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Understanding the impact of past climatic events on species may facilitate predictions of how species will respond to future climate change. To this end, we sampled populations of the common pond snail Radix balthica over the entire species range (northwestern Europe). Using a recently developed analytical framework that employs ecological niche modelling to obtain hypotheses that are subsequently tested with statistical phylogeography, we inferred the range dynamics of R. balthica over time. A Maxent modelling for present-day conditions was performed to infer the climate envelope for the species, and the modelled niche was used to hindcast climatically suitable range at the last glacial maximum (LGM) c. 21 000 years ago. Ecological niche modelling predicted two suitable areas at the LGM within the present species range. Phylogeographic model selection on a COI mitochondrial DNA data set confirmed that R. balthica most likely spread from these two disjunct refuges after the LGM. The match observed between the potential range of the species at the LGM given its present climatic requirements and the phylogeographically inferred refugial areas was a clear argument in favour of niche conservatism in R. balthica, thus allowing to predict the future range. The subsequent projection of the potential range under a global change scenario predicts a moderate pole-ward shift of the northern range limits, but a dramatic loss of areas currently occupied in France, western Great Britain and southern Germany. [ABSTRACT FROM AUTHOR]

Abstract Background Reliable taxonomic identification at the species level is the basis for many biological disciplines. In order to distinguish species, it is necessary that taxonomic characters allow for the separation of individuals into recognisable, homogeneous groups that differ from other such groups in a consistent way. We compared here the suitability and efficacy of traditionally used shell morphology and DNA-based methods to distinguish among species of the freshwater snail genus Radix (Basommatophora, Pulmonata). Results Morphometric analysis showed that shell shape was unsuitable to define homogeneous, recognisable entities, because the variation was continuous. On the other hand, the Molecularly defined Operational Taxonomic Units (MOTU), inferred from mitochondrial COI sequence variation, proved to be congruent with biological species, inferred from geographic distribution patterns, congruence with nuclear markers and crossing experiments. Moreover, it could be shown that the phenotypically plastic shell variation is mostly determined by the environmental conditions experienced. Conclusion Contrary to DNA-taxonomy, shell morphology was not suitable for delimiting and recognising species in Radix. As the situation encountered here seems to be widespread in invertebrates, we propose DNA-taxonomy as a reliable, comparable, and objective means for species identification in biological research.

The equilibrium of sex ratios in sexually reproducing species is often disrupted by various environmental and genetic factors, including endosymbionts like Wolbachia . In this study, we explore the highly female-biased sex ratio observed in the flea beetle, Altica lythri , and its underlying mechanisms. Ancient hybridization events between Altica species have led to mitochondrial DNA introgression, resulting in distinct mitochondrial haplotypes that go along with different Wolbachia infections (HT1-wLytA1, HT1*- uninfected, HT2-wLytA2, and HT3-wLytB). Notably, beetles with some haplotypes exclusively produce female offspring, suggesting potential Wolbachia -induced phenomena such as feminization of genetic males. However, the observed female bias could also be a consequence of the ancient hybridization resulting in nuclear-cytoplasmic conflicts between introgressed mtDNA and nuclear genes. Through transcriptomic analysis and the program SEX-DETector, we established markers for genotypic sex differentiation for A. lythri , enabling genetic sexing via qPCR. Our findings suggest that feminization of genetic males is contributing to the skewed sex ratios, highlighting the intricate dynamics of sex determination and reproductive strategies in this flea beetle. This study provides valuable insights into the dynamics of genetic conflicts, endosymbionts, and sex ratios, revealing the novel phenomenon of genetic male feminization in the flea beetle A. lythri ., Competing Interests: The authors declare no competing interests., (© 2024 The Author(s). Ecology and Evolution published by John Wiley & Sons Ltd.)

