New insights into the population genetics of partially clonal organisms: When seagrass data meet theoretical expectations

GenAPoPop 1.0: A user-friendly software to analyse genetic diversity and structure from partially clonal and selfed autopolyploid organisms

Autopolyploidy is quite common in most clades of eukaryotes. The emergence of sequence-based genotyping methods with individual and marker tags now enables confident allele dosage, overcoming the main obstacle to the democratization of the population genetic approaches when studying ecology and evolution of autopolyploid populations and species. Reproductive modes, including clonality, selfing and allogamy, have deep consequences on the ecology and evolution of population and species. Analysing genetic diversity and its dynamics over generations is one efficient way to infer the relative importance of clonality, selfing and allogamy in populations. GenAPoPop is a user-friendly solution to compute the specific corpus of population genetic indices, including indices about genotypic diversity, needed to analyse partially clonal, selfed and allogamous polysomic populations genotyped with confident allele dosage. It also easily provides the posterior probabilities of quantitative reproductive modes in autopolyploid populations genotyped at two-time steps and a graphical representation of the minimum spanning trees of the genetic distances between polyploid individuals, facilitating the interpretation of the genetic coancestry between individuals in hierarchically structured populations. GenAPoPop complements the previously existing solutions, including SPAGEDI and POLYGENE, to use genotypings to study the ecology and evolution of autopolyploid populations. It was specially developed with a simple graphical interface and workflow, and comes with a simulator to facilitate practical courses and teaching of population genetics for autopolyploid populations.

Clones on the run: The genomics of a recently expanded partially clonal species

Why species that in their core areas mainly reproduce sexually become enriched with clones in marginal populations ("geographic parthenogenesis") remains unclear. Earlier hypotheses have emphasized that selection might promote clonality because it protects locally adapted genotypes. On the other hand, it also hampers recombination and adaptation to changing conditions. The aim of the present study was to investigate the early stages of range expansion in a partially clonal species and what drives an increase in cloning during such expansion. We used genome-wide sequencing to investigate the origin and evolution of large clones formed in a macroalgal species (Fucus vesiculosus) during a recent expansion into the postglacial Baltic Sea. We found low but persistent clonality in core populations, while at range margins, large dominant clonal lineages had evolved repeatedly from different sexual populations. A range expansion model showed that even when asexual recruitment is less favourable than sexual recruitment in core populations, repeated bottlenecks at the expansion front can establish a genetically eroded clonal wave that spreads ahead of a sexual wave into the new area. Genetic variation decreases by drift following repeated bottlenecks at the expansion front. This results in the emerging clones having low expected heterozygosity, which corroborated our empirical observations. We conclude that Baker's Law (clones being favoured by uniparental reproductive assurance in new areas) can play an important role during range expansion in partially clonal species, resulting in a complex spatiotemporal mosaic of clonal and sexual lineages that might persist during thousands of generations.

Genetic structuring and invasion status of the perennial Ambrosia psilostachya (Asteraceae) in Europe

The perennial western ragweed (Ambrosia psilostachya DC.) arrived from North America to Europe in the late nineteenth century and behaves invasive in its non-native range. Due to its efficient vegetative propagation via root suckers, A. psilostachya got naturalized in major parts of Europe forming extensive populations in Mediterranean coastal areas. The invasion history, the spreading process, the relationships among the populations as well as population structuring is not yet explored. This paper aims to give first insights into the population genetics of A. psilostachya in its non-native European range based on 60 sampled populations and 15 Simple Sequence Repeats (SSR). By AMOVA analysis we detected 10.4% of genetic variation occurring among (pre-defined) regions. These regions represent important harbors for trading goods from America to Europe that might have served as source for founder populations. Bayesian Clustering revealed that spatial distribution of genetic variation of populations is best explained by six groups, mainly corresponding to regions around important harbors. As northern populations show high degrees of clonality and lowest levels of within-population genetic diversity (mean H_o = 0.40 ± 0.09), they could preserve the initial genetic variation levels by long-lived clonal genets. In Mediterranean populations A. psilostachya expanded to millions of shoots. Some of those were obviously spread by sea current along the coast to new sites, where they initiated populations characterized by a lower genetic diversity. For the future, the invasion history in Europe might get clearer after consideration of North American source populations of western ragweed.

