The structure of population genetic diversity in <Emphasis Type="Italic">Vallisneria</Emphasis><Emphasis Type="Italic">americana</Emphasis> in the Chesapeake Bay: implications for restoration

Submersed aquatic macrophyte beds provide important ecosystem services, yet their distribution and extent has declined worldwide in aquatic ecosystems. Effective restoration of these habitats will require, among other factors, reintroduction of genetically diverse source material that can withstand short- and long-term environmental fluctuations in environmental conditions. We examined patterns of genetic diversity in Vallisneria americana because it is a cosmopolitan freshwater submersed aquatic macrophyte and is commonly used for restoring freshwater habitats. We sampled 26 naturally occurring populations of V. americana in the Chesapeake Bay estuary and its tributaries and found that the majority of populations have high genotypic diversity and are not highly inbred. Fourteen of the populations had high allelic and genotypic diversity and could serve as source sites for restoration material. However, substantial geographic structuring of genetic diversity suggests that caution should be used in moving propagules to locations distant from their source. In particular, we suggest that propagules at least be limited within four primary geographic areas that correspond to freshwater tidal and non-tidal, oligohaline, and seasonally mesohaline areas of the Chesapeake Bay.     

Genetic Polymorphism and Transplantation Success in the Mediterranean Seagrass Posidonia oceanica

We studied the role of genetic variability of donor beds in establishing transplantation criteria for the Mediterranean seagrass Posidonia oceanica. Horizontal rhizomes, collected from three geographically distinct populations, were transplanted into a common bed at a highly human‐impacted locality. The transplantation site was located near one of the donor populations. After three years, the shoots collected in the population adjacent to the transplanting site showed the lowest growth performance. Genetic variability, assessed through the analysis of hypervariable microsatellite regions, and growth performance followed a similar trend. The shoots growing and branching at the highest rate were those collected from populations with the highest heterozygosity values, despite greater geographic distance. No genetic differences were found between the transplanted shoots and shoots from donor meadows, as expected due to the low rate of sexual reproduction in P. oceanica and the short time that had passed since the transplants. The problem of affecting the local gene pool by the introduction of foreign genotypes could arise, but introduction of new alleles could balance the degradation of genetic variability caused by human impact. In general our study suggests that the genetic variability of source material is an important aspect to consider in the development of seagrass restoration strategies.     

Random amplified polymorphic DNA assessment of diversity in western Mediterranean populations of the seagrass Posidonia oceanica

Posidonia oceanica is an endemic Mediterranean seagrass species that has often been assumed to contain low levels of genetic diversity. Random amplified polymorfic DNA (RAPD) markers were used to assess genetic diversity among five populations from three geographical regions (north, central, and south) of the western Mediterranean Sea. Stranded germinating seeds from one of the central populations were also included in the analysis. Forty-one putative genets were identified among 76 ramets based on 28 RAPD markers. Genotypic diversity strongly depended on the spatial structure, age, and maturity of the meadows. The lowest clonal diversity was found in the less structured and youngest prairies. Conversely, a high genotypic diversity was found in the highly structured meadows. The genotypic diversity in these meadows was at the same level as in P. australis and higher than previously reported data for P. oceanica populations in the Tyrrhenian Sea near the coast of Italy.     

Restoration of species‐rich grasslands by transfer of local plant material and its impact on species diversity and genetic variation—Findings of a practical restoration project in southeastern Germany

Restoration of species‐rich grasslands is a key issue of conservation. The transfer of seed‐containing local plant material is a proven technique to restore species‐rich grassland, since it potentially allows to establish genetically variable and locally adapted populations. In our study, we tested how the transfer of local plant material affected the species diversity and composition of restored grasslands and the genetic variation of the typical grassland plant species Knautia arvensis and Plantago lanceolata.For our study, we selected fifteen study sites in southeastern Germany. We analyzed species diversity and composition and used molecular markers to investigate genetic variation within and among populations of the study species from grasslands that served as source sites for restoration and grasslands, which were restored by transfer of green hay and threshed local plant material.The results revealed no significant differences in species diversity and composition between grasslands at source and restoration sites. Levels of genetic variation within populations of the study species Knautia arvensis and Plantago lanceolata were comparable at source and restoration sites and genetic variation among populations at source and their corresponding restoration sites were only marginal different.Our study suggests that the transfer of local plant material is a restoration approach highly suited to preserve the composition of species‐rich grasslands and the natural genetic pattern of typical grassland plant species.     

