The contribution of haploids, diploids and clones to fine-scale population structure in the seaweed Cladophoropsis membranacea (Chlorophyta)

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.

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.

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 Contribution of Clonality to Population Genetic Structure in the Sea Anemone, Diadumene lineata

Ecological and evolutionary processes differ depending on how genetic diversity is organized in space. For clonal organisms, the organization of both genetic and genotypic diversity can influence the fitness effects of competition, the mating system, and reproductive mode, which are key drivers of life cycle evolution. Understanding how individual reproductive behavior contributes to population genetic structure is essential for disentangling these forces, particularly in species with complex and plastic life cycles. The widespread sea anemone, Diadumene lineata, exhibits temperature-dependent fission, which contributes to predictable variation in clonal rate along the Atlantic coast of the United States, part of its non-native range. Because warmer conditions lead to higher rates of clonality, we expected to find lower genotypic and genetic diversity in lower versus higher latitude populations. We developed primers for 11 microsatellite loci and genotyped 207 anemones collected from 8 sites ranging from Florida to Massachusetts. We found clonal influence at all sites, and as predicted, the largest clones were found at lower latitude sites. We also found genetic signatures of sex in the parts of the range where gametogenesis is most common. Evidence of sex outside the native range is novel for this species and provides insights into the dynamics of this successful invader. Our findings also illustrate challenges that partially clonal taxa pose for eco-evolutionary studies, such as difficulty sampling statistically robust numbers of genets and interpretating common population genetic metrics. For example, we found high among-locus variation in FIS, which makes the meaning of mean multilocus FIS unclear.

Evolutionary Phycology: Toward a Macroalgal Species Conceptual Framework

Species concepts formalize evolutionary and ecological processes, but often conflict with one another when considering the mechanisms that ultimately lead to species delimitation. Evolutionary biologists are, however, recognizing that the conceptualization of a species is separate and distinct from the delimitation of species. Indeed, if species are generally defined as separately evolving metapopulation lineages, then characteristics, such as reproductive isolation or monophyly, can be used as evidence of lineage separation and no longer conflict with the conceptualization of a species. However, little of this discussion has addressed the formalization of this evolutionary conceptual framework for macroalgal species. This may be due to the complexity and variation found in macroalgal life cycles. While macroalgal mating system variation and patterns of hybridization and introgression have been identified, complex algal life cycles generate unique eco-evolutionary consequences. Moreover, the discovery of frequent macroalgal cryptic speciation has not been accompanied by the study of the evolutionary ecology of those lineages, and, thus, an understanding of the mechanisms underlying such rampant speciation remain elusive. In this perspective, we aim to further the discussion and interest in species concepts and speciation processes in macroalgae. We propose a conceptual framework to enable phycological researchers and students alike to portray these processes in a manner consistent with dialogue at the forefront of evolutionary biology. We define a macroalgal species as an independently evolving metapopulation lineage, whereby we can test for reproductive isolation or the occupation of distinct adaptive zones, among other mechanisms, as secondary lines of supporting evidence.

Incorporating Ploidy Diversity into Ecological and Community Genetics

Studies in ecological and community genetics have advanced our understanding of the role of intraspecific diversity in structuring communities and ecosystems. However, in near-shore marine communities, these studies have mostly been restricted to seagrasses, marsh plants, and oysters. Yet, macroalgae are critically important ecosystem engineers in these communities. Greater intraspecific diversity in a macroalgal ecosystem engineer should result in higher primary and secondary production and community resilience. The paucity of studies investigating the consequences of macroalgal intraspecific genetic variation might be due, in part, to the complexity of macroalgal life cycles. The majority of macroalgae have seemingly subtle, but in actuality, profoundly different life cycles than the more typical animal and angiosperm models. Here, we develop a novel genetic diversity metric, P_HD , that incorporates the ratio of gametophytic to sporophytic thalli in natural populations. This metric scales from 0 to 1 like many common genetic diversity metrics, such as genotypic richness, enabling comparisons among metrics. We discuss P_HD and examples from the literature, with specific reference to the widespread, red seaweed Agarophyton vermiculophyllum. We also discuss a sex diversity metric, P_FM , which also scales from 0 to 1, but fewer studies have identified males and females in natural populations. Nevertheless, by incorporating these novel metrics into the repertoire of diversity metrics, we can explore the role of genetic diversity in community and ecosystem dynamics with an emphasis on the unique biology of many macroalgae, as well as other haplodiplontic taxa such as ferns, foraminiferans, and some fungi.