Effective population size in a partially clonal plant is not predicted by the number of genetic individuals

Estimating effective population size (N _e) is important for theoretical and practical applications in evolutionary biology and conservation. Nevertheless, estimates of N _e in organisms with complex life-history traits remain scarce because of the challenges associated with estimation methods. Partially clonal plants capable of both vegetative (clonal) growth and sexual reproduction are a common group of organisms for which the discrepancy between the apparent number of individuals (ramets) and the number of genetic individuals (genets) can be striking, and it is unclear how this discrepancy relates to N _e. In this study, we analysed two populations of the orchid Cypripedium calceolus to understand how the rate of clonal versus sexual reproduction affected N _e. We genotyped >1000 ramets at microsatellite and SNP loci, and estimated contemporary N _e with the linkage disequilibrium method, starting from the theoretical expectation that variance in reproductive success among individuals caused by clonal reproduction and by constraints on sexual reproduction would lower N _e. We considered factors potentially affecting our estimates, including different marker types and sampling strategies, and the influence of pseudoreplication in genomic data sets on N _e confidence intervals. The magnitude of N _e/N _ramets and N _e/N _genets ratios we provide may be used as reference points for other species with similar life-history traits. Our findings demonstrate that N _e in partially clonal plants cannot be predicted based on the number of genets generated by sexual reproduction, because demographic changes over time can strongly influence N _e. This is especially relevant in species of conservation concern in which population declines may not be detected by only ascertaining the number of genets.

Phylogeography and genetic variation in Western Jacob's ladder (Polemonium occidentale) provide insights into the origin and conservation of rare species in the Great Lakes region

The perennial herb Western Jacob's Ladder (Polemonium occidentale, Polemoniaceae) is widespread in the mountains of western North America but reappears as a disjunct in the Great Lakes Region in Minnesota and Wisconsin, USA as the narrow endemic P. occidentale subsp. lacustre. This distribution is shown by a diverse assemblage of angiosperms. It has been hypothesized that these species became isolated just after the Last Glacial Maximum, but this has not been tested. Additionally, the genetic diversity and population connectivity of the endemic Great Lakes flora has been understudied, with important conservation implications. Using genotyping-by-sequencing, we examined the relationship of P. occidentale subsp. lacustre to its closest relatives, relationships among all known populations, and genetic diversity within these populations. Polemonium occidentale subsp. lacustre represents an isolated, unique lineage that diverged from its closest relatives 1.3 Ma and arrived in the Great Lakes Region by at least 38 ka. Nearly all extant populations diverged prior to the Last Glacial Maximum, are genetically distinct, and show little within-population genetic diversity. Clonality may mitigate reduction in diversity due to drift. Mixed population signal between Wisconsin and some Minnesota populations may be due to gene flow during the Late Pleistocene. While populations of P. occidentale subsp. lacustre may be relictual from a now extinct western relative, it is best treated as a distinct species. Conservation efforts should focus more on ensuring that current populations remain rather than maintaining large populations sizes across a few populations. However, encouraging habitat heterogeneity may accomplish both simultaneously.

Origin of scarlet gynogenetic triploid Carassius fish: Implications for conservation of the sexual-gynogenetic complex

Conservation of sperm-dependent asexual (gynogenetic) species is challenging due to their complicated ecological dynamics, which requires the stable coexistence with their sperm-providing sexual relatives, who often share similar niches. A symbolic but vulnerable gynogenetic animal is the scarlet Carassius fish, or Hibuna, which is mainly found in Lake Harutori on Hokkaido, Japan. Although Hibuna in Lake Harutori has been protected as a symbol of the Natural Monument of Japan, it has recently suffered population decline. To establish an effective conservation strategy for Hibuna, we investigated its origin, reproductive mode, and genetic diversity, with reference to the surrounding wild populations, using nuclear microsatellites and mitochondrial gene sequences. Our genetic analyses revealed that the main ploidy of Hibuna was triploid or tetraploid, and it reproduces gynogenetically. However, no co-existing sexual diploid Carassius was detected among our samples, suggesting that the sexual diploids and the gynogenetic population including Hibuna would be at risk of co-extirpation. In addition, Hibuna showed high genetic/clonal diversity and most Hibuna had nonindigenous mitochondrial haplotypes that are mostly identical to those reported from goldfish. These results indicate that Hibuna most probably originated from hybridization between indigenous gynogenetic triploids and goldfish introduced about 100 years ago, involving rare sexual reproduction. This spontaneous long-term field experiment exemplifies the recently documented diversification process of gynogenetic Carassius via complex interploidy gene flow. Although the priority to be placed on the conservation of Hibuna is controversial, the maintenance of gynogenetic Carassius, including Hibuna, requires strategic conservation of sexual populations.