Resting stages of aquatic organisms that accumulate in the sediment over time are an exceptional resource that allows direct insights into past populations and addressing evolutionary questions. This is of particular interest in taxa that face relatively new environmental challenges, e.g., climate change and eutrophication, such as the Daphnia longispina species complex, a keystone zooplankton group in European freshwater ecosystems. However, genomic analysis might be challenging as DNA yield from many of these resting stages can be low and the material degraded. To reliably allow the resequencing of single Daphnia resting eggs from different sediment layers and characterize genomic changes through time, we performed whole-genome amplification to obtain DNA amounts suitable for genome resequencing and tested multiple protocols involving egg isolation, whole-genome amplification kits, and library preparation. A pre-sequencing contamination screening was developed, consisting of amplifying mitochondrial Daphnia and bacterial markers, to quickly assess and exclude possibly contaminated samples. In total, we successfully amplified and sequenced nine genomes from Daphnia resting eggs that could be identified as Daphnia longispina species. We analyzed the genome coverage and heterozygosity of these samples to optimize this method for future projects involving population genomic investigation of the resting egg bank., Competing Interests: The authors declare that they have no conflict of interest., (© 2022 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Mutations are the ultimate source of heritable variation and therefore the fuel for evolution, but direct estimates of mutation rates exist only for few species. We estimated the spontaneous single nucleotide mutation rate among clonal generations in the waterflea Daphnia galeata with a short-term mutation accumulation approach. Individuals from eighteen mutation accumulation lines over five generations were deep sequenced to count de novo mutations that were not present in a pool of F1 individuals, representing the parental genotype. We identified 12 new nucleotide mutations in 90 clonal generational passages. This resulted in an estimated single nucleotide mutation rate of 0.745 x 10-9 (95% c.f. 0.39 x 10-9-1.26 x 10-9), which is slightly lower than recent estimates for other Daphnia species. We discuss the implications for the population genetics of Cladocerans., Competing Interests: The authors have declared that no competing interests exist.

Hybridization and introgression are recognized as an important source of variation that influence adaptive processes; both phenomena are frequent in the genus Daphnia, a keystone zooplankton taxon in freshwater ecosystems that comprises several species complexes. To investigate genome-wide consequences of introgression between species, we provide here the first high-quality genome assembly for a member of the Daphnia longispina species complex, Daphnia galeata. We further resequenced 49 whole genomes of three species of the complex and their interspecific hybrids both from genotypes sampled in the water column and from single resting eggs extracted from sediment cores. Populations from habitats with diverse ecological conditions offered an opportunity to study the dynamics of hybridization linked to ecological changes and revealed a high prevalence of hybrids. Using phylogenetic and population genomic approaches, we provide first insights into the intra- and interspecific genome-wide variability in this species complex and identify regions of high divergence. Finally, we assess the length of ancestry tracts in hybrids to characterize introgression patterns across the genome. Our analyses uncover a complex history of hybridization and introgression reflecting multiple generations of hybridization and backcrossing in the Daphnia longispina species complex. Overall, this study and the new resources presented here pave the way for a better understanding of ancient and contemporary gene flow in the species complex and facilitate future studies on resting egg banks accumulating in lake sediment., (© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

Phenotypic variation plays an important role in how species cope with environmental challenges. Pinpointing which genes and genomic regions are underlying phenotypic variability thus helps to understand the processes of acclimation and adaptation. We used Daphnia as a system to identify candidates playing a role in phenotypic variation related to a predation risk environment with a genome-wide association approach. Furthermore, a gene co-expression network analysis allowed identifying clusters of co-expressed genes which correlated to life history traits. To enhance the understanding of the functional roles of the transcripts, we identified orthologs and paralogs from related species and used ontologies to annotate the candidates of interest. Our study revealed that only one life history trait and two morphometric traits have a genetic association in the presence of predation risk (fish kairomones), whereas most genotype-phenotype associations were detected in a genotype-environment interaction analysis for reproduction-related phenotypic traits. The gene co-expression network analysis identified a total of 44 modules, of which one module correlated to another life history trait namely the 'total number of broods'. The combined use of gene co-expression network and transcriptome-wide association analysis allowed the identification of 131 candidate transcripts associated with life history traits in Daphnia galeata. These results lay the ground for targeted studies to further understand phenotypic variability in this species., (© 2020 The Authors. Journal of Evolutionary Biology published by John Wiley & Sons Ltd on behalf of European Society for Evolutionary Biology.)

