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opencc-zeroMay 2020View details →

Data from: Extreme seascape drives local recruitment and genetic divergence in brooding and spawning corals in remote northwest Australia

Management strategies designed to conserve coral reefs threatened by climate change need to incorporate knowledge of the spatial distribution of inter- and intra-specific genetic diversity. We characterised patterns of genetic diversity and connectivity using single nucleotide polymorphisms (SNPs) in two reef-building corals to explore the eco-evolutionary processes that sustain populations in northwest Australia. Our sampling focused on the unique reefs of the Kimberley; we collected the broadcast spawning coral Acropora aspera (n = 534) and the brooding coral Isopora brueggemanni (n = 612) across inter-archipelago (tens to hundreds of kilometres), inter-reef (kilometres to tens of kilometres) and within-reef (tens of metres to a few kilometres) scales. Initial analysis of A. aspera identified four highly divergent lineages that were co-occurring but morphologically similar. Subsequent population analyses focused on the most abundant and widespread lineage, Acropora asp-c. Although the overall level of geographic subdivision was greater in the brooder than in the spawner, fundamental similarities in patterns of genetic structure were evident. Most notably, limits to gene flow were observed at scales less than 35 kilometres. Further, we observed four discrete clusters and a semi-permeable barrier to dispersal that were geographically consistent between species. Finally, sites experiencing bigger tides were more connected to the metapopulation and had greater gene diversity than those experiencing smaller tides. Our data indicate that the inshore reefs of the Kimberley are genetically isolated from neighbouring oceanic bioregions, but occasional dispersal between inshore archipelagos is important for the redistribution of evolutionarily important genetic diversity. Additionally, these results suggest that networks of marine reserves that effectively protect reefs from local pressures should be spaced within a few tens of kilometres to conserve the existing patterns of demographic and genetic connectivity.

opencc-zeroOct 2021View details →

Seascape genetics of the Atlantic spotted dolphin (Stenella frontalis) based on mitochondrial DNA

The Atlantic spotted dolphin (Stenella frontalis) is endemic to tropical, subtropical, and warm temperate waters of the Atlantic Ocean. Throughout its distribution, both geographic distance and environmental variation may contribute to population structure of the species. In this study we follow a seascape genetics approach to investigate population differentiation of Atlantic spotted dolphins based on a large worldwide dataset and the relationship with marine environmental variables. The results revealed that the Atlantic spotted dolphin exhibits population genetic structure across its distribution based on mitochondrial DNA control region (mtDNA-CR) data. Analyses based on the contemporary landscape suggested, at both the individual and population-level, that the population genetic structure is consistent with the isolation-by-distance model. However, because geography and environmental matrices were correlated, and because in some, but not all analyses, we found a significant effect for the environment, we cannot rule out the addition contribution of environmental factors in structuring genetic variation. Future analyses based on nuclear data are needed to evaluate whether local processes, such as social structure and some level of philopatry within populations, may be contributing to the associations among genetic structure, geographic, and environmental distance.

publicOct 2021View details →

Seascape genetics of the Atlantic spotted dolphin (Stenella frontalis) based on mitochondrial DNA

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publicMay 2020View details →

Data from: Extreme seascape drives local recruitment and genetic divergence in brooding and spawning corals in remote northwest Australia

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opencc-zeroAug 2020View details →

Reconciling seascape genetics and fisheries science in three co-distributed flatfishes

Uncertainty hampers innovative mixed-fisheries management by the scales at which connectivity dynamics are relevant to management objectives. The spatial scale of sustainable stock management is species-specific and depends on ecology, life history and population connectivity. One valuable approach to understand these spatial scales is to determine to what extent population genetic structure correlates with the oceanographic environment. Here we compare the level of genetic connectivity in three co-distributed and commercially exploited demersal flatfish species living in the North East Atlantic Ocean. Population genetic structure was analysed based on 14, 14 and 10 neutral DNA microsatellite markers for turbot, brill and sole respectively. We then used redundancy analysis (RDA) to attribute the genetic variation to spatial (geographic location), temporal (sampling year) and oceanographic (water column characteristics) components.