Genetic variation and clonal diversity in floating aquatic plants: Comparative genomic analysis of water hyacinth species in their native range

Many eukaryotic organisms reproduce by sexual and asexual reproduction. Genetic diversity in populations can be strongly dependent on the relative importance of these two reproductive modes. Here, we compare the amounts and patterns of genetic diversity in related water hyacinths that differ in their propensity for clonal propagation - highly clonal Eichhornia crassipes and moderately clonal E. azurea (Pontederiaceae). Our comparisons involved genotype-by-sequencing (GBS) of 137 E. crassipes ramets from 60 locations (193,495 nucleotide sites) and 118 E. azurea ramets from 53 locations (198,343 nucleotide sites) among six hydrological basins in central South America, the native range of both species. We predicted that because of more prolific clonal propagation, E. crassipes would exhibit lower clonal diversity than E. azurea. This prediction was supported by all measures of clonal diversity that we examined. Eichhornia crassipes also had a larger excess of heterozygotes at variant sites, another signature of clonality. However, genome-wide heterozygosity was not significantly different between the species. Eichhornia crassipes had weaker spatial genetic structure and lower levels of differentiation among hydrological basins than E. azurea, probably because of higher clonality and more extensive dispersal of its free-floating life form. Our findings for E. crassipes contrast with earlier studies from the invasive range which have reported very low levels of clonal diversity and extensive geographic areas of genetic uniformity.

2b-RAD Genotyping of the Seagrass Cymodocea nodosa Along a Latitudinal Cline Identifies Candidate Genes for Environmental Adaptation

Plant populations distributed along broad latitudinal gradients often show patterns of clinal variation in genotype and phenotype. Differences in photoperiod and temperature cues across latitudes influence major phenological events, such as timing of flowering or seed dormancy. Here, we used an array of 4,941 SNPs derived from 2b-RAD genotyping to characterize population differentiation and levels of genetic and genotypic diversity of three populations of the seagrass Cymodocea nodosa along a latitudinal gradient extending across the Atlantic-Mediterranean boundary (i.e., Gran Canaria—Canary Islands, Faro—Portugal, and Ebro Delta—Spain). Our main goal was to search for potential outlier loci that could underlie adaptive differentiation of populations across the latitudinal distribution of the species. We hypothesized that such polymorphisms could be related to variation in photoperiod-temperature regime occurring across latitudes. The three populations were clearly differentiated and exhibited diverse levels of clonality and genetic diversity. Cymodocea nodosa from the Mediterranean displayed the highest genotypic richness, while the Portuguese population had the highest clonality values. Gran Canaria exhibited the lowest genetic diversity (as observed heterozygosity). Nine SNPs were reliably identified as outliers across the three sites by two different methods (i.e., BayeScan and pcadapt), and three SNPs could be associated to specific protein-coding genes by screening available C. nodosa transcriptomes. Two SNPs-carrying contigs encoded for transcription factors, while the other one encoded for an enzyme specifically involved in the regulation of flowering time, namely Lysine-specific histone demethylase 1 homolog 2. When analyzing biological processes enriched within the whole dataset of outlier SNPs identified by at least one method, “regulation of transcription” and “signalling” were among the most represented. Our results highlight the fundamental importance signal integration and gene-regulatory networks, as well as epigenetic regulation via DNA (de)methylation, could have for enabling adaptation of seagrass populations along environmental gradients.

Biogeography pattern of the marine angiosperm Cymodocea nodosa in the eastern Mediterranean Sea related to the quaternary climatic changes

We investigated the population dynamics of a highly clonal marine angiosperm, Cymodocea nodosa, in the eastern Mediterranean Sea, to identify the historical dynamics, demography, and connectivity of the species in the area. Eighteen microsatellite loci were used in conjunction with coalescent methods to investigate the genetic structure and demographic history of C. nodosa meadows. Approximate Bayesian computation (ABC) modeling was used to examine the pattern of divergence over time in the context of environmental change over the course of the Quaternary period. ABC analysis revealed an initial split of the C. nodosa populations between the north-western, northern, and north-eastern Aegean Sea during the Pleistocene epoch, followed by a more recent divergence of the north-western population and the central-western part of the Aegean Sea. According to the results, the most parsimonious historical scenario is that of a pervasive genetic signature of the effects of the drop in sea level during the Pleistocene epoch. This scenario supports the isolation of the north-western, north, and north-eastern area, and the subsequent recolonization after post-glaciation sea level rise that may explain the north-western differentiation as well present-day detected dispersion of C. nodosa.

