Network analysis identifies weak and strong links in a metapopulation system

Assessing fine-scale pondscape connectivity with amphibian eyes: An integrative approach using genomic and capture-mark-recapture data

In the face of habitat loss, preserving functional connectivity is essential to maintain genetic diversity and the demographic dynamics required for the viability of biotic communities. This requires knowledge of the dispersal behaviour of target species, which can be modelled as kernels, or probability density functions of dispersal distances at increasing geographic distances. We present an integrative approach to investigate the relationships between genetic connectivity and demographic parameters in organisms with low vagility focusing on five syntopic pond-breeding amphibians. We genotyped 1056 individuals of two anuran and three urodele species (1732-3913 SNPs per species) from populations located in a landscape comprising 64 ponds to characterize fine-scale genetic structure in a comparative framework, and combined these genetic data with information obtained in a previous 2-year capture-mark-recapture (CMR) study. Specifically, we contrasted graphs reconstructed from genomic data with connectivity graphs based on dispersal kernels and demographic information obtained from CMR data from previous studies, and assessed the effects of population size, population density, geographical distances, inverse movement probabilities and the presence of habitat patches potentially functioning as stepping stones on genetic differentiation. Our results show a significant effect of local population sizes on patterns of genetic differentiation at small spatial scales. In addition, movement records and cluster-derived kernels provide robust inferences on most likely dispersal paths that are consistent with genomic inferences on genetic connectivity. The integration of genetic and CMR data holds great potential for understanding genetic connectivity at spatial scales relevant to individual organisms, with applications for the implementation of management actions at the landscape level.

Past climate-driven range shifts structuring intraspecific biodiversity levels of the giant kelp (Macrocystis pyrifera) at global scales

The paradigm of past climate-driven range shifts structuring the distribution of marine intraspecific biodiversity lacks replication in biological models exposed to comparable limiting conditions in independent regions. This may lead to confounding effects unlinked to climate drivers. We aim to fill in this gap by asking whether the global distribution of intraspecific biodiversity of giant kelp (Macrocystis pyrifera) is explained by past climate changes occurring across the two hemispheres. We compared the species' population genetic diversity and structure inferred with microsatellite markers, with range shifts and long-term refugial regions predicted with species distribution modelling (SDM) from the last glacial maximum (LGM) to the present. The broad antitropical distribution of Macrocystis pyrifera is composed by six significantly differentiated genetic groups, for which current genetic diversity levels match the expectations of past climate changes. Range shifts from the LGM to the present structured low latitude refugial regions where genetic relics with higher and unique diversity were found (particularly in the Channel Islands of California and in Peru), while post-glacial expansions following ~ 40% range contraction explained extensive regions with homogenous reduced diversity. The estimated effect of past climate-driven range shifts was comparable between hemispheres, largely demonstrating that the distribution of intraspecific marine biodiversity can be structured by comparable evolutionary forces across the global ocean. Additionally, the differentiation and endemicity of regional genetic groups, confers high conservation value to these localized intraspecific biodiversity hotspots of giant kelp forests.

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.

Larval Dispersal Modeling Reveals Low Connectivity among National Marine Protected Areas in the Yellow and East China Seas