Resilience of Zostera muelleri seagrass to small‐scale disturbances: the relative importance of asexual versus sexual recovery

Resilience is the ability of an ecosystem to recover from disturbance without loss of essential function. Seagrass ecosystems are key marine and estuarine habitats that are under threat from a variety of natural and anthropogenic disturbances. The ability of these ecosystems to recovery from disturbance will to a large extent depend on the internsity and scale of the disturbance, and the relative importance of sexual versus asexual reproduction within populations. Here, we investigated the resilience of Zostera muelleri seagrass (Syn. Zostera capricorni) to small‐scale disturbances at four locations in Lake Macquarie – Australia's largest coastal lake – and monitored recovery over a 65‐week period. Resilience of Z. muelleri varied significantly with disturbance intensity; Z. muelleri recovered rapidly (within 2 weeks) from low‐intensity disturbance (shoot loss), and rates of recovery appeared related to initial shoot length. Recovery via rhizome encroachment (asexual regeneration) from high‐intensity disturbance (loss of entire plant) varied among locations, ranging from 18‐35 weeks, whereas the ability to recover was apparently lost (at least within the time frame of this study) when recovery depended on sexual regeneration, suggesting that seeds do not provide a mechanism of recovery against intense small‐scale disturbances. The lack of sexual recruits into disturbed sites is surprising as our initial surveys of genotypic diversity (using nine polymorphic microsatellite loci) at these location indicate that populations are maintained by a mix of sexual and asexual reproduction (genotypic diversity [R] varied from 0.24 to 0.44), and populations consisted of a mosaic of genotypes with on average 3.6 unique multilocus genotypes per 300 mm diameter plot. We therefore conclude that Z. muelleri populations within Lake Macquarie rely on clonal growth to recover from small‐scale disturbances and that ongoing sexual recruitment by seeds into established seagrass beds (as opposed to bare areas arising from disturbance) must be the mechanism responsible for maintaining the observed mixed genetic composition of Z. muelleri seagrass meadows.     

Genetic diversity in threatened Posidonia australis seagrass meadows

Recognising patterns of genetic diversity and connectivity is integral to understanding the mechanisms behind population declines and formulating management plans for the conservation of threatened or endangered species. This is particularly important for clonal organisms such as seagrasses, which are experiencing rapid global decline. This study quantifies genetic diversity within 12 naturally fragmented Posidonia australis meadows on the east coast of Australia, using a set of eight microsatellite DNA markers. Genetic diversity increased with latitude, moving away from the range-edge, and was significantly lower in six mid-range endangered meadows and the two northernmost meadows. These meadows also showed evidence of shared multilocus genotypes despite significant geographic separation. The four southernmost meadows were genetically differentiated from all other meadows further north, and all multilocus genotypes identified were unique to their sample locations. We conclude that patterns of low diversity in the endangered and northern meadows are likely due to a population bottleneck caused by a range-edge effect. A common ancestral source meadow existing prior to historical sea level changes may explain the sharing of multilocus genotypes, as contemporary gene flow between these geographically isolated meadows is unlikely. Our findings have important implications for conservation, highlighting the endangered and range-edge populations as those potentially most at risk of extinction should environmental conditions change. These results can be utilised for the location of suitable donor populations for transplanting purposes as a means of mitigating further declines.     

Contribution of genetics and genomics to seagrass biology and conservation

Genetic diversity is one of three forms of biodiversity recognized by the IUCN as deserving conservation along with species and ecosystems. Seagrasses provide all three levels in one. This review addresses the latest advances in our understanding of seagrass population genetics and genomics within the wider context of ecology and conservation. Case studies are used from the most widely studied, northern hemisphere species Zostera marina, Z. noltii, Posidonia oceanica and Cymodocea nodosa.

We begin with an analysis of the factors that have shaped population structure across a range of spatial and temporal scales including basin-level phylogeography, landscape-scale connectivity studies, and finally, local-scale analyses at the meadow level—including the effects of diversity, clonality and mating system. Genetic diversity and clonal architecture of seagrass meadows differ within and among species at virtually all scales studied. Recent experimental studies that have manipulated seagrass genetic biodiversity indicate that genotypic diversity matters in an immediate ecological context, and enhances population growth, resistance and resilience to perturbation, with positive effects on abundance and diversity of the larger community. In terms of the longer term, evolutionary consequences of genetic/genotypic diversity in seagrass beds, our knowledge remains meagre. It is here that the new tools of ecogenomics will assist in unravelling the genetic basis for adaptation to both biotic and abiotic change. Gene expression studies will further assist in the assessment of physiological performance which may provide an early warning system under complex disturbance regimes that seagrasses are at or near their tolerance thresholds.

