Environmental suitability throughout the late quaternary explains population genetic diversity.

During my Ph.D., I used the next generation sequencing technology to investigate patterns of recombination and the genetic consequences of different reproductive modes of Daphnia magna. More precisely, I have used Restriction site Associated (RAD) sequencing to construct a high-density genetic map that can be coupled with the draft genome assembly of D. magna, thus, providing an essential tool for genome investigations in this widely used model organism (Chapter I). Such a map has enabled characterization of variation in the meiotic recombination rates across the genome of D. magna for the first time. Since recombination rates are an important parameter in almost any type of genetic research, this newly gained insight into the recombination landscape of D. magna offers a fundamental information for future studies of genome evolution, identification of genes underlying phenotypic traits and population genetic analyses. 
\nIn addition to sexual reproduction, D. magna can also reproduce asexually to generate clutches of clonal offspring (ameiotic parthenogenesis). This feature of Daphnia biology is extremely useful for scientific experimentation where the genetic variation among tested individuals has to be minimized. However, over the last decade, reports of genome homogenization (loss of heterozygosity - LOH) in asexual lineages of D. pulex have indicated that asexual genomes are not static as it was previously assumed and that some levels of ameiotic recombination, in addition to mutation, may induce genetic variation among putative clones. However, comparing parthenogenetic offspring with their mothers at several thousand genetic markers generated by RAD-sequencing, I was not able to detect any LOH events in D. magna (Chapter II). I cannot exclude the possibility that ameiotic recombination indeed occurs in D. magna, however, my results indicate that such phenomenon is extremely rare or restricted to the very short genomic regions that I was unable to investigate, despite a high-density of markers used in this study. 
\nNevertheless, the implementation of RAD-sequencing protocol for the genome studies of D. magna still enables interrogation of the transmission of genetic information from parents to offspring at unprecedented resolution. For an example, a RAD-sequencing based analysis of reduction in parental heterozygosity among rare ephippial hatchlings (typically produced by sexual reproduction) found in non-male producing populations of D. magna, has enabled differentiation between self-fertilization and automixis (meiotic parthenogenesis), by uncovering the subtle differences in genetic consequences of these reproductive strategies (Chapter III). Harnessing the ability of high-resolution genetic analysis it was demonstrated that, in the absence of males, D. magna can produce diapause eggs by automixis, and an additional type of asexual reproduction that was not previously reported for this species.
\nFinally, RAD-sequencing European populations of D. magna revealed an association of genetic variation with the geographic location of individual samples (Chapter IV), a task which was not previously amenable using mitochondrial or microsatellite markers. This study provided a better insight into population genetic structure of D. magna and suggested that genetic differentiation is mainly driven by geographic distance. These results set a foundation for forthcoming studies aiming to disentangle past and future evolutionary processes shaping populations of this intriguing model organism.
\nTaken together, research presented in my thesis illustrates the practicality of reduced representation genome sequencing for tackling diverse topics in evolutionary biology. By increasing awareness of non-randomness of meiotic recombination across the genome of D. magna, the diversity of reproductive mechanisms it can employ, and its large-scale population structure, I hope this work will contribute to further understanding of the remarkable adaptive capacity this crustacean is famous for.
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Editorial and retrospective 2010

Genetic variation is expected to be influenced by the interaction between reproductive mode and dispersal traits on the one hand and environmental and habitat setting affecting establishment success on the other. We evaluated how environmental/habitat setting affects population genetic variation (i.e. variation in genetic diversity and structure) when regulated by contrasting dispersal traits. We used fungus-specific microsatellite markers to examine genetic diversity and structure of two closely related epiphytic lichen fungi that differ in their primary reproductive mode: Nephroma laevigatum (sexually reproducing, n = 191, 10 microsatellites) and N. parile (asexually reproducing, n = 182, 12 microsatellites), along a steep climatic gradient in Scotland. Despite their reproductive differences, we found a high proportion of clones in both species and a background pattern of genetic structure related to climatic gradients. We also demonstrated that woodland connectivity, rather than geographic distance, explained genetic diversity in both species. Environmental/habitat setting, modulated by the reproductive mode of the species, affects genetic diversity and structure, but the putative dissimilarity in their reproductive mode is less important than has been previously assumed. We reinforce the importance of protecting highly connected populations, positioned along a gradient capturing the segregation of gene pool differences in response to climatic variation.

