Admitted students

	Marcin Bogusz There is accumulating evidence that the conclusions of molecular evolutionary and genomic studies are dependent on the multiple sequence alignment methodology used in those studies, with alignment error leading to systematic biases in the estimates of evolutionary parameters, such as divergence estimates and dN/dS. My project will address these problems through the development of new methodology for aligning sequences that better describe the evolutionary processes that generated the observed data and through the explicit incorporation of uncertainty in downstream alignment.These new methods may includes novel algorithm developments, the creation of statistical models of sequence evolution, and the testing of biologically informed heuristics.
	Elodie Chapurlat In my PhD project, I study the role of pollinators as drivers of floral evolution, using the fragrant and nectar-rewarding orchid Gymnadenia conopsea as the study system. More precisely, I study the geographical context of floral evolution using a combination of field experiments, population genetics and demographic monitoring. I aim at quantifying pollinator-mediated selection and costs of reproduction in a set of natural populations distributed along a latitudinal gradient in Europe. Personal Webpage
	Hwei-yen Chen My research interests lie in the field of evolutionary biology of aging, especially in how condition-dependent selection and sex-specific selection affect aging process. The classical Medawar-William theory predicts that higher extrinsic mortality should lead to more rapid aging - deleterious mutations that have late-life detrimental effects, or pleiotropic mutations that have beneficial effect at young ages but deleterious effects at late ages, would rise in frequencies in population because of the decline of selection force later in life. However, condition-environment interaction may result in the evolution of decelerated aging under increased extrinsic mortality. Increased environments stress, as a source of extrinsic mortality, can select for decreased deterioration in traits affecting susceptibility to the stress, resulting in postponed aging. There are strong evidences suggesting that the genes involved in stress resistance, such as thermal tolerance, can also prolong lifespan. Besides, recent studies provide evidences that males and females have different basic dietary requirements for age-specific effects on fitness, and different genetic architecture of lifespan and aging, suggesting that sex difference plays a key role in shaping the evolution of aging. To test the hypothesis, I use nematode Caenorhabditis remanei as a model organism. Its short generation time (~3 days) and dioecious nature make it very suitable for experimental evolution studies involving sex-specific selection. Personal Webpage
	Maria Cortazar My research interest it will be base on the following ideas. 1. Study the prevalence of Batrachochytrium in Sweden 2. Study the susceptibility of amphibian population to Bd fungi desease. 3. Wether a latitundinal gradient is found in inmunogenetic variation 4. Study whether immunogenetic variation is reduced in small fringe populations. For that, I will study variation among populations of two common (common frog, common toad Bufo bufo) and three rare (pool frog Rana lessonae, green toad B. viridis and natterjack toad) amphibian species all over sweden. The answer of these questions will be very relevant to understand why amphibian populations are declining all over the world. Also, it will be paussible to stablish recent endangered species situation for a general amphibian conservation perspective. Personal Webpage
	Ludovic Dutoit
	Kirsten Ellegaard "My primary research interest is the biology and evolution of endosymbiotic bacteria, adapted to insects. I currently work with the bacterium Wolbachia pipientis, which has successfully invaded many arthropod populations by manipulating host reproduction. Recent estimates say that Wolbachia may be infecting as much as 70% of all insect species, with reproductive alterations ranging from feminization and induction of parthenogenesis to reproductive incompatibility between males and females with different infection status. While many discoveries have been made at the phenotypic level, the Wolbachia are still poorly characterized at the molecular level. As for other obligate intracellular bacteria, Wolbachia cannot be grown in culture, which is a prerequisite for most molecular methods. The aim of my project is to learn more about the biology and evolution of theWolbachia using a comparative genomics approach. By employing recent technologies for DNA amplification prior to next-generation sequencing, I aim to obtain the complete genomic sequences of several well characterized Wolbachia strains. Through comparative analysis the goal is to connect known phenotypic characteristics of the strains with their genomic variability."
	Kevin Fletcher My research interests lie in the field of host-parasite dynamics, particularly host behavioural, anatomical and physiological responses to parasitic disease. Parasites are an important evolutionary agent that continually adapt to diverse host resistant genotypes and promote genetic polymorphisms in their host. I will research both the virulence and prevalence of the various avian Haemosporidian parasite lineages found in a collared flycatcher Ficedula albicollis population and determine how this relates to host immunity. The cost of mounting an immune response must be balanced with other resource dependent traits, which means that immunity is involved in resource trade-offs that are integral to life history theory. My research will also focus on the effect of parasitism on collared flycatcher life history strategies, while also considering the underlying physiological mechanisms involved in resource trade-offs.
	Karoline Fritzsche I am conducting my PhD in the field of sexual selection, and I am especially interested in how sexual selection as well as sexual conflict is present in the sex role reversed seed beetle Megabruchidius dorsalis. Since in the past years of research people put a lot of effort into unraveling the role of sexual selection and sexual conflict in males but disregarded females, my prior aim is to understand to which extent these occur in and effect females. For this project a sex role reversed species like M. dorsalis is perfectly suitable. Furthermore, I would like to find out the causes for sex role reversal and whether these roles are genetically fixed or adjustable (plastic) and thus influenced by environmental conditions, e.g. species density and temperature. To solve these questions I am going to use the powerful approach of experimental evolution. I think the outcome of this study could provide a better understanding why two clearly distinct behaving genders (males and females) are so successful in many species throughout evolution.
