Isolation and characterization of microsatellite markers for the seagrass Cymodocea nodosa

In order to study the spatial patterns of genetic diversity of a clonal marine angiosperm, the seagrass Cymodocea nodosa, microsatellite markers were obtained by screening a genomic library enriched for the (CT) dinucleotide motif. Of 38 primer pairs defined, 15 amplified polymorphic microsatellites and are described. These loci identified a number of alleles ranging from two to seven, and showed expected heterozygosity ranging from 0.35 to 0.76, when a group of 40 individuals from Cadiz Bay in Spain was analysed. Additionally, we describe here the multiplexing conditions for 12 of these loci.     

Polymorphic microsatellite loci for the marine angiosperm Cymodocea nodosa

The seagrass Cymodocea nodosa (UCRIA) Ascherson represents a good model to assess the relative contribution of clonal and sexual reproduction to genetic structure in marine plant populations. Seven microsatellite loci with repeat units consisting of one trinucleotide, four simple dinucleotides and two complex dinucleotides are described here. The seven loci are characterized by high number of alleles (from three to 13) and high heterozygosity (H_O ranging from 0.240 to 0.860) in the tested populations. Conditions for multiplex polymerase chain reactions are also described.     

Genetic differentiation and secondary contact zone in the seagrass Cymodocea nodosa across the Mediterranean–Atlantic transition region

Aim A central question in evolutionary ecology is the nature of environmental barriers that can limit gene flow and induce population genetic divergence, a first step towards speciation. Here we study the geographical barrier constituted by the transition zone between the Atlantic Ocean and the Mediterranean Sea, using as our model Cymodocea nodosa, a seagrass distributed throughout the Mediterranean and in the Atlantic, from central Portugal to Mauritania. We also test predictions about the genetic footprints of Pleistocene glaciations. Location The Atlantic–Mediterranean transition region and adjacent areas in the Atlantic (Mauritania to south‐west Portugal) and the Mediterranean. Methods We used eight microsatellite markers to compare 20 seagrass meadows in the Atlantic and 27 meadows in the Mediterranean, focusing on the transition between these basins. Results Populations from these two regions form coherent groups containing several unique, high‐frequency alleles for the Atlantic and for the Mediterranean, with some admixture west of the Almeria–Oran Front (Portugal, south‐west Spain and Morocco). These are populations where only one or a few genotypes were found, for all but Cadiz, but remarkably still show the footprint of a contact zone. This extremely low genotypic richness at the Atlantic northern edge contrasts with the high values (low clonality) at the Atlantic southern edge and in most of the Mediterranean. The most divergent populations are those at the higher temperature range limits: the southernmost Atlantic populations and the easternmost Mediterranean, both potential footprints of vicariance. Main conclusions A biogeographical transition region occurs close to the Almeria–Oran front. A secondary contact zone in Atlantic Iberia and Morocco results from two distinct dispersal sources: the Mediterranean and southernmost Atlantic populations, possibly during warmer interglacial or post‐glacial periods. The presence of high‐frequency diagnostic alleles in present‐day disjunct populations from the southernmost Atlantic region indicates that their separation from all remaining populations is ancient, and suggests an old, stable rear edge.     

Isolation and characterization of novel microsatellite markers for Cymodocea serrulata (Cymodoceaceae), a seagrass distributed widely in the Indo‐Pacific region

Cymodocea serrulata is a tropical seagrass species distributed widely in the Indo‐Pacific region. We developed 16 novel microsatellite (simple sequence repeat) markers for C. serrulata using next‐generation sequencing for use in genetic studies. The applicability of these markers was attested by genotyping of 40 individuals collected from a natural population in the Philippines. Of the 16 loci, 15 showed polymorphism. For the 15 polymorphic markers, the number of alleles per locus ranged from two to seven, and the observed and expected heterozygosities ranged from 0.131–1.000 and 0.124–0.788, respectively. These markers are useful tools for elucidating genetic diversity, connectivity, and structure in this foundational coastal 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.     