Marine protected areas (MPAs) are vital for protecting biodiversity, maintaining ecosystem integrity, and tackling future climate change. The effectiveness of MPA networks relies on connectivity, yet connectivity assessments are often skipped in the planning process. Here we employed a multi-species biophysical model to examine the connectivity patterns formed among the 21 national MPAs in the Yellow and East China Seas. We simulated the potential larval dispersal of 14 oviparous species of five classes. Larvae of non-migratory species with pelagic larval duration (PLD) were assumed to be passive floating particles with no explicit vertical migration. A total of 217,000 particles were released according to spawning period, living depth, and species distribution, and they were assumed to move with currents during the PLD. Most larvae were dispersed around the MPAs (0–60 m isobaths) and consistent with the currents. Larval export increased with PLD and current velocity, but if PLD was too long, few larvae survived due to high daily mortality during pelagic dispersal. The overall connectivity pattern exhibited a north-to-south dispersal trend corresponding to coastal currents. Our results indicated that the national MPAs in the Yellow and East China Seas did not form a well-connected network and nearly 30% of them were isolated. These MPAs formed three distinct groups, one in the Yellow Sea ecoregion and two in the East China Sea ecoregion. Four MPAs (all in coastal Zhejiang) emerged as key nodes for ensuring multi-generational connectivity. Under the pressure of future climate change, high self-recruitment and low connectivity present significant challenges for building well-connected MPA networks. We suggest adding new protected areas as stepping stones for bioecological corridors. Focused protection of the Yellow Sea ecoregion could have a good effect on the southern part of the population recruitment downstream. Conservation management should be adjusted according to the life cycles and distributions of vulnerable species, as well as seasonal changes in coastal currents. This study provides a scientific basis for improving ecological connectivity and conservation effectiveness of MPAs in the Yellow and East China Seas.

Species assemblage networks identify regional connectivity pathways among hydrothermal vents in the Northwest Pacific

The distribution of species among spatially isolated habitat patches supports regional biodiversity and stability, so understanding the underlying processes and structure is a key target of conservation. Although multivariate statistics can infer the connectivity processes driving species distribution, such as dispersal and habitat suitability, they rarely explore the structure. Methods from graph theory, applied to distribution data, give insights into both connectivity pathways and processes by intuitively formatting the data as a network of habitat patches. We apply these methods to empirical data from the hydrothermal vent habitats of the Northwest Pacific. Hydrothermal vents are "oases" of biological productivity and endemicity on the seafloor that are imminently threatened by anthropogenic disturbances with unknown consequences to biodiversity. Here, we describe the structure of species assemblage networks at hydrothermal vents, how local and regional parameters affect their structure, and the implications for conservation. Two complementary networks were formed from an extensive species assemblage dataset: a similarity network of vent site nodes linked by weighted edges based on their pairwise assemblage similarity and a bipartite network of species nodes linked to vent site nodes at which they are present. Using these networks, we assessed the role of individual vent sites in maintaining network connectivity and identified biogeographic sub-regions. The three sub-regions and two outlying sites are separated by their spatial arrangement and local environmental filters. Both networks detected vent sites that play a disproportionately important role in regional pathways, while the bipartite network also identified key vent sites maintaining the distinct species assemblages of their sub-regions. These regional connectivity pathways provide insights into historical colonization routes, while sub-regional connectivity pathways are of value when selecting sites for conservation and/or estimating the multivent impacts from proposed deep-sea mining.

Applying novel connectivity networks to wood turtle populations to provide comprehensive conservation management strategies for species at risk

Genetic diversity within and among populations is frequently used in prioritization processes to rank populations based on their vulnerability or distinctiveness, however, connectivity and gene flow are rarely considered within these frameworks. Using a wood turtle (Glyptemys insculpta) population graph, we introduce BRIDES as a new tool to evaluate populations for conservation purpose without focusing solely on individual nodes. BRIDES characterizes different types of shortest paths among the nodes of a subgraph and compares the shortest paths among the same nodes in a complete network. The main objectives of this study were to (1) introduce a BRIDES selection process to assist conservation biologists in the prioritization of populations, and (2) use different centrality indices and node removal statistics to compare BRIDES results and assess gene flow among wood turtle populations. We constructed six population subgraphs and used a stepwise selection algorithm to choose the optimal number of additional nodes, representing different populations, required to maximize network connectivity under different weighting schemes. Our results demonstrate the robustness of the BRIDES selection process for a given scenario, while inconsistencies were observed among node-based metrics. Results showed repeated selection of certain wood turtle populations, which could have not been predicted following only genetic diversity and distinctiveness estimation, node-based metrics and node removal analysis. Contrary to centrality measures focusing on static networks, BRIDES allowed for the analysis of evolving networks. To our knowledge, this study is the first to apply graph theory for turtle conservation genetics. We show that population graphs can reveal complex gene flow dynamics and population resiliency to local extinction. As such, BRIDES offers an interesting complement to node-based metrics and node removal to better understand the global processes at play when addressing population prioritization frameworks.

