Mega Clonality in an Aquatic Plant-A Potential Survival Strategy in a Changing Environment

Going With the Flow? Relative Importance of Riverine Hydrologic Connectivity Versus Tidal Influence for Spatial Structure of Genetic Diversity and Relatedness in a Foundational Submersed Aquatic Plant

Genetic connectivity in rivers is generally high, and levels of genotypic and genetic diversity of riverine species are expected to accumulate in downstream locations. Genetic structure of marine and estuarine species is less predictable, even though hydrologic connectivity is also expected to be relatively high in those ecosystems. These observations have been generated across different species and locations such that our understanding of the effects of hydrologic connectivity in the same river, spanning tidal and nontidal habitats, remains incomplete. To control for species and location, we quantified diversity in 941 samples of Vallisneria americana Michx. (Hydrocharitaceae) collected from 36 sites along the species' entire distribution in the tidal and nontidal Potomac River of Maryland, Virginia, and the District of Columbia, USA. Using 10 microsatellite loci, we found 507 unique multilocus genotypes (MLGs) that were collapsed to 482 multilocus lineages (MLLs). Fifty-three MLLs were found multiple times across the riverscape, accounting for over 54% of the genotyped shoots. We found some evidence supporting connectivity throughout the river and stronger evidence that tidal regime drives genotypic and genetic structure within V. americana. Extensive clonality, including two MLLs spanning 230 and 152 km, limits diversity in the nontidal reaches and contrasts with very little evidence of clonal reproduction in tidal reaches. Genetic differentiation, structure, and pairwise relatedness of sampled shoots and MLLs also differed by tidal reach, with the nontidal Potomac having higher levels of relatedness, lower allelic diversity, and higher heterozygosity. The differences in spatial distribution of genetic diversity suggest very different outlooks for V. americana adaptation and acclimation to perturbations in tidal and nontidal regions of the Potomac, which lead to different recommendations for restoration of the same species in the same river.

Mosaic of Somatic Mutations in Earth's Oldest Living Organism, Pando

Understanding how mutations arise and spread through individuals and populations is fundamental to evolutionary biology. Most organisms have a life cycle with unicellular bottlenecks during reproduction. However, some organisms like plants, fungi, or colonial animals can grow indefinitely, changing the manner in which mutations spread throughout both the individual and the population. Furthermore, clonally reproducing organisms may also achieve exceedingly long lifespans, making somatic mutation an important mechanism of creating heritable variation for Darwinian evolution by natural selection. Yet, little is known about intra-organism mutation rates and evolutionary trajectories in long-lived species. Here, we study the Pando aspen clone, the largest known quaking aspen (Populus tremuloides) clone founded by a single seedling and thought to be one of the oldest studied organisms. Aspen reproduce vegetatively via new root-borne stems forming clonal patches, sometimes spanning several hectares. To study the evolutionary history of the Pando clone, we collected and sequenced over 500 samples from Pando and neighboring clones, as well as from various tissue types within Pando, including leaves, roots, and bark. We applied a series of filters to distinguish somatic mutations from the pool of both somatic and germline mutations, incorporating a technical replicate sequencing approach to account for uncertainty in somatic mutation detection. Despite root spreading being spatially constrained, we observed only a modest positive correlation between genetic and spatial distance, suggesting the presence of a mechanism preventing the accumulation and spread of mutations across units. Phylogenetic models estimate the age of the clone to between ~16,000-80,000 years. This age is generally corroborated by the near-continuous presence of aspen pollen in a lake sediment record collected from Fish Lake near Pando. Overall, this work enhances understanding of mutation accumulation and dispersal within and between ramets of long-lived, clonally-reproducing organisms.