	Lucie Gattepaille Personal Webpage
	Karl Grieshop My research aims to characterize the architecture of sexually antagonistic genetic variation. I am first using a quantitative genetic approach (the diallel cross) to assess the extent to which standing additive genetic variation for fitness and life history traits (e.g. metabolic rate, development time, lifespan, etc.) is sexually antagonistic in the seed beetle Callosobruchus maculatus. I will then investigate the molecular genetic underpinnings of these phenotypes (via genome wide association and possibly QTL mapping), with respect to their intersexual genetic correlations. Personal Webpage
	Robert Griffin The subject of my PhD is sexual dimorphism in life history traits. I am using Drosophila melanogaster to investigate how sex specific fitness optima can drive the evolution of life history traits. Traits, such as aging rate, can have sex specific optima resulting from the trade-off between reproduction and maintenance. I will also study the effects of genetic constraints that may prevent sexes from reaching their optima. Personal Webpage
	Peter Halvarsson Personal Webpage
	Ding He My research interests is molecular evolution in nuclear-encoded mitochondrial proteomes (NcMt). The goal of my project is to define the core components of the NcMt proteome by identifying the universal set of nuclear-encoded mitochondrial proteins using high-throughput phylogenetic screening. The strategy is based on endosymbiosis theory that these components are originated from bacteria. Hence, we are actually looking for bacterial homologs in mitochondrion. These data will then be used to tackle another important outstanding question in eukaryote evolution, the position of the root of the eukaryote tree of life. Personal Webpage
	Friederike Heinrich I am working with a bacterial clade called SAR11. SAR11 is the most abundant organism in marine systems and plays pivotal roles in element cycling. Just recently the scientific community became aware of the existence of the freshwater sister group called LD12. So far there was not much known about the ecology of this organism. The aim of my studies was to bring light into the enigma if the freshwater sister group of SAR11, LD12 is first of all a numerical similar important component of the bacterial community like in marine systems, secondly what the ecological drivers for this group are and finally if LD12 features similar ecological characteristics like the marine sibling. In order to target these questions I look at different spatial and temporal scales in freshwater and marine ecosystems. Especially for organisms with unknown ecology it is pivotal to look at temporal data since the dynamic over time and its relationship to biotic and abiotic properties of the environment can provide important first clues on the ecology of so far uncultivated bacteria like the LD12 clade. Furthermore I plan experiments in which I will look at the response of SAR11 / LD12 to biotic and abiotic environmental changes. Personal Webpage
	Sofia Bodare (Hemmilä) My main interests are population and conservation genetics in trees. I am focusing on three medicinally and economically important tree species that are endemic to the Western Ghats area in India: Dysoxylum malabaricum, Dysoxylum binectariferum and Myristica malabarica. I have developed microsatellite markers that will be used to study ecologically important factors such as the population structure and genetic diversity in the species. Personal Webpage
	Kajsa Himmelstrand I work with Heterobasidion annosum s.l., a fungal species complex that is pathogenic on a variety of conifers. My aim in the thesis work is to study the evolution and pathogenicity of the H. annosum s.l. complex. In order to get a better understanding of how the species complex have evolved, I will analyze the variation in the mitochondrial genomes of the five Heterobasidion species and 24 isolates from one of the European species. I will also examine if it is possible to couple the mitochondrial variation to differences in the virulence. Personal Webpage
	Nina Hollfelder I am interested in the demographic history of humans. In my PhD studies I will be exploring genome wide data of modern East African populations to infer demographic events in the history and prehistory of East Africa and the implications of these on a global scale. Adding ancient samples from this region will provide an additional depth. Africa is the cradle of humankind and East Africa plays an important role for the anatomically modern human as there are indications that the Out-of-Africa migration originated from East Africa 50 000 to 100 000 years ago. By comparing new data to previously published data of Africans and non-Africans I will address questions revolving around recent population history and the Out-of-Africa Migration, such as different routes, time and population size.
	Karl Holm Personal Webpage
	Cosima Hotzy I am interested in the role of haploid selection in animals. Selection during the haploid phase of the life cycle has been assumed to be insignificant in animals, but there is growing evidence that genes are indeed expressed post meiosis and hence may be under haploid selection. The aim of my PhD project is to assess the importance of haploid gene expression and to test for the existence of haploid selection and its (potentially antagonistic) effects on the diploid phase in the zebrafish Danio rerio. Personal Webpage
	Magnus Johansson The importance of divergent natural selection in creating and maintaining biological diversity is increasingly being realized in ecological and evolutionary studies. Thermal selection is expected to be ubiquitous in natural systems, but our understanding of thermal adaptation is in many ways incomplete. My PhD-project will focus on the interplay between factors maintaining (selection, reproductive isolation) and acting against (gene flow) thermal adaptation and population divergence along thermal gradients in Icelandic lakes subjected to geothermal activity, using a freshwater snail as a model system. These lakes have low and high temperature areas, providing a unique opportunity to study divergent thermal selection whilst allowing migration of individuals among the habitats.
