High genetic diversity and connectivity in the polyploid invasive seaweedAsparagopsis taxiformis(Bonnemaisoniales) in the Mediterranean, explored with microsatellite alleles and multilocus genotypes

Macroalgal detrital systems: an overlooked ecological niche for heterotrophic nitrogen fixation

Diazotrophic macroalgal associations (DMAs) can contribute fixed nitrogen (N) to the host macroalgae. Biological nitrogen fixation (BNF) rates investigated using acetylene reduction assays with living macroalgae surrounding Santa Catalina Island were low (maximum: 36 nmol N × g^-1 (dw) × h^-1 ) and probably insufficient towards helping meet macroalgal N demand. However, DMAs were observed during periods of low nitrate availability in Southern California coastal waters, highlighting the potential importance of diazotrophs during N depleted conditions. Eleven long-term (16-32 days) litter bag decomposition experiments with various macroalgae, especially those with high (> 10) C:N ratios, resulted in much higher BNF rates (maximum: 693 nmol N × g^-1 (dw) × h^-1 ) than observed with living macroalgae. BNF rates were lower at the beginning of macroalgal decomposition but rapidly increased during the second phase before declining towards the end of decomposition. Labile carbon availability is likely influencing BNF rates throughout macroalgal degradation and limits BNF in the final decomposition stage. Comparable dark and light BNF rates with most macroalgae surveyed suggest macroalgal detrital systems are an overlooked, potentially global, niche for heterotrophic N₂ fixation. Lastly, suppressed BNF rates with sodium molybdate additions highlight the prevalence of sulfate reducing diazotrophs.

Diversity Analysis of Sweet Potato Genetic Resources Using Morphological and Qualitative Traits and Molecular Markers

The European Union (EU) market for sweet potatoes has increased by 100% over the last five years, and sweet potato cultivation in southern European countries is a new opportunity for the EU to exploit and introduce new genotypes. In view of this demand, the origins of the principal Italian sweet potato clones, compared with a core collection of genotypes from Central and Southern America, were investigated for the first time. This was accomplished by combining a genetic analysis, exploiting 14 hypervariable microsatellite markers, with morphological and chemical measurements based on 16 parameters. From the molecular analyses, Italian accessions were determined to be genetically very similar to the South American germplasm, but they were sub-clustered into two groups. This finding was subsequently confirmed by the morphological and chemical measurements. Moreover, the analysis of the genetic structure of the population suggested that one of the two groups of Italian genotypes may have descended from one of the South American accessions, as predicted on the basis of the shared morphological characteristics and molecular fingerprints. Overall, the combination of two different characterization methods, genetic markers and agronomic traits, was effective in differentiating or clustering the sweet potato genotypes, in agreement with their geographical origin or phenotypic descriptors. This information could be exploited by both breeders and farmers to detect and protect commercial varieties, and hence for traceability purposes.

Genetic diversity and genetic structure of Decalobanthus boisianus in Hainan Island, China

Decalobanthus boisianus is a native plant of Hainan Island, China, which has caused considerable damage to tropical forest ecosystems in recent decades. Understanding the genetic diversity and structure of this species can facilitate uncovering the molecular mechanism of its invasive ability. Here, we collected 77 individuals of D. boisianus spanning 8 distribution areas with a gradient of human disturbance intensity (i.e., low, moderate, and high disturbance intensity groups) to assess patterns of genetic diversity and structure using inter simple sequence repeat (ISSR) markers. We found that a total of 220 loci were scored with 13 primers using ISSR methods, and that 198 loci were polymorphic. The genetic diversity of D. boisianus among these eight forests decreased with increasing human disturbance intensity. Over 70% of the total genetic variation was present within populations, while less than 30% of variation was found among populations. There was a high gene flow (1.27) among them due to a lack of effective geographic barriers. The mean Nei's genetic distance of D. boisianus populations was found to be relatively small (i.e., 0.07), and the average genetic similarity of the eight populations was high (i.e., 0.93). Our findings indicate that the genetic diversity of D. boisianus correlated to human disturbance density, and that D. boisianus populations in Hainan Island have frequent gene exchange. We suggest that reduce deforestation to decrease human disturbance may be a good way to prevent the invasion of D. boisianus.

Intraorganismal genetic heterogeneity as a source of genetic variation in modular macroalgae

Genetic diversity is considered a key factor of population survival and evolution, especially in changing environments. Genetic diversity arises from mutations in the DNA sequence of cell lines and from there it reaches the level of organisms, populations, and regions. However, many previous studies have not considered the organism architecture or pattern of thallus construction, ignoring the potential genetic complexities that intraorganismal genetic heterogeneity could generate in modular organisms. In seaweeds, modularity and clonality exist in many species. Modular organization has been related to advantages in terms of rapid construction and recovery after the loss of individual modules, which have their own demographic properties as they generate, mature, senesce, and die. Based on recent evidence from the literature, we suggest that modules also have their own genetic properties. Specifically, modular seaweeds have two possible sources of genetic diversity at the individual level: the heterozygosity of the genotypes composing the genet, and genetic heterogeneity among the modules within a genet (i.e., intraclonal genetic variability). Both sources of genetic diversity can have ecological and evolutionary consequences, and most of them must be considered in research on modular seaweeds. Linking intraorganismal genetic diversity with clonal architecture and propagation styles may help us to understand important ecological and evolutionary processes such as speciation modes, invasive capacities, or farming potential.