Calm after the storm? Similar patterns of genetic variation in a riverine foundation species before and after severe disturbance

In summer 2011, Tropical storms Lee and Irene caused an estimated 90% decline of the submersed aquatic plant Vallisneria americana Michx. (Hydrocharitaceae) in the Hudson River of New York (USA). To understand the genetic impact of such large-scale demographic losses, we compared diversity at 10 microsatellite loci in 135 samples collected from five sites just before the storms with 239 shoots collected from nine sites 4 years after. Although 80% of beds sampled in 2011 lacked V. americana in 2015, we found similar genotypic and genetic diversity and effective population sizes in pre-storm versus post-storm sites. These similarities suggest that despite local extirpations concentrated at the upstream end of the sampling area, V. americana was regionally resistant to genetic losses. Similar geographically based structure among sites in both sampling periods suggested that cryptic local refugia at previously occupied sites facilitated re-expansion after the storms. However, this apparent resistance to disturbance may lead to a false sense of security. Low effective population sizes and high clonality in both time periods suggest that V. americana beds were already small and had high frequency of asexual reproduction before the storms. Dispersal was not sufficient to recolonize more isolated sites that had been extirpated. Chronic low diversity and reliance on asexual reproduction for persistence can be risky when more frequent and intense storms are paired with ongoing anthropogenic stressors. Monitoring genetic diversity along with extent and abundance of V. americana will give a more complete picture of long-term potential for resilience.

Genomic analysis of the emergent aquatic plant Sparganium stoloniferum provides insights into its clonality, local adaptation and demographic history

Clonal propagation and extensive dispersal of seeds and asexual propagules are two important features of aquatic plants that help them adapt to aquatic environments. Accurate measurements of clonality and effective clonal dispersal are essential for understanding the evolution of aquatic plants. Here, we first assembled a high-quality chromosome-level genome of a widespread emergent aquatic plant Sparganium stoloniferum to provide a reference for its population genomic study. We then performed high-depth resequencing of 173 individuals from 20 populations covering different basins across its range in China. Population genomic analyses revealed three genetic lineages reflecting the northeast (NE), southwest (SW) and northwest (NW) of its geographical distribution. The NE lineage diverged in the middle Pleistocene while the SW and NW lineages diverged until about 2400 years ago. Clonal relationship analyses identified nine populations as monoclonal population. Dispersal of vegetative propagules was identified between five populations covering three basins in the NE lineage, and dispersal distance was up to 1041 km, indicating high dispersibility in emergent aquatic plant species. We also identified lineage-specific positively selected genes that are likely to be involved in adaptations to saline wetlands and high-altitude environments. Our findings accurately measure the clonality, determine the dispersal range and frequency of vegetative propagules, and detect genetic signatures of local adaptation in a widespread emergent aquatic plant species, providing new perspectives on the evolution of aquatic plants.

Long range gene flow beyond predictions from oceanographic transport in a tropical marine foundation species

The transport of passively dispersed organisms across tropical margins remains poorly understood. Hypotheses of oceanographic transportation potential lack testing with large scale empirical data. To address this gap, we used the seagrass species, Halodule wrightii, which is unique in spanning the entire tropical Atlantic. We tested the hypothesis that genetic differentiation estimated across its large-scale biogeographic range can be predicted by simulated oceanographic transport. The alternative hypothesis posits that dispersal is independent of ocean currents, such as transport by grazers. We compared empirical genetic estimates and modelled predictions of dispersal along the distribution of H. wrightii. We genotyped eight microsatellite loci on 19 populations distributed across Atlantic Africa, Gulf of Mexico, Caribbean, Brazil and developed a biophysical model with high-resolution ocean currents. Genetic data revealed low gene flow and highest differentiation between (1) the Gulf of Mexico and two other regions: (2) Caribbean-Brazil and (3) Atlantic Africa. These two were more genetically similar despite separation by an ocean. The biophysical model indicated low or no probability of passive dispersal among populations and did not match the empirical genetic data. The results support the alternative hypothesis of a role for active dispersal vectors like grazers.