	Anna Karlgren The purpose of my thesis is to start elucidating the molecular mechanism controlling growth rhythm in Norway spruce studying candidate genes, homologues to genes involved in photoperiodic responses in Arabidopsis thaliana. My work is mainly focused on functional genomics and I have mainly been focusing on genes involved in the circadian clock and genes which are believed to induce bud set. I have been performing functional analysis on both Arabidopsisand spruce transformants, studied RNA localization with in situ hybridization and RNA expression with real-time PCR. Except for the great interest in the genetics of adaptation from an evolutionary perspective, the genetic control of growth rhythm is of significance also for tree breeding, conservation biology and future challenges caused by climate change. Personal Webpage
	Berrit Kiehl I recently started my PhD education at the Evolutionary Biology Center of Uppsala University in Sweden (15.08.2013) with a project investigating sperm mediated epigenetic effects. The aim of my PhD project is to assess where in the sperm the trigger for this mechanism lies and how this is transferred into the offspring. The experiments will be conducted with the zebrafish as a model organism. This is an ideal study system, as its entire genome is sequenced, many genes are annotated and it has external fertilization allowing in vitro fertilization assays. Personal webpage
	Radoslav Kozma My work aims to combine the field of genetics with the application of population structure modeling as well as a more individual based genome modeling. The species of my study is the willow grouse (Lagopus lagopus), which has an interesting phenotypic diversity across its range. In Scandinavia, individuals adopt a white plumage during winter, while individuals in the northern UK forgo moulting and remain brown. Interestingly, snow free islands off the coast of Norway harbor the Scandinavian populations in fluctuating densities, which are seemingly maladapted seeing as their white plumage stands out. With the help of population modeling, one of the aims is to model the dynamics of movement to identify conditions required for local adaptation (i.e. what would it take for the island populations to stop their winter moulting). Furthermore, the genome of the willow grouse will be sequenced with the aim of finding potential genes responsible for this variation in moulting behaviour. In turn, models of the genomic data will be constructed to find out which parts of the genome are likely to respond to local selection pressures and random forces such as drift. Is it the case that local populations become divergent throughout the genome (as predicted by drift) or at key loci (as predicted by selection)? As such, the project aims to tackle these questions from an empirical as well as a theoretical perspective.
	Dmytro Kryvokhyzha I am interested in the role of interspecific hybridization and polyploidy in speciation. My previous research projects were dedicated to the diversity of diploid-polyploid complexes of spined loaches of the genus Cobitis, incipient hybrid speciation of invasive sculpins of the genus Cottus and speciation with gene flow in Heliconius butterflies. My current PhD project aims to investigate genomic and phenotypic changes associated with polyploidy and hybrid origin in Capsella bursa-pastoris, a recently formed allotetraploid weed. Unlike its parental species, which are found in Southern Europe and Central Asia, C. bursa-pastoris occurs all over the world. I analyze whole-genome DNA and RNA sequencing data of this tetraploid and its diploid parents to assess genomic consequences of allotetraploidization. I also attempt to link the identified genetic changes with variation in major adaptive traits such as flowering time and circadian rhythms to infer a possible explanation of the world-wide distribution of this weed.
	Katarzyna Kulma I am interested in host-parasite interactions in various ecological contexts as well as in evolutionary outcome that such relation may produce. The study system I use for my research involves two host species – pied (Ficedula hypoleuca) and collared flycatcher (F. albicolis) – and their malaria parasites (Plasmodium andHaemoproteus genera). Flycatchers, that are closely related, migratory passerines, in the contact zone on Baltic island (Gotland and Öland) compete fiercely over nest sites and food resources. Moreover, if conspecific mates are rare, they hybridize occasionally. Such situation is very interesting from ecological and evolutionary point of view! Parasites tightly co-evolve with their hosts and thereby influence the evolution of life-history and sexual traits of the host. Thus parasites may affect not only competitive interactions e.g. when they cause shifts in the relative fitness of the hosts across environments, but also costs of hybridization costs when hybrids are less or more infected as compared to the parental species. Different costs of infection/competition/hybridization may result in completely different evolutionary outcomes. Undoubtedly, my PhD studies are full of exciting research and important lessons I can learn! Personal Webpage
	Warren Kunce I work on the potential impacts of common insecticides on aquatic biodiversity. Project focuses are traditional LC50 testing, developing new tests for ecological settings and as well as investigating the combined (?cocktail?) effects of the insecticides found in Swedish surface waters.