At the most fundamental level, ecological interactions of seagrasses with their environment depends on the genetic architecture and response diversity underlying critical traits. Hence, given the rapid progress in data acquisition and analysis, we predict an increasing role of genetic and genomic tools for seagrass ecology and conservation.     

A genetic assessment of a successful seagrass meadow (Posidonia australis) restoration trial

Seagrass meadows are in decline globally. Although numerous experimental methods have been implemented to restore meadows, few have been successful in the long term. Poor decisions on the sourcing of transplants from donor sites, including poor genetic integration and/or low genetic diversity, may impact on restoration success. However, despite evidence to suggest a positive association between genetic diversity and ecological resilience, there is usually little or no input from genetic data to inform on the genetic management of ecological restoration. Cockburn Sound has seen a 77% decline in seagrass cover since 1967. A transplant trial was conducted between 2004 and 2008 with sprigs of Posidonia australis being planted into a bare sand area. Survival was monitored annually, and in 2012, we compared genetic diversity in this transplant area with the original donor site. Genetic diversity in the restored meadow was very high and comparable to the donor site, with no genetic differentiation detected. The high level of genetic diversity and choice of site may have played an important role in the success of this restoration trial. The observed natural recruits around the site after establishment of transplants suggest that local restoration efforts may improve seafloor habitat and facilitate natural expansion of the meadow.     

A meta‐analysis reveals a positive correlation between genetic diversity metrics and environmental status in the long‐lived seagrass Posidonia oceanica

The seagrass Posidonia oceanica is a key engineering species structuring coastal marine systems throughout much of the Mediterranean basin. Its decline is of concern, leading to the search for short‐ and long‐term indicators of seagrass health. Using ArcGIS maps from a recent, high‐resolution (1–4 km) modelling study of 18 disturbance factors affecting coastal marine systems across the Mediterranean (Micheli et al. 2013, http://globalmarine.nceas.ucsb.edu/mediterranean/ ), we tested for correlations with genetic diversity metrics (allelic diversity, genotypic/clonal diversity and heterozygosity) in a meta‐analysis of 56 meadows. Contrary to initial predictions, weak but significantly positive correlations were found for commercial shipping, organic pollution (pesticides) and cumulative impact. This counterintuitive finding suggests greater resistance and resilience of individuals with higher genetic and genotypic diversity under disturbance (at least for a time) and/or increased sexual reproduction under an intermediate disturbance model. We interpret the absence of low and medium levels of genetic variation at impacted locations as probable local extinctions of individuals that already exceeded their resistance capacity. Alternatively, high diversity at high‐impact sites is likely a temporal artefact, reflecting the mismatch with pre‐environmental impact conditions, especially because flowering and sexual recruitment are seldom observed. While genetic diversity metrics are a valuable tool for restoration and mitigation, caution must be exercised in the interpretation of correlative patterns as found in this study, because the exceptional longevity of individuals creates a temporal mismatch that may falsely suggest good meadow health status, while gradual deterioration of allelic diversity might go unnoticed.     

Population genetics information for the regional conservation of a tropical seagrass, <Emphasis Type="Italic">Enhalus acoroides</Emphasis>, around the Guimaras Strait,Philippines

Seagrasses are marine angiosperms and play an essential ecological role in coastal ecosystems; however, seagrass meadows are threatened locally by anthropogenic disturbances. Understanding the dispersal patterns of seagrasses is essential for appropriate ecosystem management and establishment of marine protected areas (MPAs) in coastal ecosystems. In the Guimaras Strait in the Philippines, Banate (BAN) has been established as an MPA. However, there is a lack of information on the genetic diversity of seagrasses in BAN and the surrounding areas. In the present study, population genetics analysis of Enhalus acoroides was performed by using polymorphic microsatellite markers, for the estimation of genetic diversity, differentiation, and migration patterns of seagrasses within the regional geographical scale (~200 km) around the Guimaras Strait. The results showed that the genetic diversity of BAN is extremely low, although the Guimaras Strait is located in the tropical central habitat. Guimaras Island geographically divides the populations of E. acoroides into south and north. However, the genetic structure did not show any relationship between the geographical location and distance. The floating, buoyant fruits of E. acoroides may play a role in their long-distance dispersal; however, such dispersal is not frequent. Almost all of the seeds and fruits are derived from self-recruitment in the natal meadow. This study suggests that E. acoroides populations possess a weak genetic connectivity, and that the persistence of the meadow is threatened due to the low genetic diversity and high degree of population isolation in BAN. To maintain and enhance the genetic diversity of seagrasses within the MPA, the seagrass meadows in the surrounding areas should also be conserved.     