Facultative Annual Life Cycles in Seagrasses

Plant species usually have either annual or perennial life cycles, but facultative annual species have annual or perennial populations depending on their environment. In terrestrial angiosperms, facultative annual species are rare, with wild rice being one of the few examples. Our review shows that in marine angiosperms (seagrasses) facultative annual species are more common: six (of 63) seagrass species are facultative annual. It concerns Zostera marina, Z. japonica, Halophila decipiens, H. beccarii, Ruppia maritima, and R. spiralis. The annual populations generally produce five times more seeds than their conspecific perennial populations. Facultative annual seagrass species occur worldwide. Populations of seagrasses are commonly perennial, but the facultative annual species had annual populations when exposed to desiccation, anoxia-related factors, shading, or heat stress. A system-wide 'experiment' (closure of two out of three connected estuaries for large-scale coastal protection works) showed that the initial annual Z. marina population could shift to a perennial life cycle within 5 years, depending on environmental circumstances. We discuss potential mechanisms and implications for plant culture. Further exploration of flexible life histories in plant species, and seagrasses in particular, may aid in answering questions about trade-offs between vegetative and sexual reproduction, and preprogrammed senescence.

Detecting clonemate pairs in multicellular diploid clonal species based on a shared heterozygosity index

Clonal reproduction, the formation of nearly identical individuals via mitosis in the absence of genetic recombination, is a very common reproductive mode across plants, fungi and animals. To detect clonal genetic structure, genetic similarity indices based on shared alleles are widely used, such as the Jaccard index, or identity by state. Here we propose a new pairwise genetic similarity index, the SH index, based on segregating genetic marker loci (typically single nucleotide polymorphisms) that are identically heterozygous for pairs of samples (N_SH ). To test our method, we analyse two old seagrass clones (Posidonia australis, estimated to be around 8500 years old; Zostera marina, >750 years old) along with two young Z. marina clones of known age (17 years old). We show that focusing on shared heterozygosity amplifies the power to distinguish sample pairs belonging to different clones compared to methods focusing on all shared alleles. Our proposed workflow can successfully detect clonemates at a location dominated by a single clone. When the collected samples involve two or more clones, the SH index shows a clear gap between clonemate pairs and interclone sample pairs. Ideally N_SH should be on the order of approximately ≥3000, a number easily achievable via restriction-site associated DNA (RAD) sequencing or whole-genome resequencing. Another potential application of the SH index is to detect possible parent-descendant pairs under selfing. Our proposed workflow takes advantage of the availability of the larger number of genetic markers in the genomic era, and improves the ability to distinguish clonemates from nonclonemates in multicellular diploid clonal species.

Multiplexed ISSR Genotyping by Sequencing (MIG-Seq)

Multiplexed inter-simple sequence repeat (ISSR) genotyping by sequencing (MIG-seq) is a simple, rapid, and inexpensive method for detecting single-nucleotide polymorphisms (SNPs) using next-generation sequencing (NGS). The advantages of MIG-seq include easy application to various species without prior genetic information. In addition, this method opens the door to genome-wide nucleotide sequence analyses of low-quality and trace-level deoxyribonucleic acid (DNA) samples, which have previously been difficult to analyze. Another advantage is that the procedure is simple, time-saving, and inexpensive. Recently, MIG-seq has been applied to wild and cultivated plants and has produced novel results. Using invisible DNA information, questions related to gene flow through pollination and seed dispersal, the genetic structure and diversity of populations, clonality, and the hybridization of wild and cultivated plants are being rapidly answered. In this chapter, I present the results of plant research based on MIG-seq and describe the procedure for this method as a user of MIG-seq.

Extensive polyploid clonality was a successful strategy for seagrass to expand into a newly submerged environment

Polyploidy has the potential to allow organisms to outcompete their diploid progenitor(s) and occupy new environments. Shark Bay, Western Australia, is a World Heritage Area dominated by temperate seagrass meadows including Poseidon's ribbon weed, Posidonia australis. This seagrass is at the northern extent of its natural geographic range and experiences extremes in temperature and salinity. Our genomic and cytogenetic assessments of 10 meadows identified geographically restricted, diploid clones (2n = 20) in a single location, and a single widespread, high-heterozygosity, polyploid clone (2n = 40) in all other locations. The polyploid clone spanned at least 180 km, making it the largest known example of a clone in any environment on earth. Whole-genome duplication through polyploidy, combined with clonality, may have provided the mechanism for P. australis to expand into new habitats and adapt to new environments that became increasingly stressful for its diploid progenitor(s). The new polyploid clone probably formed in shallow waters after the inundation of Shark Bay less than 8500 years ago and subsequently expanded via vegetative growth into newly submerged habitats.

