Return of the native facilitated by the invasive? Population composition,substrate preferences and epibenthic species richness of a recently discovered shellfish reef with native European flat oysters (Ostrea edulis) in the North Sea

After being ecologically extinct for almost a century, the discovery of a shellfish reef with native European flat oysters (Ostrea edulis) in the Dutch coastal area of the North Sea by the authors of this study called for an extensive survey to better understand some of the key requirements for the return of the native oyster in coastal waters. We assessed habitat conditions, its potential for increasing biodiversity, and the role of substrate provision by other bivalves such as the invasive alien Pacific oyster (Crassostrea gigas). Using underwater visual census, O. edulis size-frequency distributions and attachment substrate was investigated, as well as the composition of the epibenthic community and substrata types inside quadrats that were distributed across the reef. This reef was found to be composed of native European flat oysters, invasive alien Pacific oysters and blue mussels (Mytilus edulis), alternated with sandy patches. The O. edulis population (6.8?±?0.6 oysters m^?2) consisted of individuals of different size classes. In quadrats with native and non-native oysters the number of epibenthic species was 60% higher compared to adjacent sand patches within the reef. Notably, our results showed that the native oyster predominantly used shell (fragments) of the invasive Pacific oyster as settlement substrate (81% of individuals). Our results optimistically show that conditions for native oyster restoration can be suitable at a local scale in the coastal North Sea area and suggest that the return of native oysters may be facilitated by novel substrate provided by invasive oysters at sites where their distribution overlap.     

Strategies for the retention of high genetic variability in European flat oyster (<Emphasis Type="Italic">Ostrea edulis</Emphasis>) restoration programmes

The native European flat oyster Ostrea edulis is listed in the OSPAR Convention for the Protection of the Marine Environment of the North-East Atlantic (species and habitat protection) and in the UK Biodiversity Action Plan. Once extremely abundant in the nineteenth century, European stocks of O. edulis have declined during the twentieth century to rare, small, localised populations due to overexploitation, habitat degradation and, most recently, the parasitic disease bonamiosis. Selective breeding programmes for resistance to bonamiosis have been initiated in France and Ireland. High genetic diversity and bonamiosis-resistance would be important features of any sustainable restoration programmes for O. edulis. Oysters were sampled across Europe from four hatchery sources, four pond-cultured sources and four wild, but managed fisheries and were genotyped at five microsatellite loci. Hatchery-produced populations from small numbers of broodstock showed a significant loss of genetic diversity relative to wild populations and pedigree reconstruction revealed that they were each composed of a single large full-sib family and several small full-sib families. This extremely low effective population size highlights the variance in reproductive success among the potential breeders. Pond-cultured oysters were intermediate in genetic diversity and effective population size between hatchery and wild populations. Controlled hatchery production allows the development of bonamiosis-resistant strains, but at the expense of genetic diversity. Large scale pond culture on the other hand can provide a good level of genetic diversity. A mixture of these two approaches is required to ensure a healthy and sustainable restoration programme for O. edulis in Europe.     

Living with bonamiasis: Irish research since 1987

The main oyster species produced in Ireland up to the 1980's was the European flat oyster Ostrea edulis. However, since then, production of this species has been severely affected by the presence of the protistan Bonamia ostreae, which was diagnosed in a population of flat oysters on the south coast following heavy mortalities. Research has been ongoing since the first diagnosis in Ireland and has concentrated on aspects of the biology of both the host and the parasite. In recent years research has concentrated on screening populations of oysters to identify any with reduced susceptibility to the parasite.     

Recently established <Emphasis Type="Italic">Crassostrea</Emphasis>-reefs versus native <Emphasis Type="Italic">Mytilus</Emphasis>-beds: differences in ecosystem engineering affects the macrofaunal communities (Wadden Sea of Lower Saxony,southern German Bight)

