Applying genomic data to seagrass conservation

Background: Walleye (Sander vitreus), a valuable sportfish and an important ecological apex predator, exhibits genetic structuring across their range and localized structuring as a result of stocking. Methods: Walleye from 17 sampling locations across West Virginia were sequenced using a ddRAD protocol, generating various SNP datasets to assess population structuring and genomic diversity, with specific emphasis on the native Eastern Highlands strain. Different minor allele frequency filter thresholds were tested to assess impacts on genetic diversity and differentiation metrics. Results: High genetic differentiation was observed between the Eastern Highlands and Great Lakes strains, with further sub-structuring within the Eastern Highlands strain between the Ohio River populations and the other populations. Increasing MAF thresholds generally reduced the distinctiveness of clusters, but the overall inference of the number of clusters was minimally impacted. Genetic diversity metrics indicated some variability among Eastern Highlands walleye populations, with isolated populations, including the New River and Summersville Lake, showing higher inbreeding coefficients. MAF filters generally increased diversity metrics, but the trend of diversity metrics among populations remained relatively consistent. Several SNPs were found to be potentially undergoing selection, with the minor allele frequencies of these SNPs being found to be highest in Summersville Lake, highlighting potential adaptive divergence between the riverine populations and a large lentic system. Conclusions: The use of any MAF filter generated the same trends of population structuring and genomic diversity inferences regardless of the MAF threshold used. Further management of Eastern Highlands walleye in West Virginia needs to emphasize protecting the genetic integrity of the Kanawha River population and ongoing genomic screening of broodstock to conserve native genetic diversity.

Evaluating different approaches to integrate genome-wide genetic diversity in spatial conservation prioritization

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.

Genetic diversity is critical for adaptation in response to changing environments and provides a valuable metric for predicting species’ extinction risk. The International Union for Conservation of Nature (IUCN) and broader scientific community have acknowledged that genetic diversity is a critical component to biodiversity conservation. However, there remain gaps in the incorporation or application of genetic data to extinction risk assessments. Here, we describe how genetic diversity metrics can inform species extinction risk. Specifically, we focus on how information gained from genetic diversity metrics, and temporal reporting of changes in genetic diversity can complement existing IUCN Red List of Threatened Species criteria. We conclude by advocating for standardized reporting of genetic sequence data and calculated diversity metrics to facilitate the use of genetic data in threat assessments for IUCN and Red List-assessed species. This perspective highlights a critical need for, and a critical step towards, integration of genetic diversity metrics into Red List assessments. We expect our recommendations will complement ongoing work by the IUCN Species Survival Commission’s Conservation Genetics Specialist Group to protect genetic diversity globally.

The restricted distribution and isolation of island endemics often produces unique genetic and phenotypic diversity of conservation interest to management agencies. However, these isolated species, especially those with sensitive life history traits, are at high risk for the adverse effects of genetic drift and habitat degradation by non-native wildlife. Here, we study the population genetic diversity, structure, and stability of a classic “island giant” (Xantusia riversiana, the Island Night Lizard) on San Clemente Island, California following the removal of feral goats. Using DNA microsatellites, we found that this population is reasonably genetically robust despite historical grazing, with similar effective population sizes and genetic diversity metrics across all sampling locations irrespective of habitat type and degree of degradation. However, we also found strong site-specific patterns of genetic variation and low genetic diversity compared to mainland congeners, warranting continued special management as an island endemic. We identify both high and low elevation areas that remain valuable repositories of genetic diversity and provide a case study for other low-dispersal coastal organisms in the face of future climate change.

Studies in ecological and community genetics have advanced our understanding of the role of intraspecific diversity in structuring communities and ecosystems. However, in near-shore marine communities, these studies have mostly been restricted to seagrasses, marsh plants, and oysters. Yet, macroalgae are critically important ecosystem engineers in these communities. Greater intraspecific diversity in a macroalgal ecosystem engineer should result in higher primary and secondary production and community resilience. The paucity of studies investigating the consequences of macroalgal intraspecific genetic variation might be due, in part, to the complexity of macroalgal life cycles. The majority of macroalgae have seemingly subtle, but in actuality, profoundly different life cycles than the more typical animal and angiosperm models. Here, we develop a novel genetic diversity metric, PHD , that incorporates the ratio of gametophytic to sporophytic thalli in natural populations. This metric scales from 0 to 1 like many common genetic diversity metrics, such as genotypic richness, enabling comparisons among metrics. We discuss PHD and examples from the literature, with specific reference to the widespread, red seaweed Agarophyton vermiculophyllum. We also discuss a sex diversity metric, PFM , which also scales from 0 to 1, but fewer studies have identified males and females in natural populations. Nevertheless, by incorporating these novel metrics into the repertoire of diversity metrics, we can explore the role of genetic diversity in community and ecosystem dynamics with an emphasis on the unique biology of many macroalgae, as well as other haplodiplontic taxa such as ferns, foraminiferans, and some fungi.