Low genetic diversity contrasts with high phenotypic variability in heptaploid Spartina densiflora populations invading the Pacific coast of North America

Species can respond to environmental pressures through genetic and epigenetic changes and through phenotypic plasticity, but few studies have evaluated the relationships between genetic differentiation and phenotypic plasticity of plant species along changing environmental conditions throughout wide latitudinal ranges. We studied inter‐ and intrapopulation genetic diversity (using simple sequence repeats and chloroplast DNA sequencing) and inter‐ and intrapopulation phenotypic variability of 33 plant traits (using field and common‐garden measurements) for five populations of the invasive cordgrass Spartina densiflora Brongn. along the Pacific coast of North America from San Francisco Bay to Vancouver Island. Studied populations showed very low genetic diversity, high levels of phenotypic variability when growing in contrasted environments and high intrapopulation phenotypic variability for many plant traits. This intrapopulation phenotypic variability was especially high, irrespective of environmental conditions, for those traits showing also high phenotypic plasticity. Within‐population variation represented 84% of the total genetic variation coinciding with certain individual plants keeping consistent responses for three plant traits (chlorophyll b and carotenoid contents, and dead shoot biomass) in the field and in common‐garden conditions. These populations have most likely undergone genetic bottleneck since their introduction from South America; multiple introductions are unknown but possible as the population from Vancouver Island was the most recent and one of the most genetically diverse. S. densiflora appears as a species that would not be very affected itself by climate change and sea‐level rise as it can disperse, establish, and acclimate to contrasted environments along wide latitudinal ranges.

Assessing global range expansion in a cryptic species complex: insights from the red seaweed genus Asparagopsis (Florideophyceae)

The mitochondrial genetic diversity, distribution and invasive potential of multiple cryptic operational taxonomic units (OTUs) of the red invasive seaweed Asparagopsis were assessed by studying introduced Mediterranean and Hawaiian populations. Invasive behavior of each Asparagopsis OTU was inferred from phylogeographic reconstructions, past historical demographic dynamics, recent range expansion assessments and future distributional predictions obtained from demographic models. Genealogical networks resolved Asparagopsis gametophytes and tetrasporophytes into four A. taxiformis and one A. armata cryptic OTUs. Falkenbergia isolates of A. taxiformis L3 were recovered for the first time in the western Mediterranean Sea and represent a new introduction for this area. Neutrality statistics supported past range expansion for A. taxiformis L1 and L2 in Hawaii. On the other hand, extreme geographic expansion and an increase in effective population size were found only for A. taxiformis L2 in the western Mediterranean Sea. Distribution models predicted shifts of the climatically suitable areas and population expansion for A. armata L1 and A. taxiformis L1 and L2. Our integrated study confirms a high invasive risk for A. taxiformis L1 and L2 in temperate and tropical areas. Despite the differences in predictions among modelling approaches, a number of regions were identified as zones with high invasion risk for A. taxiformis L2. Since range shifts are likely climate-driven phenomena, future invasive behavior cannot be excluded for the rest of the lineages.

Population structure in two geographically sympatric and congeneric ectoparasites (Cimex adjunctus and Cimex lectularius) in the North American Great Lakes region

Subdivided populations can be described by different models of population structure that reflect population organization, dynamics, and connectivity. We used genetic data to investigate population structure in two geographically sympatric, congeneric species of generalist ectoparasites of warm-blooded animals. We characterized the spatial genetic structure of the eastern bat bug (Cimex adjunctus Barber, 1939), an understudied and fairly abundant species, using microsatellite markers at a spatial scale representing contemporary dispersal of the species. We found seven genetic clusters, global [Formula: see text] of 0.2, 33% of genetic variation among sites, and nonsignificant isolation-by-distance. We compared these results with the common bed bug (Cimex lectularius L., 1758), a closely related but conversely well-known species, in the same geographic area. We found stronger genetic structuring in C. lectularius than in C. adjunctus, with 11 genetic clusters, [Formula: see text] of 0.7, 57% of genetic variation among sites, and significant but weak isolation-by-distance (R2 = 0.09). These results suggest that while both species can be described as having classic metapopulation structure, C. adjunctus leans more towards a patchy population and C. lectularius leans more towards a nonequilibrium metapopulation. The difference in population structure between these species may be attributable to differences in movement potential and extinction–colonization dynamics.