Cloning and Selfing Affect Population Genetic Variation in Simulations of Outcrossing, Sexual Sea Stars

AbstractMany sea stars are well known for facultative or obligate asexual reproduction in both the adult and larval life-cycle stages. Some species and lineages are also capable of facultative or obligate hermaphroditic reproduction with self-fertilization. However, models of population genetic variation and empirical analyses of genetic data typically assume only sexual reproduction and outcrossing. A recent reanalysis of previously published empirical data (microsatellite genotypes) from two studies of one of the most well-known sea star species (the crown-of-thorns sea star; Acanthaster sp.) concluded that cloning and self-fertilization in that species are rare and contribute little to patterns of population genetic variation. Here we reconsider that conclusion by simulating the contribution of cloning and selfing to genetic variation in a series of models of sea star demography. Simulated variation in two simple models (analogous to previous analyses of empirical data) was consistent with high rates of cloning or selfing or both. More realistic scenarios that characterize population flux in sea stars of ecological significance, including outbreaks of crown-of-thorns sea stars that devastate coral reefs, invasions by Asterias amurensis, and epizootics of sea star wasting disease that kill Pisaster ochraceus, also showed significant but smaller effects of cloning and selfing on variation within subpopulations and differentiation between subpopulations. Future models or analyses of genetic variation in similar study systems might benefit from simulation modeling to characterize possible contributions of cloning or selfing to genetic variation in population samples or to understand the limits on inferring the effects of cloning or selfing in nature.

The Population of Sclerotinia sclerotiorum in Brazil Is Structured by Mycelial Compatibility Groups

The genetic structure of the population of Sclerotinia sclerotiorum was analyzed using 238 individuals collected from different hosts. Individuals were characterized for microsatellite genotypes and mycelial compatibility groups (MCGs). A total of 22 MCGs and 64 multilocus lineages (MLLs) were identified. There was a close relationship between the MCGs and MLLs, but there was no association between MLLs and hosts or regions. At least 39 MCGs are present in Brazil, and 68.5% of the isolates were assigned to either MCG 1 or MCG 2. Eight new MCGs were found. Seven genetic groups were identified and associated with MCGs. Most genetic variation (70.0%) was because of differences among MCGs. High values of estimates of linkage disequilibrium among loci were more frequent in the total population (all MCGs). By contrast, there was evidence of random mating in subpopulations defined by MCGs 1 and 2. Additionally, there was evidence of outcrossing in the population of S. sclerotiorum in Brazil. The population was structured by MCGs; lineages originating from asexual reproduction or selfing prevail and are widely distributed in space, are persistent in time, and affect many hosts, but there is evidence of some degree of outcrossing, which may lead to a more genetically variable population in the future.

Genetic homogeneity, lack of larvae recruitment, and clonality in absence of females across western Mediterranean populations of the starfish Coscinasterias tenuispina

We here analysed the populations' genetic structure of Coscinasterias tenuispina, an Atlantic-Mediterranean fissiparous starfish, focusing on the western Mediterranean, to investigate: the distribution and prevalence of genetic variants, the relative importance of asexual reproduction, connectivity across the Atlantic-Mediterranean transition, and the potential recent colonisation of the Mediterranean Sea. Individuals from 11 Atlantic-Mediterranean populations of a previous study added to 172 new samples from five new W Mediterranean sites. Individuals were genotyped at 12 microsatellite loci and their gonads histologically analysed for sex determination. Additionally, four populations were genotyped at two-time points. Results demonstrated genetic homogeneity and low clonal richness within the W Mediterranean, due to the dominance of a superclone, but large genetic divergence with adjacent areas. The lack of new genotypes recruitment over time, and the absence of females, confirmed that W Mediterranean populations were exclusively maintained by fission and reinforced the idea of its recent colonization. The existence of different environmental conditions among basins and/or density-depend processes could explain this lack of recruitment from distant areas. The positive correlation between clonal richness and heterozygote excess suggests that most genetic diversity is retained within individuals in the form of heterozygosity in clonal populations, which might increase their resilience.

