Tim Sierens

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 December 2009-31 January 2010

This article documents the addition of 220 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Allanblackia floribunda, Amblyraja radiata, Bactrocera cucurbitae, Brachycaudus helichrysi, Calopogonium mucunoides, Dissodactylus primitivus, Elodea canadensis, Ephydatia fluviatilis, Galapaganus howdenae howdenae, Hoplostethus atlanticus, Ischnura elegans, Larimichthys polyactis, Opheodrys vernalis, Pelteobagrus fulvidraco, Phragmidium violaceum, Pistacia vera, and Thunnus thynnus. These loci were cross‐tested on the following species: Allanblackia gabonensis, Allanblackia stanerana, Neoceratitis cyanescens, Dacus ciliatus, Dacus demmerezi, Bactrocera zonata, Ceratitis capitata, Ceratitis rosa, Ceratits catoirii, Dacus punctatifrons, Ephydatia mülleri, Spongilla lacustris, Geodia cydonium, Axinella sp., Ischnura graellsii, Ischnura ramburii, Ischnura pumilio, Pistacia integerrima and Pistacia terebinthus.

Genetic differentiation of submerged plant populations and taxa between habitats

Ceratophyllum spp., Callitriche spp., Zannichellia spp. and Potamogeton pectinatus L. are widespread submerged macrophyte species, often occurring at high abundance and forming an integral part of the vegetation of many types of shallow aquatic systems. Several species occur in both freshwater and brackish water habitats. Most have a mixed reproduction system and can reproduce sexually by seeds and propagate asexually by rhizomes, turions, root tubers or axillary tubers. It is hypothesized that sexual propagules are more important than vegetative fragments to ensure long-distance-dispersal, which in case of frequent bird or water flow-mediated dispersal should lead to lowered genetic differentiation. At a regional level, we used dominant ISSR markers in a multi-species approach and observed the largest clonal differentiation between brackish water and freshwater populations of the western European lowland (Belgium). Differentiation was pronounced at taxon level (e.g. Zannichellia), as a salinity gradient (P. pectinatus) or as a coastal-to-inland conductivity gradient (Callitriche obtusangula). These differences and trends suggested a very limited dispersal at regional level across both habitats and regions. To test the hypothesis whether vegetative reproduction and dispersal may have an important function in maintenance of the species at local scale, we investigated the microsatellite diversity and clonal distribution within and between populations of P. pectinatus from a single catchment, representing upstream forest ponds and downstream river sites along the Woluwe (Brussels, Belgium). Clonal diversity was low on average, however, with a higher number of multilocus genotypes in upstream forest ponds than in downstream river sites. A few but abundant clones were present along various stretches of the river indicating clonal spread and establishment over larger distances within the river. Clonal dispersal at a local scale was more pronounced in river than in pond habitats, indicating a higher relative importance of water flow than bird-mediated dispersal for establishment of P. pectinatus in river sites. Dispersal of seeds and establishment of seedlings were assumed more effective within ponds than in river habitats. Upstream forest ponds can be regarded as source populations and refuges of clonal diversity for recolonization of the more stressful downstream river habitat.

Seagrass radiation after Messinian salinity crisis reflected by strong genetic structuring and out-of-Africa scenario (Ruppiaceae).

Many aquatic plant and seagrass species are widespread and the origin of their continent-wide ranges might result from high gene flow levels. The response of species when extending northwards since the Last Glacial Maximum can be opposed to the structuring of their populations that survived glaciation cycles in southern regions. The peri-Mediterranean is a complex series of sea basins, coastlines, islands and river deltas with a unique history since the Messinian Crisis that potentially influenced allopatric processes of aquatic life. We tested whether vast ranges across Europe and the peri-Mediterranean of a global seagrass group (Ruppia species complexes) can be explained by either overall high levels of gene flow or vicariance through linking population genetics, phylogeography and shallow phylogenetics. A multigene approach identified haplogroup lineages of two species complexes, of ancient and recent hybrids with most of the diversity residing in the South. High levels of connectivity over long distances were only observed at recently colonized northern ranges and in recently-filled seas following the last glaciation. A strong substructure in the southern Mediterranean explained an isolation-by-distance model across Europe. The oldest lineages of the southern Mediterranean Ruppia dated back to the period between the end of the Messinian and Late Pliocene. An imprint of ancient allopatric origin was left at basin level, including basal African lineages. Thus both vicariance in the South and high levels of connectivity in the North explained vast species ranges. Our findings highlight the need for interpreting global distributions of these seagrass and euryhaline species in the context of their origin and evolutionary significant units for setting up appropriate conservation strategies.

Multiplexing 15 microsatellite loci for European primrose (Primula vulgaris)

Primula vulgaris is a perennial herb from moist native forest vegetation. In western European lowlands, it has become rare, still declining and occurring in forest remnants embedded within an agricultural matrix. In Belgium and The Netherlands, it received special attention for conservation. We developed 12 novel polymorphic microsatellite loci and two multiplex PCR including 15 loci. For seven European populations, they displayed 7–28 alleles. Observed and expected heterozygosities at population level ranged from 0.28–0.61 and 0.24–0.70, respectively. Genetic differentiation was high between western, central and eastern European populations. The variability recorded will allow investigating genetic diversity and structure patterns at local and continental scales, but also quantifying gene dispersal at a fine scale to estimate effects of habitat fragmentation on connectivity.