	Anders Larsson The working title of my PhD thesis is "Phylogeny, historical biogeography, and phylogeography of the fern genus Woodsia". The assumption that ferns are easily dispersed by wind has been put forward in many studies, based for example on the fact that the frequency of endemics on islands are lower for ferns than for angiosperms. Lately with a better understanding of the fern reproduction, and then especially that ferns are mainly outcrossing and not inbreeding as often assumed, the idea of almost freely dispersed ferns have been questioned. Yet, although biogeography is discussed in phylogenetic studies of ferns, studies explicitly testing hypothesis on distribution patterns in ferns are few. This is were I hopefully will contribute with my studies on Woodsia ferns. Personal Webpage
	Lina Lehndal In my Phd project, I will study the effects of insect herbivory on plant population dynamics. I will combine field and greenhouse experiments to explore ecological and evolutionary consequences of interactions between the perennial herbLythrum salicaria and its herbivores. My aims include quantifying genetic variation among and within populations in resistance and tolerance to herbivory, determining the effects of herbivory on the structure and growth of local populations and examining factors governing variation in intensity of herbivory at local and regional scales.
	Anders Lind In my research I am exploring the microbial dark matter, the 99% of all prokaryotes that cannot be grown, nor sequenced, from a pure culture.This is done using single-cell and metagenomics approaches using samples obtained from all over the world. My focus lies on the third domain of life, the archaea. By sampling environments known to be naturally enriched for such organisms, such as hot-springs, hydrothermal vents etc., I hope to be able to sequence and study the evolutionary past of the archaea. Apart from being interesting from a strict academic view, very little is known about them, the archaea are also closely related to ourselves, he eukaryotes, and by finding archaea that is evolutionary old, I hope to be able to learn more about the relationship these two domains share. Recently I have also been looking at the genome structure of the only known archaeal endosymbiont. Here we hope to find out why endosymbiosis is so widespread in the bacteria and rare in the archaea.
	Anna-Malin Linde
	Camille Madec The aim of my project is to understand processes influencing the genetic structure and the evolution of floral display in the perennial herb Primula farinosa, which is dimorphic for the stem length. I use a combination of field experiments and genetic analysis to study the degree to which populations are locally adapt to their environment and to estimate the level of gene flow between populations. Personal Webpage
	Mayank Mahajan The main goal of my thesis is to indentify the mechanisms and selective forces that drive the emergence of the cellular complexity in bacteria, using Planctomycetes as a model organism. To understand why and how eukaryotic cells with a nucleus and a complicated internal membrane structure have evolved in the past The main focus of the project is on the Planctomycetes, a gram -ve bacterial phylum, about which not much is known. Most of the organisms in this phylum have elaborate membrane systems which we want to study. Specially the Gemmata taxa is known to have the most elaborate membrane system in the phylum. We are sequencing four new genomes and also trying to close/finish/complete one or two genomes if possible. After the genomes are assembled and annotated we plan on doing comparative genomics for this phylum. As part of this project my role is to perform the bioinformatic analysis of the genomic, metagenomic and single cell genomics data that will be collected as part of this project. Personal Webpage
	Joran Martijn My main research interests are the evolutionary origins of eukaryotes and mitochondria. My project is part of a larger, ERC Starting grant-funded project led by my supervisor dr. Thijs Ettema that aims to gain insight in the evolutionary origin of the eukaryotic cell. We aim to do so by searching for clues present in microbial lineages for which at present there is no genomic data available because they are either hard or impossible to cultivate. The amount of genomically uncharacterized microbial lineages at the moment is so large that they are often referred to as 'the biological dark matter'. We will explore this dark matter by applying novel genomics approaches like single-cell genomics and metagenomics on samples harvested from extreme environments such as hydrothermal vents, black smokers and hot springs. As the project is currently in the starting stages my work involves assisting in the development of experimental design and bioinformatics pipelines that later on will be used to analyze the genomic data that will be streaming in on a very large scale. In addition I'm currently working on five novel Alphaproteobacteria, which are candidate members of new alphaproteobacterial lineages: two endosymbionts of the amoeba Acanthamoeba for which we have standard genomic data and three bacteria which were harvested from a lake for which we have single-cell genomic data. By assembling, annotating and performing phylogenomics I'm trying to figure out what kind of bacteria they are and what their phylogenetic placement is in the Alphaproteobacteria tree. Furthermore, using the new lineages, it will be possible to estimate with greater accuracy the nature of the mitochondrial ancestor.
	Glib Mazepa I am focused on the evolutionary consequences of the clonal inheritance using the water frogs genus Pelophylax as a study system. These animals are famous for the unusual reproduction mode called hybridogenesis, which results from incomplete postzygotic isolation: the interbreeding parental species produce fertile hybrids, which lack recombination between the parental chromosome sets. My means of backcrossing to one of the parental species, such hybrids establish clonal lines that can persist for many generations. The existing data point onto the multiple independent origin of the clonal lineages all across Europe, which presumably also differ in their age of formation. The simultaneous existence of the ancestral state (= sexual species) on the one hand and the numerous clones of different age on the other hand altogether provide a unique opportunity to study the processes similar to ones accompanying sex chromosome evolution: cessation of recombination, Mueller’s ratchet, gene conversion, etc. As for the beginning of my PhD, I am trying to establish a robust phylogenetic framework for the sexual species which later on will be complemented with the clonal lines using both RAD sequencing and sanger markers produced from the genomic and transcriptomic data.