Predicting the cumulative effect of multiple disturbances on seagrass connectivity

The rate of exchange, or connectivity, among populations effects their ability to recover after disturbance events. However, there is limited information on the extent to which populations are connected or how multiple disturbances affect connectivity, especially in coastal and marine ecosystems. We used network analysis and the outputs of a biophysical model to measure potential functional connectivity and predict the impact of multiple disturbances on seagrasses in the central Great Barrier Reef World Heritage Area (GBRWHA), Australia. The seagrass networks were densely connected, indicating that seagrasses are resilient to the random loss of meadows. Our analysis identified discrete meadows that are important sources of seagrass propagules and that serve as stepping stones connecting various different parts of the network. Several of these meadows were close to urban areas or ports and likely to be at risk from coastal development. Deep water meadows were highly connected to coastal meadows and may function as a refuge, but only for non‐foundation species. We evaluated changes to the structure and functioning of the seagrass networks when one or more discrete meadows were removed due to multiple disturbance events. The scale of disturbance required to disconnect the seagrass networks into two or more components was on average >245 km, about half the length of the metapopulation. The densely connected seagrass meadows of the central GBRWHA are not limited by the supply of propagules; therefore, management should focus on improving environmental conditions that support natural seagrass recruitment and recovery processes. Our study provides a new framework for assessing the impact of global change on the connectivity and persistence of coastal and marine ecosystems. Without this knowledge, management actions, including coastal restoration, may prove unnecessary and be unsuccessful.     

Population structure and genetic diversity among eelgrass (Zostera marina) beds and depths in San Francisco Bay

The seagrass Zostera marina is widely distributed in coastal regions throughout much of the northern hemisphere, forms the foundation of an important ecological habitat, and is suffering population declines. Studies in the Atlantic and Pacific oceans indicate that the degree of population genetic differentiation is location dependent. San Francisco Bay, California, USA, is a high-current, high-wind environment where rafting of seed-bearing shoots has the potential to enhance genetic connectivity among Z. marina populations. We tested Z. marina from six locations, including one annual population, within the bay to assess population differentiation and to compare levels of within-population genetic diversity. Using 7 microsatellite loci, we found significant differentiation among all populations. The annual population had significantly higher clonal diversity than the others but showed no detectible differences in heterozygosity or allelic richness. There appears to be sufficient input of genetic variation through sexual reproduction or immigration into the perennial populations to prevent significant declines in the number and frequency of alleles. In additional depth comparisons, we found differentiation among deep and shallow portions in 1 of 3 beds evaluated. Genetic drift, sweepstakes recruitment, dispersal limitation, and possibly natural selection may have combined to produce genetic differentiation over a spatial scale of 3-30 km in Z. marina. This implies that the scale of genetic differentiation may be smaller than expected for seagrasses in other locations too. We suggest that populations in close proximity may not be interchangeable for use as restoration material.     

Rapid restoration of belowground structure and fauna of a seagrass habitat

Seagrass meadows are habitat for an abundance and diversity of animal life, and their continuing global loss has focused effort on their restoration. This restoration not only aims to re‐establish the structure of the seagrass, but also to restore its function, particularly as habitat. The success of seagrass restoration is typically measured by the recovery of aboveground structure, but this ignores the important role of the belowground component of seagrass ecosystems, which may not recover at the same rate, and is equally important for faunal communities. We quantify infaunal communities (abundance, richness, and composition) within expanding plots of restored seagrass, and relate their change to the recovery of belowground seagrass biomass and sediment properties. We found that infaunal abundance and composition converged on that found in natural seagrass within 2 years, while the overall infaunal richness was not affected by habitat. The carbon content of surface sediments also recovered within 2 years, although recovery of belowground biomass and sediment grain size took 4 to 6 years. These results suggest that the structure of recovering seagrass habitats may not need to attain that of natural meadows before they support infauna that is comparable to natural communities. This pace and effectiveness of recovery provides some optimism for future seagrass restoration.     

