Spatial genetic structure among and within populations of Primula sieboldii growing beside separate streams

Population genetic structure and connectivity of a riparian selfing herb Caulokaempferia coenobialis at a fine-scale geographic level in subtropical monsoon forest

BACKGROUND

Rivers and streams facilitate movement of individuals and their genes across the landscape and are generally recognized as dispersal corridors for riparian plants. Nevertheless, some authors have reported directly contrasting results, which may be attributed to a complex mixture of factors, such as the mating system and dispersal mechanisms of propagules (seed and pollen), that make it difficult to predict the genetic diversity and population structure of riparian species. Here, we investigated a riparian self-fertilizing herb Caulokaempferia coenobialis, which does not use anemochory or zoochory for seed dispersal; such studies could contribute to an improved understanding of the effect of rivers or streams on population genetic diversity and structure in riparian plants. Using polymorphic ISSR and cpDNA loci, we studied the effect at a microgeographic scale of different stream systems (a linear stream, a dendritic stream, and complex transverse hydrological system) in subtropical monsoon forest on the genetic structure and connectivity of C. coenobialis populations across Dinghu Mountain (DH) and Nankun Mountain (NK).

RESULTS

The results indicate that the most recent haplotypes (DH: H7, H8; NK: h6, h7, h11, h12) are not shared among local populations of C. coenobialis within each stream system. Furthermore, downstream local populations do not accumulate genetic diversity, whether in the linear streamside local populations across DH (H: 0.091 vs 0.136) or the dendritic streamside local populations across NK (H: 0.079 vs 0.112, 0.110). Our results show that the connectivity of local C. coenobialis populations across DH and NK can be attributed to historical gene flows, resulting in a lack of spatial genetic structure, despite self-fertilization. Selfing C. coenobialis can maintain high genetic diversity (H = 0.251; I = 0.382) through genetic differentiation (GST = 0.5915; FST = 0.663), which is intensified by local adaptation and neutral mutation and/or genetic drift in local populations at a microgeographic scale.

CONCLUSION

We suggest that streams are not acting as corridors for dispersal of C. coenobialis, and conservation strategies for maintaining genetic diversity of selfing species should be focused on the protection of all habitat types, especially isolated fragments in ecosystem processes.

Comparative analysis of spatial genetic structures in sympatric populations of two riparian plants, Saxifraga acerifolia and Saxifraga fortunei

PREMISE

The genetic structure between plant populations is facilitated by the spatial population arrangement and limited dispersal of seed and pollen. Saxifraga acerifolia, a local endemic species in Japan, is a habitat specialist that is confined to waterfalls in riparian environments. Its sister species, Saxifraga fortunei, is a generalist that is widely distributed along riverbanks. Here, we examined sympatric populations of the two Saxifraga species to test whether the differences in habitat preference and colonization process influenced regional and local genetic structures.

METHODS

To reveal genetic structures, we examined chloroplast microsatellite variations and genome-wide nucleotide polymorphisms obtained by genotyping by sequencing. We also estimated the gene flow among and within populations and performed landscape genetic analyses to evaluate seed and pollen movement and the extent of genetic isolation related to geographic distance and/or habitat differences.

RESULTS

We found strong genetic structure in the specialist S. acerifolia, even on a small spatial scale (<1 km part); each population on a different waterfall in one river system had a completely different predominant haplotype. By contrast, the generalist S. fortunei showed no clear genetic differentiation.

CONCLUSIONS

Our findings suggest that the level of genetic isolation was increased in S. acerifolia by the spatially fragmented habitat and limited seed and pollen dispersal over waterfalls. Habitat differentiation between the sister taxa could have contributed to the different patterns of gene flow and then shaped the contrasting genetic structures.

By Animal, Water, or Wind: Can Dispersal Mode Predict Genetic Connectivity in Riverine Plant Species?

Seed dispersal is crucial to gene flow among plant populations. Although the effects of geographic distance and barriers to gene flow are well studied in many systems, it is unclear how seed dispersal mediates gene flow in conjunction with interacting effects of geographic distance and barriers. To test whether distinct seed dispersal modes (i.e., hydrochory, anemochory, and zoochory) have a consistent effect on the level of genetic connectivity (i.e., gene flow) among populations of riverine plant species, we used unlinked single-nucleotide polymorphisms (SNPs) for eight co-distributed plant species sampled across the Rio Branco, a putative biogeographic barrier in the Amazon basin. We found that animal-dispersed plant species exhibited higher levels of genetic diversity and lack of inbreeding as a result of the stronger genetic connectivity than plant species whose seeds are dispersed by water or wind. Interestingly, our results also indicated that the Rio Branco facilitates gene dispersal for all plant species analyzed, irrespective of their mode of dispersal. Even at a small spatial scale, our findings suggest that ecology rather than geography play a key role in shaping the evolutionary history of plants in the Amazon basin. These results may help improve conservation and management policies in Amazonian riparian forests, where degradation and deforestation rates are high.