Dinamica dei sistemi a Cymodocea nodosa,Zostera marina e Zostera noltii nel Mediterraneo

Abstract

Data on geographical and depth distribution, sediment granulometry, salinity, biomass variability, below/aboveground biomass ratio, and reproductive strategies of seagrass communities in the Mediterranean Sea were analysed to describe their dynamics patterns.

Notwithstanding their different latitudinal distribution, they have a similar seasonal biomass variability, deriving both from extrinsic forcing (e.g. light and temperature) and intrinsic species-specific components (e.g. reproduction pattern), these latter being responsible for their different structure and seasonal dynamics.     

New microsatellite markers for the endemic Mediterranean seagrass Posidonia oceanica

The seagrass Posidonia oceanica is endemic to the Mediterranean Sea, where it plays an important role in coastal ecosystem dynamics. Because of this important role and concerns about the observed regression of some meadows, population genetic studies of this species have been promoted. However, the markers used until now were not polymorphic enough to efficiently assess the level and spatial pattern of genetic variability. Hypervariable molecular markers were obtained by screening a genomic library enriched for microsatellite dinucleotide repeats. Among 25 primer pairs defined, eight amplified polymorphic microsatellites with an encouraging level of variability at the two geographical scales sampled.     

Comparison of spatial scale variability of shoot density and epiphytic leaf assemblages of Halophila stipulacea and Cymodocea nodosa on the Eastern Coast of Tunisia

Abstract

A study was undertaken to compare the patterns of spatial variability, epiphytic percentage cover, and distribution of epiphytic fauna and flora between the two adjacent seagrasses Cymodocea nodosa and the invasive species Halophila stipulucea. Samples were taken at six stations separated by 600?m and exposed to different current conditions. The stations G2 and G5 were affected by a high current tide, while G4 was directly exposed to the northern marine currents. The station G3 was situated in the middle of a Posidonia oceanica bed and was less exposed to hydrodynamism, whereas the other stations were relatively protected. Results indicate that for both H. stipulacea and C. nodosa, shoot density and epiphytic cover biomass decreased when exposed to high levels of hydrodynamic activity. In terms of epiphytic leaf assemblages, our results showed significant differences for the two host plants in their mean cover and for the six stations at the largest and smallest spatial scale. Our observations highlight the dominance of Rhodophyta and the low number of epiphytic species and the epiphytic cover on H. stipulacea compared to C. nodosa. In addition, results indicate the absence of two taxa Hydrozoans and Annelida in the epiphytic assemblage of H. stipulacea leaves.     

Genetic structure of the clonal herb Tanakaea radicans (Saxifragaceae) at multiple spatial scales,revealed by nuclear and mitochondrial microsatellite markers

The genus Tanakaea is a plant genus that consists of one or two evergreen herbaceous species in Japan and China. As rithophytic plant species occur on shaded rocks, the populations are usually isolated and sporadically found in disjunct areas. To evaluate the genetic structure of the species at multiple spatial scales, 10 nuclear and mitochondrial microsatellite markers were developed. The novel markers showed high genetic variations (two to 15 alleles and H_e from 0.400 to 0.894). Clonal samples were identified with the probability of identity of 9.0E‐8. When evaluated with 11 populations in Japan, significant genetic differentiation between regional population groups was detected (F_ST = 0.313 between Shikoku and Honshu islands), suggesting they have long been isolated from each other. Overall, these markers will be useful for population genetic research to investigate clonal structure and genetic diversity and levels of genetic differentiation between the geographically isolated populations.     

野古草种群克隆的遗传变异和遗传结构

用酶电泳法和同工酶分析对东北松嫩草原西北部野古草种群克隆遗传变异性和种群遗传结构做了探讨。讨论了遗传多样性、地理距离和遗传距离之间的关系、大种群和小种群的遗传变异性和种群间的基因流 ;种群间 ,包括大种群和小种群间基因流、遗传和地理距离对遗传多样性的影响、昆虫和风传粉、种群籽苗的补充、遗传多样性的发生和保持 ,自交不亲和性和无性繁殖及体细胞突变     

Diel and Seasonal Changes in the Structure of a Decapod (Crustacea: Decapoda) Community of Cymodocea nodosa from Southeastern Spain (West Mediterranean Sea)