海草场生态系统及其修复研究进展

海草场能够提供重要的生态系统服务。自20世纪末以来,由于人类活动和自然灾害的影响,全球范围内的海草场出现了急剧衰退,由此也促进了海草场生态系统的研究以及海草场人工修复技术的发展。近年来,针对海草场生境流失的现状,中国也开始开展海草场修复工作。从以下方面进行论述:(1)海草的种类、分布,海草场生态系统功能及其生态系统服务:与陆地系统相比,全球海草物种多样性较低,了解海草的分布特征有助于通过了解海草如何适应当地环境压力,以揭示海草适应环境的能力;海草场提供重要而广泛的自然生态系统服务,特别是在维护近岸生态系统健康和满足人类需求过程中起到重要的作用;(2)海草场的衰退及其原因:认识并缓解人类压力对海草场的危害是促进海草场生态系统可持续发展的重要一环;(3)国内外海草场修复现状:以此阐明海草场修复原理,为海草场修复提供科学的方法;(4)总结与讨论:基于科学研究背景,为中国海草场生态系统保护和修复提出建议。海草场的修复和保护应当相辅相成,并与我国海岸长远规划相结合,以此推动我国海草场生态系统服务的可持续发展。     

Demographic and genetic connectivity: the role and consequences of reproduction,dispersal and recruitment in seagrasses

Accurate estimation of connectivity among populations is fundamental for determining the drivers of population resilience, genetic diversity, adaptation and speciation. However the separation and quantification of contemporary versus historical connectivity remains a major challenge. This review focuses on marine angiosperms, seagrasses, that are fundamental to the health and productivity of temperate and tropical coastal marine environments globally. Our objective is to understand better the role of sexual reproduction and recruitment in influencing demographic and genetic connectivity among seagrass populations through an integrated multidisciplinary assessment of our present ecological, genetic, and demographic understanding, with hydrodynamic modelling of transport. We investigate (i) the demographic consequences of sexual reproduction, dispersal and recruitment in seagrasses, (ii) contemporary transport of seagrass pollen, fruits and seed, and vegetative fragments with a focus on hydrodynamic and particle transport models, and (iii) contemporary genetic connectivity among seagrass meadows as inferred through the application of genetic markers. New approaches are reviewed, followed by a summary outlining future directions for research: integrating seascape genetic approaches; incorporating hydrodynamic modelling for dispersal of pollen, seeds and vegetative fragments; integrating studies across broader geographic ranges; and incorporating non‐equilibrium modelling. These approaches will lead to a more integrated understanding of the role of contemporary dispersal and recruitment in the persistence and evolution of seagrasses.     

Assessing the effect of genetic diversity on the early establishment of the threatened seagrass Posidonia australis using a reciprocal‐transplant experiment

Two common goals for restoration are rapid plant establishment and long‐term plant persistence. The success of transplanted populations may be jeopardized if the donor transplants are not genetically diverse, and/or poorly matched to their new environment. Here, we test the effects of local adaptation and plot‐level genetic diversity on the early establishment phase of a threatened seagrass species, Posidonia australis, by performing a reciprocal transplant experiment across two genetically and geographically distinct populations in southeastern Australia. Posidonia australis is a long‐lived, slow‐growing species that has no seed bank, and the successful transplantation of live shoots and seedlings is the only available restoration method. Our results show a strong effect of local adaptation and genetic diversity on P. australis survivorship and performance over the first 6 months following transplantation. High‐genetic diversity plots displayed higher survival rates and exhibited reduced productivity and increased carbohydrate reserves within the rhizome. This suggests that high‐diversity plots included shoots that were conserving energy stores by actively reducing growth rates during the early stages of transplantation. The lowest diversity plots exhibited high leaf and root productivity and corresponding low carbohydrate reserves. This may be a sign of stress in the low‐diversity transplants, potentially explaining the very low survival rate. We suggest that future restoration efforts source donor transplants from multiple local sources to ensure both local adaptation and sufficient genetic diversity to increase the likelihood of early establishment success.     