Multi-scale spatial genetic structure of the vector-borne pathogen 'Candidatus Phytoplasma prunorum' in orchards and in wild habitats

Inferring the dispersal processes of vector-borne plant pathogens is a great challenge because the plausible epidemiological scenarios often involve complex spread patterns at multiple scales. The spatial genetic structure of 'Candidatus Phytoplasma prunorum', responsible for European stone fruit yellows disease, was investigated by the application of a combination of statistical approaches to genotype data of the pathogen sampled from cultivated and wild compartments in three French Prunus-growing regions. This work revealed that the prevalence of the different genotypes is highly uneven both between regions and compartments. In addition, we identified a significant clustering of similar genotypes within a radius of 50 km or less, but not between nearby wild and cultivated Prunus. We also provide evidence that infected plants are transferred between production areas, and that both species of the Cacopsylla pruni complex can spread the pathogen. Altogether, this work supports a main epidemiological scenario where 'Ca. P. prunorum' is endemic in - and generally acquired from - wild Prunus by its immature psyllid vectors. The latter then migrate to shelter plants that epidemiologically connect sites less than 50 km apart by later providing infectious mature psyllids to their "migration basins". Such multi-scale studies could be useful for other pathosystems.

Bridging population genetics and the metacommunity perspective to unravel the biogeographic processes shaping genetic differentiation of Myriophyllum alterniflorum DC

The degree to which dispersal limitation interacts with environmental filtering has intrigued metacommunity ecologists and molecular biogeographers since the beginning of both research disciplines. Since genetic methods are superior to coarse proxies of dispersal, understanding how environmental and geographic factors influence population genetic structure is becoming a fundamental issue for population genetics and also one of the most challenging avenues for metacommunity ecology. In this study of the aquatic macrophyte Myriophyllum alterniflorum DC., we explored the spatial genetic variation of eleven populations from the Iberian Plateau by means of microsatellite loci, and examined if the results obtained through genetic methods match modern perspectives of metacommunity theory. To do this, we applied a combination of robust statistical routines including network analysis, causal modelling and multiple matrix regression with randomization. Our findings revealed that macrophyte populations clustered into genetic groups that mirrored their geographic distributions. Importantly, we found a significant correlation between genetic variation and geographic distance at the regional scale. By using effective (genetic) dispersal estimates, our results are broadly in line with recent findings from metacommunity theory and re-emphasize the need to go beyond the historically predominant paradigm of understanding environmental heterogeneity as the main force driving macrophyte diversity patterns.

Is the São Francisco River a geographic barrier to gene flow in trees ofHandroanthus ochraceus?

Many landscape features represent geographic barriers to gene flow, and promote genetic discontinuity. Rivers are effective barriers. However, most studies on this subject have focused on animals and only a few have focused on plants. We studied the genetic structure and gene flow of the tropical treeHandroanthus ochraceus(Bignoniaceae) on both banks of the São Francisco River in a Brazilian seasonally dry tropical forest. The São Francisco is located in eastern Brazil and is 600 m wide at the study site. Our hypothesis was that the river is a geographic barrier to gene flow ofH. ochraceustrees. We sampled two populations on the left bank and one population on the right bank. We used seven microsatellites to genotype 212 individual plants. All populations had low polymorphism and genetic diversity, but high inbreeding. There was no genetic differentiation among populations and, consequently, the estimated gene flow was high for all pairs of populations. The genetic relatedness among individuals from populations of the same margin did not differ from the relatedness among individuals from populations of opposite margins. Hence, the São Francisco River is not an effective geographic barrier to gene flow amongH. ochraceuspopulations.