	Rhiannon Mondav The ultra micro end of my research is an investigation of microbes with reduced genomes. There are many highly abundant ecologically relevant microbes that have streamlined genomes and together they are thought to significantly contribute to global carbon and sulfur cycling. I am investigating data and theories that suggest streamlined microbes are affected by certain evolutionary mechanisms than organisms with larger genomes. During this research into genomic mechanisms I will test and compare bacteria that exist at the boundaries of free-living / exo-symbiotic / endo-symbiotic lifestyles. Microbes will be sourced from Lake Erken. I’ll also be exploring mechanistic aspects of microbial evolution and establishing new model bacteria for laboratory experiments. Personal Webpage
	Thijessen Naidoo My PhD research seeks to utilize the gene regulatory network as a functional framework, to examine the effects of human variation on regulatory elements and, thus, on the regulation of gene expression. This will allow us to unearth possible differences among regulatory elements with regard to the presence and potential consequence of variation. The use of a population-based approach will assist in examining how functional variation has assorted across human populations, and whether anyY differences found among populations could result in differences in phenotype. Such knowledge will add to discussions on human evolution, while also clarifying differential disease burden and susceptibility among populations. Personal Webpage
	Ioana Onut Brännström In my PhD I would like to sequence the entire genome of both main symbiotic partners of T. vermicularis and use a novel and modern approach to study lichens by combining genomic, ecologic and evolutionary methods. In order to understand the life history of T. vermicularis in particular and the biology of lichens in general, some of my project objectives are: World-wide phylogeography of Thamnolia vermicularis seen as a dual symbiotic organism This type of study will be a first for lichens. By sequencing markers from both main symbionts using samples from all over the world I will be able to understand the biology of this species. I am planning to use sequences from seven fungal markers and at least three algal markers. Following on from this analysis, demographic inference can be carried out with estimation of divergence time, post divergent gene flow between populations and whether bottlenecks have occured in the history of a species. Understanding population structure within these species will be another concern, and modern methods of extracting such information shall be utilised. Understanding the symbiotic nature of lichens In many species of lichens it was discovered that the fungal- algal association is not permanently maintained and apparently when the lichen is colonizing new environments the fungus can associate with a new algal species or strain. This phenomenon is called algal-switching but how it takes place and how new lichen is formed is not still understood. It is strongly suspected that the lichens ability for algal-switching plays a key role for adaptation and surviving climate changes. Personal webpage
	Kalicharan Patra
	Erik Pelve My field of interest is Archaea – the most recently discovered and still least studied domain of living organisms. The archaea can be found in any environment, from the human gut flora to the extreme environments they are most renowned for. Ecologically they are important parts of the global cycling of matters and they are the only organisms known to produce the powerful greenhouse gas methane. From a cell biological point of view the Archaea constitute a very early diverged group with unique solutions to basal cell biological problems, sometimes combining bacterial and eukaryal traits, sometimes featuring previously unknown solutions. My research focuses on the function and regulation of the cell cycle of the crenarchaea Sulfolobus, a hot-spring dweller which we grow in 80°C. Using an array of techniques, including transcriptomics, flow cytometry and microscopy we have identified the CDV-system, a crenarchaeal cell division machinery, related to an eukaryal vesicle forming system. Evolutionary, archaea are more closely related to eukaryotes than bacteria, and therefore these findings of the basal cellular machinery of archaea can serve as a model for the eukaryal cell. Personal Webpage
	Allison Perrigo My PhD project focuses on the ecology and systematics of Dictyostelids, or cellular slime molds. I am preliminarily looking at the diversity and distribution of these protists within Sweden. I will then work towards using culture independent methods to quantitativly measure their diversity and abundance in a variety of environmental conditions, as it is presently quite difficult to measure species abundance using traditional cultivation techniques. Finally, I will be looking at the numerous "species complexes" within the group and will address the issue of cryptic species, as well as their geographic variation, using phylogenetic techniques.
	Froukje Postma
	Monica Ricao Canelhos My studies will focus on investigating the bacterioplankton species which play a major role in substrate cycling and the extent to which their metabolic function can be correlated to their phylogenetic group. Microorganisms are the main contributors to the remineralization of organic matter and play a vital role for our ecosystem. Bacteria live mostly under limited substrate conditions and must adapt spatialy and temporally to their environmental conditions. To further understand how environmental patterns shape these processes I will look at spatial and temporal change, including factors of temperature, light radiation, along with substrate limitation. The strategies of remineralization will be analyzed using single-cell methods and comparing substrate aquistion startegies (specialist and generalist groups). Substrates relevant for the aquatic systems of interest will be used to guide experimental setups and study assemblages of bacterioplankton in vitro.