Genetic diversity and population structure of the endangered plant Salix taishanensis based on CDDP markers

Eukaryotic phytoplankton exhibit an enormous species richness, displaying a range of phylogenetic, morphological and physiological diversity. Yet, until recently, very little was known about the diversity, genetic variation and evolutionary processes within species and populations. An approach to explore this diversity and to understand evolution of phytoplankton is to use population genetics as a conceptual framework and methodology. Here, we discuss the patterns, processes and questions that population genetic studies have revealed in eukaryotic phytoplankton. First, we describe the main biological processes generating genetic variation. We specifically discuss the importance of life-cycle complexity for genetic and phenotypic diversity and consider how such diversity can be maintained during blooms when rapid asexual proliferation dominates. Next, we explore how genetic diversity is partitioned over time and space, with a focus on the processes shaping this structure, in particular selection and genetic exchange. Our aim is also to show how population genetics can be used to make inferences about realized dispersal and sexual recombination, as these processes are so difficult to study directly. Finally, we highlight important open questions and suggest promising avenues for future studies that will be made possible by new sequencing technologies

Sophora moorcroftiana is a perennial leguminous low shrub endemic to the Yarlung Zangbo River basin in Tibet with irreplaceable economic and ecological value. To determine the drivers of evolution in this species, 225 individuals belonging to 15 populations from different geographic locations were sampled, and population genetics was studied using high-throughput genotyping-by-sequencing (GBS). Based on genetic diversity analysis, phylogenetic analysis, principal component analysis, and structure analysis, 15 natural populations were clustered into the following five subgroups: subgroup I (Shigatse subgroup) was located in the upper reaches of the Yarlung Zangbo River with a relatively high level of population genetic variation (means for PIC, Shannon and PI were 0.173, 0.326 and 0.0000305, respectively), and gene flow within the subgroup was also high (mean value for Nm was 4.67). Subgroup II (including Pop 7 and Pop 8; means for PIC, Shannon and PI were 0.182, 0.345 and 0.0000321, respectively), located in the middle reaches of the Yarlung Zangbo River had relatively high levels of gene flow with the populations distributed in the upper and lower reaches. The Nm between subgroup II with subgroups I and III was 3.271 and 2.894, respectively. Considering all the genetic diversity indices Pop 8 had relatively high genetic diversity. Subgroup III (the remaining mixed subgroup of Lhasa and Shannan) was located in the middle reaches of the Yarlung Zangbo River and the means for PIC, Shannon and PI were 0.172, 0.324 and 0.0000303, respectively. Subgroup IV (Nyingchi subgroup), located in the lower reaches of the Yarlung Zangbo River basin, showed a further genetic distance from the other subgroups and the means for PIC, Shannon and PI were 0.147, 0.277 and 0.0000263, respectively. Subgroup V (Nyingchi Gongbu Jiangda subgroup), located in the upper reaches of the Niyang River, had the lowest level of genetic variation (means for PIC, Shannon and PI were 0.106, 0.198 and 0.0000187, respectively) and gene flow with other populations (mean value for Nm was 0.42). According to the comprehensive analysis, the S. moorcroftiana populations generally expanded from upstream to downstream and displayed a high level of genetic differentiation in the populations in the upper and lower reaches. There were high levels of gene exchange between the central populations with upstream and downstream populations, and wind-induced seed dispersal was an important factor in the formation of this gene exchange mode.

AimThe centre‐periphery hypothesis (CPH) states that peripheral populations exhibit lower genetic diversity, abundance and size, and higher differentiation compared to central populations, due to a decline in environmental suitability towards range margins. Here, we tested if neutral genetic diversity and functional leaf trait diversity fit the predicted patterns of the CPH.LocationCerrado, Brazil.TaxonQualea grandiflora (Vochysiaceae) and Annona crassiflora (Annonaceae).MethodsVariation in eight functional leaf traits and nine or eight microsatellite loci were analysed in 37 populations (777 individuals) of Q. grandiflora and 21 populations (397 individuals) of A. crassiflora. We tested CPH using three distinct centres of species’ range: geographical (centre of species’ geographic occurrence), historical (centre of species’ refugia) and ecological (centre of species’ current suitability areas). Generalised linear regressions were performed between genetic diversity and differentiation, coefficients of variation and means of leaf metamer traits of populations and their distances from each centre.ResultsA decrease in allele richness was observed from central towards peripheral populations for ecological (both species) and geographical centres (Q. grandiflora). Overall, the results for both species pointed to a decrease in metamer vigour towards marginal populations, pattern consistent with a decrease in environmental suitability towards periphery as predicted by CPH. Besides geographical and ecological centres, leaf traits fitted CPH considering historical centre.Main ConclusionsResults for leaf traits and genetic diversity of two phylogenetically distant species indicate the consistency of the CPH for Cerrado species. Our results highlight the importance of considering distinct centres and a great number of populations along species’ range to better determinate the processes underlying the distribution of genetic diversity and functional traits. The low genetic diversity and metamer vigour in marginal populations can explain the Cerrado endemism of studied species and suggest that the ongoing climatic changes can be critical for their survival.