Connectivity in a pond system influences migration and genetic structure in threespine stickleback

Neutral genetic structure of natural populations is primarily influenced by migration (the movement of individuals and, subsequently, their genes) and drift (the statistical chance of losing genetic diversity over time). Migration between populations is influenced by several factors, including individual behavior, physical barriers, and environmental heterogeneity among populations. However, drift is expected to be stronger in populations with low immigration rate and small effective population size. With the technological advancement in geological information systems and spatial analysis tools, landscape genetics now allows the development of realistic migration models and increased insight to important processes influencing diversity of natural populations. In this study, we investigated the relationship between landscape connectivity and genetic distance of threespine stickleback (Gasterosteus aculeatus) inhabiting a pond complex in Belgjarskógur, Northeast Iceland. We used two landscape genetic approaches (i.e., least-cost-path and isolation-by-resistance) and asked whether gene flow, as measured by genetic distance, was more strongly associated with Euclidean distance (isolation-by-distance) or with landscape connectivity provided by areas prone to flooding (as indicated by Carex sp. cover)? We found substantial genetic structure across the study area, with pairwise genetic distances among populations (DPS) ranging from 0.118 to 0.488. Genetic distances among populations were more strongly correlated with least-cost-path and isolation-by-resistance than with Euclidean distance, whereas the relative contribution of isolation-by-resistance and Euclidian distance could not be disentangled. These results indicate that migration among stickleback populations occurs via periodically flooded areas. Overall, this study highlights the importance of transient landscape elements influencing migration and genetic structure of populations at small spatial scales.

QTL analysis of heterostyly in Primula sieboldii and its application for morph identification in wild populations

BACKGROUND AND AIMS

Primula sieboldii is a perennial clonal herb that is distributed around the Sea of Japan and is endangered in Japan. Its breeding system is characterized by heteromorphic self-incompatibility, and the morph ratio within a population is very important for reproductive success. The aims of this study were to construct a linkage map, map the S locus as a qualitative trait and quantitative trait loci (QTLs) for floral morphological traits related to heterostyly, and predict the morph type in wild populations by using molecular markers for devising a conservation strategy.

METHODS

A linkage map was constructed with 126 markers. The QTLs for four floral traits and the S locus were mapped. Using the genotypes of loci that were located near both the S locus and the QTLs with large effects, morphs of 59 wild genets were predicted.

KEY RESULTS

The linkage map consisted of 14 linkage groups (LGs). The S locus was mapped to LG 7. Major QTLs for stigma and anther heights were detected in the same region as the S locus. These QTLs exhibited high logarithm of the odds scores and explained a high percentage of the phenotypic variance (>85 %). By analysing these two traits within each morph, additional QTLs for each trait were detected. Using the four loci linked to the S locus, the morphs of 43 genets in three wild populations could be predicted.

CONCLUSIONS

This is the first report of a linkage map and QTL analysis for floral morphology related to heterostyly in P. sieboldii. Floral morphologies related to heterostyly are controlled by the S locus in LG 7 and by several QTLs in other LGs. Additionally, this study showed that molecular markers are effective tools for investigating morph ratios in a population containing the non-flowering individuals or during the non-flowering seasons.

Landscape genetics of plants

Landscape genetics is the amalgamation of landscape ecology and population genetics to help with understanding microevolutionary processes such as gene flow and adaptation. In this review, we examine why landscape genetics of plants lags behind that of animals, both in number of studies and consideration of landscape elements. The classical landscape distance/resistance approach to study gene flow is challenging in plants, whereas boundary detection and the assessment of contemporary gene flow are more feasible. By contrast, the new field of landscape genetics of adaptive genetic variation, establishing the relationship between adaptive genomic regions and environmental factors in natural populations, is prominent in plant studies. Landscape genetics is ideally suited to study processes such as migration and adaptation under global change.

Landscape genetics: where are we now?

Landscape genetics has seen rapid growth in number of publications since the term was coined in 2003. An extensive literature search from 1998 to 2008 using keywords associated with landscape genetics yielded 655 articles encompassing a vast array of study organisms, study designs and methodology. These publications were screened to identify 174 studies that explicitly incorporated at least one landscape variable with genetic data. We systematically reviewed this set of papers to assess taxonomic and temporal trends in: (i) geographic regions studied; (ii) types of questions addressed; (iii) molecular markers used; (iv) statistical analyses used; and (v) types and nature of spatial data used. Overall, studies have occurred in geographic regions proximal to developed countries and more commonly in terrestrial vs. aquatic habitats. Questions most often focused on effects of barriers and/or landscape variables on gene flow. The most commonly used molecular markers were microsatellites and amplified fragment length polymorphism (AFLPs), with AFLPs used more frequently in plants than animals. Analysis methods were dominated by Mantel and assignment tests. We also assessed differences among journals to evaluate the uniformity of reporting and publication standards. Few studies presented an explicit study design or explicit descriptions of spatial extent. While some landscape variables such as topographic relief affected most species studied, effects were not universal, and some species appeared unaffected by the landscape. Effects of habitat fragmentation were mixed, with some species altering movement paths and others unaffected. Taken together, although some generalities emerged regarding effects of specific landscape variables, results varied, thereby reinforcing the need for species-specific work. We conclude by: highlighting gaps in knowledge and methodology, providing guidelines to authors and reviewers of landscape genetics studies, and suggesting promising future directions of inquiry.