Hybridization, polyploidy and clonality influence geographic patterns of diversity and salt tolerance in the model halophyte seashore paspalum (Paspalum vaginatum)

In plant species, variation in levels of clonality, ploidy and interspecific hybridization can interact to influence geographic patterns of genetic diversity. These factors commonly vary in plants that specialize on saline habitats (halophytes) and may play a role in how they adapt to salinity variation across their range. One such halophyte is the turfgrass and emerging genomic model system seashore paspalum (Paspalum vaginatum Swartz). To investigate how clonal propagation, ploidy variation, and interspecific hybridization vary across ecotypes and local salinity levels in wild P. vaginatum, we employed genotyping-by-sequencing, cpDNA sequencing and flow cytometry in 218 accessions representing > 170 wild collections from throughout the coastal southern United States plus USDA germplasm. We found that the two morphologically distinct ecotypes of P. vaginatum differ in their adaptive strategies. The fine-textured ecotype is diploid and appears to reproduce in the wild both sexually and by clonal propagation; in contrast, the coarse-textured ecotype consists largely of clonally-propagating triploid and diploid genotypes. The coarse-textured ecotype appears to be derived from hybridization between fine-textured P. vaginatum and an unidentified Paspalum species. These clonally propagating hybrid genotypes are more broadly distributed than clonal fine-textured genotypes and may represent a transition to a more generalist adaptive strategy. Additionally, the triploid genotypes vary in whether they carry one or two copies of the P. vaginatum subgenome, indicating multiple evolutionary origins. This variation in subgenome composition shows associations with local ocean salinity levels across the sampled populations and may play a role in local adaptation.

Somatic genetic drift and multilevel selection in a clonal seagrass

All multicellular organisms are genetic mosaics owing to somatic mutations. The accumulation of somatic genetic variation in clonal species undergoing asexual (or clonal) reproduction may lead to phenotypic heterogeneity among autonomous modules (termed ramets). However, the abundance and dynamics of somatic genetic variation under clonal reproduction remain poorly understood. Here we show that branching events in a seagrass (Zostera marina) clone or genet lead to population bottlenecks of tissue that result in the evolution of genetically differentiated ramets in a process of somatic genetic drift. By studying inter-ramet somatic genetic variation, we uncovered thousands of single nucleotide polymorphisms that segregated among ramets. Ultra-deep resequencing of single ramets revealed that the strength of purifying selection on mosaic genetic variation was greater within than among ramets. Our study provides evidence for multiple levels of selection during the evolution of seagrass genets. Somatic genetic drift during clonal propagation leads to the emergence of genetically unique modules that constitute an elementary level of selection and individuality in long-lived clonal species.

Diversity and microhabitat associations of Labyrinthula spp. in the Indian River Lagoon System

Seagrasses create foundational habitats in coastal ecosystems. One contributing factor to their global decline is disease, primarily caused by parasites in the genus Labyrinthula. To explore the relationship between seagrass and Labyrinthula spp. diversity in coastal waters, we examined the diversity and microhabitat association of Labyrinthula spp. in 2 inlets on Florida's Atlantic Coast, the Indian River Lagoon (IRL) and Banana River. We used amplicon-based high throughput sequencing with 2 newly designed primers to amplify Labyrinthula spp. from 5 seagrass species, water, and sediments to determine their spatial distribution and microhabitat associations. The SSU primer set identified 12 Labyrinthula zero-radius operational taxonomic units (ZOTUs), corresponding to at least 8 putative species. The ITS1 primer set identified 2 ZOTUs, corresponding to at least 2 putative species. Based on our phylogenetic analyses, which include sequences from previous studies that assigned seagrass-related pathogenicity to Labyrinthula clades, all but one of the ZOTUs that we recovered with the SSU primers were from non-pathogenic species, while the 2 ZOTUs recovered with the ITS1 primers were from pathogenic species. Some of the ZOTUs were widespread across the sampling sites and microhabitats (e.g. SSU ZOTU_10), and most were present in more than one site. Our results demonstrate that targeted metabarcoding is a useful tool for examining the relationships between seagrass and Labyrinthula diversity in coastal waters.