	Inga Richert I study microbial communities in aquatic systems. With their functional role as decomposers, microbes bring an enormous metabolic capability of demineralizing even toxic and highly persistent compounds into nutrients within the natural cycle of matter. I want to understand microbial demineralization processes in heavily oil spill contaminated sites and further which environmental factors are responsible for shaping the microbial community structure. My special research interest is to link fine scale biogeochemical analysis with microbial, DNA based, identification of key-species and their individual activity in the demineralization process. Personal Webpage
	Francisco J. Ruiz-Ruano I am a PhD student from Granada (Spain) invited to work in the lab. I study the nature, origin and expression of supernumerary chromosomes in grasshoppers. I am starting to apply next generation sequencing to my material and I am here to get more experience in the experimental design and analysis for this kind of data. Personal Webpage
	Jakub Rybinski [Personal webpage]
	Sanea Sheikh My PhD mainly focuses on the annotation of the genome of Acrasis kona which will help define the nature of the last common ancestor of the eukaryotes and how features that are unique to eukaryotes have evolved. I will work with identification of genes, proteins, metabolic pathways and gene expression patterns in the genome of Acrasis kona. I will then perform a phylogenetic analysis to analyze the gene families and study the origin of genes. I will use my analysis to understand the origin and function of different genes, metabolic pathways and gene expression patterns which will in turn answer questions about how eukaryote specific features evolved and how some proteins are different over the branches of the eukaryotic tree. I will also use my results to analyze how cells communicate and cooperate to form multicellular structures.
	André Silva Climate is changing in Southern Asia and its biodiversity hotspots are under this additional threat. Biodiversity in the region is particularly susceptible to climate modifications due to its evolutionary adaptation to the monsoon cycle. The magnitude of this impact is poorly known and current protected areas may fail their purpose under future climate. Comprehensive and accurate ways of predicting such effects of climate change are urgently needed but still scarce. This PhD thesis will use small felids as models organisms to develop and test an approach, combining ecological and genetic data, for investigating the future efficiency of current protected areas under predicted climate change. So far, alternative strategies to this goal have either used only ecological models for a large number of species or combined genetic and ecological information for single species. Here I aim to develop an integrative approach that may represent an optimal trade-off between those two extremes. Personal webpage
	Willian Silva I am interested in the mechanisms and processes responsible for the generation of developmental patterns and variation and how they affect phenotypic evolution. Development is controlled by numerous factors, both genetic and environmental, which interact to produce the developmental patterns observed during morphogenesis. The DNA sequence per se is not responsible for all the phenotypic variation observed in a population. Instead, epigenetic processes, both at the level of physico-chemical dynamics and at the level of gene regulation and chromosome organization, are also responsible for the complexity of the genotype-phenotype map. With a theoretical-experimental approach of the genotype-phenotype-fitness map and its role in population dynamics, we can understand the basis of phenotypic variation and evolution. I am using the zebrafish as my model species to understand how environmental factors (e.g. intra-sexual competition) affect developmental patterns (in particular, morphological patterns) through epigenetic changes and how these changes affect the evolution of phenotypic traits. We aim to answer three main questions: 1. Which traits are affected by epigenetic changes? 2. What are the effects of epigenetic changes on developmental patterns in populations under different environmental conditions? 3. How does epigenetic effects affect the evolution of phenotypic traits? The study of epigenetics is essential to understand the developmental mechanisms and processes responsible for phenotypic variation and the role of development in phenotypic evolution. Personal webpage
	Lucas Sinclair Personal webpage
	Agnes Sjöstrand
	Kim Steige My research interest is mainly about regulatory evolution in plants. I will focus on two diploid species, Capsella rubella and Capsella grandiflora, that differ markedly in floral traits although they diverged less than 50,000 years ago. The main aim of the project is to test hypotheses on the effects and adaptive significance of regulatory changes, and to elucidate the role of regulatory changes for recent phenotypic evolution in Capsella. There are three specific aims: 1) to empirically assess the degree of pleiotropy of regulatory changes, 2) to quantify natural selection on cis-regulatory regions and 3) to test for a role of regulatory variation in floral and reproductive trait evolution in Capsella.