Since 1998 the non-indigenous Pacific oyster Crassostrea gigas (Thunberg 1793) has been invading the Wadden Sea of Lower Saxony, southern German Bight. C. gigas settles predominantly on intertidal Mytilus-beds (M. edulis L.) and subsequently create rigid reef-like structures. Both bivalve species are ecosystem engineers in sedimentary tidal flats. They provide hard substrate for sessile species, mobile organisms find refuge within the habitat matrix of dense suspension feeders, and biodeposits enrich the sediments with organic matter. The transformation of Mytilus-beds into Crassostrea-reefs gives rise to the question whether the invader may affect the native community. We investigated two parts of a changing bivalve bed in the backbarrier area of the island of Juist in March 2005. One part was still dominated by M. edulis whereas the other part was already densely colonized by C. gigas. Crassostrea-reefs compensate for the conceivable loss of Mytilus-beds in the intertidal of the Wadden Sea by replacing the ecological function of M. edulis. There was no indication of a suppression of indigenous species. This even applied to M. edulis, which persisted at the site invaded by C. gigas. The associated macrofaunal community showed increased species richness, abundance, biomass, and diversity in the Crassostrea-reef. The latter particularly favored sessile species like anthozoans, hydrozoans, and barnacles. Higher abundance and biomass for vagile epizoic species like the shore crab Carcinus maenas and the periwinkle Littorina littorea also occurred among oysters. Abundance of deposit feeding oligochaetes was enhanced by oysters as well. More opportunistic, facultative filter-feeding polychaetes occurred in the Crassostrea-reef.     

Heat Shock Protein 90 of Bonamia ostreae: Characterization and Possible Correlation with Infection of the Flat Oyster,Ostrea edulis

In this study, we described the cytosolic HSP90 of Bonamia ostreae, an intracellular parasite of Ostrea edulis hemocytes. The complete open reading frame was assembled by Rapid Amplification cDNA Ends reactions on cDNA of B. ostreae‐infected hemocytes. HSP90 amplification was corroborated in infected oysters and B. ostreae purified cells. The functionality of the HSP90, studied by inhibitory assays with radicicol, suggests that this protein may play a role in hemocyte invasion. Our results inform the molecular basis that governs B. ostreae–O. edulis interactions.     

Variability of haemocyte and haemolymph parameters in European flat oyster Ostrea edulis families obtained from brood stocks of different geographical origins and relation with infection by the protozoan Bonamia ostreae

A research project to compare productive traits (growth and mortality), disease susceptibility and immune capability between Ostrea edulis stocks was performed. This article reports the results on the immune capability and its relation with infection by the intrahaemocytic protozoan Bonamia ostreae. Four to five oyster spat families were produced from each of four European flat oyster populations (one from Ireland, one from Greece and two from Galicia, Spain) in a hatchery. The spat were transferred to a raft in the Ría de Arousa (Galicia) for on growing for 2 years. Total haemocyte count (THC) and differential haemocyte count (DHC) were estimated monthly through the second year of growing-out. Three types of haemocytes were distinguished: granulocytes (GH), large hyalinocytes (LHH) and small hyalinocytes (SHH). Significant correlations between the mean relative abundance of GH and SHH of the families and the mean prevalence of B. ostreae, the overall incidence of pathological conditions and the cumulative mortality of the families were found; these correlations supported the hypothesis that high %GH and low %SHH would enhance oyster immune ability and, consequently, would contribute to lower susceptibility to disease and longer lifespan. Infection by B. ostreae involved a significant increase of circulating haemocytes, which affected more markedly the LHH type. The higher the infection intensity the higher the %LHH. This illustrates the ability of B. ostreae to modulate the immune responses of the O. edulis to favour its own multiplication. A significant reduction of the phenoloxidase activity in the haemolymph of oysters O. edulis infected by B. ostreae was observed. Nineteen enzymatic activities in the haemolymph of O. edulis and Crassostrea gigas (used as a B. ostreae resistant reference) were measured using the kit api ZYM^®, Biomerieux. Qualitative and quantitative differences in enzyme activities in both haemocyte and plasma fractions between B. ostreae noninfected O. edulis from different origins were recorded. However, no clear positive association between enzyme activity and susceptibility to bonamiosis was found. The only enzyme detected in the resistant species C. gigas that was not found in the susceptible one O. edulis was β-glucosidase (in plasma). B. ostreae infected O. edulis showed significant increase of some enzyme activities and the occurrence of enzymes that were not detected in noninfected oysters. These changes could be due to infection-induced enzyme synthesis by the host or to enzyme synthesis by the parasite.     