Bidirectional gene flow on a mangrove river landscape and between-catchment dispersal of Rhizophora racemosa (Rhizophoraceae)

Understanding how landscape structure shapes the genetic structure of populations of keystone species is important for their long-term management. We tested the unidirectional dispersal hypothesis on the linear river landscape of the Wouri River and the one catchment-one gene pool hypothesis on red mangrove (Rhizophora racemosa) populations of the Cameroon Estuary complex. Therefore, we conducted release–recapture experiments in the field, and sampled 649 adult trees for plant material for genetic analyses. This allowed for estimating genetic diversity and structure, as well as dispersal directionality. Genetic diversity in populations downstream did not differ significantly from upstream populations and the molecular variance of populations did not correlate with their position on the linear landscape. Contemporary and historical migration estimates indicated bidirectional dispersal, i.e. in both the downstream and the upstream direction along the Wouri River. This was confirmed by the propagule dispersal directions derived from our field experiments. Bayesian clustering analysis assigned all individuals of this estuary into one cluster, suggesting high inter-catchment connectivity. River flow currents, tides, and wind plausibly operate together to ensure the high genetic connectivity within this complex estuary.

Clonal growth strategy, diversity and structure: A spatiotemporal response to sedimentation in tropical Cyperus papyrus swamps

Land degradation and soil erosion in the upper catchments of tropical lakes fringed by papyrus vegetation can result in a sediment load gradient from land to lakeward. Understanding the dynamics of clonal modules (ramets and genets) and growth strategies of plants on such a gradient in both space and time is critical for exploring a species adaptation and processes regulating population structure and differentiation. We assessed the spatial and temporal dynamics in clonal growth, diversity, and structure of an emergent macrophyte, Cyperus papyrus (papyrus), in response to two contrasting sedimentation regimes by combining morphological traits and genotype data using 20 microsatellite markers. A total of 636 ramets from six permanent plots (18 x 30 m) in three Ethiopian papyrus swamps, each with discrete sedimentation regimes (high vs. low) were sampled for two years. We found that ramets under the high sedimentation regime (HSR) were significantly clumped and denser than the sparse and spreading ramets under the low sedimentation regime (LSR). The HSR resulted in significantly different ramets with short culm height and girth diameter as compared to the LSR. These results indicated that C. papyrus ameliorates the effect of sedimentation by shifting clonal growth strategy from guerrilla (in LSR) to phalanx (in HSR). Clonal richness, size, dominance, and clonal subrange differed significantly between sediment regimes and studied time periods. Each swamp under HSR revealed a significantly high clonal richness (R = 0.80) as compared to the LSR (R = 0.48). Such discrepancy in clonal richness reflected the occurrence of initial and repeated seedling recruitment strategies as a response to different sedimentation regimes. Overall, our spatial and short-term temporal observations highlighted that HSR enhances clonal richness and decreases clonal subrange owing to repeated seedling recruitment and genets turnover.

Inferring Connectivity Range in Submerged Aquatic Populations (Ruppia L.) Along European Coastal Lagoons From Genetic Imprint and Simulated Dispersal Trajectories

Coastal salt- and brackish water lagoons are unique shallow habitats characterized by beds of submerged seagrasses and salt-tolerant Ruppia species. Established long-term and large-scale patterns of connectivity in lagoon systems can be strongly determined by patterns of nearshore and coastal currents next to local bird-mediated seed dispersal. Despite the importance of dispersal in landscape ecology, characterizing patterns of connectivity remains challenging in aquatic systems. Here, we aimed at inferring connectivity distances of Ruppia cirrhosa along European coastal lagoons using a population genetic imprint and modeled dispersal trajectories using an eddy-resolving numerical ocean model that includes tidal forcing. We investigated 1,303 individuals of 46 populations alongside subbasins of the Mediterranean (Balearic, Tyrrhenian, Ionian) and the Atlantic to Baltic Sea coastline over maximum distances of 563–2,684 km. Ten microsatellite loci under an autotetraploid condition revealed a mixed sexual and vegetative reproduction mode. A pairwise FST permutation test of populations revealed high levels of historical connectivity only for distance classes up to 104–280 km. Since full range analysis was not fully explanatory, we assessed connectivity in more detail at coastline and subbasin level using four approaches. Firstly, a regression over restricted geographical distances (300 km) was done though remained comparable to full range analysis. Secondly, piecewise linear regression analyses yielded much better explained variance but the obtained breakpoints were shifted toward greater geographical distances due to a flat slope of regression lines that most likely reflect genetic drift. Thirdly, classification and regression tree analyses revealed threshold values of 47–179 km. Finally, simulated ocean surface dispersal trajectories for propagules with floating periods of 1–4 weeks, were congruent with inferred distances, a spatial Bayesian admixed gene pool clustering and a barrier detection method. A kinship based spatial autocorrelation showed a contemporary within-lagoon connectivity up to 20 km. Our findings indicate that strong differentiation or admixtures shaped historical connectivity and that a pre- and post LGM genetic imprint of R. cirrhosa along the European coasts was maintained from their occurrence in primary habitats. Additionally, this study demonstrates the importance of unraveling thresholds of genetic breaks in combination with ocean dispersal modeling to infer patterns of connectivity.