Hatching resting stages of ecologically important organisms such as Daphnia from lake sediments, referred to as resurrection ecology, is a powerful approach to assess changes in alleles and traits over time. However, the utility of the approach is constrained by a few obstacles, including low and/or biased hatching among genotypes. Here, we eliminated such bottlenecks by investigating DNA sequences isolated directly (i.e. without hatching) from resting eggs found in the sediments of Lake Constance spanning pre-, peri-, and post-eutrophication. While we expected genome-wide changes, we specifically expected changes in alleles related to pathways involved in mitigating effects of cyanobacterial toxins. We used pairwise F ST -analyses to identify transcripts that showed strongest divergence among the four different populations and a clustering analysis to identify correlations between allele frequency shifts and changes in abiotic and biotic lake parameters. In a cluster that correlated with the increased abundance of cyanobacteria in Lake Constance we find genes that have been reported earlier to be differentially expressed in response to the cyanobacterial toxin microcystin and to microcystin-free cyanobacteria. We further reveal the enrichment of gene ontology terms that have been shown to be involved in microcystin-related responses in other organisms but not yet in Daphnia and as such are candidate loci for adaptation of natural Daphnia populations to increased cyanobacterial abundances. In conclusion this approach of investigating DNA extracted from Daphnia resting stages allowed to determine frequency changes of loci in a natural population over time., (Copyright © 2021 Elsevier GmbH. All rights reserved.)

We present four new complete mitochondrial genomes for Dasypoda hirtipes, Melitta schultzei , Capicola nanula and Samba griseonigra belonging to the basally branching bee family Melittidae covering four genera in three tribes (Melittini, Hesperaspini, Dasypodaini) and two subfamilies (Melittinae, Dasypodainae). The mitogenomes vary between 15,884 and 20,324 bp in length and consist of the typical set of 13 protein-coding genes, 22 tRNAs, two rRNAs and the control region. These new mitogenomes raise the number of available mitochondrial genomes for the family Melittidae to five and will help to shed light on the phylogenetic relationships within Melittidae and their position within the Anthophila., Competing Interests: There is no financial interest or benefit arising from the here presented data. No potential conflict of interest was reported by the author(s)., (© 2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

Phenotypic plastic responses allow organisms to rapidly adjust when facing environmental challenges-these responses comprise morphological, behavioral but also life-history changes. Alteration of life-history traits when exposed to predation risk have been reported often in the ecological and genomic model organism Daphnia . However, the molecular basis of this response is not well understood, especially in the context of fish predation. Here, we characterized the transcriptional profiles of two Daphnia galeata clonal lines with opposed life histories when exposed to fish kairomones. First, we conducted a differential gene expression, identifying a total of 125 candidate transcripts involved in the predator-induced response, uncovering substantial intraspecific variation. Second, we applied a gene coexpression network analysis to find clusters of tightly linked transcripts revealing the functional relations of transcripts underlying the predator-induced response. Our results showed that transcripts involved in remodeling of the cuticle, growth, and digestion correlated with the response to environmental change in D .  galeata . Furthermore, we used an orthology-based approach to gain functional information for transcripts lacking gene ontology (GO) information, as well as insights into the evolutionary conservation of transcripts. We could show that our candidate transcripts have orthologs in other Daphnia species but almost none in other arthropods. The unique combination of methods allowed us to identify candidate transcripts, their putative functions, and evolutionary history associated with predator-induced responses in Daphnia . Our study opens up to the question as to whether the same molecular signature is associated with fish kairomones-mediated life-history changes in other Daphnia species., Competing Interests: None declared., (© 2020 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Sexual reproduction is pervasive in animals and has led to the evolution of sexual dimorphism. In most animals, males and females show marked differences in primary and secondary sexual traits. The formation of sex-specific organs and eventually sex-specific behaviors is defined during the development of an organism. Sex determination processes have been extensively studied in a few well-established model organisms. While some key molecular regulators are conserved across animals, the initiation of sex determination is highly diverse. To reveal the mechanisms underlying the development of sexual dimorphism and to identify the evolutionary forces driving the evolution of different sexes, sex determination mechanisms must thus be studied in detail in many different animal species beyond the typical model systems. In this perspective article, we argue that spiders represent an excellent group of animals in which to study sex determination mechanisms. We show that spiders are sexually dimorphic in various morphological, behavioral, and life history traits. The availability of an increasing number of genomic and transcriptomic resources and functional tools provides a great starting point to scrutinize the extensive sexual dimorphism present in spiders on a mechanistic level. We provide an overview of the current knowledge of sex determination in spiders and propose approaches to reveal the molecular and genetic underpinnings of sexual dimorphism in these exciting animals.