Resilience of beach grasses along a biogeomorphic successive gradient: resource availability vs. clonal integration

Coastal ecosystems are often formed through two-way interactions between plants and their physical landscape. By expanding clonally, landscape-forming plants can colonize bare unmodified environments and stimulate vegetation-landform feedback interactions. Yet, to what degree these plants rely on clonal integration for overcoming physical stress during biogeomorphological succession remains unknown. Here, we investigated the importance of clonal integration and resource availability on the resilience of two European beach grasses (i.e. Elytrigia juncea and Ammophila arenaria) over a natural biogeomorphic dune gradient from beach (unmodified system) to foredune (biologically modified system). We found plant resilience, as measured by its ability to recover and expand following disturbance (i.e. plant clipping), to be independent on the presence of rhizomal connections between plant parts. Instead, resource availability over the gradient largely determined plant resilience. The pioneer species, Elytrigia, demonstrated a high resilience to physical stress, independent of its position on the biogeomorphic gradient (beach or embryonic dune). In contrast, the later successional species (Ammophila) proved to be highly resilient on the lower end of its distribution (embryonic dune), but it did not fully recover on the foredunes, most likely as a result of nutrient deprivation. We argue that in homogenously resource-poor environments as our beach system, overall resource availability, instead of translocation through a clonal network, determines the resilience of plant species. Hence, the formation of high coastal dunes may increase the resistance of beach grasses to the physical stresses of coastal flooding, but the reduced marine nutrient input may negatively affect the resilience of plants.

Shared genomic outliers across two divergent population clusters of a highly threatened seagrass

The seagrass, Zostera capensis, occurs across a broad stretch of coastline and wide environmental gradients in estuaries and sheltered bays in southern and eastern Africa. Throughout its distribution, habitats are highly threatened and poorly protected, increasing the urgency of assessing the genomic variability of this keystone species. A pooled genomic approach was employed to obtain SNP data and examine neutral genomic variation and to identify potential outlier loci to assess differentiation across 12 populations across the ∼9,600 km distribution of Z. capensis. Results indicate high clonality and low genomic diversity within meadows, which combined with poor protection throughout its range, increases the vulnerability of this seagrass to further declines or local extinction. Shared variation at outlier loci potentially indicates local adaptation to temperature and precipitation gradients, with Isolation-by-Environment significantly contributing towards shaping spatial variation in Z. capensis. Our results indicate the presence of two population clusters, broadly corresponding to populations on the west and east coasts, with the two lineages shaped only by frequency differences of outlier loci. Notably, ensemble modelling of suitable seagrass habitat provides evidence that the clusters are linked to historical climate refugia around the Last Glacial Maxi-mum. Our work suggests a complex evolutionary history of Z. capensis in southern and eastern Africa that will require more effective protection in order to safeguard this important ecosystem engineer into the future.

Some Like It Hot: Maternal-Switching With Climate Change Modifies Formation of Invasive Spartina Hybrids

Climate change can induce temporary, spatial or behavioral changes in species, so that only some species can adapt to the new climatic conditions. In the case of invasive species, it is expected that they will be promoted in a context of global change, given their high tolerance to environmental factors and phenotypic plasticity. Once in the invaded range, these species can hybridize with native species thus introducing their genotype in the native biota. However, the effects that climate change will have on this process of invasion by hybridization remain unclear. We evaluated the historical establishment of the reciprocal hybrids between the native Spartina maritima and the invasive S. densiflora in the Gulf of Cadiz (SW Iberian Peninsula) and we related it to climatic changes during the period 1955-2017. Our results showed that, according to their dating based on their rate of lateral expansion rates, the establishment of S. maritima × densiflora and S. densiflora × maritima in the Gulf of Cadiz has occurred in the last two centuries and has been related to changes in air temperature and rainfall during the flowering periods of their parental species, with antagonist impacts on both hybrids. Thus, the hybrid S. densiflora × maritima has been established in years with mild ends of spring and beginning of summer when the flowering of S. maritima lengthened and its pollen production was higher, and it coincided with the beginning of the flowering period of S. densiflora. Moreover, the establishment of this hybrid was related to higher spring/summer rainfalls, probably due to the reduction in salinity in middle marshes. However, the hybrid S. maritima × densiflora, was established mainly in warmer spring/summers in which the proportion of pollen:ovule of S. maritima was reduced favoring its pollination by S. densiflora. As a consequence of the promotion of S. maritima × densiflora with climate change, the native and endangered species S. maritima would be threatened, as both taxa share the same habitat and the hybrid shows a remarkably higher competitive potential.

