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Different photoperiodic responses in diapause induction can promote the maintenance of genetic diversity via the storage effect in Daphnia pulex

Understanding mechanisms that promote the maintenance of biodiversity (genetic and species diversity) has been a central topic in evolution and ecology. Previous studies have revealed that dormancy can contribute to coexistence of competing genotypes or species in fluctuating environments via the storage effect. However, they tended to focus on differences in reproductive success (e.g., seed yield) and diapause termination (e.g., germination) timing. Here we tested whether different photoperiodic responses in diapause induction can promote coexistence of two parthenogenetic (asexual) genotypes of Daphnia pulex in Lake Fukami-ike, Japan. Through laboratory experiments, we confirmed that short day length and low food availability induced the production of diapausing eggs. Furthermore, we found that one genotype tended to produce diapausing eggs in broader environmental conditions than the other. Terminating parthenogenetic reproduction earlier decreases total clonal production, but the early-diapausing genotype becomes advantageous by assuring reproduction in "short" years where winter arrival is earlier than usual. Empirically parameterized theoretical analyses suggested that different photoperiodic responses can promote coexistence via the storage effect with fluctuations of the growing season length. Therefore, timing of diapause induction may be as important as diapause termination timing for promoting the maintenance of genetic diversity in fluctuating environments.

Dataset: T-DNA characterization of genetically modified 3-R-gene late blight resistant potato events with a novel procedure utilizing the Samplix Xdrop® Enrichment Technology

Before commercialization of genetically modified crops, the events carrying the novel DNA must be thoroughly evaluated for agronomic, nutritional, and molecular characteristics. Over the years, Polymerase Chain Reaction-based methods, Southern blot, and short-read sequencing techniques have been utilized for collecting molecular characterization data. Multiple genomic applications are necessary to determine the insert location, flanking sequence analysis, characterization of the inserted DNA, and determination of any interruption of native genes. These techniques are time-consuming and labor-intensive, making it difficult to characterize multiple events. Current advances in sequencing technologies are enabling whole genomic sequencing of modified crops to obtain full molecular characterization. However, in polyploids, such as the tetraploid potato, it is a challenge to obtain whole genomic sequencing coverage that meets regulatory approval of the genetic modification. Here we describe an alternative to labor-intensive applications with a novel procedure using Samplix Xdrop® enrichment technology and next-generation Nanopore sequencing technology to more efficiently characterize the T-DNA insertions of four genetically modified potato events developed by the Feed the Future Global Biotech Potato Partnership: DIA_MSU_UB015, DIA_MSU_UB255, GRA_MSU_UG234 and GRA_MSU_UG265 (derived from regionally important varieties Diamant and Granola). Using the Xdrop® /Nanopore technique, we obtained a very high sequence read coverage within the T-DNA and junction regions. In three of the four events, we were able to use the data to confirm single T-DNA insertions, identify insert locations, identify flanking sequences, and characterize the inserted T-DNA. We further used the characterization data to identify native gene interruption and confirm the stability of the T-DNA across clonal cycles. These results demonstrate the functionality of using the Xdrop® /Nanopore technique for T-DNA characterization. This research will contribute to meeting regulatory safety and regulatory approval requirements for commercialization with small shareholder farmers in target countries within our partnership.

Data from: Genetic mechanism of non-targeted-site resistance to diquat in Spirodela polyrhiza

Understanding non-target-site resistance (NTSR) to herbicides represents a pressing challenge as NTSR is widespread in many weeds. Using the giant duckweed (Spirodela polyrhiza) as a model, we systematically investigated genetic and molecular mechanisms of diquat resistance, which can only be achieved via NTSR. Screening the diquat resistance among 138 genotypes suggested more than 8.5-fold resistance differences. Further experiments suggested that diquat uptake and antioxidant-related processes jointly contributed to diquat resistance in S. polyrhiza. Using a genome-wide association approach, we identified candidate genes that are associated with diquat resistance in S. polyrhiza, which includes a homolog of dienelactone hydrolase.