Multiple spatial scale patterns of genetic diversity in riparian populations of Ainsliaea faurieana (Asteraceae) on Yakushima Island, Japan

Habitat and geographical features of river systems strongly influence gene flow and spatial genetic patterning in riparian plant populations. We investigated the patterns of genetic diversity within and among populations of Ainsliaea faurieana relative to different spatial conditions (along a river, among rivers, and among regions on an island), based on nuclear and chloroplast microsatellite DNA variations. Within an individual river system, we found higher haplotype diversities in downstream populations, and in a Bayesian analysis of recent migration, we detected unidirectional gene movements from upstream to downstream, indicating water-mediated dispersal along the river. Mantel tests detected no isolation-by-distance in genetic variation, suggesting the maintenance of a metapopulation with wide-range seed dispersal by water. Moreover, the observed high level of genetic differentiation, especially in the cpDNA (F(ST) = 0.539), indicated a metapopulation structure with frequent extinction and colonization. On a larger scale, we found high population differentiation and clear genetic structuring among regions, suggesting that gene flow was restricted by geographical features (mountains separating river systems) for relatively long periods. Our findings of genetic structures based on different spatial conditions elucidated patterns and ranges of historical and contemporary gene movement in a plant species that is persistent in extremely disturbed riparian environments.

Reconsideration for conservation units of wildPrimula sieboldiiin Japan based on adaptive diversity and molecular genetic diversity

Primula sieboldiiE. Morren is a perennial clonal herb that is widely distributed in Japan, but in danger of extinction in the wild. In a previous study, we revealed the genetic diversity of the species using chloroplast and nuclear DNA and used this information to define conservation units. However, we lacked information on adaptive genetic diversity, which is important for long-term survival and, thus, for the definition of conservation units. In order to identify adaptive traits that showed adaptive differentiation among populations, we studied the genetic variation in six quantitative traits within and among populations for 3 years in a common garden using 110 genets from five natural populations from three regions of Japan. The number of days to bud initiation was adaptive quantitative trait for which the degree of genetic differentiation among populations (QST) was considerably larger than that in eight microsatellite markers (FST). The relationship between this trait and environmental factors revealed that the number of days to bud initiation was negatively correlated, with the mean temperature during the growing period at each habitat. This suggests that adaptive differentiation in the delay before bud initiation was caused by selective pressure resulting from temperature differences among habitats. Our results suggest that based on adaptive diversity and neutral genetic diversity, the Saitama population represents a new conservation unit.

The landscape genetics of yellow perch (Perca flavescens) in a large fluvial ecosystem

Landscape genetics is being increasingly applied to elucidate the role of environmental features on the population structure of terrestrial organisms. However, the potential of this framework has been little explored in aquatic ecosystems such as large rivers. Here, we used a landscape genetics approach in order to (i) document the population structure of the yellow perch (Perca flavescens) by means of genetic variation at microsatellite markers, (ii) assess to what extent the structure was explained by landscape heterogeneity, and (iii) interpret the relevance of interactions between genetics and landscape for management and conservation. Analysis of the genetic variation among 1715 individuals from 16 localities and distributed over 310 km in the freshwater section of the Saint Lawrence River (Québec, Canada) revealed a relatively modest level of genetic structuring (F(ST) = 0.039). Application of the Monmonier's algorithm combining geographical and genetic information identified three zones of restricted gene flow defining four distinct populations. Physical barriers played a more important role on gene flow and genetic structure than waterway geographical distance. We found correlations between genetic differentiation and presence of distinct water masses in the sector of Lake Saint-Louis (r = 0.7177, P = 0.0340) and with fragmentation of spawning habitats in the sector of Lake Saint-Pierre (r = 0.8578, P = 0.0095). Our results support the treatment of four distinct biological units, which is in contrast with the current basis for yellow perch management. Finally, this study showed that landscape genetics is a powerful means to identify environmental barriers to gene flow causing genetic discontinuities in apparently highly connected aquatic landscapes.

