Several methods based on the Sequential Markovian coalescence (SMC) have been developed that make use of genome sequence data to uncover population demographic history, which is of interest in its own right and is a key requirement to generate a null model for selection tests. While these methods can be applied to all possible kind of species, the underlying assumptions are sexual reproduction in each generation and nonoverlapping generations. However, in many plants, invertebrates, fungi and other taxa, those assumptions are often violated due to different ecological and life history traits, such as self-fertilization or long term dormant structures (seed or egg-banking). We develop a novel SMC-based method to infer 1) the rates/parameters of dormancy and of self-fertilization, and 2) the populations' past demographic history. Using simulated data sets, we demonstrate the accuracy of our method for a wide range of demographic scenarios and for sequence lengths from one to 30 Mb using four sampled genomes. Finally, we apply our method to a Swedish and a German population of Arabidopsis thaliana demonstrating a selfing rate of ca. 0.87 and the absence of any detectable seed-bank. In contrast, we show that the water flea Daphnia pulex exhibits a long lived egg-bank of three to 18 generations. In conclusion, we here present a novel method to infer accurate demographies and life-history traits for species with selfing and/or seed/egg-banks. Finally, we provide recommendations for the use of SMC-based methods for non-model organisms, highlighting the importance of the per site and the effective ratios of recombination over mutation.

Natural selection leaves distinct signatures in the genome that can reveal the targets and history of adaptive evolution. By analysing high-coverage genome sequence data from 4 major colour pattern loci sampled from nearly 600 individuals in 53 populations, we show pervasive selection on wing patterns in the Heliconius adaptive radiation. The strongest signatures correspond to loci with the greatest phenotypic effects, consistent with visual selection by predators, and are found in colour patterns with geographically restricted distributions. These recent sweeps are similar between co-mimics and indicate colour pattern turnover events despite strong stabilising selection. Using simulations, we compare sweep signatures expected under classic hard sweeps with those resulting from adaptive introgression, an important aspect of mimicry evolution in Heliconius butterflies. Simulated recipient populations show a distinct 'volcano' pattern with peaks of increased genetic diversity around the selected target, characteristic of sweeps of introgressed variation and consistent with diversity patterns found in some populations. Our genomic data reveal a surprisingly dynamic history of colour pattern selection and co-evolution in this adaptive radiation.

A combination of selective and neutral evolutionary forces shape patterns of genetic diversity in nature. Among the insects, most previous analyses of the roles of drift and selection in shaping variation across the genome have focused on the genus Drosophila. A more complete understanding of these forces will come from analyzing other taxa that differ in population demography and other aspects of biology. We have analyzed diversity and signatures of selection in the neotropical Heliconius butterflies using resequenced genomes from 58 wild-caught individuals of Heliconius melpomene and another 21 resequenced genomes representing 11 related species. By comparing intraspecific diversity and interspecific divergence, we estimate that 31% of amino acid substitutions between Heliconius species are adaptive. Diversity at putatively neutral sites is negatively correlated with the local density of coding sites as well as nonsynonymous substitutions and positively correlated with recombination rate, indicating widespread linked selection. This process also manifests in significantly reduced diversity on longer chromosomes, consistent with lower recombination rates. Although hitchhiking around beneficial nonsynonymous mutations has significantly shaped genetic variation in H. melpomene, evidence for strong selective sweeps is limited overall. We did however identify two regions where distinct haplotypes have swept in different populations, leading to increased population differentiation. On the whole, our study suggests that positive selection is less pervasive in these butterflies as compared to fruit flies, a fact that curiously results in very similar levels of neutral diversity in these very different insects.KEYWORDS background selection; genetic hitchhiking; recombination rate; selective sweeps; effective population size G ENETIC variation within and between populations is shaped by numerous factors. In particular, genetic drift is stronger in smaller populations, such that organisms with larger population sizes should be more diverse under neutral evolution. However, it has long been known that the amount of genetic variation does not always scale as expected with population size, with a deficit of genetic variability in larger populations as compared to the neutral expectation (Lewontin 1974). This has become known as "Lewontin's paradox." It is likely that this paradox can be explained by considering the influence of natural selection (Ohta and Gillespie 1996;Leffler et al. 2012;Cutter and Payseur 2013;. Since drift can act to retard selection, natural selection tends to be more efficient in organisms with larger population sizes. Consistent with this, estimated rates of adaptive evolution are often greater for smaller organisms with larger population sizes. For example, it has been estimated that .50% of amino acid substitutions between fruit fly species are driven by positive selection (Sella et al. 2009;, but in humans, ,15% of recent amino acid substitutions appear to have been driven by selection (E...

21When species occur in repeated ecologically distinct habitats across their range, adaptation may proceed 22 surprisingly fast and result in parallel evolution. There is increasing evidence that such cases of rapid parallel 23 evolution are fueled by standing genetic variation, but the origin of this genetic variation remains poorly 24 understood. In Pogonus chalceus beetles, short-and long-winged ecotypes have diverged in response to 25 contrasting hydrological regimes and can be repeatedly found along the Atlantic European coast. By 26 analyzing genomic variation across the beetles' distribution, we reveal that genomically widespread short-27 wing selected alleles evolved during a singular divergence event, estimated at ~0.19 Mya. The ancient and 28 differentially selected alleles are currently polymorphic in all populations across the range, allowing for the 29 fast evolution of one ecotype from a small number of random individuals, as low as 5 to 15, of the 30 populations of the other ecotype. Our results suggest that cases of fast parallel ecological divergence might 31 be the result of evolution at two different time frames: ecological divergence in isolation in the past, 32 followed by repeated selection on the divergently evolved alleles after admixture. We suggest that this 33 mechanism may be common and potentially driven by large-scale environmental changes such as glacial 34 cycles. 35 36 37 Introduction 38