The importance of effective sampling for exploring the population dynamics of haploid-diploid seaweeds

The mating system partitions genetic diversity within and among populations and the links between life history traits and mating systems have been extensively studied in diploid organisms. As such most evolutionary theory is focused on species for which sexual reproduction occurs between diploid male and diploid female individuals. However, there are many multicellular organisms with biphasic life cycles in which the haploid stage is prolonged and undergoes substantial somatic development. In particular, biphasic life cycles are found across green, brown and red macroalgae. Yet, few studies have addressed the population structure and genetic diversity in both the haploid and diploid stages in these life cycles. We have developed some broad guidelines with which to develop population genetic studies of haploid-diploid macroalgae and to quantify the relationship between power and sampling strategy. We address three common goals for studying macroalgal population dynamics, including haploid-diploid ratios, genetic structure and paternity analyses.

Development and characterization of microsatellite loci for the haploid-diploid red seaweed Gracilaria vermiculophylla

Microsatellite loci are popular molecular markers due to their resolution in distinguishing individual genotypes. However, they have rarely been used to explore the population dynamics in species with biphasic life cycles in which both haploid and diploid stages develop into independent, functional organisms. We developed microsatellite loci for the haploid-diploid red seaweed Gracilaria vermiculophylla, a widespread non-native species in coastal estuaries of the Northern hemisphere. Forty-two loci were screened for amplification and polymorphism. Nine of these loci were polymorphic across four populations of the extant range with two to eleven alleles observed. Mean observed and expected heterozygosities ranged from 0.265 to 0.527 and 0.317 to 0.387, respectively. Overall, these markers will aid in the study of the invasive history of this seaweed and further studies on the population dynamics of this important haploid-diploid primary producer.

Understanding macroalgal dispersal in a complex hydrodynamic environment: a combined population genetic and physical modelling approach

Gene flow in macroalgal populations can be strongly influenced by spore or gamete dispersal. This, in turn, is influenced by a convolution of the effects of current flow and specific plant reproductive strategies. Although several studies have demonstrated genetic variability in macroalgal populations over a wide range of spatial scales, the associated current data have generally been poorly resolved spatially and temporally. In this study, we used a combination of population genetic analyses and high-resolution hydrodynamic modelling to investigate potential connectivity between populations of the kelp Laminaria digitata in the Strangford Narrows, a narrow channel characterized by strong currents linking the large semi-enclosed sea lough, Strangford Lough, to the Irish Sea. Levels of genetic structuring based on six microsatellite markers were very low, indicating high levels of gene flow and a pattern of isolation-by-distance, where populations are more likely to exchange migrants with geographically proximal populations, but with occasional long-distance dispersal. This was confirmed by the particle tracking model, which showed that, while the majority of spores settle near the release site, there is potential for dispersal over several kilometres. This combined population genetic and modelling approach suggests that the complex hydrodynamic environment at the entrance to Strangford Lough can facilitate dispersal on a scale exceeding that proposed for L. digitata in particular, and the majority of macroalgae in general. The study demonstrates the potential of integrated physical-biological approaches for the prediction of ecological changes resulting from factors such as anthropogenically induced coastal zone changes.

GENETIC POPULATION STRUCTURE AND MATING SYSTEM IN CHONDRUS CRISPUS (RHODOPHYTA)1

Chondrus crispus Stackh. has been intensely studied, yet no study to date has elucidated its population structure or mating system despite many populations in which there was a haploid bias and lack of male gametophytes. Therefore, 12 nuclear microsatellite loci were identified in this red alga. Microsatellite markers were developed and tested against a panel of specimens collected from two shore levels at two sites in Brittany, France: Pointe de Primel and Pointe de la Jument, Concarneau. Single locus genetic determinism was verified at eight polymorphic loci, as only one band was observed for haploid genotypes, whereas one or two bands were observed for diploids. These markers enabled the detection of unique genotypes within sampled populations, indicating that very few fronds shared the same multilocus genotype. This finding suggests that asexual reproduction was not the prevailing mode of reproduction. In addition, we explored the hierarchical population structure showing that gene flow is restricted at small spatial scales (<50 m) between upper and lower Chondrus-range populations within a shore. Sexual reproduction predominated in the populations of C. crispus studied, but probably due to fine-scale spatial substructuring, inbreeding was also significant. In conclusion, this study reveals that fine-scale genetic variation is of major importance in C. crispus, suggesting that differences between microhabitats should be essential in understanding evolutionary processes in this species.