Population transcriptomic sequencing reveals allopatric divergence and local adaptation in Pseudotaxus chienii (Taxaceae)

BACKGROUND

Elucidating the effects of geography and selection on genetic variation is critical for understanding the relative importance of adaptation in driving differentiation and identifying the environmental factors underlying its occurrence. Adaptive genetic variation is common in tree species, especially widely distributed long-lived species. Pseudotaxus chienii can occupy diverse habitats with environmental heterogeneity and thus provides an ideal material for investigating the process of population adaptive evolution. Here, we characterize genetic and expression variation patterns and investigate adaptive genetic variation in P. chienii populations.

RESULTS

We generated population transcriptome data and identified 13,545 single nucleotide polymorphisms (SNPs) in 5037 unigenes across 108 individuals from 10 populations. We observed lower nucleotide diversity (π = 0.000701) among the 10 populations than observed in other gymnosperms. Significant negative correlations between expression diversity and nucleotide diversity in eight populations suggest that when the species adapts to the surrounding environment, gene expression and nucleotide diversity have a reciprocal relationship. Genetic structure analyses indicated that each distribution region contains a distinct genetic group, with high genetic differentiation among them due to geographical isolation and local adaptation. We used FST outlier, redundancy analysis, and latent factor mixed model methods to detect molecular signatures of local adaptation. We identified 244 associations between 164 outlier SNPs and 17 environmental variables. The mean temperature of the coldest quarter, soil Fe and Cu contents, precipitation of the driest month, and altitude were identified as the most important determinants of adaptive genetic variation. Most candidate unigenes with outlier signatures were related to abiotic and biotic stress responses, and the monoterpenoid biosynthesis and ubiquitin-mediated proteolysis KEGG pathways were significantly enriched in certain populations and deserve further attention in other long-lived trees.

CONCLUSIONS

Despite the strong population structure in P. chienii, genomic data revealed signatures of divergent selection associated with environmental variables. Our research provides SNPs, candidate unigenes, and biological pathways related to environmental variables to facilitate elucidation of the genetic variation in P. chienii in relation to environmental adaptation. Our study provides a promising tool for population genomic analyses and insights into the molecular basis of local adaptation.

Phenotypic plasticity under rapid global changes: The intrinsic force for future seagrasses survival

Coastal oceans are particularly affected by rapid and extreme environmental changes with dramatic consequences for the entire ecosystem. Seagrasses are key ecosystem engineering or foundation species supporting diverse and productive ecosystems along the coastline that are particularly susceptible to fast environmental changes. In this context, the analysis of phenotypic plasticity could reveal important insights into seagrasses persistence, as it represents an individual property that allows species' phenotypes to accommodate and react to fast environmental changes and stress. Many studies have provided different definitions of plasticity and related processes (acclimation and adaptation) resulting in a variety of associated terminology. Here, we review different ways to define phenotypic plasticity with particular reference to seagrass responses to single and multiple stressors. We relate plasticity to the shape of reaction norms, resulting from genotype by environment interactions, and examine its role in the presence of environmental shifts. The potential role of genetic and epigenetic changes in underlying seagrasses plasticity in face of environmental changes is also discussed. Different approaches aimed to assess local acclimation and adaptation in seagrasses are explored, explaining strengths and weaknesses based on the main results obtained from the most recent literature. We conclude that the implemented experimental approaches, whether performed with controlled or field experiments, provide new insights to explore the basis of plasticity in seagrasses. However, an improvement of molecular analysis and the application of multi-factorial experiments are required to better explore genetic and epigenetic adjustments to rapid environmental shifts. These considerations revealed the potential for selecting the best phenotypes to promote assisted evolution with fundamental implications on restoration and preservation efforts.