Genetic and morphological variation in an ecosystem engineer, Lithophyllum byssoides (Corallinales, Rhodophyta)

Lithophyllum byssoides is a common coralline alga in the intertidal zone of Mediterranean coasts, where it produces biogenic concretions housing a high algal and invertebrate biodiversity. This species is an ecosystem engineer and is considered a target for conservation efforts, but designing effective conservation strategies currently is impossible due to lack of information about its population structure. The morphological and molecular variation of L. byssoides was investigated using morphoanatomy and DNA sequences (psbA and cox2,3) obtained from populations at 15 localities on the Italian and Croatian coasts. Lithophyllum byssoides exhibited a high number of haplotypes (31 psbA haplotypes and 24 cox2,3 haplotypes) in the central Mediterranean. The psbA and cox2,3 phylogenies were congruent and showed seven lineages. For most of these clades, the distribution was limited to one or a few localities, but one of them (clade 7) was widespread across the central Mediterranean, spanning the main biogeographic boundaries recognized in this area. The central Mediterranean populations formed a lineage separate from Atlantic samples; psbA pair-wise divergences suggested that recognition of Atlantic and Mediterranean L. byssoides as different species may be appropriate. The central Mediterranean haplotype patterns of L. byssoides were interpreted as resulting from past climatic events in the hydrogeological history of the Mediterranean Sea. The high haplotype diversity and the restricted spatial distribution of the seven lineages suggest that individual populations should be managed as independent units.

Speciation and genetic diversity in Centaurea subsect. Phalolepis in Anatolia

Mountains of Anatolia are one of the main Mediterranean biodiversity hotspots and their richness in endemic species amounts for 30% of the flora. Two main factors may account for this high diversity: the complex orography and its role as refugia during past glaciations. We have investigated seven narrow endemics of Centaurea subsection Phalolepis from Anatolia by means of microsatellites and ecological niche modelling (ENM), in order to analyse genetic polymorphisms and getting insights into their speciation. Despite being narrow endemics, all the studied species show moderate to high SSR genetic diversity. Populations are genetically isolated, but exchange of genes probably occurred at glacial maxima (likely through the Anatolian mountain arches as suggested by the ENM). The lack of correlation between genetic clusters and (morpho) species is interpreted as a result of allopatric diversification on the basis of a shared gene pool. As suggested in a former study in Greece, post-glacial isolation in mountains would be the main driver of diversification in these plants; mountains of Anatolia would have acted as plant refugia, allowing the maintenance of high genetic diversity. Ancient gene flow between taxa that became sympatric during glaciations may also have contributed to the high levels of genetic diversity.

Trophic interactions between indigenous and non-indigenous species in Lampedusa Island, Mediterranean Sea

Using stable isotope analysis, we investigated trophic interactions between indigenous benthic taxa and the non-indigenous species (NIS): the green alga Caulerpa cylindracea, the red alga Asparagopsis taxiformis, the crab Percnon gibbesi and the sea hare Aplysia dactylomela. The study was conducted on Lampedusa Island, Mediterranean Sea. We evaluated the trophic positions and isotopic niches of consumers. Using Bayesian mixing models, we quantified the food source contribution to diets of indigenous and non-indigenous herbivores. Isotopic niche of NIS showed no overlap with the ones of indigenous macroinvertebrates and fish. Caulerpa cylindracea provided the largest contribution to the diet of P. gibbesi (0.431-1), while the dietary contribution estimates overlapped considerably for all sources of A. dactylomela and indigenous herbivores. From these results, we conclude that the invasion of C. cylindracea is increasing the diversity of available prey and might facilitate the expansion of other NIS.

Host and Environmental Specificity in Bacterial Communities Associated to Two Highly Invasive Marine Species (Genus Asparagopsis)

As habitats change due to global and local pressures, population resilience, and adaptive processes depend not only on their gene pools but also on their associated bacteria communities. The hologenome can play a determinant role in adaptive evolution of higher organisms that rely on their bacterial associates for vital processes. In this study, we focus on the associated bacteria of the two most invasive seaweeds in southwest Iberia (coastal mainland) and nearby offshore Atlantic islands, Asparagopsis taxiformis and Asparagopsis armata. Bacterial communities were characterized using 16S rRNA barcoding through 454 next generation sequencing and exploratory shotgun metagenomics to provide functional insights and a backbone for future functional studies. The bacterial community composition was clearly different between the two species A. taxiformis and A. armata and between continental and island habitats. The latter was mainly due to higher abundances of Acidimicrobiales, Sphingomonadales, Xanthomonadales, Myxococcales, and Alteromonadales on the continent. Metabolic assignments for these groups contained a higher number of reads in functions related to oxidative stress and resistance to toxic compounds, more precisely heavy metals. These results are in agreement with their usual association with hydrocarbon degradation and heavy-metals detoxification. In contrast, A. taxiformis from islands contained more bacteria related to oligotrophic environments which might putatively play a role in mineralization of dissolved organic matter. The higher number of functional assignments found in the metagenomes of A. taxiformis collected from Cape Verde Islands suggest a higher contribution of bacteria to compensate nutrient limitation in oligotrophic environments. Our results show that Asparagopsis-associated bacterial communities have host-specificity and are modulated by environmental conditions. Whether this environmental effect reflects the host's selective requirements or the locally available bacteria remains to be addressed. However, the known functional capacities of these bacterial communities indicate their potential for eco-physiological functions that could be valuable for the host fitness.

