High Interannual Variability in Connectivity and Genetic Pool of a Temperate Clingfish Matches Oceanographic Transport Predictions

The contribution of nearshore oceanography to temporal variation in larval dispersal

Patterns of population connectivity shape ecological and evolutionary phenomena from population persistence to local adaptation and can inform conservation strategy. Connectivity patterns emerge from the interaction of individual behavior with a complex and heterogeneous environment. Despite ample observation that dispersal patterns vary through time, the extent to which variation in the physical environment can explain emergent connectivity variation is not clear. Empirical studies of its contribution promise to illuminate a potential source of variability that shapes the dynamics of natural populations. We leveraged simultaneous direct dispersal observations and oceanographic transport simulations of the clownfish Amphiprion clarkii in the Camotes Sea, Philippines, to assess the contribution of oceanographic variability to emergent variation in connectivity. We found that time-varying oceanographic simulations on both annual and monsoonal timescales partly explained the observed dispersal patterns, suggesting that temporal variation in oceanographic transport shapes connectivity variation on these timescales. However, interannual variation in observed mean dispersal distance was nearly 10 times the expected variation from biophysical simulations, revealing that additional biotic and abiotic factors contribute to interannual connectivity variation. Simulated dispersal kernels also predicted a smaller scale of dispersal than the observations, supporting the hypothesis that undocumented abiotic factors and behaviors such as swimming and navigation enhance the probability of successful dispersal away from, as opposed to retention near, natal sites. Our findings highlight the potential for coincident observations and biophysical simulations to test dispersal hypotheses and the influence of temporal variability on metapopulation persistence, local adaptation, and other population processes.

Indicators to assess temporal variability in marine connectivity processes: A semi-theoretical approach

Oceanographic connectivity in an effective network of protected areas is crucial for restoring and stabilising marine populations. However, temporal variability in connectivity is rarely considered as a criterion in designing and evaluating marine conservation planning. In this study, indicators were defined to characterise the temporal variability in occurrence, flux, and frequency of connectivity in a northwestern Mediterranean Sea area. Indicators were tested on semi-theoretically-estimated connections provided by the runs of a passive particle transport model in a climatological year and in three years between 2006-2020, showing large deviation from the climatological year. The indicators allowed comparing the temporal variability in connectivity of four zones, highlighted differences in connectivity due to their locations and the mesoscale hydrodynamics, and identified areas that require further investigation. The three indicators also showed that the temporal variability in connectivity was influenced by the duration and depth of particle transport, although no consistent pattern was observed in the indicator variations of the compared zones. Provided that specific objectives will be given when parameterising transport models (i.e., selection of focus species and time period), indicators of temporal variability in connectivity have potential to support spatial conservation planning, prioritise the protection of marine resources, and measure the effectiveness of Marine Protected Areas, in line with a long-term vision of ocean management.

Multidisciplinary estimates of connectivity and population structure suggest the use of multiple units for the conservation and management of meagre, Argyrosomus regius

Information on population structure and connectivity of targeted species is key for proper implementation of spatial conservation measures. We used a combination of genomics, biophysical modelling, and biotelemetry to infer the population structure and connectivity of Atlantic meagre, an important fisheries resource throughout its distribution. Genetic samples from previously identified Atlantic spawning locations (Gironde, Tejo, Guadalquivir, Banc d'Arguin) and two additional regions (Algarve and Senegal) were analysed using genome-wide SNP-genotyping and mitochondrial DNA analyses. Biophysical models were conducted to investigate larval dispersal and connectivity from the known Atlantic spawning locations. Additionally, thirteen fish were double-tagged with biotelemetry transmitters off the Algarve (Portugal) to assess movement patterns and connectivity of adult individuals. This multidisciplinary approach provided a robust overview of meagre population structure and connectivity in the Atlantic. Nuclear SNP-genotyping showed a clear differentiation between the European and African populations, with significant isolation of the few known Atlantic spawning sites. The limited level of connectivity between these subpopulations is potentially driven by adults, capable of wide-ranging movements and connecting sites 500 km apart, as evidenced by tagging studies, whilst larval dispersal inferred by modelling is much more limited (average of 52 km; 95% of connectivity events up to 174 km). Our results show sufficient evidence of population structure, particularly between Africa and Europe but also within Europe, for the meagre to be managed as separate stocks. Additionally, considering the low degree of larvae connectivity, the implementation of marine protected areas in key spawning sites could be crucial towards species sustainability.