The South Carolina Department of Natural Resources began a stock enhancement research program for red drum, Sciaenops ocellatus, as a possible management strategy for augmenting the availability of juveniles for recreational harvest in South Carolina estuaries. Between 1999 and 2011, approximately 6 million juveniles and 260 million larvae were stocked into the Charleston Harbor (CH) estuary, and proportions of stocked fish were found through standardized sampling as high as 49.6% within a subadult year‐class and up to 12% within the spatially separate spawning population. This study evaluated the genetic influences of stocking on the spawning population, using microsatellite loci, and examined any changes in genetic diversity metrics over the course of the stock enhancement program. Percent contribution of stocked fish among subadult and adult collections was compared against measures of genetic diversity. No statistically significant correlations were found among genetic diversity metrics, suggesting that responsible stocking of red drum as small juveniles has not altered the genetic diversity of adults spawning offshore the CH. Life‐history characteristics likely play a large role in mitigating changes in genetic diversity, despite high contributions of stocked fish in some years, because red drum exhibit a long adult life span and benefit from overlapping generations.

Whether natural or man‐made, landscape features often influence the patterns of genetic variation within a species and can have important conservation implications. This is especially true for Brook Trout Salvelinus fontinalis, which are typically restricted to high‐quality headwater streams. In this study, we characterized the patterns of genetic partitioning and diversity among Brook Trout populations in the Laurel Hill of southwestern Pennsylvania with respect to landscape features and potential barriers to migration. In total, 354 wild Brook Trout samples collected across 10 streams were analyzed using 12 microsatellite loci. Our results showed a wide range of genetic diversity (allelic richness AR = 3.404–7.124; expected heterozygosity He = 0.432–0.727) and effective population size estimates (Ne = 13.5–1,106.6) and indicated that some sites contained small, low‐diversity populations of Brook Trout. Three populations were located upstream of reservoirs; however, our results did not show significant differences in the genetic diversity metrics between upstream and downstream populations. Although isolation by distance could be a factor, the patterns of genetic differentiation revealed minimal contemporary gene flow between watersheds and among most streams. Overall, our results highlight the need for continued population monitoring and habitat restoration for Brook Trout populations in southwestern Pennsylvania.

To relate base populations in genomic evaluations, the theory of metafounders has been developed during the last decade. From this theory, relationships within and between populations can be estimated with the gamma parameter. Recently, it has been demonstrated that several genetic diversity metrics such as fixation index (Fst), Nei’s minimum genetic distance (D), and population inbreeding coefficients based on homozygosity (Fhom), drift (Fdrift) or average heterozygosity (Fb) can be estimated based on this gamma matrix. However, how these derived formulas behave in real populations, compared to their traditionally estimated counterparts, has not yet been studied. Therefore, the objective of this study is to compare traditional and gamma-based genetic diversity parameters. For this purpose, we will apply formulas found in Table 1 to different cattle populations. Formulas derived from the gamma parameter assume allelic frequencies of 0.5 in the base population. Unless the formulas are more robust to changes in allelic frequencies than expected, we should probably expect different results between the traditional and novel metrics based on gamma.