Although genetic diversity has been recognized as a key component of biodiversity since the first Convention on Biological Diversity (CBD) in 1993, it has rarely been included in conservation policies and regulations. Even less appreciated is the role that ancient and historical DNA (aDNA and hDNA, respectively) could play in unlocking the temporal dimension of genetic diversity, allowing key conservation issues to be resolved, including setting baselines for intraspecies genetic diversity, estimating changes in effective population size (N e) , and identifying the genealogical continuity of populations. Here, we discuss how genetic information from ancient and historical specimens can play a central role in preserving biodiversity and highlight specific conservation policies that could incorporate such data to help countries meet their CBD obligations. Genetic biodiversityThree levels of biodiversity constitute the variation of life on our planet: diversity of ecosystems, species diversity (number and distribution of species), and genetic diversity (amount and distribution of genetic variation within species or populations). The need to monitor biodiversity at all three levels has been globally recognized in international policy since 1993 when the Convention on Biological Diversity i (CBD) came into effect. Today, we face dramatic biodiversity loss due to the combined effects of habitat damage, fragmentation and alteration, climate change, and other global change stressors. Most frequently, this loss is calculated in terms of the number of species, but relatively little is known about loss of diversity within species and populations at the genome level (but see [1]). Genetic diversity within species and populations is necessary for long-term survival as it allows resilience and adaptation not only for individuals, but also for populations, species, and entire ecosystems [2]. This diversity is particularly relevant in the Anthropocene, characterized by significant, rapid, and global changes to habitats and environmental conditions. Despite the importance of genetic diversity in biodiversity protection and management, it has rarely been included in policies and regulations [3]. But, with the ongoing development of the CBD post-2020 Global Biodiversity Framework (expected to be concluded in May 2022), there is an opportunity to address this significant blind spot by adopting genetic diversity targets and indicators.

Organic contaminants detected in sediments from Lake Greifensee and other compounds falling in the log Dow range from 1 to 7 were selected to study the bioconcentration of organic contaminants in sediments in Daphnia resting eggs (ephippia). Our results show that octocrylene, tonalide, triclocarban, and other personal care products, along with pesticides and biocides can accumulate in ephippia with log BCF values up to 3. Data on the uptake and depuration kinetics show a better fit toward a two compartment organism model over a single compartment model due to the differences in ephippial egg content in the environment. The obtained BCFs correlate with hydrophobicity for neutral compounds. Independence between BCF and hydrophobicity was observed for partially ionized compounds with log Dow values around 1. Internal concentrations in ephippia in the environment were predicted based on sediment concentrations using the equilibrium partitioning model and calculated BCFs. Estimated internal concentration values ranged between 1 and 68,000 μg/kglip with triclocarban having the highest internal concentrations followed by tonalide and triclosan. The outcomes indicate that contaminants can be taken up by ephippia from the water column or the pore water in the sediment and might influence fitness and sexual reproduction in the aquatic key species of the genus Daphnia.

Natural selection leaves distinct signatures in the genome that can reveal the targets and history of adaptive evolution. By analysing high-coverage genome sequence data from four major colour pattern loci sampled from nearly 600 individuals in 53 populations, we show pervasive selection on wing patterns across the Heliconius adaptive radiation. The strongest signatures correspond to loci with the greatest phenotypic effects, consistent with visual selection by predators, and are found in colour patterns with geographically restricted distributions. These recent sweeps are similar between co-mimics and indicate colour pattern turn-over events despite strong stabilizing selection. Using simulations we compare sweep signatures expected under classic hard sweeps with those resulting from adaptive introgression, an important aspect of mimicry evolution in Heliconius. Simulated recipient populations show a distinct 'volcano' pattern with peaks of increased genetic diversity around the selected target, consistent with patterns found in some populations. Our genomic data provide unprecedented insights into the recent history of selection across the Heliconius adaptive radiation.

Reconstruction of species histories is a central aspect of evolutionary biology. Patterns of genetic variation within and among populations can be leveraged to elucidate evolutionary processes and demographic histories. However, interpreting genetic signatures and unraveling the contributing processes can be challenging, in particular for non-model organisms with complex reproductive modes and genome organization.One way forward is the combined consideration of patterns revealed by different molecular markers (nuclear vs. mitochondrial) and types of variants (common vs. rare) that differ in their age, mode, and rate of evolution. Here, we applied this approach to RNAseq data generated for Machilis pallida (Archaeognatha), an Alpine jumping bristletail considered parthenogenetic and triploid. We generated de novo transcriptome and mitochondrial assemblies to obtain high-density data to investigate patterns of mitochondrial and common and rare nuclear variation in 17 M. pallida individuals sampled from all known populations. We find that the different variant types capture distinct aspects of the evolutionary history and discuss the observed patterns in the context of parthenogenesis, polyploidy, and survival during glaciation. This study highlights the potential of different variant types to gain insights into evolutionary scenarios even from challenging but often available data and the suitability of M. pallida and the genus Machilis as a study system for the evolution of sexual strategies and polyploidization during environmental change. We also emphasize the need for further research which will be stimulated and facilitated by these newly generated resources and insights.