Oceanographic connectivity explains the intra-specific diversity of mangrove forests at global scales

The distribution of mangrove intra-specific biodiversity can be structured by historical demographic processes that enhance or limit effective population sizes. Oceanographic connectivity (OC) may further structure intra-specific biodiversity by preserving or diluting the genetic signatures of historical changes. Despite its relevance for biogeography and evolution, the role of oceanographic connectivity in structuring the distribution of mangrove's genetic diversity has not been addressed at global scale. Here we ask whether connectivity mediated by ocean currents explains the intra-specific diversity of mangroves. A comprehensive dataset of population genetic differentiation was compiled from the literature. Multigenerational connectivity and population centrality indices were estimated with biophysical modeling coupled with network analyses. The variability explained in genetic differentiation was tested with competitive regression models built upon classical isolation-by-distance (IBD) models considering geographic distance. We show that oceanographic connectivity can explain the genetic differentiation of mangrove populations regardless of the species, region, and genetic marker (significant regression models in 95% of cases, with an average R-square of 0.44 ± 0.23 and Person's correlation of 0.65 ± 0.17), systematically improving IBD models. Centrality indices, providing information on important stepping-stone sites between biogeographic regions, were also important in explaining differentiation (R-square improvement of 0.06 ± 0.07, up to 0.42). We further show that ocean currents produce skewed dispersal kernels for mangroves, highlighting the role of rare long-distance dispersal events responsible for historical settlements. Overall, we demonstrate the role of oceanographic connectivity in structuring mangrove intra-specific diversity. Our findings are critical for mangroves' biogeography and evolution, but also for management strategies considering climate change and genetic biodiversity conservation.

Weak biodiversity connectivity in the European network of no-take marine protected areas

The need for international cooperation in marine resource management and conservation has been reflected in the increasing number of agreements aiming for effective and well-connected networks of Marine Protected Areas (MPAs). However, the extent to which individual MPAs are connected remains mostly unknown. Here, we use a biophysical model tuned with empirical data on species dispersal ecology to predict connectivity of a vast spectrum of biodiversity in the European network of marine reserves (i.e., no-take MPAs). Our results highlight the correlation between empirical propagule duration data and connectivity potential and show weak network connectivity and strong isolation for major ecological groups, resulting from the lack of direct connectivity corridors between reserves over vast regions. The particularly high isolation predicted for ecosystem structuring species (e.g., corals, sponges, macroalgae and seagrass) might potentially undermine biodiversity conservation efforts if local retention is insufficient and unmanaged populations are at risk. Isolation might also be problematic for populations' persistence in the light of climate change and expected species range shifts. Our findings provide novel insights for management directives, highlighting the location of regions requiring additional marine reserves to function as stepping-stone connectivity corridors.

Unravelling the taxonomy of an interstitial fish radiation: Three new species of Gouania (Teleostei: Gobiesocidae) from the Mediterranean Sea and redescriptions of G. willdenowi and G. pigra

The clingfish (Gobiesocidae) genus Gouania Nardo, 1833 is endemic to the Mediterranean Sea and inhabits, unlike any other vertebrate species in Europe, the harsh intertidal environment of gravel beaches. Following up on a previous phylogenetic study, we revise the diversity and taxonomy of this genus by analysing a comprehensive set of morphological (meristics, morphometrics, microcomputed tomography imaging), geographical and genetic (DNA-barcoding) data. We provide descriptions of three new species, G. adriatica sp. nov., G. orientalis sp. nov. and G. hofrichteri sp. nov., as well as redescriptions of G. willdenowi (Risso, 1810) and G. pigra (Nardo, 1827) and assign neotypes for the latter two species. In addition to elucidating the complex taxonomic situation of Gouania, we discuss the potential of this enigmatic clingfish genus for further ecological, evolutionary and biodiversity studies that might unravel even more diversity in this unique Mediterranean fish radiation.

Unraveling hierarchical genetic structure in a marine metapopulation: A comparison of three high-throughput genotyping approaches

Marine metapopulations often exhibit subtle population structure that can be difficult to detect. Given recent advances in high-throughput sequencing, an emerging question is whether various genotyping approaches, in concert with improved sampling designs, will substantially improve our understanding of genetic structure in the sea. To address this question, we explored hierarchical patterns of structure in the coral reef fish Elacatinus lori using a high-resolution approach with respect to both genetic and geographic sampling. Previously, we identified three putative E. lori populations within Belize using traditional genetic markers and sparse geographic sampling: barrier reef and Turneffe Atoll; Glover's Atoll; and Lighthouse Atoll. Here, we systematically sampled individuals at ~10 km intervals throughout these reefs (1,129 individuals from 35 sites) and sequenced all individuals at three sets of markers: 2,418 SNPs; 89 microsatellites; and 57 nonrepetitive nuclear loci. At broad spatial scales, the markers were consistent with each other and with previous findings. At finer spatial scales, there was new evidence of genetic substructure, but our three marker sets differed slightly in their ability to detect these patterns. Specifically, we found subtle structure between the barrier reef and Turneffe Atoll, with SNPs resolving this pattern most effectively. We also documented isolation by distance within the barrier reef. Sensitivity analyses revealed that the number of loci (and alleles) had a strong effect on the detection of structure for all three marker sets, particularly at small spatial scales. Taken together, these results illustrate empirically that high-throughput genotyping data can elucidate subtle genetic structure at previously-undetected scales in a dispersive marine fish.