opencc-zeroDec 2017View details →

Data from: Geographic isolation and larval dispersal shape seascape genetic patterns differently according to spatial scale

Genetic variation, as a basis of evolutionary change, allows species to adapt and persist in different climates and environments. Yet, a comprehensive assessment of the drivers of genetic variation at different spatial scales is still missing in marine ecosystems. Here, we investigated the influence of environment, geographic isolation, and larval dispersal on the variation in allele frequencies, using an extensive spatial sampling (47 locations) of the striped red mullet (Mullus surmuletus) in the Mediterranean Sea. Univariate multiple regressions were used to test the influence of environment (salinity and temperature), geographic isolation, and larval dispersal on Single Nucleotide Polymorphisms (SNPs) allele frequencies. We used Moran's Eigenvector Maps (db-MEMs) and Asymmetric Eigenvector Maps (AEMs) to decompose geographic and dispersal distances in predictors representing different spatial scales. We found that salinity and temperature had only a weak effect on the variation in allele frequencies. Our results revealed the predominance of geographic isolation to explain variation in allele frequencies at large spatial scale (> 1,000km) while larval dispersal was the major predictor at smaller spatial scale (< 1,000km). Our findings stress the importance of including spatial scales to understand the drivers of spatial genetic variation. We suggest that larval dispersal allows to maintain gene flows at small to intermediate scale, while at broad scale, genetic variation may be mostly shaped by adult mobility, demographic history or multi-generational stepping stone dispersal. These findings bring out important spatial scale considerations to account for in the design of a protected areas network that would efficiently enhance protection and persistence capacity of marine species.

opencc-zeroDec 2016View details →

Data from: Seascape genetics and biophysical connectivity modelling support conservation of the seagrass Zostera marina in the Skagerrak-Kattegat region of the eastern North Sea

Maintaining and enabling evolutionary processes within meta-populations is critical to resistance, resilience and adaptive potential. Knowledge about which populations act as sources or sinks, and the direction of gene flow, can help to focus conservation efforts more effectively and forecast how populations might respond to future anthropogenic and environmental pressures. As a foundation species and habitat provider, Zostera marina (eelgrass) is of critical importance to ecosystem functions including fisheries. Here we estimate connectivity of Z. marina in the Skagerrak-Kattegat region of the North Sea based on genetic and biophysical modelling. Genetic diversity, population structure and migration were analysed at 23 locations using 20 microsatellite loci and a suite of analytical approaches. Oceanographic connectivity was analysed using Lagrangian dispersal simulations based on contemporary and historical distribution data dating back to the late 19th century. Population clusters, barriers and networks of connectivity were found to be very similar based on either genetic or oceanographic analyses. A single-generation model of dispersal was not realistic, whereas multi-generation models that integrate stepping-stone dispersal and extant and historic distribution data were able to capture and model genetic connectivity patterns well. Passive rafting of flowering shoots along oceanographic currents is the main driver of gene flow at this spatial-temporal scale and extant genetic connectivity strongly reflects the "ghost of dispersal past" sensu Benzie 1999. The identification of distinct clusters, connectivity hotspots and areas where connectivity has become limited over the last century is critical information for spatial management, conservation and restoration of eelgrass.

opencc-zeroDec 2013View details →

Data from: Seascape continuity plays an important role in determining patterns of spatial genetic structure in a coral reef fish

Detecting patterns of spatial genetic structure (SGS) can help identify intrinsic and extrinsic barriers to gene flow within metapopulations. For marine organisms such as coral reef fishes, identifying these barriers is critical to predicting evolutionary dynamics and demarcating evolutionarily significant units for conservation. In this study, we adopted an alternative hypothesis-testing framework to identify the patterns and predictors of SGS in the Caribbean reef fish Elacatinus lori. First, genetic structure was estimated using nuclear microsatellites and mitochondrial cytochrome b sequences. Next, clustering and network analyses were applied to visualize patterns of SGS. Finally, logistic regressions and linear mixed models were used to identify the predictors of SGS. Both sets of markers revealed low global structure: mitochondrial ΦST = 0.12, microsatellite FST = 0.0056. However, there was high variability among pairwise estimates, ranging from no differentiation between sites on contiguous reef (ΦST = 0) to strong differentiation between sites separated by ocean expanses ≥ 20 km (maximum ΦST = 0.65). Genetic clustering and statistical analyses provided additional support for the hypothesis that seascape discontinuity, represented by oceanic breaks between patches of reef habitat, is a key predictor of SGS in E. lori. Notably, the estimated patterns and predictors of SGS were consistent between both sets of markers. Combined with previous studies of dispersal in E. lori, these results suggest that the interaction between seascape continuity and the dispersal kernel plays an important role in determining genetic connectivity within metapopulations.