	Michael Stocks I am interested in using polymorphism and divergence data to make inferences about both selection and past demographic events. Multilocus data is being accumulated from multiple spruce species, with the aim being to establish an extensive comparative dataset. Spruce (Picea) are conifers whose distribution spans most of the northern hemisphere and are characterised by long generation times and high levels of outcrossing, and so consequently offer an interesting contrast to most model organisms. My initial research will focus on complementing this empirical data with population genetic predictions and simulation studies to shed light on adaptation and population genetic processes in diverging populations. Personal Webpage
	Oddny Sverrisdottir Personal Webpage
	Venkat Talla Our research aims to resolve the most long-term and fundamental biological question; understanding the factors that underlie in speciation and diversification processes. Using the three Leptidea butterflies with the combinations of classical genetics, ecology and genomic tools, various factors responsible for speciation and diversification can be pointed out. Even though these three Leptidea butterflies look unidentifiably similar, they can be separated by genital morphology. A set of genes responsible for the genital morphology in closest relatives are used to identify the similar effect on the genitals of these three butterflies. Unravelling the factors responsible for the reproductive isolation will be a key factor in this study. Previous work also suggests high variance in the karyotype between populations within one of the species in this cryptic complex (L. sinapis). Illumina libraries obtained from a set of ten individuals of each species respectively are currently used for the population genomics approach to identify rates of mutation and variance between each of the species in this cryptic complex. These differences identified between the species inside the cryptic complex can be related to important ecological and evolutionary factors like host plant selection, diapause and direct development. As no previous attempt to sequence the genomes of these cryptic species was performed before, we aim to obtain a high quality genome assembly and linkage map through the larvae obtained from four generations of inbreeding Swedish L.sinapis. A set of Bioinformatics and genomic approaches will be used to find the chromosomal synteny and genomic rearrangements across the cryptic complex. Large pedigrees of Spanish and Swedish butterflies are reared in natural conditions to perform a genetic mapping and population genomic analysis to identify rates of recombination and variation. [Personal webpage]
	Masahito Tsuboi My general research interest is the diversity of nature. How is the diversity maintained? What originates diversity? When and why diversification occurred? These are the fundamental questions that I have been bearing throughout my career. My PhD project will deal with the diversity of teleost brain using phylogenetic comparative method. Brain is the key organ that control the entire operation of organisms among vertebrates. Not only the brain has been shown to correlated with life history traits and ecological characteristics such as diet preference, recent studies have even suggested that the brain size influences evolutionarily critical events such as invasion success and extinction rate. However, although teleost fish represents by far the most remarkable diversity among all vertebrates, this group has been paid less attention in brain evolution compared to mammals and birds. Thus, insights from comparative study on teleost brain will significantly enhance our knowledge on vertebrate brain evolution. Obvious advantage of using teleost fish over birds and mammals is the enormous diversity. I specifically chose three groups, cichlid, pipefish, and cardinalfish as model systems to maximize the variation. First, cichlids from East African lakes exhibits extraordinary variation in morphology, ecology and behavior within a single group. However, in terms of the sexual role, all cichlid species except for one have conventional sex roles. Second group, pipefish, is chosen to compensate this variation. This group is entirely sex role reversed with a huge amount of variation in the extent of paternal investment. Notably, this variation is not even existing among extant birds and mammals. Third, cardinal fish was chosen as a control group that the sexual investment is not largely biased to one sex. Importantly, since robust molecular phylogenies for these three groups are already available, recently advanced statistical analyses can be fully exploited. Throughout my PhD project, I aim to enhance insights on vertebrate brain evolution and also to find a new knowledge in the relationship between sexual behavior and brain evolution. [Personal webpage]
	Severin Uebbing I will work mainly within the flycatcher genome sequencing project. The focus of my studies will be on analyses of the flycatcher transcriptome. Therefore we have acquired Illumina high throughput next generation sequencing data from ten collared (Ficedula albicollis) and ten pied flycatchers (F. hypoleuca) of both sexes. We have sequenced eight different tissues from each bird plus several embryos. The aim is to find established differences in expression patterns between the two species which speciated only about one million years ago and do still hybridise where they occur in sympatry. I am analysing differential gene expression patterns between both species, sex-biased gene expression, dosage compensation between male ZZ and female ZW chromosome system, and allele-specific gene expression (i.e. expression level differences of different alleles of the same gene in one individual). Personal webpage
	Maria Uscka-Perzanowska
	Nagarjun Vijay Initially I will focus on genome assembly of the Hooded crow (Corvus cornix) using Next-Generation sequencing data. After establishing a high quality draft assembly, I will perform annotation of the genome using both in-silico methods and trascriptome data. The aim of the project is to detect genomic regions that significantly different between carrion and hooded crows (Corvus [c.] corone and C. [c.] cornix) and potentially contribute to speciation. Population genetic data will also be generated to analyse the differences between the two species. Later, depending on the outcome, validation of the candidate loci might be feasible with traditional sequencing methods on a larger set of populations samples. It would also be interesting to look at similar plumage differences in sister species within the genus Corvid. Personal webpage
	Biao Wang The major histocompatibility complex, which plays a central role in the immune system, is the most variable functional gene cluster described in vertebrates. It is fitness related, and therefore can reflect a natural population's evolutionary potential and population viability. Previous MHC studies mostly relied on the analysis of short antigen-presenting sequences. However, MHC is comprised of large gene families, it's necessary to study it from a broader perspective. In my PhD project, I focus on the MHC of Black Grouse(Tetrao tetrix) at a genomic level. I use 454 GS FLX Titanium platform to sequence the spleen transcriptome to discovery MHC and MHC-related genes. I also made a Fosmid library to obtain the entire genomic map of MHC. By using an improved screening method, I have found clones containing MHC Class I, Class II, Class III and BG genes, ranging about 100kb. The Fosmid clones are under Sanger shotgun sequencing. After finishing the MHC map, I will re-sequence this gene region in wild populations. The re-sequencing will also rely on 454 platform and will include some advanced technologies such as targeted enrichment and individual tagging. Personal webpage
	Mi Wang My research interest is to study the gene expression and regulation using statistical analysis. The hypothesis that differences in regulation of gene expression have an important role in speciation and adaptation is more than 40 years old. Although the relative contribution of changes in gene regulation to speciation continues to be debated, it has become clear now that variation in gene expression patterns often plays a key part in the evolution. The advant of Next Generation Sequencing makes it possible to charaterize this hypothesis at an unprecedemted resolution and scale. I aim to address this question from flycatchers by for example, identifying allele-specific expression, studying cisand/or trans- regulatory changes and exploreing the relationship between nature selection and regulatory divergence. Personal webpage
	Stina Weststrand Spore dispersed plants are underrepresented in plant biogeography studies. In my project I will focus on spikemosses (Selaginellaceae), a cosmopolitan group of lycophytes with a disjunct distribution. The main question that I am posing is whether the distribution patterns seen are due to long-distance dispersal or historical vicariance events. Studies will be conducted at different spatial and temporal scales using phylogenetic techniques and biogeographical analyses.