Heavy metal complexation in polluted molluscs II. Oysters (Ostrea edulis and Crassostrea gigas)

Cadmium, zinc and copper, accumulated from polluted habitats by the oysters Ostrea edulis and Crassostrea gigas, were studied. Three distinct low molecular weight (less than 3000 daltons) zinc complexes were separated from highly contaminated C. gigas, one of which may be a complex with the amino acid taurine. Only one of these zinc complexes was present in less contaminated specimens of O. edulis. On gel permeation chromatography of oyster extracts, copper was eluted together with amino acids (principally taurine) and the betaine homarine. No evidence of metallothionein type proteins was found.     

Weak effects of the exotic invasive <Emphasis Type="Italic">Carpobrotus edulis</Emphasis> on the structure and composition of Portuguese sand-dune communities

Sand dune ecosystems have a high conservation value worldwide, but they are highly threatened by exotic plant invasion. We investigated the impacts of the exotic invasive species Carpobrotus edulis on the composition and structure (spatial pattern, total cover, species diversity and species co-occurrence) of native sand dune communities in the western coast of Portugal. We studied eight sites following a north-south gradient; in each site we established 8–10 transects of 25 contiguous quadrats of one square meter. C. edulis had a significantly clumped pattern in five of the study sites, which, however, was not related to the spatial pattern of native species. The effects of climate on the community structure variables were on average three times stronger than those of C. edulis. This species also had small effects on the floristic composition of native species. Our results indicate that the success and impacts of C. edulis are habitat-dependent and context-specific. They also provide evidence of a strong resilience to the impacts of invasion in the studied sand dune ecosystems: C. edulis did not reach large abundances or exert negative impacts on native communities to the extent expected. These ecosystems provide a unique opportunity to increase our understanding on the origin of impacts by invasive species, and on how particular communities resist the impacts of an invader.     

Infestation of oysters and mussels by mytilicolid copepods: differences between natural coastal habitats and two offshore cultivation sites in the German Bight

The aim of this study was to determine the macro‐parasitic infestation level of oysters from the southern German Bight focussing on copepods of the genus Mytilicola. Crassostrea gigas, Ostrea edulis and Mytilus edulis were collected at five locations: three nearshore sites in the eastern Wadden Sea and two offshore cultivation sites in the German Bight. To reveal seasonal variations one sampling site was investigated in winter and summer. At the nearshore sites, Mytilicola orientalis was regularly detected in C. gigas. Prevalences ranged between 32.3% and 45.1%, intensity between 3.0 ± 0.6 and 8.2 ± 1.5. Infestation rates of C. gigas within the southern German Bight decreased from west to east: Apparently, M. orientalis has started its range extension along the German coast with gradual retardation eastwards but generally followed the invasion route of its main host, the Pacific oyster. Interestingly, we detected not only M. intestinalis but also M. orientalis as an intestinal parasite in M. edulis, which has sofar not previously been described as host within this region. We conclude that M. orientalis is flexible in its host choice. Furthermore, in the eastern Wadden Sea infestation rates of oysters and mussels by copepods are similar. These results deviate from the patterns observed for the northern Wadden Sea in terms of infestation level and host specificity. No macro‐parasites were found in oysters and mussels from the offshore sites. This absence can be considered as potentially beneficial for aquaculture activities in the open ocean in terms of stamina and physiological performance.     

Ecosystem engineering by a canopy‐forming kelp facilitates the recruitment of native oysters

Ecosystem engineers are species that influence the abiotic and biotic environment around them and may assist the restoration of associated species, including other habitat‐forming species. We deployed an array of 28 artificial reefs with transplanted Ecklonia radiata, the dominant canopy‐forming kelp species across southern Australia, to investigate how the patch size and density of E. radiata influenced the establishment of the associated communities of plants and animals. Many of the reefs were rapidly colonized by Ostrea angasi, a critically depleted reef‐forming oyster. Over the 24‐month deployment of the reefs, thick oyster mats formed across the entire surface of many of the reefs with estimated biomass densities exceeding 5 kg of live oysters/m²; however, oyster density was dependent on E. radiata patch size and density. Increasing patch size and the presence of kelp resulted in significantly higher densities of oysters 5 months after the reefs were deployed and at the end of the experiment, where oysters were approximately three times more numerous on reefs with kelp compared to those without kelp. E. radiata appeared to facilitate the establishment of O. angasi largely through its capacity to reduce benthic light and thus suppress competition from turfing algae. These results may inform the development of novel approaches to tackle recruitment bottlenecks affecting the restoration of O. angasi reefs.     