The history of introduction of the African baobab (Adansonia digitata, Malvaceae: Bombacoideae) in the Indian subcontinent

To investigate the pathways of introduction of the African baobab, Adansonia digitata, to the Indian subcontinent, we examined 10 microsatellite loci in individuals from Africa, India, the Mascarenes and Malaysia, and matched this with historical evidence of human interactions between source and destination regions. Genetic analysis showed broad congruence of African clusters with biogeographic regions except along the Zambezi (Mozambique) and Kilwa (Tanzania), where populations included a mixture of individuals assigned to at least two different clusters. Individuals from West Africa, the Mascarenes, southeast India and Malaysia shared a cluster. Baobabs from western and central India clustered separately from Africa. Genetic diversity was lower in populations from the Indian subcontinent than in African populations, but the former contained private alleles. Phylogenetic analysis showed Indian populations were closest to those from the Mombasa-Dar es Salaam coast. The genetic results provide evidence of multiple introductions of African baobabs to the Indian subcontinent over a longer time period than previously assumed. Individuals belonging to different genetic clusters in Zambezi and Kilwa may reflect the history of trafficking captives from inland areas to supply the slave trade between the fifteenth and nineteenth centuries. Baobabs in the Mascarenes, southeast India and Malaysia indicate introduction from West Africa through eighteenth and nineteenth century European colonial networks.

The Polyploid Series of the Achillea millefolium Aggregate in the Iberian Peninsula Investigated Using Microsatellites

The Achillea millefolium aggregate is one of the most diverse polyploid complexes of the Northern hemisphere and has its western Eurasian boundary in the Iberian Peninsula. Four ploidy levels have been detected in A. millefolium, three of which have already been found in Iberia (diploid, hexaploid and octoploid), and a fourth (tetraploid) reported during the preparation of this paper. We collected a sample from 26 Iberian populations comprising all ploidy levels, and we used microsatellite markers analyzed as dominant in view of the high ploidy levels. Our goals were to quantify the genetic diversity of A. millefolium in the Iberian Peninsula, to elucidate its genetic structure, to investigate the differences in ploidy levels, and to analyse the dispersal of the species. The lack of spatial genetic structure recovered is linked to both high levels of gene flow between populations and to the fact that most genetic variability occurs within populations. This in turn suggests the existence of a huge panmictic yarrow population in the Iberian Peninsula. This is consistent with the assumption that recent colonization and rapid expansion occurred throughout this area. Likewise, the low levels of genetic variability recovered suggest that bottlenecks and/or founder events may have been involved in this process, and clonal reproduction may have played an important role in maintaining this genetic impoverishment. Indeed, the ecological and phenologic uniformity present in the A. millefolium agg. in Iberia compared to Eurasia and North America may be responsible for the low number of representatives of this complex of species present in the Iberian Peninsula. The low levels of genetic differentiation between ploidy levels recovered in our work suggest the absence of barriers between them.

Influence of niche similarity on hybridization between Myriophyllum sibiricum and M. spicatum

The impact of ecological factors on natural hybridization is of widespread interest. Here, we asked whether climate niche influences hybridization between the two closely related plant species Myriophyllum sibiricum and M. spicatum. Eight microsatellite loci and two chloroplast fragments were used to investigate the occurrence of hybridization between these two species in two co-occurring regions: north-east China (NEC) and the Qinghai-Tibetan Plateau (QTP). The climate niches of the species were quantified by principal component analysis with bioclimatic data, and niche comparisons were performed between the two species in each region. Reciprocal hybridization was observed, and M. sibiricum was favoured as the maternal species. Furthermore, hybrids were rare in NEC but common in the QTP. Accordingly, in NEC, the two species were climatically distinct, and hybrids only occurred in the narrow geographical or ecological transition zone, whereas in the QTP, obvious niche overlaps were found for the two species, and hybrids occurred in multiple contact zones. This association between hybridization pattern and climate niche similarity suggests that the level of hybridization was promoted by niche overlap. Compared with the parental species, similar climate niches were found for the hybrid populations in the QTP, indicating that other environmental factors rather than climate were important for hybrid persistence. Our findings highlight the significance of climate niche with respect to hybridization patterns in plants.

The more we search, the more we find: discovery of a new lineage and a new species complex in the genus Asparagopsis

In the past few decades, in the marine realm in particular, the use of molecular tools has led to the discovery of hidden taxonomic diversity, revealing complexes of sister species. A good example is the red algal genus Asparagopsis. The two species (A. armata and A. taxiformis) recognized in this genus have been introduced in many places around the world. Within the nominal species A. taxiformis, previous molecular analyses have uncovered several lineages, suggesting the existence of sister species or subspecies. Although the genus has been well studied in some regions (e.g., the Mediterranean Sea and Hawaii), it remains poorly investigated in others (e.g., South Pacific). Our study mainly focused on these latter areas to clarify lineages and better determine lineage status (i.e., native vs. introduced). A total of 188 specimens were collected from 61 sites, 58 of which had never been sampled before. We sequenced the DNA from samples for three markers and obtained 112 sequences for the chloroplastic RuBisCo spacer, 118 sequences for the nuclear LSU rRNA gene, and 174 for the mitochondrial spacer cox2-3. Phylogenetic analyses using all three markers suggested the existence of two cryptic sister species with the discovery of a new clade within A. armata. This clade was found only in Western Australia, Tasmania and New Zealand, and is thus restricted to a subregional biogeographic unit. We also discovered a new, fifth lineage for A. taxiformis restricted to the South Pacific and Western Australia. Except for this newly described lineage, all other lineages showed a global distribution influenced by introduction events. These results illustrate the difficulty in accurately defining cosmopolitan species. Our findings also highlight the need for targeted (i.e., in poorly studied areas) and geographically extensive sampling efforts when studying taxa that have been introduced globally and that are likely to hide species complexes.