Anthropogenic disturbance homogenizes seagrass fish communities

Anthropogenic activities have led to the biotic homogenization of many ecological communities, yet in coastal systems this phenomenon remains understudied. In particular, activities that locally affect marine habitat‐forming foundation species may perturb habitat and promote species with generalist, opportunistic traits, in turn affecting spatial patterns of biodiversity. Here, we quantified fish diversity in seagrass communities across 89 sites spanning 6° latitude along the Pacific coast of Canada, to test the hypothesis that anthropogenic disturbances homogenize (i.e., lower beta‐diversity) assemblages within coastal ecosystems. We test for patterns of biotic homogenization at sites within different anthropogenic disturbance categories (low, medium, and high) at two spatial scales (within and across regions) using both abundance‐ and incidence‐based beta‐diversity metrics. Our models provide clear evidence that fish communities in high anthropogenic disturbance seagrass areas are homogenized relative to those in low disturbance areas. These results were consistent across within‐region comparisons using abundance‐ and incidence‐based measures of beta‐diversity, and in across‐region comparisons using incidence‐based measures. Physical and biotic characteristics of seagrass meadows also influenced fish beta‐diversity. Biotic habitat characteristics including seagrass biomass and shoot density were more differentiated among high disturbance sites, potentially indicative of a perturbed environment. Indicator species and trait analyses revealed fishes associated with low disturbance sites had characteristics including stenotopy, lower swimming ability, and egg guarding behavior. Our study is the first to show biotic homogenization of fishes across seagrass meadows within areas of relatively high human impact. These results support the importance of targeting conservation efforts in low anthropogenic disturbance areas across land‐ and seascapes, as well as managing anthropogenic impacts in high activity areas.     

Spatiotemporal variability in the structure of seagrass meadows and associated macrofaunal assemblages in southwest England (UK): Using citizen science to benchmark ecological pattern

Seagrass meadows underpin a variety of ecosystem services and are recognized as globally important habitats and a conservation priority. However, seagrass populations are currently impacted by a range of biotic and abiotic stressors, and many are in decline globally. As such, improved understanding of seagrass populations and their associated faunal assemblages is needed to better detect and predict changes in the structure and functioning of these key habitats. Here, we analyzed a large dataset—collected by recreational scuba divers volunteering on a citizen science project—to examine spatiotemporal patterns in ecological structure and to provide a robust and reliable baseline against which to detect future change. Seagrass (Zostera marina) shoot density and the abundance of associated faunal groups were quantified across 2 years at 19 sites nested within three locations in southwest UK, by collecting in situ quadrat samples (2,518 in total) during 328 dives. Seagrass shoot density and meadow fragmentation was comparable across locations but was highly variable among sites. Faunal abundance and assemblage structure varied between areas with or without seagrass shoots; this pattern was largely consistent between locations and years. Overall, increased seagrass density was related to increased faunal abundance and explained shifts in faunal assemblage structure, although individual faunal groups were affected differently. More broadly, our study shows that well‐funded and orchestrated citizen science projects can, to some extent, gather fundamental information needed to benchmark ecological structure in poorly studied nearshore marine habitats.     

Strengths and potential pitfalls of hay transfer for ecological restoration revealed by RAD‐seq analysis in floodplain Arabis species

Achieving high intraspecific genetic diversity is a critical goal in ecological restoration as it increases the adaptive potential and long‐term resilience of populations. Thus, we investigated genetic diversity within and between pristine sites in a fossil floodplain and compared it to sites restored by hay transfer between 1997 and 2014. RAD‐seq genotyping revealed that the stenoecious floodplain species Arabis nemorensis is co‐occurring with individuals that, based on ploidy, ITS‐sequencing and morphology, probably belong to the close relative Arabis sagittata, which has a documented preference for dry calcareous grasslands but has not been reported in floodplain meadows. We show that hay transfer maintains genetic diversity for both species. Additionally, in A. sagittata, transfer from multiple genetically isolated pristine sites resulted in restored sites with increased diversity and admixed local genotypes. In A. nemorensis, transfer did not create novel admixture dynamics because genetic diversity between pristine sites was less differentiated. Thus, the effects of hay transfer on genetic diversity also depend on the genetic make‐up of the donor communities of each species, especially when local material is mixed. Our results demonstrate the efficiency of hay transfer for habitat restoration and emphasize the importance of prerestoration characterization of microgeographic patterns of intraspecific diversity of the community to guarantee that restoration practices reach their goal, that is maximize the adaptive potential of the entire restored plant community. Overlooking these patterns may alter the balance between species in the community. Additionally, our comparison of summary statistics obtained from de novo‐ and reference‐based RAD‐seq pipelines shows that the genomic impact of restoration can be reliably monitored in species lacking prior genomic knowledge.