Wild gregarious settlements of Ostrea edulis in a semi‐enclosed sea lough: a case study for unassisted restoration

Ostrea edulis was once prolific throughout Europe and considered as the continent's native oyster. However, O. edulis currently exists in small fragmented assemblages where natural unaided recovery is rarely encountered. This research identified the small semi‐enclosed sea Lough of Strangford on the northeast coast of Northern Ireland as one of the few locations within Europe where the native oyster displayed gregarious natural rejuvenation. On close examination, four influential parameters appeared to assist in concentrated settlement; raised topographical cultch formations, shell coverage, the number of fecund in situ adults, and site protection. If these components were to be combined and managed as part of reintroduction and restoration initiatives, high‐density settlements and self‐sustaining populations may be possible. The research also identified that unregulated harvesting of intertidal O. edulis assemblages has the potential to seriously hinder natural recoveries. Indeed, the findings suggest that a review of policy in regards to intertidal hand gathering is necessary. However, naturally occurring high‐density settlements recorded during this research should be inspirational to all involved in the restoration of the native oyster.     

Oysters as habitat for limpets in a temperate mangrove forest

In temperate mangrove forests in New South Wales, Australia, the limpet Patelloida mimula Iredale lives on the oyster Saccostrea commercialis Iredale and Roughley, which, along with mangrove trees, provide the only hard substrata in a habitat otherwise dominated by soft-sediment. The objective of this study was to ascertain the degree of association between the limpet and the oyster by examining their patterns of co-occurrence in the forest and the relationship between individual pairs of limpets and oysters. Sampling of the distribution and abundance of limpets and oysters throughout the mangrove forest revealed that limpets were rarely present on substrata other than oysters. Patterns of abundance of limpets were, however, not directly related to the amount of habitat provided by the oysters. For example, there was a dramatic decline in the abundance of oysters from seaward to landward in the mangrove forest which was not reflected in the densities of limpets. Consequently, oysters appear to set the limits of distribution of limpets, but other factors modify their broad-scale patterns of distribution and abundance within these bounds. Limpets leave scars on oysters which might be home sites. About 98% of oysters with limpets had only one limpet per surface of oyster, and the distribution of limpets was overdispersed or repulsed. Moreover, in some areas of the forest, the lengths of limpets were directly related to lengths of oysters. Tracking of individual limpets for 13 days revealed that > 70% remained on the same scar of an oyster. This evidence suggests that for some limpets there is a strong association with particular oysters. Factors determining the distribution, abundance, and sizes of oysters are likely to be important sources of variation to the structure of populations of P. mimula in temperate mangrove forests.     

Unusual conservation of mitochondrial gene order in <Emphasis Type="Italic">Crassostrea</Emphasis>oysters: evidence for recent speciation in Asia

Background  

Oysters are morphologically plastic and hence difficult subjects for taxonomic and evolutionary studies. It is long been suspected, based on the extraordinary species diversity observed, that Asia Pacific is the epicenter of oyster speciation. To understand the species diversity and its evolutionary history, we collected five Crassostrea species from Asia and sequenced their complete mitochondrial (mt) genomes in addition to two newly released Asian oysters (C. iredalei and Saccostrea mordax) for a comprehensive analysis.     

Cloning of cDNAs and hybridization analysis of lysozymes from two oyster species, Crassostrea gigas and Ostrea edulis

In bivalve molluscs including oysters, lysozymes play an important role in the host defense mechanisms against invading microbes. However, it remains unclear in which sites/cells the lysozyme genes are expressed and which subsequently produced the enzyme. This study cloned lysozyme cDNAs from the digestive organs of Pacific oyster Crassostrea gigas and European flat oyster Ostrea edulis. Both complete sequences of two oysters' lysozymes were composed of 137 amino acids. Two translated proteins present a high content in cysteine residues. Phylogenetic analyses showed that these oysters' lysozymes clustered with the invertebrate-type lysozymes of other bivalve species. In the Pacific oyster, lysozyme mRNA was expressed in all tissues except for those of the adductor muscle. In situ hybridization analyses revealed that lysozyme mRNA was expressed strongly in basophil cells in the digestive gland tubule of C. gigas, but not in digestive cells. Results indicated that the basophil cells of the oyster digestive gland are the sites of lysozyme synthesis.     