opencc-zeroDec 2014View details →

Data from: Seascape genetics along environmental gradients in the Arabian Peninsula: insights from ddRAD sequencing of anemonefishes

Understanding the processes that shape patterns of genetic structure across space is a central aim of landscape genetics. However, it remains unclear how geographic features and environmental variables shape gene flow, particularly for marine species in large complex seascapes. Here, we evaluated the genomic composition of the two-band anemonefish Amphiprion bicinctus across its entire geographic range in the Red Sea and Gulf of Aden, as well as its close relative, Amphiprion omanensis endemic to the southern coast of Oman. Both the Red Sea and the Arabian Sea are complex and environmentally heterogeneous marine systems that provide an ideal scenario to address these questions. Our findings confirm the presence of two genetic clusters previously reported for A. bicinctus in the Red Sea. Genetic structure analyses suggest a complex seascape configuration, with evidence of both Isolation by Distance (IBD) and Isolation by Environment (IBE). In addition to IBD and IBE, genetic structure among sites was best explained when two barriers to gene flow were also accounted for. One of these coincides with a strong oligotrophic-eutrophic gradient at around 16-20˚N in the Red Sea. The other agrees with an historical bathymetric barrier at the straight of Bab al Mandab. Finally, these data support the presence of inter-specific hybrids at an intermediate suture zone at Socotra and indicate complex patterns of genomic admixture in the Gulf of Aden with evidence of introgression between species. Our findings highlight the power of recent genomic approaches to resolve subtle patterns of gene flow in marine seascapes.

opencc-zeroDec 2013View details →

Data from: Matching oceanography and genetics at the basin scale. Seascape connectivity of the Mediterranean shore crab in the Adriatic Sea

Investigating the interactions between the physical environment and early life history is crucial to understand the mechanisms that shape the genetic structure of marine populations. Here, we assessed the genetic differentiation in a species with larval dispersal, the Mediterranean shore crab (Carcinus aestuarii) in the Adriatic Sea (central Mediterranean), and we investigated the role of oceanic circulation in shaping population structure. To this end, we screened 11 polymorphic microsatellite loci from 431 individuals collected at eight different sites. We found a weak, yet significant, genetic structure into three major clusters: a northern Adriatic group, a central Adriatic group, and one group including samples from southern Adriatic and Ionian seas. Genetic analyses were compared, under a seascape genetics approach, with estimates of potential larval connectivity obtained with a coupled physical-biological model that integrates a water circulation model and a description of biological traits affecting dispersal. The cross-validation of the results of the two approaches supported the view that genetic differentiation reflects an oceanographic subdivision of the Adriatic Sea into three sub-basins, with circulation patterns allowing the exchange of larvae through permanent connections linking north Adriatic sites and ephemeral connections like those linking the central Adriatic with northern and southern locations.

opencc-zeroDec 2017View details →

Data from: Seascape habitat patchiness and hydrodynamics explain genetic structuring of kelp populations

