Exploring the Genetic Consequences of Clonality in Haplodiplontic Taxa

Let's talk about sex: Why reproductive systems matter for understanding algae

Sex is a crucial process that has molecular, genetic, cellular, organismal, and population-level consequences for eukaryotic evolution. Eukaryotic life cycles are composed of alternating haploid and diploid phases but are constrained by the need to accommodate the phenotypes of these different phases. Critical gaps in our understanding of evolutionary drivers of the diversity in algae life cycles include how selection acts to stabilize and change features of the life cycle. Moreover, most eukaryotes are partially clonal, engaging in both sexual and asexual reproduction. Yet, our understanding of the variation in their reproductive systems is largely based on sexual reproduction in animals or angiosperms. The relative balance of sexual versus asexual reproduction not only controls but also is in turn controlled by standing genetic variability, thereby shaping evolutionary trajectories. Thus, we must quantitatively assess the consequences of the variation in life cycles on reproductive systems. Algae are a polyphyletic group spread across many of the major eukaryotic lineages, providing powerful models by which to resolve this knowledge gap. There is, however, an alarming lack of data about the population genetics of most algae and, therefore, the relative frequency of sexual versus asexual processes. For many algae, the occurrence of sexual reproduction is unknown, observations have been lost in overlooked papers, or data on population genetics do not yet exist. This greatly restricts our ability to forecast the consequences of climate change on algal populations inhabiting terrestrial, aquatic, and marine ecosystems. This perspective summarizes our extant knowledge and provides some future directions to pursue broadly across micro- and macroalgal species.

The eco-evolutionary importance of reproductive system variation in the macroalgae: Freshwater reds as a case study

The relative frequency of sexual versus asexual reproduction governs the distribution of genetic diversity within and among populations. Most studies on the consequences of reproductive variation focus on the mating system (i.e., selfing vs. outcrossing) of diploid-dominant taxa (e.g., angiosperms), often ignoring asexual reproduction. Although reproductive systems are hypothesized to be correlated with life-cycle types, variation in the relative rates of sexual and asexual reproduction remains poorly characterized across eukaryotes. This is particularly true among the three major lineages of macroalgae (green, brown, and red). The Rhodophyta are particularly interesting, as many taxa have complex haploid-diploid life cycles that influence genetic structure. Though most marine reds have separate sexes, we show that freshwater red macroalgae exhibit patterns of switching between monoicy and dioicy in sister taxa that rival those recently shown in brown macroalgae and in angiosperms. We advocate for the investigation of reproductive system evolution using freshwater reds, as this will expand the life-cycle types for which these data exist, enabling comparative analyses broadly across eukaryotes. Unlike their marine cousins, species in the Batrachospermales have macroscopic gametophytes attached to filamentous, often microscopic sporophytes. While asexual reproduction through monospores may occur in all freshwater reds, the Compsopogonales are thought to be exclusively asexual. Understanding the evolutionary consequences of selfing and asexual reproduction will aid in our understanding of the evolutionary ecology of all algae and of eukaryotic evolution generally.

Red macroalgae in the genomic era

Rhodophyta (or red algae) are a diverse and species-rich group that forms one of three major lineages in the Archaeplastida, a eukaryotic supergroup whose plastids arose from a single primary endosymbiosis. Red algae are united by several features, such as relatively small intron-poor genomes and a lack of cytoskeletal structures associated with motility like flagella and centrioles, as well as a highly efficient photosynthetic capacity. Multicellular red algae (or macroalgae) are one of the earliest diverging eukaryotic lineages to have evolved complex multicellularity, yet despite their ecological, evolutionary, and commercial importance, they have remained a largely understudied group of organisms. Considering the increasing availability of red algal genome sequences, we present a broad overview of fundamental aspects of red macroalgal biology and posit on how this is expected to accelerate research in many domains of red algal biology in the coming years.