Successful validation of a larval dispersal model using genetic parentage data

Larval dispersal is a critically important yet enigmatic process in marine ecology, evolution, and conservation. Determining the distance and direction that tiny larvae travel in the open ocean continues to be a challenge. Our current understanding of larval dispersal patterns at management-relevant scales is principally and separately informed by genetic parentage data and biological-oceanographic (biophysical) models. Parentage datasets provide clear evidence of individual larval dispersal events, but their findings are spatially and temporally limited. Biophysical models offer a more complete picture of dispersal patterns at regional scales but are of uncertain accuracy. Here, we develop statistical techniques that integrate these two important sources of information on larval dispersal. We then apply these methods to an extensive genetic parentage dataset to successfully validate a high-resolution biophysical model for the economically important reef fish species Plectropomus maculatus in the southern Great Barrier Reef. Our results demonstrate that biophysical models can provide accurate descriptions of larval dispersal at spatial and temporal scales that are relevant to management. They also show that genetic parentage datasets provide enough statistical power to exclude poor biophysical models. Biophysical models that included species-specific larval behaviour provided markedly better fits to the parentage data than assuming passive behaviour, but incorrect behavioural assumptions led to worse predictions than ignoring behaviour altogether. Our approach capitalises on the complementary strengths of genetic parentage datasets and high-resolution biophysical models to produce an accurate picture of larval dispersal patterns at regional scales. The results provide essential empirical support for the use of accurately parameterised biophysical larval dispersal models in marine spatial planning and management.

Our understanding of marine fish larva dispersal is currently limited by sparse data and unvalidated models; combining DNA parentage matches with an oceanographic model of fish larvae on Australia’s Great Barrier Reef allows the authors to ground-truth a vital tool for sustainably managing coral reef fisheries.

Drivers of Cape Verde archipelagic endemism in keyhole limpets

Oceanic archipelagos are the ideal setting for investigating processes that shape species assemblages. Focusing on keyhole limpets, genera Fissurella and Diodora from Cape Verde Islands, we used an integrative approach combining molecular phylogenetics with ocean transport simulations to infer species distribution patterns and analyse connectivity. Dispersal simulations, using pelagic larval duration and ocean currents as proxies, showed a reduced level of connectivity despite short distances between some of the islands. It is suggested that dispersal and persistence driven by patterns of oceanic circulation favouring self-recruitment played a primary role in explaining contemporary species distributions. Mitochondrial and nuclear data revealed the existence of eight Cape Verde endemic lineages, seven within Fissurella, distributed across the archipelago, and one within Diodora restricted to Boavista. The estimated origins for endemic Fissurella and Diodora were 10.2 and 6.7 MY, respectively. Between 9.5 and 4.5 MY, an intense period of volcanism in Boavista might have affected Diodora, preventing its diversification. Having originated earlier, Fissurella might have had more opportunities to disperse to other islands and speciate before those events. Bayesian analyses showed increased diversification rates in Fissurella possibly promoted by low sea levels during Plio-Pleistocene, which further explain differences in species richness between both genera.

Habitat continuity and stepping-stone oceanographic distances explain population genetic connectivity of the brown alga Cystoseira amentacea

Effective predictive and management approaches for species occurring in a metapopulation structure require good understanding of interpopulation connectivity. In this study, we ask whether population genetic structure of marine species with fragmented distributions can be predicted by stepping-stone oceanographic transport and habitat continuity, using as model an ecosystem-structuring brown alga, Cystoseira amentacea var. stricta. To answer this question, we analysed the genetic structure and estimated the connectivity of populations along discontinuous rocky habitat patches in southern Italy, using microsatellite markers at multiple scales. In addition, we modelled the effect of rocky habitat continuity and ocean circulation on gene flow by simulating Lagrangian particle dispersal based on ocean surface currents allowing multigenerational stepping-stone dynamics. Populations were highly differentiated, at scales from few metres up to thousands of kilometres. The best possible model fit to explain the genetic results combined current direction, rocky habitat extension and distance along the coast among rocky sites. We conclude that a combination of variable suitable habitat and oceanographic transport is a useful predictor of genetic structure. This relationship provides insight into the mechanisms of dispersal and the role of life-history traits. Our results highlight the importance of spatially explicit modelling of stepping-stone dynamics and oceanographic directional transport coupled with habitat suitability, to better describe and predict marine population structure and differentiation. This study also suggests the appropriate spatial scales for the conservation, restoration and management of species that are increasingly affected by habitat modifications.