Gene expression patterns help to measure and characterize the effect of environmental perturbations at the cellular and organism-level. Complicating interpretation is the presence of uncharacterized or "hypothetical" gene functions for a large percentage of genomes. This is particularly evident in Daphnia genomes, which contains many regions coding for "hypothetical proteins" and are significantly divergent from many of the available arthropod model species, but might be ecologically important. In the present study, we developed a gene expression database, the Daphnia stressor database (http://www.daphnia-stressordb.uni-hamburg.de/dsdbstart.php), built from 90 published studies on Daphnia gene expression. Using a comparative genomics approach, we used the database to annotate D. galeata transcripts. The extensive body of literature available for Daphnia species allowed to associate stressors with gene expression patterns. We believe that our stressor based annotation strategy allows for better understanding and interpretation of the functional role of the understudied hypothetical or uncharacterized Daphnia genes, thereby increasing our understanding of Daphnia's genetic and phenotypic variability.

Understanding the genetic basis of local adaptation has long been a focus of evolutionary biology. Recently, there has been increased interest in deciphering the evolutionary role of Daphnia 's plasticity and the molecular mechanisms of local adaptation. Using transcriptome data, we assessed the differences in gene expression profiles and sequences in four European Daphnia galeata populations. In total, ~33% of 32,903 transcripts were differentially expressed between populations. Among 10,280 differentially expressed transcripts, 5,209 transcripts deviated from neutral expectations and their population-specific expression pattern is likely the result of local adaptation processes. Furthermore, a SNP analysis allowed inferring population structure and distribution of genetic variation. The population divergence at the sequence level was comparatively higher than the gene expression level by several orders of magnitude consistent with strong founder effects and lack of gene flow between populations. Using sequence homology, the candidate transcripts were annotated using a comparative genomics approach. Additionally, we also performed a weighted gene co-expression analysis to identify population-specific regulatory patterns of transcripts in D. galeata . Thus, we identified candidate transcriptomic regions for local adaptation in this key species of aquatic ecosystems in the absence of any laboratory-induced stressor., Competing Interests: None declared.

Phenotypic plasticity is the ability of a genotype to produce different phenotypes depending on the environment. It has an influence on the adaptive potential to environmental change and the capability to adapt locally. Adaptation to environmental change happens at the population level, thereby contributing to genotypic and phenotypic variation within a species. Predation is an important ecological factor structuring communities and maintaining species diversity. Prey developed different strategies to reduce their vulnerability to predators by changing their behaviour, their morphology or their life history. Predator-induced life history responses in Daphnia have been investigated for decades, but intra-and inter-population variability was rarely addressed explicitly. We addressed this issue by conducting a common garden experiment with 24 clonal lines of European Daphnia galeata originating from four populations, each represented by six clonal lines. We recorded life history traits in the absence and presence of fish kairomones. Additionally, we looked at the shape of experimental individuals by conducting a geometric morphometric analysis, thus assessing predator-induced morphometric changes. Our data revealed high intraspecific phenotypic variation within and between four D. galeata populations, the potential to locally adapt to a vertebrate predator regime as well as an effect of the fish kairomones on morphology of D. galeata ., Competing Interests: The authors declare that they have no competing interests.