The study of a decapod community in a Cymodocea nodosa meadow from Southeastern Spain (Western Mediterranean Sea) showed a stable structure, in which the families Hippolytidae, Processidae, Majidae and Portunidae were the most abundant and the species Hippolyte niezabitowskii dominated. The animal community was more numerous and diverse during the night, showing the existence of nychthemeral movements, which are essentially related to the trophic behaviour and shelter. In this way, many species increased their abundance as a result of an increasing activity and, also, of an influx of other species and specimens from adjacent sandy bottoms, such as Processa spp. (mainly P. modica) Sicyonia carinata, Liocarcinus spp. (mainly juveniles) and several species of hermit crabs, which were rare or absent during the day. All these changes produced modifications in the dominance curves and in the values of all ecological indices (richness, diversity and evenness). Monthly samples were grouped and ordered (MDS) by the factor “day–night”, which showed slight qualitative and quantitative differences (SIMPER, dissimilarity average of the factor day–night = 61.67). On the other hand, no global seasonal differences have been found (one way ANOSIM), but there was a significant level of similarity between winter and spring, while the summer samples were the most different. The differentiation of the summer 1999 can be attributed to a decrease in species abundance and richness, probably due to the dynamics of the decapod populations and the balance with predators (fishes), while that of the summer 2000, to an anomalous event: the massive proliferation of filamentous algae, mainly Ectocarpus s.l., which modified the environmental conditions.     

Fine‐scale genetic structure and flowering output of the seagrass Enhalus acoroides undergoing disturbance

Seagrass are under great stress in the tropical coast of Asia, where Enhalus acoroides is frequently the dominant species with a large food web. Here, we investigate the question of the fine‐scale genetic structure of this ecologically important foundation species, subject to severe anthropogenic disturbance in China. The genetic structure will illuminate potential mechanisms for population dynamics and sustainability, which are critical for preservation of biodiversity and for decision‐making in management and restoration. We evaluated the fine‐scale spatial genetic structure (SGS) and flowering output of E. acoroides, and indirectly estimated the relative importance of sexual versus asexual reproduction for population persistence using spatial autocorrelation analysis. Results reveal high clonal diversity for this species, as predicted from its high sexual reproduction output. The stronger Sp statistic at the ramet‐level compared with genet‐level indicates that clonality increases the SGS pattern for E. acoroides. Significant SGS at the genet‐level may be explained by the aggregated dispersal of seed/pollen cohorts. The estimated gene dispersal variance suggests that dispersal mediated by sexual reproduction is more important than clonal growth in this study area. The ongoing anthropogenic disturbance will negatively affect the mating pattern and the SGS patterns in the future due to massive death of shoots, and less frequency of sexual reproduction.     

Nutrient availability in the sediment and the reciprocal effects between the native seagrass Cymodocea nodosa and the introduced rhizophytic alga Caulerpa taxifolia

Two reciprocal experiments testing for the effects of nutrient addition in the sediment and competitive interactions between the native seagrass Cymodocea nodosa (Ucria) Ascherson and the introduced alga Caulerpa taxifolia (Vahl) C. Agardh were performed. This study was conducted for 13 months (August 1995 until September 1996) in a bay on the south coast of Elba Island (Italy). Each experiment consisted of the manipulation of the level of nutrients (addition vs. control) and the manipulation of the neighbours (presence vs. removal). Response variables were blade density and size for one experiment and shoot density and leaf length of seagrass in the other. Results indicated that the presence of Caulerpa taxifolia did not affect significantly Cymodocea nodosa shoot density and the increased nutrient availability in the sediment did not alter this pattern. Neither the removal of the canopy of the seagrass nor the fertilization of the sediment has influenced significantly the density of the alga. Both species, where co-occurring, show larger size than where the neighbour is removed. Hence, results of this study suggest that the two species on the long term are likely to coexist and that the high nutrient supply of the sediment would not enhance the probability of success neither of the seagrass nor of the alga. Predictions made on the basis of short-term results, that high nutrient loads of the substratum would have represented an even more suitable condition for C. taxifolia to colonize C. nodosa beds and that on the long-term the alga has a high probability of success, did not occur.     