Genomic signatures of clonality in the deep water kelp Laminaria rodriguezii

The development of population genomic approaches in non-model species allows for renewed studies of the impact of reproductive systems and genetic drift on population diversity. Here, we investigate the genomic signatures of partial clonality in the deep water kelp Laminaria rodriguezii, known to reproduce by both sexual and asexual means. We compared these results with the species Laminaria digitata, a closely related species that differs by different traits, in particular its reproductive mode (no clonal reproduction). We analysed genome-wide variation with dd-RAD sequencing using 4,077 SNPs in L. rodriguezii and 7,364 SNPs in L. digitata. As predicted for partially clonal populations, we show that the distribution of FIS within populations of L. rodriguezii is shifted toward negative values, with a high number of loci showing heterozygote excess. This finding is the opposite of what we observed within sexual populations of L. digitata, characterized by a generalized deficit in heterozygotes. Furthermore, we observed distinct distributions of FIS among populations of L. rodriguezii, which is congruent with the predictions of theoretical models for different levels of clonality and genetic drift. These findings highlight that the empirical distribution of FIS is a promising feature for the genomic study of asexuality in natural populations. Our results also show that the populations of L. rodriguezii analysed here are genetically differentiated and probably isolated. Our study provides a conceptual framework to investigate partial clonality on the basis of RAD-sequencing SNPs. These results could be obtained without any reference genome, and are therefore of interest for various non-model species.

The Genetic Component of Seagrass Restoration: What We Know and the Way Forwards

Seagrasses are marine flowering plants providing key ecological services and functions in coasts and estuaries across the globe. Increased environmental changes fueled by human activities are affecting their existence, compromising natural habitats and ecosystems’ biodiversity and functioning. In this context, restoration of disturbed seagrass environments has become a worldwide priority to reverse ecosystem degradation and to recover ecosystem functionality and associated services. Despite the proven importance of genetic research to perform successful restoration projects, this aspect has often been overlooked in seagrass restoration. Here, we aimed to provide a comprehensive perspective of genetic aspects related to seagrass restoration. To this end, we first reviewed the importance of studying the genetic diversity and population structure of target seagrass populations; then, we discussed the pros and cons of different approaches used to restore and/or reinforce degraded populations. In general, the collection of genetic information and the development of connectivity maps are critical steps for any seagrass restoration activity. Traditionally, the selection of donor population preferred the use of local gene pools, thought to be the best adapted to current conditions. However, in the face of rapid ocean changes, alternative approaches such as the use of climate-adjusted or admixture genotypes might provide more sustainable options to secure the survival of restored meadows. Also, we discussed different transplantation strategies applied in seagrasses and emphasized the importance of long-term seagrass monitoring in restoration. The newly developed information on epigenetics as well as the application of assisted evolution strategies were also explored. Finally, a view of legal and ethical issues related to national and international restoration management is included, highlighting improvements and potential new directions to integrate with the genetic assessment. We concluded that a good restoration effort should incorporate: (1) a good understanding of the genetic structure of both donors and populations being restored; (2) the analysis of local environmental conditions and disturbances that affect the site to be restored; (3) the analysis of local adaptation constraints influencing the performances of donor populations and native plants; (4) the integration of distribution/connectivity maps with genetic information and environmental factors relative to the target seagrass populations; (5) the planning of long-term monitoring programs to assess the performance of the restored populations. The inclusion of epigenetic knowledge and the development of assisted evolution programs are strongly hoped for the future.

The Combined Effect of Haplodiplonty and Partial Clonality on Genotypic and Genetic Diversity in a Finite Mutating Population

Partial clonality is known to affect the genetic composition and evolutionary trajectory of diplontic (single, free-living diploid stage) populations. However, many partially clonal eukaryotes exhibit life cycles in which somatic development occurs in both haploid and diploid individuals (haplodiplontic life cycles). Here, we studied how haplodiplontic life cycles and partial clonality structurally constrain, as immutable parameters, the reshuffling of genetic diversity and its dynamics in populations over generations. We assessed the distribution of common population genetic indices at different proportions of haploids, rates of clonality, mutation rates, and sampling efforts. Our results showed that haplodiplontic life cycles alone in finite populations affect effective population sizes and the ranges of distributions of population genetic indices. With nonoverlapping generations, haplodiplonty allowed the evolution of 2 temporal genetic pools that may diverge in sympatry due to genetic drift under full sexuality and clonality. Partial clonality in these life cycles acted as a homogenizing force between those 2 pools. Moreover, the combined effects of proportion of haploids, rate of clonality, and the relative strength of mutation versus genetic drift impacts the distributions of population genetics indices, rendering it difficult to transpose and use knowledge accumulated from diplontic or haplontic species. Finally, we conclude by providing recommendations for sampling and analyzing the population genetics of partially clonal haplodiplontic taxa.