Environment predicts seagrass genotype, phenotype, and associated biodiversity in a temperate ecosystem

Coastal vegetative ecosystems are among the most threatened in the world, facing multiple anthropogenic stressors. A good example of this is seagrass, which supports carbon capture, coastal stabilization, and biodiversity, but is declining globally at an alarming rate. To understand the causes and consequences of changes to these ecosystems, we need to determine the linkages between different biotic and abiotic components. We used data on the seagrass, Zostera marina, collected by citizen scientists across 300 km of the south coast of the United Kingdom as a case study. We assembled data on seagrass genotype, phenotype, infauna, and associated bathymetry, light, sea surface temperature, and wave and current energy to test hypotheses on the distribution and diversity of this temperate sub-tidal ecosystem. We found spatial structure in population genetics, evident through local assortment of genotypes and isolation by distance across a broader geographic scale. By integrating our molecular data with information on seagrass phenotype and infauna, we demonstrate that these ecosystem components are primarily linked indirectly through the effects of shared environmental factors. It is unusual to examine genotypic, phenotypic, and environmental data in a single study, but this approach can inform both conservation and restoration of seagrass, as well as giving new insights into a widespread and important ecosystem.

High gene flow in the silverlip pearl oyster Pinctada maxima between inshore and offshore sites near Eighty Mile Beach in Western Australia

An understanding of stock recruitment dynamics in fisheries is fundamental to successful management. Pinctada maxima is a bivalve mollusc widely distributed throughout the Indo-Pacific and is the main species targeted for cultured pearl and pearl shell production in Australia. Pearl production in Australia relies heavily on wild-caught individuals, the majority of which come from the Eighty Mile Beach region near Broome in Western Australia. In this study, we used a genotyping by sequencing approach to explore fine-scale patterns of genetic connectivity among inshore shallow and offshore deep populations of P. maxima near Eighty Mile Beach. Our results revealed high-levels of gene flow among inshore and offshore sites and no differences in genetic diversity between depths. Global estimates of genetic differentiation were low (F ST = 0.006) but significantly different from zero, and pairwise estimates of genetic differentiation among sites were significant in only 3% of comparisons. Moreover, Bayesian clustering detected no separation of inshore and offshore sample sites, and instead showed all samples to be admixed among sites, locations and depths. Despite an absence of any clear spatial clustering among sites, we identified a significant pattern of isolation by distance. In a dynamic environment like Eighty Mile Beach, genetic structure can change from year-to-year and successive dispersal and recruitment events over generations likely act to homogenize the population. Although we cannot rule out the null hypothesis of panmixia, our data indicate high levels of dispersal and connectivity among inshore and offshore fishing grounds.

Assessing the influence of the amount of reachable habitat on genetic structure using landscape and genetic graphs

Genetic structure, i.e. intra-population genetic diversity and inter-population genetic differentiation, is influenced by the amount and spatial configuration of habitat. Measuring the amount of reachable habitat (ARH) makes it possible to describe habitat patterns by considering intra-patch and inter-patch connectivity, dispersal capacities and matrix resistance. Complementary ARH metrics computed under various resistance scenarios are expected to reflect both drift and gene flow influence on genetic structure. Using an empirical genetic dataset concerning the large marsh grasshopper (Stethophyma grossum), we tested whether ARH metrics are good predictors of genetic structure. We further investigated (i) how the components of the ARH influence genetic structure and (ii) which resistance scenario best explains these relationships. We computed local genetic diversity and genetic differentiation indices in genetic graphs, and ARH metrics in the unified and flexible framework offered by landscape graphs, and we tested the relationships between these variables. ARH metrics were relevant predictors of the two components of genetic structure, providing an advantage over commonly used habitat metrics. Although allelic richness was significantly explained by three complementary ARH metrics in the best PLS regression model, private allelic richness and MIW indices were essentially related with the ARH measured outside the focal patch. Considering several matrix resistance scenarios was also key for explaining the different genetic responses. We thus call for further use of ARH metrics in landscape genetics to explain the influence of habitat patterns on the different components of genetic structure.