Mahorones, highly brominated cyclopentenones from the red alga Asparagopsis taxiformis

The red alga Asparagopsis taxiformis (Rhodophyta, Bonnemaisoniaceae) has been shown to produce a large diversity of halogenated volatile organic compounds, with one to four carbons. As the distribution of this alga may expand worldwide, we implemented a research program that aims to understand the functions of its specialized metabolome in marine ecosystems. Phytochemical investigations performed on A. taxiformis gametophyte stages from the Indian Ocean revealed two new highly brominated cyclopentenones named mahorone (1) and 5-bromomahorone (2). They are the first examples of natural 2,3-dibromocyclopentenone derivatives. Their structure elucidation was achieved using spectrometric methods including NMR and MS. A standardized ecotoxicological assay was used as an assessment of their role in the environment, revealing high toxicities for both compounds (EC50 0.16 μM for 1 and 2). Additionally, both compounds were evaluated in antibacterial, antifungal, and cytotoxicity assays. Compounds 1 and 2 exhibit mild antibacterial activities against the human pathogen Acinetobacter baumannii.

Homogeneous population of the brown alga Sargassum polycystum in Southeast Asia: possible role of recent expansion and asexual propagation

Southeast Asia has been known as one of the biodiversity hotspots in the world. Repeated glacial cycles during Pleistocene were believed to cause isolation of marine taxa in refugia, resulting in diversification among lineages. Recently, ocean current was also found to be another factor affecting gene flow by restricting larval dispersal in animals. Macroalgae are unique in having mode of reproduction that differs from that of animals. Our study on the phylogeographical pattern of the brown macroalga Sargassum polycystum using nuclear Internal Transcribed Spacer 2 (ITS2), plastidal RuBisCO spacer (Rub spacer) and mitochondrial cytochrome oxidase subunit-III (Cox3) as molecular markers revealed genetic homogeneity across 27 sites in Southeast Asia and western Pacific, in sharp contrast to that revealed from most animal studies. Our data suggested that S. polycystum persisted in single refugium during Pleistocene in a panmixia pattern. Expansion occurred more recently after the Last Glacial Maximum and recolonization of the newly flooded Sunda Shelf could have involved asexual propagation of the species. High dispersal ability through floating fronds carrying developing germlings may also contribute to the low genetic diversity of the species.

Population genetics structure of glyphosate-resistant Johnsongrass (Sorghum halepense L. Pers) does not support a single origin of the resistance

Single sequence repeats (SSR) developed for Sorghum bicolor were used to characterize the genetic distance of 46 different Sorghum halepense (Johnsongrass) accessions from Argentina some of which have evolved toward glyphosate resistance. Since Johnsongrass is an allotetraploid and only one subgenome is homologous to cultivated sorghum, some SSR loci amplified up to two alleles while others (presumably more conserved loci) amplified up to four alleles. Twelve SSR providing information of 24 loci representative of Johnsongrass genome were selected for genetic distance characterization. All of them were highly polymorphic, which was evidenced by the number of different alleles found in the samples studied, in some of them up to 20. UPGMA and Mantel analysis showed that Johnsongrass glyphosate-resistant accessions that belong to different geographic regions do not share similar genetic backgrounds. In contrast, they show closer similarity to their neighboring susceptible counterparts. Discriminant Analysis of Principal Components using the clusters identified by K-means support the lack of a clear pattern of association among samples and resistance status or province of origin. Consequently, these results do not support a single genetic origin of glyphosate resistance. Nucleotide sequencing of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) encoding gene from glyphosate-resistant and susceptible accessions collected from different geographic origins showed that none presented expected mutations in aminoacid positions 101 and 106 which are diagnostic of target-site resistance mechanism.

Genetic guidelines for the conservation of the endangered polyploid Centaurea borjae (Asteraceae)

Appropriate management of species of conservation concern requires designing strategies that should include genetic information as small population size and restricted geographic range can reduce genetic variation. We used AFLPs to investigate genetic variation within and among populations of the endangered narrow endemic Centaurea borjae, and found no evidence for genetic impoverishment despite its <40 km range and potential for vegetative propagation. Genetic variation was comparable to other plants with similar life history (88 % occurring within populations) and potential clone mates were less frequent than expected. Nonetheless, populations separated by few hundred meters showed signs of significant genetic differentiation suggesting low gene flow between them. Our results suggested that the three geographically closer populations located at the center of the range might be treated as a single management unit, while the remaining ones could be considered independent units. We found evidence of fine-scale spatial genetic structure up to 80 m indicating that the collection of germplasm for ex-situ conservation should focus on individuals separated >80 m to maximize genetic variation.