Population genetics and gene flow of the seagrass, Syringodium isoetifolium based on Start codon targeted (SCoT) marker from Palk Bay and Chilika Lake, India

Marine angiosperms, or seagrasses, continue to be a major focus of marine biologists because of their important ecological role in many coastal ecosystems. Seagrass population biology could benefit from a population genetic perspective because genetic data enable the extraction of useful demographic information such as isolation and gene flow between demes. Moreover, population genetic processes may contribute to the growing ecological risks of local population extinction. Progress in seagrass genetics is partly driven by novel genetic markers which detect variation at the DNA level and overcome the limited polymorphism of allozymes. Key results of studies in the past decade, mostly using RAPD and microsatellites, were (1) considerable genetic and genotypic (clonal) diversity is present in several species in contrast to earlier notions of low polymorphism detected at allozyme loci, and (2) genetic differentiation among populations seems to be the rule despite earlier reports of genetic uniformity. Pronounced genetic structure was detected between populations of 4 species examined thus far (Posidonia oceanica, P. australis, Zostera marina, Thalassia testudinum). The FST estimates varied widely and ranged from 0.01 to 0.623 across studies and species. Genetic differentiation at a systematic range of scales was only studied in eelgrass Zostera marina, where it was positively correlated with geographic distance. The high polymorphism of RAPD or microsatellite markers will allow the augmention of indirect estimates of gene flow by methods detecting individual immigration events through paternity analysis or assignment tests. Important conservation related issues such as the level of inbreeding and the effective population size have also been obtained from genetic marker data, but results are too scarce at the moment to allow generalizations. In Zostera marina and Posidonia australis, several population genetic attributes such as clonal diversity, mating system and effective population size varied among populations within species, highlighting that there is no Œtypical¹ population. An important gap in our knowledge is whether the effects of natural population fragmentation and patchiness enhance the genetic isolation of populations due to anthropogenic disturbances. It is also unclear whether genetic differentiation displayed at marker loci are correlated with fitness-related plant traits, and whether genetic or genotypic diversity is important for medium- to long-term meadow persistence. An assessment of the genetic and genotypic diversity at marker loci should be combined with experiments on the ecological plasticity and reaction norms of genotypes composing the populations in question. This way, the role of genetic diversity for seagrass population maintenance and growth in the face of changing environmental conditions can be evaluated.

BackgroundPrunus tomentosa Thunb, a fruit tree native to China, is an important and excellent plant material. It exhibits high adaptability to almost all soil types and climatic conditions. The germplasm resources are found in the six geographical regions of China, covering a vast expanse, and comprise a variety of ecological types. However, little is known about genetic diversity and population structure, with its abundant genetic information. Nuclear simple sequence repeat markers, with biparentally inherited characteristics, is powerful for evaluating the genetic diversity of population. Therefore, this research assessed the genetic diversity and population structure of P. tomentosa by collecting extensive samples. The finding will contribute to not only proposing scientific conservation strategies of P. tomentosa but also developing the germplasm to breed novel cherry cultivar.ResultsA total of 822 germplasms from 40 populations were used for assessing. The indicators of genetic diversity showed high values, including observable heterozygosity (0.546), expected heterozygosity (0.819), Shannon’s information index (I = 1.951), polymorphism information content (0.799). The populations displaying the greatest diversity—Gan-XlM, Shaan-HM, and Gan-ZhC. In addition, extensive genetic differentiation was detected. The genetic differentiation coefficient (FST) values calculated from heterozygosity and analysis of molecular variance were greater than 0.15. Gene flow was relatively stable (number of migrants [Nm] = 1.065). Mantel test analysis showed that there was a significant correlation (R2 = 0.065, P < 0.05) between the genetic distance and the geographical distance of the populations. Integrated cluster, structure, and principal component analysis indicated that the 40 populations were clustered into a Northwest Group and a Northeast Group. However, the Chuan-Aba, Xin-TKS, and Xin-ALR populations were clearly differentiated.ConclusionsThe P. tomentosa populations showed high or moderate polymorphism. The genetic differentiation within each population was higher than that between populations. There was a significant correlation between the genetic distance and the geographical distance. Based on genetic diversity and population differentiation levers, the most diverse populations—Gan-XlM, Shaan-HS, and Gan-PL from Gansu and Shaanxi provinces, should first be protected and applied to the innovation of cherry germplasm, followed by significantly differentiated populations, including Chuan-Aba, Ning-HlM, and Gan-PL.