MULTISCALE GENETIC STRUCTURE OF AN ENDANGERED SEAWEED AHNFELTIOPSIS PUSILLA (RHODOPHYTA): IMPLICATIONS FOR ITS CONSERVATION(1)

Although marine macroalgae have recently entered the lists of endangered species, conservation efforts are still limited by a lack of data, particularly for naturally rare species. One example is the turf-forming Ahnfeltiopsis pusilla (Mont.) P. C. Silva et DeCew. Albeit cataloged as vulnerable in the Northwest Iberian Peninsula (NWIP), where it occurs only at five enclaves separated by 1,200 km from the closest recorded presence of the species, nothing is known about its genetic diversity and population connectivity. We used amplified fragment length polymorphism (AFLP) and sequences of the intergenic region between the mitochondrial cytochrome oxidase subunit 2 and subunit 3 genes (cox2-3) to investigate its genetic structure at large (1,200 km), regional (<125 km), fine (<250 m), and patch (<1 m) scales. While cox2-3 variability was too low for the intraspecific study, AFLP revealed that most of the genetic diversity was due to differences between populations. Locally, genetic diversity was always low, and clones were frequent, suggesting that asexual reproduction may be common; patches of turf, however, often were composites of various genetic individuals. Genetic structure at local, regional, and large scales indicated that A. pusilla is a poor disperser, and an assignment test found no evidence of real-time dispersal between NWIP sites. Therefore, it is proposed that the five NWIP enclaves are designated independent management units (MUs). Bayesian-clustering approaches suggested that the three southernmost sites are particularly valuable for conservation since they concentrate most of the genetic heritage of A. pusilla in NWIP. Our study shows that the approaches of conservation genetics may provide useful insights for endangered seaweeds.

Microsatellite markers in an invasive strain of Asparagopsis taxiformis (Bonnemaisoniales, Rhodophyta): insights in ploidy level and sexual reproduction

Eight polymorphic nuclear microsatellite loci were identified from the invasive Indo-Pacific Mediterranean strain of Asparagopsis taxiformis. Microsatellite markers were tested against a panel of specimens collected along the Italian (Elba, Naples) and Californian (Catalina Island) coasts, all belonging to the same mitochondrial lineage. In addition, we used Hawaiian specimens, belonging to a closely related mitochondrial lineage. The markers amplified in all of the specimens but failed consistently in thalli of two more distantly related mitochondrial lineages of A. taxiformis as well as in specimens belonging to the sister species Asparagopsis armata. Since haploid female individuals among the Mediterranean specimens contained cystocarps, genotyping was performed on supposedly haploid female specimens and supposedly diploid cystocarps separately. As expected, external allelic contribution was detected in the cystocarps. However, even after removal of these reproductive structures, gametophyte thalli exhibited patterns consisting of up to three alleles in all of the tested populations indicating polyploidy. An elevated number of distinct genotypes (up to 85%) were found per population, suggesting high intra-population variation. Results showed high genetic similarity between the two Mediterranean populations screened and lower similarity between these two and the Californian one within the same mitochondrial lineage. Lowest similarity was found between these three and the Hawaiian population belonging to the other related mitochondrial lineage 1.

Landscape structure, clonal propagation, and genetic diversity in Scandinavian populations of Arabidopsis lyrata (Brassicaceae)

Colonization history, landscape structure, and environmental conditions may influence patterns of neutral genetic variation because of their effects on gene flow and reproductive mode. We compared variation at microsatellite loci within and among 26 Arabidopsis lyrata populations in two disjunct areas of its distribution in northern Europe (Norway and Sweden). The two areas probably share a common colonization history but differ in size (Norwegian range markedly larger than Swedish range), landscape structure (mountains vs. coast), and habitat conditions likely to affect patterns of gene flow and opportunities for sexual reproduction. Within-population genetic diversity was not related to latitude but was higher in Sweden than in Norway. Population differentiation was stronger among Norwegian than among Swedish populations (F(ST) = 0.23 vs. F(ST) = 0.18). The frequency of clonal propagation (proportion of identical multilocus genotypes) increased with decreasing population size, was higher in Norwegian than in Swedish populations, but was not related to altitude or substrate. Differences in genetic structure are discussed in relation to population characteristics and range size in the two areas. The results demonstrate that the possibility of clonal propagation should be considered when developing strategies for sampling and analyzing data in ecological and genetic studies of this emerging model species.