Phenology and thallus size in a non-native population of Gracilaria vermiculophylla

Phenology, or seasonal variation in life cycle events, is poorly described for many macroalgal species. We describe the phenology of a non-native population of Gracilaria vermiculophylla whose thalli are free-living or anchored by decorating polychaetes to tube caps. At a site in South Carolina, USA, we sampled 100 thalli approximately every month from January 2014 to January 2015. We assessed the reproductive state and measured thallus size based on wet weight, thallus length, and thallus surface area from herbarium mounts. Because life cycle stage cannot be assigned using morphology, we implemented a PCR assay to determine the life cycle stage-tetrasporophyte, female gametophyte, or male gametophyte-of each thallus. Tetrasporophytes dominated throughout the year, making up 81%-100% of thalli sampled per month. Reproductive tetrasporophytes varied between 0% and 65% of monthly samples and were most common in warm summer months (July through September) when thalli also tended to be larger. The vast majority of the reproductive thalli were worm-anchored and not fixed to hard substratum via a holdfast. Thus, free-living thalli can be reproductive and potentially seed new non-native populations. Given G. vermiculophylla reproduction seems tied closely to temperature, our work suggests phenology may change with climate-related changes in seawater temperatures. We also highlight the importance of understanding the natural history of macroalgae to better understand the consequence of range expansions on population dynamics.

Tetrasporophytic bias coupled with heterozygote deficiency in Antarctic Plocamium sp. (Florideophyceae, Rhodophyta)

Meiosis and syngamy generate an alternation between two ploidy stages, but the timing of these two processes varies widely across taxa, thereby generating life cycle diversity. One hypothesis suggests that life cycles with long-lived haploid stages are correlated with selfing, asexual reproduction, or both. Though mostly studied in angiosperms, selfing and asexual reproduction are often associated with marginal habitats. Yet, in haploid-diploid macroalgae, these two reproductive modes have subtle but unique consequences whereby predictions from angiosperms may not apply. Along the western Antarctic Peninsula, there is a thriving macroalgal community, providing an opportunity to explore reproductive system variation in haploid-diploid macroalgae at high latitudes where endemism is common. Plocamium sp. is a widespread and abundant red macroalga observed within this ecosystem. We sampled 12 sites during the 2017 and 2018 field seasons and used 10 microsatellite loci to describe the reproductive system. Overall genotypic richness and evenness were high, suggesting sexual reproduction. Eight sites were dominated by tetrasporophytes, but there was strong heterozygote deficiency, suggesting intergametophytic selfing. We observed slight differences in the prevailing reproductive mode among sites, possibly due to local conditions (e.g., disturbance) that may contribute to site-specific variation. It remains to be determined whether high levels of selfing are characteristic of macroalgae more generally at high latitudes, due to the haploid-diploid life cycle, or both. Further investigations of algal life cycles will likely reveal the processes underlying the maintenance of sexual reproduction more broadly across eukaryotes, but more studies of natural populations are required.

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.

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.

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.

Sex and Asex: A Clonal Lexicon

Organisms across the tree of life have complex life cycles that include both sexual and asexual reproduction or that are obligately asexual. These organisms include ecologically dominant species that structure many terrestrial and marine ecosystems, as well as many pathogens, pests, and invasive species. We must consider both the evolution and maintenance of these various reproductive modes and how these modes shape the genetic diversity, adaptive evolution, and ability to persist in the species that exhibit them. Thus, having a common framework is a key aspect of understanding the biodiversity that shapes our planet. In the 2019 AGA President's Symposium, Sex and Asex: The genetics of complex life cycles, researchers investigating a wide range of taxonomic models and using a variety of modes of investigation coalesced around a common theme-understanding not only how such complex life cycles may evolve, but how they are shaped by the evolutionary and ecological forces around them. In this introduction to the Special Issue from the symposium, we give an overview of some of the key ideas and areas of investigation (a common clonal lexicon, we might say) and introduce the breadth of work submitted by symposium participants.