Minchinia armoricana sp. nov. (Haplosporida), a parasite of the European flat oyster, Ostrea edulis

Examination of European flat oysters, Ostrea edulis, from the Dutch oyster culture, but originating in France, revealed a new disease due to a protistan parasite. Light and electron microscope studies revealed that the parasite belongs to the haplosporidan genus Minchinia. Since comparison with other Minchinia spp. indicate that it is new, the name Minchinia armoricana nov. sp. is proposed. Thus far, the parasite was very rare; only two diseased oysters were observed among ca. 3700 specimens examined histologically during a 2.5-year period. The diseased oysters showed macroscopically a peculiar brown discoloration and microscopically many sporocysts with spores in the connective tissue. Beside the two diseased oysters, another one was observed with an infection of unidentified plasmodial stages in the connective tissue. These may be developmental stages of the new species M. armoricana.     

Evaluation of the sample size used for the rapid bioassessment of rivers using macroinvertebrates

Experiments were designed to investigate selective predation by medium (40–55 mm carapace width: CW) and large (55–70 mm CW) Carcinus maenas when feeding on four bivalves of contrasting shell morphology. Size-selection was examined by presenting individual crabs with a wide size range of Mytilus edulis, Ostrea edulis, Crassostrea gigas and Cerastoderma edule. Medium-sized crabs preferred mussels 5–15 mm shell length (maximum shell dimension: SL) and cockles 5–10 mm SL, whereas large crabs preferred mussels 15–25 mm and cockles 10–20 mm SL. Crabs generally showed no preference for any particular size of either oyster species. Species-selection was examined by presenting individual crabs with paired combinations of the four bivalves in various proportions. When offered mussels and oysters simultaneously, both size categories of crabs consistently selected mussels, and food choice was independent of prey relative abundance. By contrast, C. maenas selected mussels and cockles as expected by the frequency in which each size category of crab encountered the preferred size ranges of prey. Crab preference clearly paralleled the rank order of prey profitability, which in turn was mainly determined by prey biomass, suggesting that active selection takes place at some point of the predation cycle. Experiments with epoxy resin models showed that initial reluctance of crabs to attack oysters was not associated with the ultimate energy reward. Moreover, they suggest that foraging decisions are partly based on evaluations of overall prey shape and volume, and that the minimum dimension of the shell constitutes an important feature which crabs recognise and associate with prey value.     

Coastal sponge communities of the West Indian Ocean: taxonomic affinities, richness and diversity

Sponges assemblages were sampled in four coastal study regions (Malindi, Kenya; Quirimba Archipelago, northern Mozambique; Inhaca Island, Southern Mozambique and Anakao, Madagascar) in the west Indian Ocean. Sponge species were counted in multiple 0.5 m² quadrats at depths of between 0 and 20 m at a number of sites within localities within each region. Despite the relatively small areas sampled, sponge samples comprised a total of 130 species and 70 genera of the classes Demospongiae and Calcarea. Sponges are clearly a major taxon in these regions in terms of numbers of species, percentage cover or biomass, although their ecology in the west Indian Ocean is virtually unknown. Nearly half of the genera, e.g. Iotrochota, found were species with a so‐called Tethyan distribution. Most of the other genera were cosmopolitan, e.g. Clathria, but some were cold water (Coelosphaera), Indo‐Australian (Ianthella) or circum‐African (Crambe). Many of the species encountered in the present study occurred in at least two study regions, many in more and could occupy large areas of substratum. Some of these, e.g. Xestospongia exigua, are commonly found throughout the Indo‐west Pacific region where they also occupy much space. The endemicity of the shallow water sponge faunas in East Africa (20–25%) seem to be high within the Indo‐Pacific realm but are lower than northern Papua New Guinea. The tropical regions (Kenya and Northern Mozambique) were more speciose than subtropical regions (southern Mozambique and Madagascar) but not significantly more diverse (Shannon H′). Although latitude was not a major influence on sponge community patterns, hard substratum assemblages did form a cline from the tropics to Southern Mozambique, linked by Madagascar. Substratum nature (habitat) was most important in influencing the suite and number of species present. Sponge assemblages of soft substrata were much more dissimilar, both within and between habitats, than those on hard substrata. There was a predictable variability in species richness between hard substratum habitats: coral reefs being speciose and caves being less so. Our findings showed that both patterns and influences on species richness may be decoupled from those influencing diversity. In our data species richness, but not diversity, showed striking regional and bathymetric trends. In addition, sponge species richness mainly split at coral reef vs. non‐reef habitats, whilst diversity divided principally into assemblages on hard and soft substrata. We consider this dichotomy of findings between species richness and diversity values to be important, as these are two principal measures used for the interpretation of biodiversity.     