The complex interplay of forces influencing genetic divergence among populations complicates the discovery of the genetic basis underlying local adaptation. Here, we utilized for the first time a combined reverse ecology and population transcriptomic approach to assess the contribution of thermal selection to population differentiation, thereby considering transcriptome-wide variation in both gene expression profiles and DNA sequences. We compared transcriptomes among four Daphnia galeata populations and identified transcripts potentially responding to local thermal selection based on an extensive literature search for candidate genes possibly under thermal selection in arthropods. Over-representation of temperature-relevant candidate genes among transcripts strongly contributing to sequence divergence among two populations indicates that local thermal selection acted on the coding sequence level. We identified a large number of transcripts, which may contribute to local thermal adaptation based on outlier tests and distinctive expression profiles. However, among these, temperature-relevant candidate genes were not over-represented compared to the global gene set, suggesting that thermal selection played a minor role in divergence among Daphnia populations. Interestingly, although the majority of genes contributing strongly to sequence divergence did not contribute strongly to divergence at the expression level and vice versa, the affected gene functions were largely consistent between the two data sets. This suggests that genetic and regulatory variation constitutes alternative routes for responses to natural selection. Our combined utilization of a population transcriptomics approach and literature-based identification of ecologically informative candidate genes represents a useful and powerful methodology with a wide range of applications in evolutionary biology., (© 2017 John Wiley & Sons Ltd.)

Altering thermal environments impose strong selection pressures on organisms, whose local persistence depends on adaptive phenotypic plastic and genetic responses. Thus far, adaptive change is monitored using phenotypic shifts or molecular markers, although inevitable obstacles are inherent in both methods. In order to circumvent these, it is necessary to find a causal link between adaptive alleles and fitness. Combining both approaches by linking genetic analyses and life-history measurements, a potential genotype-phenotype relationship can be assessed and adaptation at the molecular level demonstrated. For our study, clonal lineages of the freshwater keystone species D. galeata from seven different populations distributed along a latitudinal gradient across Europe were tested for local thermal adaptation in common garden experiments. Fitness-related life-history responses were quantified under different thermal regimes and experimental clones were genotyped at three candidate gene marker loci to investigate a potential genotype-phenotype association. The analyses of the life-history data showed a significant temperature effect on several fitness-related life-history traits recorded in our experiments. However, we could not detect evidence for a direct association at neither candidate gene locus between genotypes and life-history traits. The observed phenotypic shifts might therefore not be based on the tested marker loci EA, M and TF, or in general not coding sequence-based and thus rather reveal phenotypic plasticity in response to thermal variation. Nonetheless, we revealed significant genotype by environment (GxE) interactions at all tested loci, potentially reflecting a contribution of marker loci to certain life-history trait values and contribution of multiple genetic loci to phenotypic traits., (© 2017 Wiley Periodicals, Inc.)

