to incorporate effects of demographic history and population structure. But important design problems (e.g. focus on populations as units, focus on hard selective sweeps, no hypothesis-based framework in the design of the statistical tests) reduce their capability of detecting adaptive genetic variation. In parallel, landscape genomics offers a solution to several of these problems and provides a number of advantages (e.g. fast computation, landscape heterogeneity integration). But the approach makes several implicit assumptions that should be carefully considered (e.g. selection has had enough time to create a functional relationship between the allele distribution and the environmental variable, or this functional relationship is assumed to be constant). To address the respective strengths and weaknesses mentioned above, the workshop brought together a panel of experts from both disciplines to present their work and discuss the relevance of combining these approaches, possibly resulting in a joint software solution in the future.