Range-wide population genetic structure of the Caribbean marine angiosperm Thalassia testudinum

Many marine species have widespread geographic ranges derived from their evolutionary and ecological history particularly their modes of dispersal. Seagrass (marine angiosperm) species have ranges that are unusually widespread, which is not unexpected following recent reviews of reproductive strategies demonstrating the potential for long-distance dispersal combined with longevity through clonality. An exemplar of these dual biological features is turtle grass (Thalassia testudinum) which is an ecologically important species throughout the tropical Atlantic region. Turtle grass has been documented to have long-distance dispersal via floating fruits and also extreme clonality and longevity. We hypothesize that across its range, Thalassia testudinum will have very limited regional population structure due to these characteristics and under typical models of population structure would expect to detect high levels of genetic connectivity. There are very few studies of range-wide genetic connectivity documented for seagrasses or other sessile marine species. This study presents a population genetic dataset that represents a geographic area exceeding 14,000 km2. Population genetic diversity was evaluated from 32 Thalassia testudinum populations sampled across the Caribbean and Gulf of Mexico. Genotypes were based on nine microsatellites, and haplotypes were based on chloroplast DNA sequences. Very limited phylogeographic signal from cpDNA reduced the potential comparative analyses possible. Multiple analytical clustering approaches on population genetic data revealed two significant genetic partitions: (a) the Caribbean and (b) the Gulf of Mexico. Genetic diversity was high (H E = 0.641), and isolation by distance was significant; gene flow and migration estimates across the entire range were however modest, we suggest that the frequency of successful recruitment across the range is uncommon. Thalassia testudinum maintains genetic diversity across its entire distribution range. The genetic split may be explained by genetic drift during recolonization from refugia following relatively recent reduction in available habitat such as the last glacial maxima.

Individual-based genetic analyses support asexual hydrochory dispersal in Zostera noltei

Dispersal beyond the local patch in clonal plants was typically thought to result from sexual reproduction via seed dispersal. However, evidence for the separation, transport by water, and re-establishment of asexual propagules (asexual hydrochory) is mounting suggesting other important means of dispersal in aquatic plants. Using an unprecedented sampling size and microsatellite genetic identification, we describe the distribution of seagrass clones along tens of km within a coastal lagoon in Southern Portugal. Our spatially explicit individual-based sampling design covered 84 km2 and collected 3 185 Zostera noltei ramets from 803 sites. We estimated clone age, assuming rhizome elongation as the only mechanism of clone spread, and contrasted it with paleo-oceanographic sea level change. We also studied the association between a source of disturbance and the location of large clones. A total of 16 clones were sampled more than 10 times and the most abundant one was sampled 59 times. The largest distance between two samples from the same clone was 26.4 km and a total of 58 and 10 clones were sampled across more than 2 and 10 km, respectively. The number of extremely large clone sizes, and their old ages when assuming the rhizome elongation as the single causal mechanism, suggests other processes are behind the span of these clones. We discuss how the dispersal of vegetative fragments in a stepping-stone manner might have produced this pattern. We found higher probabilities to sample large clones away from the lagoon inlet, considered a source of disturbance. This study corroborates previous experiments on the success of transport and re-establishment of asexual fragments and supports the hypothesis that asexual hydrochory is responsible for the extent of these clones.