Tidal marshes at the Paul S. Sarbanes Ecosystem Restoration Project at Poplar Island (PI) are part of a large‐scale restoration project to replace lost island habitat in Chesapeake Bay, United States. However, observations of Spartina alterniflora die‐back prompted questions about the impact on genetic diversity and resilience of restored versus natural marshes, leading to an investigation of genetic diversity and population structure. Transects were established across three distinct restored marshes with different ages and histories of die‐back and across two local, non‐restored native marshes. Plants were genotyped at eight microsatellite markers to examine metrics of genetic diversity, population structure, and clonality. Allelic richness but not heterozygosity was higher in restored marshes compared to reference marshes, which showed significantly higher clonality and spatial genetic autocorrelation. Restored marsh areas experiencing die‐back had slightly lower multilocus diversity indices than non‐die back areas in two third cases, but not a third comparison. Significant genetic differentiation was observed between the native and restored marshes (mean GST approximately 0.06), which reflects the approximately 100 km distance between native marshes and restored seed source in New Jersey. Overall, die‐back in restored marshes did not substantially affect genetic diversity or composition, but substantial differences in diversity were observed between restored and native marshes. Reduced clonal diversity in mature, native marshes may be a function of their greater age, as has been reported elsewhere. Future monitoring of neutral genetic diversity in PI marshes will be useful for understanding longer‐term patterns of genetic change and diversity in planted, restored marshes.

The common bottlenose dolphin (Tursiops truncatus) is a key marine mammal species in the Gulf of Mexico, playing an essential role as a top predator. This study investigates the genetic diversity and population structure of bottlenose dolphins stranded in the Mississippi Sound from 2010 to 2021. Tissue samples (muscle, liver, lung, kidney, and brain) were collected from 511 stranded dolphins, and mitochondrial DNAs (mtDNA) were extracted for analysis. A total of 417 samples were successfully amplified and sequenced using high throughput sequencing, yielding 386 complete mitogenomes. Genetic diversity metrics, such as nucleotide and haplotype diversity, were calculated, and population structure was inferred for both mitochondrial control region (mtCR) and whole mitogenome sequences. Using the whole mitogenome, the study identified four genetically distinct populations within the Mississippi Sound, demonstrating regional variation in dolphin populations. Notably, two stranded individuals likely originated from populations outside the sampled area. The use of whole mitogenomes allowed for improved resolution of genetic diversity and population differentiation compared to previous studies using partial mtDNA sequences. These findings enhance our understanding of bottlenose dolphin population structure in the region and underscore the value of stranded animals for population genetic studies.

AimThe impacts of Holocene fires on the genetic architecture of fire‐intolerant species have largely been overlooked. Here, we investigate the relative impacts of the last glacial climate versus Holocene fires on the genetic diversity of two co‐occurring, fire‐intolerant conifers using a comparative population genetic study.LocationThe palaeoendemic plant‐rich montane rain forests and alpine coniferous heath of Tasmania, Australia.MethodsThe Tasmanian endemic conifersAthrotaxis cupressoidesD. Don (461 samples from 20 populations) andDiselma archeriHook.f. (576 samples from 23 populations, 16 of which were for sites sampled forA. cupressoides), were genotyped using eight and nineESTnuclear microsatellites respectively. Genetic diversity and structure was compared between the two species and the factors underlying genetic patterns in both species were investigated by examining isolation by distance, correlations with Last Glacial Maximum modelled distributions and the fossil record, and a fire history index of the sampled stands.ResultsThe range‐wide genetic structure of the two species was similar (Fst = 0.09 andF’st = 0.21 forA. cupressoidesversusD. archeri;Fst = 0.06 andF’st = 0.24), and there were significant correlations between species for population‐based expected heterozygosity, allelic richness, private allelic richness and pairwise genetic divergences. Furthermore, genetic diversity metrics decreased significantly with an index of fire history. Given fossil evidence and modelling evidence that both species occurred near their current ranges during the last glaciation and a lack of evidence for isolation by distance in either species, the plausible explanation for the patterns of diversity is genetic decline resulting from repeated Holocene fires.Main conclusionsOur study suggests that fire can have substantial impacts on genetic structure and diversity of plant species, particularly those without fire‐tolerant traits, and that any increases in fire resulting from climate change may impose substantial threats to such species. In Tasmania, the observed increase in dry lightning in recent years, combined with periods of abnormally dry conditions, may therefore further degrade the range and genetic diversity of fire‐intolerant palaeoendemic species.