Exploring the Genetic Consequences of Clonality in Haplodiplontic Taxa

Partially clonality is an incredibly common reproductive mode found across all the major eukaryotic lineages. Yet, population genetic theory is based on exclusive sexuality or exclusive asexuality, and partial clonality is often ignored. This is particularly true in haplodiplontic eukaryotes, including algae, ferns, mosses, and fungi, where somatic development occurs in both the haploid and diploid stages. Haplodiplontic life cycles are predicted to be correlated with asexuality, but tests of this prediction are rare. Moreover, there are unique consequences of having long-lived haploid and diploid stages in the same life cycle. For example, clonal processes uncouple the life cycle such that the repetition of the diploid stage via clonality leads to the loss of the haploid stage. Here, we surveyed the literature to find studies that had genotyped both haploid and diploid stages and recalculated population genetic summary metrics for seven red algae, one green alga, three brown algae, and three mosses. We compared these data to recent simulations that explicitly addressed the population genetic consequences of partial clonality in haplodiplontic life cycles. Not only was partial clonality found to act as a homogenizing force, but the combined effects of proportion of haploids, rate of clonality, and the relative strength of mutation versus genetic drift impacts the distributions of population genetic indices. We found remarkably similar patterns across commonly used population genetic metrics between our empirical and recent theoretical expectations. To facilitate future studies, we provide some recommendations for sampling and analyzing population genetic parameters for haplodiplontic taxa.

The discernible and hidden effects of clonality on the genotypic and genetic states of populations: Improving our estimation of clonal rates

Partial clonality is widespread across the tree of life, but most population genetic models are designed for exclusively clonal or sexual organisms. This gap hampers our understanding of the influence of clonality on evolutionary trajectories and the interpretation of population genetic data. We performed forward simulations of diploid populations at increasing rates of clonality (c), analysed their relationships with genotypic (clonal richness, R, and distribution of clonal sizes, Pareto β) and genetic (F_IS and linkage disequilibrium) indices, and tested predictions of c from population genetic data through supervised machine learning. Two complementary behaviours emerged from the probability distributions of genotypic and genetic indices with increasing c. While the impact of c on R and Pareto β was easily described by simple mathematical equations, its effects on genetic indices were noticeable only at the highest levels (c > 0.95). Consequently, genotypic indices allowed reliable estimates of c, while genetic descriptors led to poorer performances when c < 0.95. These results provide clear baseline expectations for genotypic and genetic diversity and dynamics under partial clonality. Worryingly, however, the use of realistic sample sizes to acquire empirical data systematically led to gross underestimates (often of one to two orders of magnitude) of c, suggesting that many interpretations hitherto proposed in the literature, mostly based on genotypic richness, should be reappraised. We propose future avenues to derive realistic confidence intervals for c and show that, although still approximate, a supervised learning method would greatly improve the estimation of c from population genetic data.

Integrating genetics, biophysical, and demographic insights identifies critical sites for seagrass conservation

The eelgrass Zostera marina is an important foundation species of coastal areas in the Northern Hemisphere, but is continuing to decline, despite management actions. The development of new management tools is therefore urgent in order to prioritize limited resources for protecting meadows most vulnerable to local extinctions and identifying most valuable present and historic meadows to protect and restore, respectively. We assessed 377 eelgrass meadows along the complex coastlines of two fjord regions on the Swedish west coast-one is currently healthy and the other is substantially degraded. Shoot dispersal for all meadows was assessed with Lagrangian biophysical modeling (scale: 100-1,000 m) and used for barrier analysis and clustering; a subset (n = 22) was also assessed with population genetic methods (20 microsatellites) including diversity, structure, and network connectivity. Both approaches were in very good agreement, resulting in seven subpopulation groupings or management units (MUs). The MUs correspond to a spatial scale appropriate for coastal management of "waterbodies" used in the European Water Framework Directive. Adding demographic modeling based on the genetic and biophysical data as a third approach, we are able to assess past, present, and future metapopulation dynamics to identify especially vulnerable and valuable meadows. In a further application, we show how the biophysical approach, using eigenvalue perturbation theory (EPT) and distribution records from the 1980s, can be used to identify lost meadows where restoration would best benefit the present metapopulation. The combination of methods, presented here as a toolbox, allows the assessment of different temporal and spatial scales at the same time, as well as ranking of specific meadows according to key genetic, demographic and ecological metrics. It could be applied to any species or region, and we exemplify its versatility as a management guide for eelgrass along the Swedish west coast.