Microsatellite genetic diversity and differentiation of native and introduced grass carp populations in three continents

Grass carp (Ctenopharyngodon idella), a freshwater species native to China, has been introduced to about 100 countries/regions and poses both biological and environmental challenges to the receiving ecosystems. In this study, we analyzed genetic variation in grass carp from three introduced river systems (Mississippi River Basin in US, Danube River in Hungary, and Tone River in Japan) as well as its native ranges (Yangtze, Pearl, and Amur Rivers) in China using 21 novel microsatellite loci. The allelic richness, observed heterozygosity, and within-population gene diversity were found to be lower in the introduced populations than in the native populations, presumably due to the small founder population size of the former. Significant genetic differentiation was found between all pairwise populations from different rivers. Both principal component analysis and Bayesian clustering analysis revealed obvious genetic distinction between the native and introduced populations. Interestingly, genetic bottlenecks were detected in the Hungarian and Japanese grass carp populations, but not in the North American population, suggesting that the Mississippi River Basin grass carp has experienced rapid population expansion with potential genetic diversification during the half-century since its introduction. Consequently, the combined forces of the founder effect, introduction history, and rapid population expansion help explaining the observed patterns of genetic diversity within and among both native and introduced populations of the grass carp.

Species replacement along a linear coastal habitat: phylogeography and speciation in the red alga Mazzaella laminarioides along the south east Pacific

Background

The Chilean shoreline, a nearly strait line of coast expanding across 35 latitudinal degrees, represents an interesting region to assess historical processes using phylogeographic analyses. Stretching along the temperate section of the East Pacific margin, the region is characterized by intense geologic activity and has experienced drastic geomorphological transformations linked to eustatic and isostatic changes during the Quaternary. In this study, we used two molecular markers to evaluate the existence of phylogeographic discontinuities and detect the genetic footprints of Pleistocene glaciations among Patagonian populations of Mazzaella laminarioides, a low-dispersal benthic intertidal red seaweed that inhabits along ~3,700 km of the Chilean coastal rocky shore.

Results

Three main genetic lineages were found within M. laminarioides. They are distributed along the Chilean coast in strict parapatry. The deep divergence among lineages suggests that they could be considered putative genetic sibling species. Unexpectedly, genetic breaks were not strictly concordant with the biogeographic breaks described in the region. A Northern lineage was restricted to a broad transition zone located between 30°S and 33°S and showed signals of a recent bottleneck. The reduction of population size could be related to warm events linked to El Niño Southern Oscillation, which is known to cause massive seaweed mortality in this region. To the south, we propose that transient habitat discontinuities driven by episodic tectonic uplifting of the shoreline around the Arauco region (37°S-38°S); one of the most active forearc-basins in the South East Pacific; could be at the origin of the Central/South genetic break. The large beaches, located around 38°S, are likely to contribute to the lineages’ integrity by limiting present gene flow. Finally, the Southern lineage, occupies an area affected by ice-cover during the last glaciations. Phylogeny suggested it is a derived clade and demographic analyses showed the lineage has a typical signature of postglacial recolonization from a northern glacial refugium area.

Conclusions

Even if environmental adaptation could have strengthened divergence among lineages in M. laminarioides, low dispersal capacity and small population size are sufficient to generate phylogeographic discontinuities determined by genetic drift alone. Interestingly, our results confirm that seaweed population connectivity over large geographic scales does not rely only on dispersal capacity but also seem to depend highly on substratum availability and population density of the receiving locality.

Intraspecific cytotypic variation and complicated genetic structure in the Phlox amabilis-P. woodhousei (Polemoniaceae) complex

PREMISE OF THE STUDY

Polyploidy is widely recognized as an important process in the evolution of plants, but less attention has been paid to the study of intraspecific polyploidy, including its prevalence, formation, taxonomic implications, and effect on genetic diversity, structure, and gene flow within and among individuals and populations. Here we studied intraspecific ploidy level variation in the Phlox amabilis-P. woodhousei complex to determine the amount and distribution of cytotypic and genetic variation present and measure the extent of gene flow among species, cytotypes, and populations.

METHODS

Flow cytometry and microsatellite analyses were used to ascertain cytotypic variation, genetic diversity, and population structure within and among eight populations of P. amabilis and 10 populations of P. woodhousei from Arizona and New Mexico.

KEY RESULTS

Our analyses support the recognition of P. amabilis and P. woodhousei as two distinct species. Both species exhibit cytotypic variation with geographically structured diploid, tetraploid, and hexaploid populations, and genetic analyses suggest a combination of auto- and allopolyploidy in their formation. Diploid, tetraploid, and most hexaploid populations within species share much of their genetic variation, while some hexaploid populations are genetically distinct. All populations maintain moderately high genetic diversity and connectivity, and genetic structure is strongly influenced by geography.

CONCLUSIONS

This study highlights the potential for complicated patterns of genetic variation relative to cytotypic variation and provides evidence for the role of cytotypic variation and geographic isolation in shaping diversity, differentiation, and potentially speciation in the P. amabilis-P. woodhousei complex.

Isolation of polymorphic microsatellite markers and tests of cross-amplification in four widespread European calcicole ferns

PREMISE OF THE STUDY

Studies on the biogeography and population genetics of the widespread European rock ferns Asplenium scolopendrium, A. trichomanessubsp. quadrivalens, Polystichum setiferum, and P. aculeatumwould potentially yield interesting new insights into the colonization capacities of ferns. Markers with sufficient resolution for detailed genetic studies are, however, not yet available.

METHODS AND RESULTS

Using genome screening with intersimple sequence repeat (ISSR) primers, a total of 16 different microsatellite markers were isolated and characterized for the four species. Some of these markers could be exchanged within each congeneric pair.