Daphnia species have become models for ecological genomics and exhibit interesting features, such as high phenotypic plasticity and a densely packed genome with many lineage-specific genes. They are also cyclic parthenogenetic, with alternating asexual and sexual cycles and environmental sex determination. Here, we present a de novo transcriptome assembly of over 32,000 D. galeata genes and use it to investigate gene expression in females and spontaneously produced males of two clonal lines derived from lakes in Germany and the Czech Republic. We find that only a low percentage (18%) of genes shows sex-biased expression and that there are many more female-biased gene (FBG) than male-biased gene (MBG). Furthermore, FBGs tend to be more conserved between species than MBGs in both sequence and expression. These patterns may be a consequence of cyclic parthenogenesis leading to a relaxation of purifying selection on MBGs. The two clonal lines show considerable differences in both number and identity of sex-biased genes, suggesting that they may have reproductive strategies differing in their investment in sexual reproduction. Orthologs of key genes in the sex determination and juvenile hormone pathways, which are thought to be important for the transition from asexual to sexual reproduction, are present in D. galeata and highly conserved among Daphnia species., (© The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

Climatic changes are projected to result in rapid adaptive events with considerable phenotypic shifts. In order to reconstruct the impact of increased mean water temperatures during past decades and to reveal possible thermal micro-evolution, we applied a resurrection ecology approach using dormant eggs of the freshwater keystone species Daphnia galeata. To this end, we compared the adaptive response of D. galeata clones from Lake Constance of two different time periods, 1965-1974 ("historical") versus 2000-2009 ("recent"), to experimentally increased temperature regimes. In order to distinguish between genetic versus environmentally induced effects, we performed a common garden experiment in a flow-through system and measured variation in life-history traits. Experimental thermal regimes were chosen according to natural temperature conditions during the reproductive period of D. galeata in Central European lakes, with one additional temperature regime exceeding the currently observable maximum (+2°C). Increased water temperatures were shown to significantly affect measured life-history traits, and significant "temperature × clonal age" interactions were revealed. Compared to historical clones, recent clonal lineages exhibited a shorter time to first reproduction and a higher survival rate, which may suggest temperature-driven micro-evolution over time but does not allow an explicit conclusion on the adaptive nature of such responses.

Reproductive traits are key parameters for the evolution of invasiveness in weedy crop-wild hybrids. In Beta vulgaris, cultivated beets hybridize with their wild relatives in the seed production areas, giving rise to crop-wild hybrid weed beets. We investigated the genetic structure, the variation in first-year flowering and the variation in mating system among weed beet populations occurring within sugar beet production fields. No spatial genetic structure was found for first-year populations composed of F1 crop-wild hybrid beets. In contrast, populations composed of backcrossed weed beets emerging from the seed bank showed a strong isolation-by-distance pattern. Whereas gametophytic self-incompatibility prevents selfing in wild beet populations, all studied weed beet populations had a mixed-mating system, plausibly because of the introgression of the crop-derived Sf gene that disrupts self-incompatibility. No significant relationship between outcrossing rate and local weed beet density was found, suggesting no trends for a shift in the mating system because of environmental effects. We further reveal that increased invasiveness of weed beets may stem from positive selection on first-year flowering induction depending on the B gene inherited from the wild. Finally, we discuss the practical and applied consequences of our findings for crop-weed management.

Background: Reliable taxonomic identification at the species level is the basis for many biological disciplines. In order to distinguish species, it is necessary that taxonomic characters allow for the separation of individuals into recognisable, homogeneous groups that differ from other such groups in a consistent way. We compared here the suitability and efficacy of traditionally used shell morphology and DNA-based methods to distinguish among species of the freshwater snail genus Radix (Basommatophora, Pulmonata)., Results: Morphometric analysis showed that shell shape was unsuitable to define homogeneous, recognisable entities, because the variation was continuous. On the other hand, the Molecularly defined Operational Taxonomic Units (MOTU), inferred from mitochondrial COI sequence variation, proved to be congruent with biological species, inferred from geographic distribution patterns, congruence with nuclear markers and crossing experiments. Moreover, it could be shown that the phenotypically plastic shell variation is mostly determined by the environmental conditions experienced., Conclusion: Contrary to DNA-taxonomy, shell morphology was not suitable for delimiting and recognising species in Radix. As the situation encountered here seems to be widespread in invertebrates, we propose DNA-taxonomy as a reliable, comparable, and objective means for species identification in biological research.