Resilience of seagrass populations to thermal stress does not reflect regional differences in ocean climate

The prevalence of local adaptation and phenotypic plasticity among populations is critical to accurately predicting when and where climate change impacts will occur. Currently, comparisons of thermal performance between populations are untested for most marine species or overlooked by models predicting the thermal sensitivity of species to extirpation. Here we compared the ecological response and recovery of seagrass populations (Posidonia oceanica) to thermal stress throughout a year-long translocation experiment across a 2800-km gradient in ocean climate. Transplants in central and warm-edge locations experienced temperatures > 29°C, representing thermal anomalies > 5°C above long-term maxima for cool-edge populations, 1.5°C for central and < 1°C for warm-edge populations. Cool-edge, central and warm-edge populations differed in thermal performance when grown under common conditions, but patterns contrasted with expectations based on thermal geography. Cool-edge populations did not differ from warm-edge populations under common conditions and performed significantly better than central populations in growth and survival. Our findings reveal that thermal performance does not necessarily reflect the thermal geography of a species. We demonstrate that warm-edge populations can be less sensitive to thermal stress than cooler, central populations suggesting that Mediterranean seagrasses have greater resilience to warming than current paradigms suggest.

Network topology and patch connectivity affect dynamics in experimental and model metapopulations

Biological populations are rarely isolated in space and instead interact with others via dispersal in metapopulations. Theory predicts that network connectivity patterns can have critical effects on network robustness, as certain topologies, such as scale-free networks, are more tolerant to disturbances than other patterns. However, at present, experimental evidence of how these topologies affect population dynamics in a metapopulation framework is lacking. We used experimental metapopulations of the aquatic protist Paramecium tetraurelia to determine how network topology influences occupation patterns. We created metapopulations engineered to be comparable in linkage density, but differing in their degree distribution. We compared random networks to scale-free networks by evaluating local population occupancy and abundance throughout 18-30 protist generations. In parallel, we used simulations to explore differences in patch occupation patterns among topologies. Our experimental results highlighted the importance of the balance between dispersal and extinction in the interaction with spatial network topology. Under low dispersal conditions, random metapopulations of P. tetraurelia reached higher abundance and higher occupancy (proportion of occupied patches) compared to scale-free systems in both experimental and simulated systems. Under high dispersal conditions, we did not detect differences between types of metapopulations. Increasing patch degree (i.e. number of connections per patch) reduced the probability of extinction of local populations in both types of networks. We suggest the interaction between colonization/extinction rates and network topology alters the likelihood of rescue effects which results in differential patterns of occupancy and abundance in metapopulations.

Dispersal behaviour and riverine network connectivity shape the genetic diversity of freshwater amphipod metapopulations

Theory predicts that the distribution of genetic diversity in a landscape is strongly dependent on the connectivity of the metapopulation and the dispersal of individuals between patches. However, the influence of explicit spatial configurations such as dendritic landscapes on the genetic diversity of metapopulations is still understudied, and theoretical corroborations of empirical patterns are largely lacking. Here, we used microsatellite data and stochastic simulations of two metapopulations of freshwater amphipods in a 28,000 km² riverine network to study the influence of spatial connectivity and dispersal strategies on the spatial distribution of their genetic diversity. We found a significant imprint of the effects of riverine network connectivity on the local and global genetic diversity of both amphipod species. Data from 95 sites showed that allelic richness significantly increased towards more central nodes of the network. This was also seen for observed heterozygosity, yet not for expected heterozygosity. Genetic differentiation increased with instream distance. In simulation models, depending on the mutational model assumed, upstream movement probability and dispersal rate, respectively, emerged as key factors explaining the empirically observed distribution of local genetic diversity and genetic differentiation. Surprisingly, the role of site‐specific carrying capacities, for example by assuming a direct dependency of population size on local river size, was less clear cut: while our best fitting model scenario included this feature, over all simulations, scaling of carrying capacities did not increase data‐model fit. This highlights the importance of dispersal behaviour along spatial networks in shaping population genetic diversity.