Leaf dynamics and standing stocks of intertidal Zostera noltii Hornem. and Cymodocea nodosa (Ucria) Ascherson on the Banc d'Arguin (Mauritania)

Leaf dynamics and standing stocks of intertidal seagrasses were studied in the Baie d'Aouatif (Parc National du Banc d'Arguin, Mauritania) in April and September 1988. Standing stocks of Zostera noltii Hornem. suggest a unimodal seasonal curve similar to what is found for populations at higher latitudes. Also, leaf growth rates (0.03 cm² cm^–2 day^–1 on average) were similar to those found at higher latitudes in these months. Variation in leaf loss over tidal depth, time and different locations in the Baie d'Aouatif was larger and more often significant than variation in leaf growth. In general, Z. noltii beds in the Baie d'Aouatif had comparable leaf growth rates and standing stocks. In both months losses were almost always higher than or equal to growth.Variation in leaf loss over time was much higher in the plots that were situated high in the intertidal than in lower plots. This is explained by differences in susceptibility to sloughing, which is presumably higher in periods with low tide around noon for shallow depths.In an experiment using artificial shading nets, in situ leaf growth was affected negatively from 94% shading onwards. This shading was observed to reduce the light intensity reaching the seagrass bed to a level below the reported range of light compensation points for Z. noltii. Cymodocea nodosa (Ucria) Ascherson on average had higher leaf area and relative growth rates than Z. noltii and much lower loss rates, resulting in a positive net increase in September. Standing stocks were also higher than for Z. noltii. A mixed seagrass bed containing the above two species and Halodule wrightii Ascherson had the highest observed total biomass: 335 g m^–2 ash-free dry weight.     

Temporal dynamics of genotypic diversity reveal strong clonal selection in the aphid Myzus persicae

Parthenogenetic organisms often harbour substantial genotypic diversity. This diversity may be the result of recurrent formations of new clones, or it may be maintained by environmental heterogeneity acting on ecological differences among clones. In aphids, both processes may be important because obligate and cyclical parthenogens can form mixed populations. Using microsatellites, I analysed the temporal dynamics of clonal diversity in such a population of the aphid Myzus persicae over a 1-year period. The frequency distribution of clonal genotypes was very skewed, with many rare and few common clones. The relative frequencies of common clones underwent strong and rapid changes indicative of intense clonal selection. Differences in their host associations suggest that these shifts may partly be caused by changes in the abundance of annual host plants. Other selective factors of potential importance are also discussed. New, sexually produced genotypes made a minor contribution to clonal diversity, consistent with the observed heterozygote excess characteristic of predominantly asexual populations in M. persicae.     

Clonality strongly affects the spatial genetic structure of the nurse species Aechmea nudicaulis (L.) Griseb. (Bromeliaceae)

Aechmea nudicaulis is a clonal bromeliad common to the Brazilian Atlantic forest complex and is found abundantly in the sandy coastal plain vegetation (restinga) on the north coast of Rio de Janeiro state, Brazil. This restinga site is structured in vegetation islands, and the species plays a key role as a nurse plant, much favoured by its clonality. We studied the clonal structure and consequences of clonality on the population spatial genetic structure (SGS) of this species using six nuclear microsatellites. Spatial autocorrelation analysis was performed to study the effects of sexual and clonal reproduction on the dispersal of A. nudicaulis. Analyses were performed at the genet (i.e. excluding clonal repeats) and ramet levels. Genotypic richness was moderate (R = 0.32), mostly as a result of the dominance of a few clones. The spatial distribution of genets was moderately intermingled, the mean clone size was 4.9 clonal fragments per genet and the maximum clonal spread was 25 m. Expected heterozygosities were high and comparable with those found in other clonal plants. SGS analyses at the genet level revealed significantly restricted gene dispersal (Sp = 0.074), a strong SGS compared with other herbaceous species. The clonal subrange extended across 23 m where clonality had a significant effect on SGS. The restricted dispersal and SGS pattern in A. nudicaulis, coupled with high levels of genetic diversity, indicated a recruitment at windows of opportunity (RWO) strategy. Moreover, the spatial distribution of genetic variation and the habitat occupation pattern in A. nudicaulis were dependent not only on the intrinsic biological traits of the species (such as spacer size and mating system), but also on biotic interactions with neighbouring species that determined suitable habitats for germination and the establishment of new genets. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 178 , 329–342.     