CONCLUSIONS

The developed primer sets will be very useful for analyses of the biogeography and population genetics of some widespread calcicole ferns. The observed cross-amplification rates suggest a high potential for application on additional species from the same genera.

Long-distance dispersal and high genetic diversity are implicated in the invasive spread of the common reed, Phragmites australis (Poaceae), in northeastern North America

PREMISE OF THE STUDY

The Eurasian subspecies of the common reed (Phragmites australis subsp. australis, hereafter abbreviated as P. a. australis) was introduced to North America in the late 18(th) century and rapidly expanded its range, posing an ecological threat to wetlands. In this study, we aimed to determine whether admixture among multiple lineages, dispersal mechanisms, and high genetic diversity have contributed to the invasion of P. a. australis in the northeastern part of its range. Understanding mechanisms of the P. a. australis invasion will 1) contribute to a broader understanding of the factors that facilitate plant invasion, and 2) help us to develop effective management strategies for wetlands threatened by P. a. australis invasion.

METHODS

We used a population genetics approach incorporating nine microsatellite loci to study genetic diversity and population structure in relation to biogeography of introduced North American Phragmites a. australis stands in the northeastern continental region.

KEY RESULTS

Phragmites a. australis is genetically diverse in the region studied here. Significant population structure exists, and population structure is likely influenced by both long-distance dispersal via major waterways, and short-distance dispersal overland. Different lineages sometimes colonize geographically proximate locations leading to opportunities for admixture. Clonal reproduction likely exaggerates geographical structure among some stands, although high genetic and clonal diversity within some stands implies that sexual reproduction occurs frequently in P. a. australis.

CONCLUSIONS

A variety of factors, including admixture among multiple lineages, multiple modes of dispersal, and plasticity in reproductive strategy promote the invasion success of Phragmites a. australis. Wetland managers in the St. Lawrence River/Great Lakes region should focus monitoring efforts on the shores of conservation lands to prevent the establishment of propagules from novel lineages.

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.

Population genetic structure and connectivity of the harmful dinoflagellate Alexandrium minutum in the Mediterranean Sea

The toxin-producing microbial species Alexandrium minutum has a wide distribution in the Mediterranean Sea and causes high biomass blooms with consequences on the environment, human health and coastal-related economic activities. Comprehension of algal genetic differences and associated connectivity is fundamental to understand the geographical scale of adaptation and dispersal pathways of harmful microalgal species. In the present study, we combine A. minutum population genetic analyses based on microsatellites with indirect connectivity (C(i)) estimations derived from a general circulation model of the Mediterranean sea. Our results show that four major clusters of genetically homogeneous groups can be identified, loosely corresponding to four regional seas: Adriatic, Ionian, Tyrrhenian and Catalan. Each of the four clusters included a small fraction of mixed and allochthonous genotypes from other Mediterranean areas, but the assignment to one of the four clusters was sufficiently robust as proved by the high ancestry coefficient values displayed by most of the individuals (>84%). The population structure of A. minutum on this scale can be explained by microalgal dispersion following the main regional circulation patterns over successive generations. We hypothesize that limited connectivity among the A. minutum populations results in low gene flow but not in the erosion of variability within the population, as indicated by the high gene diversity values. This study represents a first and new integrated approach, combining both genetic and numerical methods, to characterize and interpret the population structure of a toxic microalgal species. This approach of characterizing genetic population structure and connectivity at a regional scale holds promise for the control and management of the harmful algal bloom events in the Mediterranean Sea.

Characterization of microsatellite loci and reliable genotyping in a polyploid plant, Mercurialis perennis (Euphorbiaceae)

For many applications in population genetics, codominant simple sequence repeats (SSRs) may have substantial advantages over dominant anonymous markers such as amplified fragment length polymorphisms (AFLPs). In high polyploids, however, allele dosage of SSRs cannot easily be determined and alleles are not easily attributable to potentially diploidized loci. Here, we argue that SSRs may nonetheless be better than AFLPs for polyploid taxa if they are analyzed as effectively dominant markers because they are more reliable and more precise. We describe the transfer of SSRs developed for diploid Mercurialis huetii to the clonal dioecious M. perennis. Primers were tested on a set of 54 male and female plants from natural decaploid populations. Eight of 65 tested loci produced polymorphic fragments. Binary profiles from 4 different scoring routines were used to define multilocus lineages (MLLs). Allowing for fragment differences within 1 MLL, all analyses revealed the same 14 MLLs without conflicting with merigenet, sex, or plot assignment. For semiautomatic scoring, a combination of as few as 2 of the 4 most polymorphic loci resulted in unambiguous discrimination of clones. Our study demonstrates that microsatellite fingerprinting of polyploid plants is a cost efficient and reliable alternative to AFLPs, not least because fewer loci are required than for diploids.