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.

No leading-edge effect in North Atlantic harbor porpoises: Evolutionary and conservation implications

Understanding species responses to past environmental changes can help forecast how they will cope with ongoing climate changes. Harbor porpoises are widely distributed in the North Atlantic and were deeply impacted by the Pleistocene changes with the split of three subspecies. Despite major impacts of fisheries on natural populations, little is known about population connectivity and dispersal, how they reacted to the Pleistocene changes, and how they will evolve in the future. Here, we used phylogenetics, population genetics, and predictive habitat modeling to investigate population structure and phylogeographic history of the North Atlantic porpoises. A total of 925 porpoises were characterized at 10 microsatellite loci and one quarter of the mitogenome (mtDNA). A highly divergent mtDNA lineage was uncovered in one porpoise off Western Greenland, suggesting that a cryptic group may occur and could belong to a recently discovered mesopelagic ecotype off Greenland. Aside from it and the southern subspecies, spatial genetic variation showed that porpoises from both sides of the North Atlantic form a continuous system belonging to the same subspecies (Phocoena phocoena phocoena). Yet, we identified important departures from random mating and restricted dispersal forming a highly significant isolation by distance (IBD) at both mtDNA and nuclear markers. A ten times stronger IBD at mtDNA compared with nuclear loci supported previous evidence of female philopatry. Together with the lack of spatial trends in genetic diversity, this IBD suggests that migration-drift equilibrium has been reached, erasing any genetic signal of a leading-edge effect that accompanied the predicted recolonization of the northern habitats freed from Pleistocene ice. These results illuminate the processes shaping porpoise population structure and provide a framework for designing conservation strategies and forecasting future population evolution.

Analysing landscape effects on dispersal networks and gene flow with genetic graphs

Graph-theoretic approaches have relevant applications in landscape genetic analyses. When species form populations in discrete habitat patches, genetic graphs can be used (a) to identify direct dispersal paths followed by propagules or (b) to quantify landscape effects on multi-generational gene flow. However, the influence of their construction parameters remains to be explored. Using a simulation approach, we constructed genetic graphs using several pruning methods (geographical distance thresholds, topological constraints, statistical inference) and genetic distances to weight graph links (F_ST , D_PS , Euclidean genetic distances). We then compared the capacity of these different graphs to (a) identify the precise topology of the dispersal network and (b) to infer landscape resistance to gene flow from the relationship between cost-distances and genetic distances. Although not always clear-cut, our results showed that methods based on geographical distance thresholds seem to better identify dispersal networks in most cases. More interestingly, our study demonstrates that a sub-selection of pairwise distances through graph pruning (thereby reducing the number of data points) can counter-intuitively lead to improved inferences of landscape effects on dispersal. Finally, we showed that genetic distances such as the D_PS or Euclidean genetic distances should be preferred over the F_ST for landscape effect inference as they respond faster to landscape changes.