Macroalgae underpin most temperate inshore ecosystems, but increasing macroalgal loss, fragmentation and range contractions are eroding connectivity among populations. Understanding loss, and predicting the likelihood of recovery, is dependent on knowledge of population connectivity and how it is mediated by variability in local seascapes. Although many studies of marine connectivity have focussed on influences of geographic distance on genetic structure, the contribution of intervening habitat is rarely considered. We tested the extent to which geographic separation, intervening suitable habitat (reef versus sand and open water) and local hydrodynamics (inferred from particle dispersal models) explained structuring of genetic variation at microsatellite loci in the habitat forming macroalga Lessonia corrugata. Genetic structuring was best explained by the availability of suitable intervening habitat (rocky reef) rather than by geographic separation, although biologically realistic estimates of dispersal probability also became important at smaller spatial scales. Our results indicate that ecological separation can be more influential than geographic distance on population genetic structuring, and this should be considered during the assessment of connectivity and gene flow in marine species.

opencc-zeroDec 2014View details →

Data from: Seascape drivers of Macrocystis pyrifera population genetic structure in the northeast Pacific

At small spatial and temporal scales, genetic differentiation is largely controlled by constraints on gene flow, while genetic diversity across a species' distribution is shaped on longer temporal and spatial scales. We assess the hypothesis that oceanographic transport and other seascape features explain different scales of genetic structure of giant kelp, Macrocystis pyrifera. We followed a hierarchical approach to perform a microsatellite-based analysis of genetic differentiation in Macrocystis across its distribution in the northeast Pacific. We used seascape genetic approaches to identify large-scale biogeographic population clusters and investigate whether they could be explained by oceanographic transport and other environmental drivers. We then modelled population genetic differentiation within clusters as a function of oceanographic transport and other environmental factors. Five geographic clusters were identified: Alaska/Canada, central California, continental Santa Barbara, California Channel Islands and mainland southern California/Baja California peninsula. The strongest break occurred between central and southern California, with mainland Santa Barbara sites forming a transition zone between the two. Breaks between clusters corresponded approximately to previously identified biogeographic breaks, but were not solely explained by oceanographic transport. An isolation-by-environment (IBE) pattern was observed where the northern and southern Channel Islands clustered together, but not with closer mainland sites, despite the greater distance between them. The strongest environmental association with this IBE pattern was observed with light extinction coefficient, which extends suitable habitat to deeper areas. Within clusters, we found support for previous results showing that oceanographic connectivity plays an important role in the population genetic structure of Macrocystis in the Northern hemisphere.

Figure 3 in Cryptic lineages, cryptic barriers: historical seascapes and oceanic fronts drive genetic diversity in supralittoral rockpool beetles (Coleoptera: Hydraenidae)

Figure 3. Haplotype networks for COI and wingless for Ochthebius (Ochthebius) quadricollis. Colours represent the main geographic areas indicated in the legend.

Figure 2. Calibrated phylogenetic tree obtained with BEAST v.1.10.4 in Cryptic lineages, cryptic barriers: historical seascapes and oceanic fronts drive genetic diversity in supralittoral rockpool beetles (Coleoptera: Hydraenidae)

Figure 2. Calibrated phylogenetic tree obtained with BEAST v.1.10.4 of Ochthebius with focus on subgenus Cobalius (purple shade) and quadricollis species group (green shade) (former subgenus 'Calobius'). Numbers at nodes represent posterior probabilities, and 95% highest posterior density are given in blue horizontal rectangles. Calibrations points used in analysis are specified by grey dots.

Figure 5 in Cryptic lineages, cryptic barriers: historical seascapes and oceanic fronts drive genetic diversity in supralittoral rockpool beetles (Coleoptera: Hydraenidae)

Figure 5. Haplotype networks for COI and wingless for Ochthebius (Cobalius) lejolisii. Colours represent the main geographic areas indicated in the legend.

Figure 1 in Cryptic lineages, cryptic barriers: historical seascapes and oceanic fronts drive genetic diversity in supralittoral rockpool beetles (Coleoptera: Hydraenidae)

Figure 1. Distribution of sampling localities 1-57 (as listed in Table 1) and main surface marine currents and potential geographic barriers to dispersal (inset top-right).

Figure 4 in Cryptic lineages, cryptic barriers: historical seascapes and oceanic fronts drive genetic diversity in supralittoral rockpool beetles (Coleoptera: Hydraenidae)

Figure 4. Haplotype networks for COI and wingless for Ochthebius (Cobalius) subinteger. Colours represent the main geographic areas indicated in the legend.