Local genetic structure in a clonal dioecious angiosperm

We used seven microsatellite loci to characterize genetic structure and clonal architecture at three different spatial scales (from meters to centimetres) of a Cymodocea nodosa population. C. nodosa exhibits both sexual reproduction and vegetative propagation by rhizome elongation. Seeds remain buried in the sediment nearby the mother plant in a dormant stage until germination. Seed dispersal potential is therefore expected to be extremely restricted. High clonal diversity (up to 67% of distinct genotypes) and a highly intermingled configuration of genets at different spatial scales were found. No significant differences in genetic structure were found among the three spatial scales, indicating that genetic diversity is evenly distributed along the meadow. Autocorrelation analyses of kinship estimates confirmed the absence of spatial clumping of genets at small spatial scale and the expectations of a very restricted seed dispersal (observed dispersal range 1-21 m) in this species.

Maintenance of clonal diversity during a spring bloom of the centric diatom Ditylum brightwellii

Maintenance of genetic diversity in eukaryotic microbes reflects a synergism between reproductive mode (asexual vs. sexual) and environmental conditions. We determined clonal diversity in field samples of the planktonic marine diatom, Ditylum brightwellii, during a bloom, when cell number increased by seven-fold because of rapid asexual division. The genotypes at three microsatellite loci were determined for 607 individual cell lines isolated during the 11 days of sampling. Genetic diversity remained high during the bloom and 87% of the cells sampled each day were genetically distinct. Sixty-nine clonal lineages were sampled two or more times during the bloom, and two clones were sampled seven times. Based on the frequency of resampled clonal lineages, capture-recapture statistics were used to determine that at least 2400 genetically distinct clonal lineages comprised the bloom population. No significant differences in microsatellite allele frequencies were observed among daily samples indicating that the bloom was comprised of a single population. No sexual stages were observed, although linkage equilibrium at two loci, high levels of allelic and genotypic diversity, and heterozygote deficiencies were all indicative of past sexual reproduction events. At the height of the bloom, a windstorm diluted cell numbers by 51% and coincided with a change in the frequency distribution of some resampled lineages. The extensive clonal diversity generated through past sexual reproduction events coupled with frequent environmental changes appear to prevent individual clonal lineages from becoming numerically dominant, maintaining genetic diversity and the adaptive potential of the population.

Mating system and gene flow in the red seaweed Gracilaria gracilis: effect of haploid–diploid life history and intertidal rocky shore landscape on fine-scale genetic structure

The impact of haploid-diploidy and the intertidal landscape on a fine-scale genetic structure was explored in a red seaweed Gracilaria gracilis. The pattern of genetic structure was compared in haploid and diploid stages at a microgeographic scale (< 5 km): a total of 280 haploid and 296 diploid individuals located in six discrete, scattered rock pools were genotyped using seven microsatellite loci. Contrary to the theoretical expectation of predominantly endogamous mating systems in haploid-diploid organisms, G. gracilis showed a clearly allogamous mating system. Although within-population allele frequencies were similar between haploids and diploids, genetic differentiation among haploids was more than twice that of diploids, suggesting that there may be a lag between migration and (local) breeding due to the long generation times in G. gracilis. Weak, but significant, population differentiation was detected in both haploids and diploids and varied with landscape features, and not with geographic distance. Using an assignment test, we establish that effective migration rates varied according to height on the shore. In this intertidal species, biased spore dispersal may occur during the transport of spores and gametes at low tide when small streams flow from high- to lower-shore pools. The longevity of both haploid and diploid free-living stages and the long generation times typical of G. gracilis populations may promote the observed pattern of high genetic diversity within populations relative to that among populations.

Estimating F-statistics

A moment estimator of, the coancestry coefficient for alleles within a population, was described by Weir & Cockerham in 1984 (100) and is still widely cited. The estimate is used by population geneticists to characterize population structure, by ecologists to estimate migration rates, by animal breeders to describe genetic variation, and by forensic scientists to quantify the strength of matching DNA profiles. This review extends the work of Weir & Cockerham by allowing different levels of coancestry for different populations, and by allowing non-zero coancestries between pairs of populations. All estimates are relative to the average value of theta between pairs of populations. Moment estimates for within- and between-population theta values are likely to have large sampling variances, although these may be reduced by combining information over loci. Variances also decrease with the numbers of alleles at a locus, and with the numbers of populations sampled. This review also extends the work of Weir & Cockerham by employing maximum likelihood methods under the assumption that allele frequencies follow the normal distribution over populations. For the case of equal theta values within populations and zero theta values between populations, the maximum likelihood estimate is the same as that given by Robertson & Hill in 1984 (70). The review concludes by relating functions of theta values to times of population divergence under a pure drift model.