Genetic admixture between Central European and Alpine wolf populations

The recovery and expansion of formerly isolated wolf populations in Europe raise questions about the nature of their interactions and future consequences for population viability and conservation. Will fragmented populations fuse or maintain a certain level of isolation with migration? Central Europe is suitable for obtaining empirical data in this field as it represents a "crossroad" with the potential for contact among several phylogeographic lineages. In this study, non-invasive genetic samples obtained during population monitoring in the Bohemian and Bavarian Forest (BBF) mountain ranges in the Czech Republic and Germany (Bohemian Massif) were analysed at different neutral markers including mitochondrial sequence, nuclear autosomal microsatellites and gonosomal sex markers. Resultant genetic profiles were compared with reference data to study population ancestry. Both cluster analyses of microsatellite genotypes and syntopic occurrence of haplotypes HW01 and HW22 showed genetic admixture between Central European and Alpine populations. This represents secondary contact and interbreeding of formerly allopatric populations with different phylogeographic histories and distant expansion centres in different biomes in the Baltic region versus the Apennine peninsula and Alps. Moreover, the study describes the founding event and genealogy of this admixed deme, inhabiting intermediate environmental conditions compared to parental forms, and emphasises the role of protected areas as stepping stones in the range recolonization process in endangered large mammals.

Dissecting the genetic architecture of quantitative traits using genome-wide identity-by-descent sharing

Additive and dominance genetic variances underlying the expression of quantitative traits are important quantities for predicting short-term responses to selection, but they are notoriously challenging to estimate in most non-model wild populations. Specifically, large-sized or panmictic populations may be characterized by low variance in genetic relatedness among individuals which in turn, can prevent accurate estimation of quantitative genetic parameters. We used estimates of genome-wide identity-by-descent (IBD) sharing from autosomal SNP loci to estimate quantitative genetic parameters for ecologically important traits in nine-spined sticklebacks (Pungitius pungitius) from a large, outbred population. Using empirical and simulated datasets, with varying sample sizes and pedigree complexity, we assessed the performance of different crossing schemes in estimating additive genetic variance and heritability for all traits. We found that low variance in relatedness characteristic of wild outbred populations with high migration rate can impair the estimation of quantitative genetic parameters and bias heritability estimates downwards. On the other hand, the use of a half-sib/full-sib design allowed precise estimation of genetic variance components, and revealed significant additive variance and heritability for all measured traits, with negligible dominance contributions. Genome-partitioning and QTL mapping analyses revealed that most traits had a polygenic basis and were controlled by genes at multiple chromosomes. Furthermore, different QTL contributed to variation in the same traits in different populations suggesting heterogenous underpinnings of parallel evolution at the phenotypic level. Our results provide important guidelines for future studies aimed at estimating adaptive potential in the wild, particularly for those conducted in outbred large-sized populations.

Data from: The genetic basis of dispersal in a vertebrate metapopulation

Dispersal affects evolutionary processes by changing population size and genetic composition, influencing the viability and persistence of populations. Investigating which mechanisms underlie variation in dispersal phenotypes and whether populations harbor adaptive potential for dispersal is crucial to understanding the eco-evolutionary dynamics of this important trait. Here, we investigate the genetic architecture of dispersal among successfully recruited individuals in an insular metapopulation of house sparrows. We use an extensive long-term individual-based ecological data set and high-density single nucleotide polymorphism (SNP) genotypes for over 2500 individuals. We conducted a genome-wide association study (GWAS), finding a relationship between dispersal probability and an SNP located near genes known to regulate circadian rhythmic, glycogenesis and exercise performance, among other functions. However, this SNP only explained 3.8% of variance, suggesting that dispersal is a polygenic trait. We then used an animal model to estimate heritable genetic variation (σA2 ), which composes 10% of the total variation in dispersal probability. Finally, we investigated differences in σA2 across populations occupying ecologically relevant habitat types (farm vs. non-farm) using a genetic-groups animal model. We found different adaptive potentials across habitats, with higher mean breeding value, σA2 , and heritability for the habitat presenting lower dispersal rates, suggesting also different roles of environmental variation. Our results suggest a complex genetic architecture of dispersal, and demonstrate that adaptive potential may be environment-dependent in key eco-evolutionary traits. The eco-evolutionary implications of such environment-dependence and consequent spatial variation are likely to become ever more important with the increased fragmentation and loss of suitable habitats for many natural populations.