Spatial analysis of nuclear and cytoplasmic DNA diversity in wild sea beet (Beta vulgaris ssp. maritima) populations: do marine currents shape the genetic structure?

Patterns of seed dispersal in the wild sea beet (Beta vulgaris ssp. maritima) are predicted to be influenced by marine currents because populations are widely distributed along the European Atlantic coast. We investigated the potential influence of marine currents on the pattern of spatial genetic structuring in natural populations of sea beet. Populations were located along the French coasts of the Anglo-Norman gulf that features peculiar marine currents in the Channel. Thirty-three populations were sampled, among which 23 were continental and 10 were insular populations located in Jersey, Guernsey and Chausey, for a total of 1224 plants genotyped. To validate the coastal topography influence and the possibility of marine current orientated gene flow on the genetic features of sea beet populations, we assessed patterns of genetic structuring of cytoplasmic and nuclear diversity by: (i) searching for an isolation-by-distance (IBD) pattern using spatial autocorrelation tools; (ii) using the Monmonier algorithm to identify genetic boundaries in the area studied; and (iii) performing assignment tests that are based on multilocus genotype information to ascertain population membership of individuals. Our results showed a highly contrasted cytoplasmic and nuclear genetic differentiation and highlighted the peculiar situation of island populations. Beyond a classical isolation-by-distance due to short-range dispersal, genetic barriers fitting the orientation of marine currents were clearly identified. This suggests the occurrence of long-distance seed dispersal events and an asymmetrical gene flow separating the eastern and western part of the Anglo-Norman gulf.

Reproductive strategy, clonal structure and genetic diversity in populations of the aquatic macrophyte Sparganium emersum in river systems

Many aquatic and riparian plant species are characterized by the ability to reproduce both sexually and asexually. Yet, little is known about how spatial variation in sexual and asexual reproduction affects the genotypic diversity within populations of aquatic and riparian plants. We used six polymorphic microsatellites to examine the genetic diversity within and differentiation among 17 populations (606 individuals) of Sparganium emersum, in two Dutch-German rivers. Our study revealed a striking difference between rivers in the mode of reproduction (sexual vs. asexual) within S. emersum populations. The mode of reproduction was strongly related to locally reigning hydrodynamic conditions. Sexually reproducing populations exhibited a greater number of multilocus genotypes compared to asexual populations. The regional population structure suggested higher levels of gene flow among sexually reproducing populations compared to clonal populations. Gene flow was mainly mediated via hydrochoric dispersal of generative propagules (seeds), impeding genetic differentiation among populations even over river distances up to 50 km. Although evidence for hydrochoric dispersal of vegetative propagules (clonal plant fragments) was found, this mechanism appeared to be relatively less important. Bayesian-based assignment procedures revealed a number of immigrants, originating from outside our study area, suggesting intercatchment plant dispersal, possibly the result of waterfowl-mediated seed dispersal. This study demonstrates how variation in local environmental conditions in river systems, resulting in shifting balances of sexual vs. asexual reproduction within populations, will affect the genotypic diversity within populations. This study furthermore cautions against generalizations about dispersal of riparian plant species in river systems.

Distribution of genetic diversity among disjunct populations of the rare forest understory herb, Trillium reliquum

We assessed genetic diversity and its distribution in the rare southeastern US forest understory species, Trillium reliquum. In all, 21 loci were polymorphic (PS=95.5%) and the mean number of alleles per polymorphic locus was 3.05. However, genetic diversity was relatively low (Hes=0.120) considering the level of polymorphism observed for this outcrossing species. A relatively high portion of the genetic diversity (29.7%) was distributed among populations. There was no relationship between population size and genetic diversity, and we did not detect significant inbreeding. These results are best explained by the apparent self-incompatibility of this species, its longevity and clonal reproduction. To address questions regarding the history of T. reliquum's rarity, we compared results for T. reliquum with that of its more common and partially sympatric congener, T. cuneatum. Despite shared life history traits and history of land use, we observed significant genetic differences between the two species. Although T. cuneatum contains slightly lower polymorphism (Ps=85%), we detected significantly higher genetic diversity (Hes=0.217); most of its genetic diversity is contained within its populations (GST=0.092). Our results suggest that not only is there little gene flow among extant T. reliquum populations, but that rarity and population isolation in this species is of ancient origins, rather than due to more recent anthropogenic fragmentation following European colonization. The Chattahoochee River was identified as a major barrier to gene exchange.