Genetic structure and diversity of the Chilean flat oyster Ostrea chilensis (Bivalvia: Ostreidae) along its natural distribution from natural beds subject to different fishing histories

Ostrea chilensis (Küster, 1844), the flat oyster, is native to Chile and New Zealand. In Chile, it occurs in a few natural beds, from the northern part of Chiloé Island (41 ºS) to the Guaitecas Archipelago (45 ºS). This bivalve is slow growing, broods its young, and has very limited dispersal potential. The Ostrea chilensis fishery has been over-exploited for a number of decades such that in some locations oysters no longer exist. The aim of this study was to study the genetic diversity of the Chilean flat oyster along its natural distribution to quantify the possible impact of the dredge fishery on wild populations. The genetic structure and diversity of Ostrea chilensis from six natural beds with different histories of fishing activity were estimated. Based on mitochondrial (Cytb) and nuclear (ITS1) DNA sequence variation, our results provide evidence that genetic diversity is different among populations with recent history of wild dredge fishery efforts. We discuss the possible causes of these results. Ultimately, such new information may be used to develop and apply new management measures to promote the sustainable use of this valuable marine resource.     

Bioaccumulation Efficiency,Tissue Distribution,and Environmental Occurrence of Hepatitis E Virus in Bivalve Shellfish from France

Hepatitis E virus (HEV), an enteric pathogen of both humans and animals, is excreted by infected individuals and is therefore present in wastewaters and coastal waters. As bivalve molluscan shellfish are known to concentrate viral particles during the process of filter feeding, they may accumulate this virus. The bioaccumulation efficiencies of oysters (Crassostrea gigas), flat oysters (Ostrea edulis), mussels (Mytilus edulis), and clams (Ruditapes philippinarum) were compared at different time points during the year. Tissue distribution analysis showed that most of the viruses were concentrated in the digestive tissues of the four species. Mussels and clams were found to be more sensitive to sporadic contamination events, as demonstrated by rapid bioaccumulation in less than 1 h compared to species of oysters. For oysters, concentrations increased during the 24-h bioaccumulation period. Additionally, to evaluate environmental occurrence of HEV in shellfish, an environmental investigation was undertaken at sites potentially impacted by pigs, wild boars, and human waste. Of the 286 samples collected, none were contaminated with hepatitis E virus, despite evidence that this virus is circulating in some French areas. It is possible that the number of hepatitis E viral particles discharged into the environment is too low to detect or that the virus may have a very short period of persistence in pig manure and human waste.     

Contrasting population genetic structure and gene flow between <Emphasis Type="Italic">Oryza rufipogon</Emphasis> and <Emphasis Type="Italic">Oryza nivara</Emphasis>

The cross compatible wild relatives of crops have furnished valuable genes for crop improvement. Understanding the genetics of these wild species may enhance their further use in breeding. In this study, sequence variation of the nuclear Lhs1 gene was used to investigate the population genetic structure and gene flow of Oryza rufipogon and O. nivara, two wild species most closely related to O. sativa. The two species diverge markedly in life history and mating system, with O. rufipogon being perennial and outcrossing and O. nivara being annual and predominantly inbreeding. Based on sequence data from 105 plants representing 11 wild populations covering the entire geographic range of these wild species, we detected significantly higher nucleotide variation in O. rufipogon than in O. nivara at both the population and species levels. At the population level the diversity in O. rufipogon (Hd = 0.712; θ _sil = 0.0017) is 2–3 folds higher than that in O. nivara (Hd = 0.306; θ _sil = 0.0005). AMOVA partitioning indicated that genetic differentiation among O. nivara populations (78.2%) was much higher than that among O. rufipogon populations (52.3%). The different level of genetic diversity and contrasting population genetic structure between O. rufipogon and O. nivara might be explained by their distinct life histories and mating systems. Our simulation using IM models demonstrated significant gene flow from O. nivara to O. rufipogon, indicating a directional introgression from the annual and selfing species into the perennial and outcrossing species. The ongoing introgression has played an important role in shaping current patterns of genetic diversity of these two wild species. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.