Data from: The Drosophila Genetic Reference Panel (DGRP) on locomotor activity across different environmental conditions

In nature, organisms are exposed to variable and occasionally stressful environmental conditions. Responses to diurnal and seasonal fluctuations, such as temperature and food accessibility, involve adaptive behavioral and physiological changes. While much work has been done on understanding the genetic architecture and evolutionary potential of stress tolerance traits under constant thermal conditions, there has been less focus on the quantitative genetic background in variable environments. In this study, we use the Drosophila Genetic Reference Panel (DGRP) to investigate locomotor activity, a key behavioral trait, under variable natural thermal conditions during the summer in a temperate environment. Male flies from 100 DGRP lines were exposed to natural thermal and light conditions in Drosophila activity monitors across three experimental days. We found that activity was highly temperature- and time-dependent and varied between lines both within and between days. Further, we observed variation in genetic and environmental variance components, with low to moderate estimates of the heritability for locomotor activity, consistently peaking in the afternoons. Moreover, we showed that the estimated genetic correlations of locomotor activity between two time points decreased as the absolute differences in ambient temperature was increased. In conclusion, we find that the genetic background for locomotor activity is environment specific and we conclude that more variable and unpredictable future temperatures will likely have a strong impact on the evolutionary trajectories of behavioral traits in ectotherms.

Population genetics of the Four Corners potato (Solanum jamesii)

The domestication of wild plant species can begin with gathering and transport of propagules by Indigenous peoples. The effect on genomic composition, especially in clonal, self-incompatible perennials would be instantaneous and drastic with respect to new, anthropogenic populations subsequently established. Populations of the Four Corners potato, Solanum jamesii Torr., associated with archaeological sites in Utah and northern Arizona are unable to produce seeds and fruits unless crossed with non-archaeological populations. Presumably, founder events reduced genetic diversity and mating capability when tubers were transported and established in ancient gardens. Herein genetic sequencing (GBS) data is used to further examine the hypothesis of domestication in this culturally significant species by sampling 25 archaeological and non-archaeological populations. Archaeological populations from Utah, Colorado, and northern Arizona have lower levels of polymorphic loci, unique alleles, and heterozygosity than non-archaeological populations from the Mogollon Region of central Arizona and New Mexico. Principle components analysis, Fst values, and structure analysis revealed that genetic relationships among archaeological populations did not correspond to geographic proximity. Populations near Escalante, Utah were either derived from those found on the Mogollon Rim (400 km south) or related to those in Bears Ears (178 km east). Populations in Chaco Canyon are also similar to Escalante, but those in Mesa Verde, Chimney Rock, and El Morro have affinities to southern New Mexico and Texas. Movement of tubers from the Mogollon Region may have occurred many times and in multiple directions during the past, resulting in the complex genetic patterns seen in these populations from across the Four Corners Region.

Data from: The impact of plant genetic variation, drought, and leaf nitrogen on plant-herbivore interactions

Plant genotype, drought stress, and their interaction are among the factors contributing to the susceptibility of plants to herbivory. The plant's nitrogen concentration, a critical and often limiting nutrient, differs with plant genotype and drought. Still, few studies have investigated the impact of the interaction of genotype and drought on herbivory and plant nitrogen. We established a common garden in Duluth, MN, of tall goldenrod, Solidago altissima, collected from a local Minnesota site to analyze the effects of goldenrod genotype and drought stress on leaf nitrogen and the preference and performance of the chrysanthemum lace bug, Corythucha marmorata. Lace bugs had oviposition, nymph, and adult preferences among host plant genotypes, water treatments, and among genotype and water treatment combinations. Nymph and adult survival and adult mass varied significantly due to plant genotype, water treatment, the interaction of plant and water treatment, and the interaction of treatment with lace bug density. Oviposition preference and offspring performance were significantly positively related. Leaf nitrogen increased with the increasing severity of the water limitation in the absence of lace bugs. However, in the presence of lace bugs, there was no difference in nitrogen among water treatments.

Data from: Genetic consequences of improved river connectivity in brown trout (Salmo trutta)

Fragmentation of watercourses poses a significant threat to biodiversity, particularly for migratory fish species. Mitigation measures such as fishways, have been increasingly implemented to restore river connectivity and support fish migration. The effects of such restoration efforts are typically tested using telemetry and fisheries methods, which do not fully capture the broader population movements that may have important consequences for population viability. We performed a before-and-after control-impact (BACI) study using genetic tools (SNPs) to investigate the effect of a newly implemented fishway, aiming to enhance upstream spawning migration of brown trout (Salmo trutta Linnaeus) in a reservoir with two headwater tributaries fragmented by man-made weirs. Another reservoir with two barrier-free tributaries was also analysed as a control. Our results showed that the isolated brown trout population was spawning in the reservoir before the installation of the fishway, and we found genetic structuring and differentiation between fragmented headwater tributaries before the fishway construction, but not in the control reservoir. Unexpectedly, after the fishway construction we observed signals consistent with increased genetic differentiation between populations of newly recruited juvenile fish in the reservoir tributary and fish in the reservoir. We propose this was caused by newly enabled philopatric behaviour of brown trout to their natal spawning tributary. In contrast, we did not find any genetic changes in the tributary without a fishway or in the barrier-free reservoir system. Given the scarcity of similar studies, we advocate for an increased use of genetic analyses in BACI studies to monitor and evaluate the effect of efforts to restore habitat connectivity and inform future management strategies.