	Feifei Xu The overall goal of my research is to understand how different genome evolutionary processes change the biology of microbial eukaryotes (protists). Diplomonads are a group of heterotrophic flagellates (protists). They include pathogens, commensals, and free-living organisms found in anaerobic or micro-aerophilic environments. Most members of this group have two nuclei and are tetraploid. We are currently performing comparative sequencing projects on diplomonads with varying lifestyles. The main goal is to find differences that could explain their different biology.
	Katarzyna Zaremba I'm interested in microbes and evolutionary processes that make them who they are =) Many natural 'large-scale' concepts, like population or species, become very hard to define for microbes, and are tightly linked to the understanding of their evolution. I approach studying microbes with several different techniques, including traditional and single cell genomics, and metagenomics. The regular genome projects require pure culture of the organism of interest, which is a major limitation. Metagenomics and single cell genomics are the novel approaches that overcome the inability to obtain pure cultures and allow studying the mind-boggling and largely unknown diversity of microbes. One of my main interests is to combine metagenomics with single cell genomics and develop strategies for studying genomic variation in single cells and comparing it to the whole population. In practise, I deal with a lot of sequence data, mainly 454, but also Sanger and Solexa. I have started with applying metagenomic approach to the data coming from the Neanderthal genome sequencing consortium to learn more about the microbes present in an ancient bone sample. I have developed a pipeline for taxonomic analysis of a metagenomic sample, which I am now using to learn more about freshwater microbiomes. Taxonomically, my main focus is on the members of Alphaproteobacteria. I am part of a (wonderful!) Bartonella team at Molecular Evolution, that has several ongoing genome projects. Bartonellas are intra-cellular bacteria infecting mammalian hosts (humans, cats, dogs, rodents, ungulates, ...), where they can cause anything from no symptoms to a fatal disease. I am responsible for a genome of a bacterium coming from a dog, that suffered from lethal problems with heart, joints, heavy bleedings, anemia and more. We have another dog isolate, from a perfectly healthy individual, as well as bacteria coming from other animals, for example moose and kangaroo. In the freshwaters, I am especially interested in alphaproteobacterium closely related toPelagibacter ubique, the sequenced representative of an abundant oceanic bacterial clade called SAR11. Interestingly its genome is among the smallest in free-living bacteria and it is comparable in size to the endosymbionts, which are dependent on a host and are known to have reduced genomes. Many questions about SAR11 still remain open, perhaps most importantly what makes it so successful? Virtually nothing is known about its freshwater sister clade.
	Martyna Zwoinska In my PhD project I will be looking at sex-specific trade-offs between life span, reproduction and cognition in a model organism, a dioecious nematodeCaenorhabditis remanei. More specifically, I will be investigating whether sexes differ in cognitive abilities and the process of cognitive ageing, and if so, what are the causes and consequences of such patterns. I will further develop my project by including the role of condition-dependent selection and stress in the evolution of cognitive ageing. Two main questions to be addressed in the course of my studies are: i) does sex-specific selection lead to sex differences in age-related learning and memory? ; ii) does intra-locus sexual conflict prevent sexes from reaching their sex-specific optima in these traits? To test this I will employ experimental evolution approach, combined with behavioural ecology and, at later stage, genetic tools.
	Murielle Ålund My PhD-project focuses on trying to understand the role that gamete interactions play in the speciation process. Little is known about gametic isolation as a reproductive barrier since it is difficult to study, particularly for organisms with internal fertilization. I would like to learn more about how quickly gametes diverge between species and what kind of mechanisms take place after mating but before fertilization in order to reduce the costs of heterospecific mating. I am also interested in the causes of reduced fertility in hybrid offspring and the mechanisms behind it. I will be using the flycatcher system of the hybrid zone of Öland. The collared and pied flycatchers are found in sympatry there and hybridize to some extent. All the female hybrids are sterile and the males have reduced fertility. I will be using the long term data on that population and data from a few subsequent field seasons. Personal Webpage