Microsatellites reveal origin and genetic diversity of Eurasian invasions by one of the world's most notorious marine invader, Mnemiopsis leidyi (Ctenophora)

Marine invasions are taking place at an increasing rate. When occurring in blooms, zooplanktivorous comb jellies of the genus Mnemiopsis are able to cause pelagic regime shifts in coastal areas and may cause the collapse of commercially important fish populations. Using microsatellites, developed for the first time in the phylum Ctenophora, we show that Mnemiopsis leidyi has colonized Eurasia from two source regions. Our preliminary data set included four sites within the putative source region (US East Coast and Gulf of Mexico) and 10 invaded locations in Eurasian waters. Bayesian clustering and phylogeographic approaches revealed the origin of earlier invasions of the Black and Caspian Sea in the 1980s/1990s within or close to the Gulf of Mexico, while the 2006 invasion of the North and Baltic Seas can be directly traced to New England (pairwise F(ST) = 0). We found no evidence for mixing among both gene pools in the invaded areas. While the genetic diversity (allelic richness) remained similar in the Baltic Sea compared to the source region New England, it was reduced in the North Sea, supporting the view of an initial invasion of Northern Europe to a Baltic Sea port. In Black and Caspian Sea samples, we found a gradual decline in allelic richness compared to the Gulf of Mexico region, supporting a stepping-stone model of colonization with two sequential genetic founder events. Our data also suggest that current practices of ballast water treatment are insufficient to prevent repeated invasions of gelatinous zooplankton.

Fine-scale comparisons of genetic variability in seed families of asexually and sexually reproducing Crataegus (hawthorn; Rosaceae)

The reproductive system is one of the key mechanisms that determine genetic diversity at different biological levels. However, few attempts have been made to assess the consequences of asexual reproduction by comparing genetic structure and fecundity of seed families in asexually and sexually reproducing individuals. We have examined two similar hawthorn species, Crataegus crus-galli and C. punctata, that differ in ploidy level and breeding system. Fecundity (per-fruit seed set) and microsatellite genotypes for five loci were determined in 18 and 26 seed families of C. crus-galli and C. punctata (totals of 83 and 118 embryos), respectively. Compared with the sexual diploid C. punctata, tetraploid C. crus-galli shows similar fecundity, but lower genotypic diversity within and between seed families. Reproduction in the tetraploid, while predominantly apomictic, is nevertheless accompanied by outcrossing and selfing. We conclude that in C. crus-galli pollen flow between conspecific individuals is limited, and the combination of pollen fertility, self-compatibility, and pseudogamous apomixis provides reproductive assurance in these tetraploids. Reproductive assurance, in turn, may explain the derived floral architecture seen in most North American tetraploid hawthorns. We also discuss analytical approaches for inferring mating-system parameters in tetraploids and for comparing microsatellite variation across ploidy levels.

Isolation and characterization of 20 microsatellite loci for laurel species (Laurus, Lauraceae)

PREMISE OF THE STUDY

Microsatellite primers were developed for the evergreen tree Laurus to investigate population genetic structure and patterns of gene flow via animal-dispersed pollen and seeds.

METHODS AND RESULTS

Twenty polymorphic nuclear microsatellite markers were developed using CA, GA, AAC, and ATG n-enriched genomic libraries. Given the tetraploidy of the sampled populations, we analyzed our data both as dominant loci and as codominant genotypic data to calculate allele frequencies and genetic diversity. A total of 196 and 222 alleles were found in 37 Mediterranean (L. nobilis) and 26 Macaronesian islands (L. azorica) individuals, respectively.

CONCLUSIONS

Levels of polymorphism of the reported markers are adequate for studies of diversity and parentage in natural populations of this Tertiary relict tree.

Gene flow and population admixture as the primary post-invasion processes in common ragweed (Ambrosia artemisiifolia) populations in France

*An improved inference of the evolutionary history of invasive species may be achieved by analyzing the genetic variation and population differentiation of recently established populations and their ancestral (historical) populations. Employing this approach, we investigated the role of gene flow in the post-invasion evolution of common ragweed (Ambrosia artemisiifolia). *Using eight microsatellite loci, we compared genetic diversity and structure among nine pairs of historical and recent populations in France. Historical populations were reconstructed from herbarium specimens dated from the late 19th to early 20th century, whereas recent populations were collected within the last 5 yr. *Recent populations showed greater allelic and genetic diversity than did historical populations. Recent populations exhibited a lower level of population differentiation, shorter genetic distances among populations and more weakly structured populations than did historical populations. *Our results suggest that currently invasive populations have arisen from active gene flow and the subsequent admixture of historical populations, incorporating new alleles from multiple introductions.

Genetic perspectives on marine biological invasions

The extent to which the geographic distributions of marine organisms have been reshaped by human activities remains underappreciated, and so does, consequently, the impact of invasive species on marine ecosystems. The application of molecular genetic data in fields such as population genetics, phylogeography, and evolutionary biology have improved our ability to make inferences regarding invasion histories. Genetic methods have helped to resolve longstanding questions regarding the cryptogenic status of marine species, facilitated recognition of cryptic marine biodiversity, and provided means to determine the sources of introduced marine populations and to begin to recover the patterns of anthropogenic reshuffling of the ocean's biota. These approaches stand to aid materially in the development of effective management strategies and sustainable science-based policies. Continued advancements in the statistical analysis of genetic data promise to overcome some existing limitations of current approaches. Still other limitations will be best addressed by concerted collaborative and multidisciplinary efforts that recognize the important synergy between understanding the extent of biological invasions and coming to a more complete picture of both modern-day and historical marine biogeography.