The conservation genetics of Iris lacustris (Dwarf Lake Iris), a Great Lakes endemic

Iris lacustris, a northern Great Lakes endemic, is a rare species known from 165 occurrences across Lake Michigan and Huron in the United States and Canada. Due to multiple factors, including habitat loss, lack of seed dispersal, patterns of reproduction, and forest succession, the species is threatened. Early population genetic studies using isozymes and allozymes recovered no to limited genetic variation within the species. To better explore genetic variation across the geographic range of I. lacustris and to identify units for conservation, we used tunable Genotyping-by-Sequencing (tGBS) with 171 individuals across 24 populations from Michigan and Wisconsin, and because the species is polyploid, we filtered the single nucleotide polymorphism (SNP) matrices using polyRAD to recognize diploid and tetraploid loci. Based on multiple population genetic approaches, we resolved three to four population clusters that are geographically structured across the two ranges of the species. The species migrated from west to east across its geographic range, and minimal genetic exchange has occurred among populations. Four units for conservation are recognized, but nine adaptive units were identified, providing evidence for local adaptation across the geographic range of the species. Population genetic analyses with all, diploid, and tetraploid loci recovered similar results, which suggests that methods may be robust to variation in ploidy level.

opencc-zeroDec 2023View details →

Data from: Evaluating genotyping-in-thousands by sequencing as a genetic monitoring tool for a climate sentinel mammal using non-invasive and archival samples

Genetic tools for wildlife monitoring can provide valuable information on spatiotemporal population trends and connectivity, particularly in systems experiencing rapid environmental change. Though many DNA sequencing approaches still require high quality and quantity of DNA obtained from traditional sources (e.g. blood and tissue), rapid genotyping tools such as Genotyping-in-Thousands by sequencing (GT-seq) have improved our ability to make use of degraded and less concentrated DNA commonly obtained from non-invasive and archival samples. Here, we developed a multi-purpose GT-seq panel (307 single nucleotide polymorphisms) for a climate sentinel mammal (the American pika, Ochotona princeps) for use as a genetic tool for monitoring populations in the Canadian Rocky Mountains. We optimized the panel using contemporary tissue samples (n = 77) and subsequently applied it to archival tissue (n = 17) and contemporary fecal pellet samples (n = 129) to evaluate its effectiveness at identifying individuals and sex, estimating relatedness, and inferring population structure. The panel demonstrated high efficacy with contemporary and archival tissue samples (94.7% and 90.5% genotyping success, respectively) and negligible genotyping error (0.001% and 0.0%, respectively). Despite relatively high genotyping success for fecal pellet samples (79.7%), high genotyping error (28.4%) limited its power as a monitoring tool to assess genetic variation using non-invasive samples and highlighted the need for further optimization around sample and data collection.

zenodo36/100

Analysis of gene expression in the postmortem brain of neurotypical Black Americans reveals contributions of genetic ancestry: Source and Supplementary Data

Source and Supplementary data for AANRI manuscript

opencc-by-4.0Mar 2024View details →

Considerable genetic diversity and structure despite narrow endemism and limited ecological specialization in the Hayden's ringlet, Coenonympha haydenii

Understanding the processes that underlie the development of population genetic structure is central to the study of evolution. Patterns of genetic structure can reveal signatures of isolation by distance, barriers to gene flow, or even the genesis of speciation. However, it is unclear how severe range restriction might impact the processes that dominate the development of genetic structure. In narrow endemic species, is population structure likely to be adaptive in nature, or rather the result of genetic drift? In this study, we investigated patterns of genetic diversity and structure in the narrow endemic Hayden's ringlet butterfly. Specifically, we asked to what degree genetic structure in the Hayden's ringlet can be explained by isolation by distance, isolation by resistance (in the form of geographic or ecological barriers to migration between populations), and isolation by environment (in the form of differences in host plant availability and preference). We employed a genotyping-by-sequencing (GBS) approach coupled with host preference assays, Bayesian modeling, and population genomic analyses to answer these questions. Our results suggest that despite their restricted range, levels of genetic diversity in the Hayden's ringlet are comparable to those seen in more widespread butterfly species. Hayden's ringlets showed a strong preference for feeding on grasses relative to sedges, but neither larval preference nor potential host availability at sampling sites correlated with genetic structure. We conclude that geography, in the form of isolation by resistance and simple isolation by distance, was the major driver of contemporary patterns of differentiation in this narrow endemic species.