Tai-Kadai-speaking Gelao population: Forensic features, genetic diversity and population structure

Fruit‐bagging is being used as a pest management tool to control fruit moths on several continents. However, nothing is known about how this physical control method affects population genetics of these moths. Focusing on the oriental fruit moth, Grapholita (= Cydia) molesta (Busck) (Lepidoptera: Tortricidae), we used five polymorphic microsatellite loci and two mitochondrial gene sequences to investigate the genetic diversity and genetic structure of populations from three fruit‐bagged and two unbagged apple orchards in five regions of a major fruit‐growing area of China. We sampled each orchard 3× during the season and found high genetic diversity in the samples of populations collected. Populations from fruit‐bagged and unbagged orchards were genetically significantly differentiated, indicating a clear effect of the pest management method applied. Genetic structures of the populations under a given management regime changed in the course of the season in a characteristic manner, and within the same regime, patterns were always similar at a given sampling time. There was no significant isolation by geographical distance. Population genetics from both orchard types did not resemble one another at the beginning of the season, but they did rather at the end. Potential reasons for this unexpected direction of change in population genetic structure are discussed, and we hypothesize that diapause‐related characteristics may account for the patterns observed. The current study documents that pest management methods applied can have an important impact on the genetic diversity and genetic structure of targeted pest insect populations.

Human pluripotent stem (hPS) cells can, in theory, be differentiated into any cell type, making them a powerful in vitro model for human biology. Recent technological advances have facilitated large-scale hPS cell studies that allow investigation of the genetic regulation of molecular phenotypes and their contribution to high-order phenotypes such as human disease. Integrating hPS cells with single-cell sequencing makes identifying context-dependent genetic effects during cell development or upon experimental manipulation possible. Here we discuss how the intersection of stem cell biology, population genetics and cellular genomics can help resolve the functional consequences of human genetic variation. We examine the critical challenges of integrating these fields and approaches to scaling them cost-effectively and practically. We highlight two areas of human biology that can particularly benefit from population-scale hPS cell studies, elucidating mechanisms underlying complex disease risk loci and evaluating relationships between common genetic variation and pharmacotherapeutic phenotypes.

The genetic diversity and population structure of 25 natural populations of Thymus capitatus, from five ecological areas, were analysed using eight isozymes. For all populations, 11 polymorphic loci were detected, and several of them showed rare alleles. A high genetic diversity within populations (Ap = 1.82; P = 62.88%; Ho = 0.116) and an excess of heterozygosity were observed. A high level of inbreeding within populations was observed (FIS = 0.471). High differentiation and low gene flow (Nm = 0.821) were detected among populations (FST = 0.219). The genetic variation within and among ecological groups varied according to the bioclimate. Population structuration depends on geographic distance between sites rather than on bioclimate (Mantel’s test; r = 0.251; P = 0.004). Nei’s genetic distances (D) values calculated between pairs of populations were globally low with a mean of 0.047. The unweighted pairwise groups method using arithmetic average dendrogram showed fourth sub‐clusters. Population groupings occur with evident relationship to geographic location. The substantial differentiation and the high genetic similarities between populations indicate that populations have been recently isolated as a result of anthropic pressure. In situ conservation must first focus on populations with a high level of genetic diversity and rare alleles. Ex situ preservation should be elaborated by collecting seeds within populations that showed a high level of genetic diversity in each ecological group.

Aim Invasive alien species usually exhibit very high adaptation and rapid evolution in a new environment, but they often have low levels of genetic diversity (invasive species paradox). Genetic variation and population genetic structure of feral American mink, Neovison vison, in Poland was investigated to explain the invasion paradox and to assess current gene flow. Furthermore, the influence of mink farming on adaptation of the feral population was evaluated by comparing the genetic structure of feral and ranch mink.Location Samples from feral mink were collected in 11 study areas in northern and central Poland and from ranch mink at 10 farms distributed throughout the country.Methods A 373‐bp‐long mtDNA control region fragment was amplified from 276 feral and 166 ranch mink.Results Overall, 31 haplotypes, belonging to two groups from genetically diverse sources, were detected: 11 only in feral mink, 12 only in ranch mink and eight in both. The genetic differentiation of feral mink from the trapping sites was high, while that among ranch mink from various farms was moderate. There was no significant relationship between genetic and geographic distance. The number of trapping sites where given haplotypes occurred correlated with the number of farms with these haplotypes. The mink from two sites were the most divergent, both from all other feral mink and from ranch mink. Comparison of mtDNA and microsatellite differentiation suggests male‐biased dispersal in this species.Main conclusions American mink in Poland exhibit high genetic diversity and originate from different source populations of their native range. The process of colonization was triggered by numerous escapees from various farms and by immigrants from Belarus. The genetic structure of local feral mink populations was shaped by the founder effect and multiple introductions. The genomic admixture that occurred during mixing of different populations might have increased the fitness of individuals and accelerated the invasiveness of this species.