Functional uniformity underlies the common spatial structure of macrofaunal assemblages in intertidal seagrass beds

Previous work has shown that the intertidal seagrass macrobenthos at three geographically and ecologically disparate localities (in the north‐east Atlantic, south‐west Indian and south‐west Pacific Oceans) possess similar relative species occurrence distributions and uniform species densities. These common features are here demonstrated to be related to the presence in those assemblages of: (1) similar functional diversities and evennesses, (2) the same set of dominant component functional groups, and (3) similar ranked relative occurrence distributions both of those groups and of the component genera within each of the larger groups. The two lower‐latitude systems were particularly similar in all these respects. Although sharing the same subset of individual functional groups, however, the relative importance of members of that subset varied from locality to locality and even within a single locality, whilst still maintaining the same ranked relative functional‐group occurrence distribution. Therefore the broad structure of available macrobenthic functional roles and the relative occurrences of the component taxa in intertidal seagrass beds (and hence, granted stochastic assembly, the total numbers of taxa supported by unit area) are likely to be linked causally, although the form of the relationship is unclear. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 115 , 114–126.     

Population structure,seasonal genotypic differentiation,and clonal diversity of weedy dandelions in three Boston area populations (Taraxacum sp.)

Weedy dandelions have a worldwide distribution and thrive in urban environments despite a lack of sexual reproduction throughout most of its range. North American dandelions, introduced from Eurasia, are believed to be primarily, if not exclusively, apomictic triploids. In some European populations, apomicts co‐occur with diploid sexual individuals and hybridizations can create genetically unique apomicts, which may subsequently disperse and establish new populations globally. Using six nuclear microsatellite markers and a cpDNA intergenic spacer, we investigate the impact of this unusual natural history on population structure and diversity in three urban Boston area dandelion populations. Our results show high levels of genetic diversity within populations, spatial population structure, and seasonal genotypic differentiation in flowering times. We find evidence that sexual reproduction and recombination, presumably in Europe, and extensive gene flow drive these patterns of diversity and create the appearance of panmixia despite the lack of evidence for local sexual reproduction.     

Local forest environment largely affects below-ground growth, clonal diversity and fine-scale spatial genetic structure in the temperate deciduous forest herb Paris quadrifolia

Paris quadrifolia (herb Paris) is a long-lived, clonal woodland herb that shows strong differences in local population size and shoot density along an environmental gradient of soil and light conditions. This environmentally based structuring may be mediated by differences in clonal growth and seedling recruitment through sexual reproduction. To study the interrelationship between environmental conditions and spatial patterns of clonal growth, the spatial genetic structure of four P. quadrifolia populations growing in strongly contrasting sites was determined. In the first place, plant excavations were performed in order to (i) determine differences in below-ground growth of genets, (ii) investigate connectedness of ramets and (iii) determine total genet size. Although no differences in internode length were found among sites, clones in moist sites were much smaller (genets usually consisted of 1-3 interconnected shoots, most of them flowering) than genets in dry sites, which consisted of up to 15 interconnected shoots, the majority of which were vegetative. Further, amplified fragment length polymorphism (AFLP) markers were used. Clonal diversity was higher in populations located in moist and productive ash-poplar forests compared to those found in drier and less productive mixed forest sites (G/N: 0.27 and 0.14 and Simpson's D: 0.84 and 0.75, respectively). Patterns of spatial population genetic structure under dry conditions revealed several large clones dominating the entire population, whereas in moist sites many small genets were observed. Nevertheless, strong spatial genetic structure of the genet population was observed. Our results clearly demonstrate that patterns of clonal diversity and growth form of P. quadrifolia differ among environments. Limited seedling recruitment and large clone sizes due to higher connectedness of ramets explain the low clonal diversity in dry sites. In moist sites, higher levels of clonal diversity and small clone sizes indicate repeated seedling recruitment, whereas strong spatial genetic structure suggests limited seed dispersal within populations.