Data from: Vertically inherited microbiota and environment modifying behaviors conceal genetic variation in dung beetle life history

Diverse organisms actively manipulate their (sym)biotic and physical environment in ways that feedback on their own development. However, the degree to which these processes affect microevolution remains poorly understood. The gazelle dung beetle both physically modifies its ontogenetic environment and structures its biotic interactions through vertical symbiont transmission. By experimentally eliminating i) physical environmental modifications, and ii) the vertical inheritance of microbes, we assess how environment modifying behavior and microbiome transmission shape heritable variation. We found that depriving larvae from symbionts and environment modifying behaviors increased additive genetic variance and heritability for development time but not body size. This suggests that larvae's ability to manipulate their environment has the potential to modify heritable variation and to facilitate the accumulation of cryptic genetic variation. This cryptic variation may become released and selectable when organisms encounter environments that alter the degree to which they can be manipulated. Furthermore, we found heritable variation for the response to the elimination of environmental modifications, indicating that genotypes differ in their dependence on the ability to manipulate their environment. Our findings highlight that the ability of organisms to actively manipulate their environment may affect the potential of populations to evolve when encountering novel, stressful conditions.

Combining transinfected Wolbachia and a genetic sexing strain to control Aedes albopictus in laboratory-controlled conditions

The global expansion of Aedes albopictus has stimulated the development of environmental-friendly methods aiming at controlling disease transmission through the suppression of natural vector populations. Sterile male release programs are currently being deployed worldwide, and are challenged by the availability of an efficient sex separation that can be achieved mechanically at the pupal stage and/or by artificial intelligence at the adult stage, or through genetic sexing, which allows separating males and females at an early development stage. In this study, we combined the genetic sexing strain (GSS) previously established based on the linkage of dieldrin resistance to the male locus with a Wolbachia transinfected line. For this, we introduced either the wPip-I or the wPip-IV strain from Culex pipiens in an asymbiotic-Wolbachia-free Ae. albopictus line. We then measured the penetrance of CI and life history traits of both transinfected lines, selected the wPip-IV line, and combined it with the GSS. Population suppression experiments demonstrated a 90% reduction in population size and a 50% decrease in hatching rate. Presented results showed that such a combination has a high potential in terms of vector control but also highlighted associated fitness costs, which should be reduced before large-scale field assay.

Parallel evolution despite low genetic diversity in three-spined sticklebacks

The three-spined stickleback (Gasterosteus aculeatus) is a model organism for studies of parallel evolution in the wild; marine stickleback populations have repeatedly colonized and adapted to different brackish and freshwater habitats. Population genetic studies of European three-spined sticklebacks have usually been conducted only in high-latitude areas. Here, we analysed southern and northern European samples of marine and freshwater three-spined stickleback to test two hypotheses. First, southern European freshwater populations – which currently lack or have limited connection to marine populations – have lost genetic diversity due to population bottlenecks and inbreeding compared to their northern European counterparts. Second, the degree of genetic parallelism in response to freshwater colonisation is higher among northern than southern European populations as the latter have been isolated and likely subjected to strong genetic drift. The results show that southern populations exhibit lower genetic diversity but a higher degree of genetic parallelism than northern populations. Hence, they confirm the hypothesis that southern populations have lost genetic diversity, but this loss likely happened after they had already adapted to freshwater conditions, explaining the high degree of genetic parallelism in the south.

opencc-by-4.0Mar 2024View details →

zenodo36/100

Minimal dataset for the manuscript "Better together against genetic heterogeneity: a sex-combined joint main and interaction analysis of 290 quantitative traits in the UK Biobank".