American Aberdeen (AD) cattle in the USA descend from an Aberdeen Angus herd originally brought to the Trangie Agricultural Research Centre, New South Wales, AUS. Although put under specific selection pressure for yearling growth rate, AD remain genomically uncharacterized. The objective was to characterize the genetic diversity and structure of purebred and crossbred AD cattle relative to seven common USA beef breeds using available whole-genome SNP data. A total of 1140 animals consisting of 404 purebred (n = 8 types) and 736 admixed individuals (n = 10 types) was used. Genetic diversity metrics, an analysis of molecular variance, and a discriminant analysis of principal components were employed. When linkage disequilibrium was not accounted for, markers influenced basic diversity parameter estimates, especially for AD cattle. Even so, intrapopulation and interpopulation estimates separate AD cattle from other purebred types (e.g., Latter's pairwise FST ranged from 0.1129 to 0.2209), where AD cattle were less heterozygous and had lower allelic richness than other purebred types. The admixed AD-influenced cattle were intermediate to other admixed types for similar parameters. The diversity metrics separation and differences support strong artificial selection pressures during and after AD breed development, shaping the evolution of the breed and making them genomically distinct from similar breeds.

Seagrass meadows are some of the most productive marine plant ecosystems in the world, yet their loss continues on a global scale. Zostera marina, an ecologically important foundation species, reproduces both sexually and asexually, yielding different levels of genetic diversity throughout its range, which in turn can influence resistance to, and resilience from, environmental disturbances. Understanding the genetic structure and diversity of these populations, and how they fluctuate over space and time, will aid in the conservation and management of seagrasses in an environment where the effects of climate change are likely to be chronic. Using microsatellite data, we examined spatiotemporal genetic structure and genetic diversity of Z. marina over a 10 yr period at 2 sites in North Carolina (USA), the southern limit of its geographic range in the Western Atlantic. Both meadows were genetically diverse, with very little spatial genetic structure existing within and between sites, and relative temporal stability between decadal time points. Within-site kin structure was more pronounced in the earlier years, and allelic richness increased over time at both sites, suggesting an increase in sexual reproduction, potentially in response to thermal stress. Despite the genetic similarities between sites, life history strategies showed phenotypic plasticity, and several metrics of genetic diversity were associated with meadow health. These findings point to the adaptive potential of Z. marina and provide promising insight into how the species will perform as the effects of climate change continue to amplify over the next century.

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 532:111-122 (2015) - DOI: https://doi.org/10.3354/meps11355 The importance of genetic make-up in seagrass restoration: a case study of the seagrass Zostera noltei Marlene Jahnke1,*,**, Ilia Anna Serra2,**, Guillaume Bernard3, Gabriele Procaccini1 1Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy 2Dipartimento di Chimica e Tecnologie Chimiche, Università̀ della Calabria, 87036 Rende (CS), Italy 3GIPREB Syndicat Mixte, Cours Mirabeau, 13130 Berre-l’Etang, France *Corresponding author: marlene.jahnke@szn.it**These authors contributed equally to this work ABSTRACT: Seagrass meadows are among the most important coastal ecosystems. Their ongoing decline is of concern, and transplantations are carried out in many parts of the world to restore the ecosystem services seagrass meadows provide. Several studies have highlighted the importance of genetic diversity for transplantation success in seagrasses, but this is still rarely taken into account in transplantation trials. Here we assess a transplantation experiment of the seagrass Zostera noltei in one of the largest saline Mediterranean lagoons 4 yr after transplantations were carried out with low success rates. We compare genetic diversity values of a transplant site, 2 relict meadows and newly appeared patches in the lagoon to genetic diversity metrics measured before the transplantation experiment inside and outside the lagoon. We show that genotypic richness of the transplant site assessed 4 yr after the transplantation is very low. Moreover, the transplants are genetically distinct from the genetic stock in the lagoon, with low migration rates, low effective population size and signs of a recent population bottleneck. Relict meadows and newly appeared patches show, in contrast, signs of high levels of sexual reproduction and are connected via gene flow. The newly appeared patches likely did not originate from the transplantation. The lack of success of transplanted shoots could be due to an adaptation mismatch of the marine donor material to lagoon conditions or to low plasticity of the transplanted shoots. KEY WORDS: Zostera noltei · Microsatellites · Ecosystem recovery · Genetic diversity · Transplantation Full text in pdf format Supplementary material PreviousNextCite this article as: Jahnke M, Serra IA, Bernard G, Procaccini G (2015) The importance of genetic make-up in seagrass restoration: a case study of the seagrass Zostera noltei. Mar Ecol Prog Ser 532:111-122. https://doi.org/10.3354/meps11355 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 532. Online publication date: July 21, 2015 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2015 Inter-Research.