Dataset "lin2024-sex_combined_interaction-association_signifincant_in_one_or_more_tests-summary.txt" is a minimal dataset to reproduce the figures and tables in the manuscript "Better together against genetic heterogeneity: a sex-combined joint main and interaction analysis of 290 quantitative traits in the UK Biobank".  To generate this dataset, see "https://github.com/BoxiLin/t2meta" Steps 0, 1. This dataset is the input for Steps 2, 3, 4, 5 to generate Figures 1-3 and Table 2-3.   ##### Column information ######################## The following columns are annotations on each variant in the GWAS, calculated across the analysis subset of 361,194 samples by the Neale lab: code: Phenotype identifier in the form of "[UKB Data field]_raw" variant: Unique variant identifier in the form "chr:pos:ref:alt", where "ref" is aligned to the forward strand. chr: Chromosome of the variant. pos: Position of the variant in GRCh37 coordinates. rsid: rs ID ref: Reference allele on the forward strand. alt: Alternate allele (not necessarily minor allele). p_hwe: Hardy-Weinberg p-value. info: Imputation INFO score as provided by UK Biobank.   The following columns are sex-stratified test statistics calculated by the Neale lab: minor_allele.x: Minor allele (AF < 0.5) in the female GWAS  minor_AF.x: Minor allele frequency in the female GWAS  beta.x: Estimated effect size of alt allele in the female GWAS  se.x: Estimated standard error of beta in the female GWAS tstat.x: t-statistic of beta estimate (= beta/se) in the female GWAS  pval.x: p-value of beta significance test in the female GWAS  minor_allele.y: Minor allele (AF < 0.5) in the male GWAS  minor_AF.y: Minor allele frequency in the male GWAS  beta.y: Estimated effect size of alt allele in the male GWAS  se.y: Estimated standard error of beta in the male GWAS  tstat.y: t-statistic of beta estimate (= beta/se) in the male GWAS  pval.y: p-value of beta significance test in the male GWAS    The following columns are sex-combined test statistics calculated in our analysis: T.I: test statsitic for interaction effect-only  p.T.I:  p-value of the interaction effect-only test  TSG.L:  test statsitic for inverse variance weighted meta-analysis p.TSG.L: p-value of the inverse variance weighted meta-analysis TSG.Q: test statsitic for the omnibus meta-analysis p.TSG.Q: p-value for the omnibus meta-analysis

Data for: Estimation of genetic parameters for the implementation of selective breeding in commercial insect production

Background There is a burgeoning interest in using insects as a sustainable source of food and feed, particularly by capitalising on various waste materials and by-products that are typically considered of low value. Enhancing the commercial production of insects can be achieved through two main approaches: optimising environmental conditions and implementing selective breeding strategies. In order to successfully target desirable traits through selective breeding, having a thorough understanding of the genetic parameters pertaining to those traits is essential. In this study, a full-sib half-sib mating design was used to estimate variance components and heritabilities for larval size and survival at day seven of development, development time and survival from egg to adult, and to estimate correlations between these traits, within an outbred population of house flies (Musca domestica), using high-throughput phenotyping for data collection. Results The results revealed low to intermediate heritabilities and positive genetic correlations between all traits except development time and survival to day seven of development and from egg to adulthood. Surprisingly, larval size at day seven exhibited a comparatively low heritability (0.10) in contrast to development time (0.25), a trait that is believed to have a stronger association with overall fitness. A decline in family numbers resulting from low mating success and high overall mortality reduced the amount of available data which resulted in large standard errors for the estimated parameters. Environmental factors made a substantial contribution to the phenotypic variation, which was overall high for all traits. Conclusions There is potential for genetic improvement in all studied traits and estimates of genetic correlations indicate a partly shared genetic architecture among the traits. All estimates have large standard errors. Implementing high-throughput phenotyping is imperative for the estimation of genetic parameters in fast developing insects, and facilitates age synchronisation, which is vital in a breeding population. In spite of endeavours to minimise non-genetic sources of variation, all traits demonstrated substantial influences from environmental components. This emphasises the necessity of thorough attention to the experimental design before breeding is initiated in insect populations.

Genetic insight into a polygenic trait using a novel Genome Wide Association approach in a wild amphibian population

Body size variation is central in the evolution of life history traits in amphibians, but the underlying genetic architecture of this complex trait is still largely unknown. Herein, we studied the genetic basis of body size and fecundity of the alternative morphotypes in a wild population of the Greek smooth newt (Lissotriton graecus). By combining a Genome-wide association approach with linkage disequilibrium network analysis, we were able to identify clusters of highly correlated loci thus maximizing sequence data for downstream analysis. The putatively associated variants explained 12.8% to 44.5% of the total phenotypic variation in body size and were mapped to genes with functional roles in the regulation of gene expression and cell cycle processes. Our study is the first to provide insights into the genetic basis of complex traits in newts and provides a useful tool to identify loci potentially involved in fitness related traits in small data sets from natural populations in non-model species.