Dynamic spatio-temporal patterns of metapopulation occupancy in patchy habitats

Spatio-temporal dynamics in habitat suitability and connectivity among mosaics of heterogeneous wetlands are critical for biological diversity and species persistence in aquatic patchy landscapes. Despite the recognized importance of stochastic hydroclimatic forcing in driving wetlandscape hydrological dynamics, linking such effects to emergent dynamics of metapopulation poses significant challenges. To fill this gap, we propose here a dynamic stochastic patch occupancy model (SPOM), which links parsimonious hydrological and ecological models to simulate spatio-temporal patterns in species occupancy in wetlandscapes. Our work aims to place ecological studies of patchy habitats into a proper hydrologic and climatic framework to improve the knowledge about metapopulation shifts in response to climate-driven changes in wetlandscapes. We applied the dynamic version of the SPOM (D-SPOM) framework in two wetlandscapes in the US with contrasting landscape and climate properties. Our results illustrate that explicit consideration of the temporal dimension proposed in the D-SPOM is important to interpret local- and landscape-scale patterns of habitat suitability and metapopulation occupancy. Our analyses show that spatio-temporal dynamics of patch suitability and accessibility, driven by the stochasticity in hydroclimatic forcing, influence metapopulation occupancy and the topological metrics of the emergent wetlandscape dispersal network. D-SPOM simulations also reveal that the extinction risk in dynamic wetlandscapes is exacerbated by extended dry periods when suitable habitat decreases, hence limiting successful patch colonization and exacerbating metapopulation extinction risks. The proposed framework is not restricted only to wetland studies but could also be applied to examine metapopulation dynamics in other types of patchy habitats subjected to stochastic external disturbances.

The demographic contributions of connectivity versus local dynamics to population growth of an endangered bird

Conservation and management increasingly focus on connectivity, because connectivity driven by variation in immigration rates across landscapes is thought to be crucial for maintaining local population and metapopulation persistence. Yet, efforts to quantify the relative role of immigration on population growth across the entire range of species and over time have been lacking. We assessed whether immigration limited local and range-wide population growth of the endangered snail kite Rostrhamus sociabilis in Florida, USA, over 18 years using multi-state, reverse-time modelling that accounts for imperfect detection of individuals and unobservable states. Demographic contributions of immigration varied depending on the dynamics and geographic position of the local populations, were scale-dependent and changed over time. By comparing the relative contributions of immigration versus local demography for periods of significant change in local abundance, we found empirical evidence for a disproportionately large role of immigration in facilitating population growth of a centrally located population-a connectivity 'hub'. The importance of connectivity changed depending of the spatial scale considered, such that immigration was a more important driver of population growth at small versus large spatial scales. Furthermore, the contribution of immigration was much greater during time periods when local population size was small, emphasizing abundance-dependent rescue effects. Our findings suggest that efforts aimed at improving local breeding habitat will likely be most effective at increasing snail kite population growth. More broadly, our results provide much needed information on the role of connectivity for population growth, suggesting that connectivity conservation may have the greatest benefits when efforts focus on centrally located habitat patches and small populations. Furthermore, our results highlight that connectivity is highly dynamic over time and that interpreting the effects of connectivity at local scales may not transfer to region-wide dynamics.

Hypomethylation of the aquatic invasive plant, Ludwigia grandiflora subsp. hexapetala mimics the adaptive transition into the terrestrial morphotype

Ongoing global changes affect ecosystems and open up new opportunities for biological invasion. The ability of invasive species to rapidly adapt to new environments represents a relevant model for studying short-term adaptation mechanisms. The aquatic invasive plant, Ludwigia grandiflora subsp. hexapetala, is classified as harmful in European rivers. In French wet meadows, this species has shown a rapid transition from aquatic to terrestrial environments with emergence of two distinct morphotypes in 5 years. To understand the heritable mechanisms involved in adjustment to such a new environment, we investigate both genetic and epigenetic as possible sources of flexibility involved in this fast terrestrial transition. We found a low overall genetic differentiation between the two morphotypes arguing against the possibility that terrestrial morphotype emerged from a new adaptive genetic capacity. Artificial hypomethylation was induced on both morphotypes to assess the epigenetic hypothesis. We analyzed global DNA methylation, morphological changes, phytohormones and metabolite profiles of both morphotype responses in both aquatic and terrestrial conditions in shoot and root tissues. Hypomethylation significantly affected morphological variables, phytohormone levels and the amount of some metabolites. The effects of hypomethylation depended on morphotypes, conditions and plant tissues, which highlighted differences among the morphotypes and their plasticity. Using a correlative integrative approach, we showed that hypomethylation of the aquatic morphotype mimicked the characteristics of the terrestrial morphotype. Our data suggest that DNA methylation rather than a new adaptive genetic capacity is playing a key role in L. grandiflora subsp. hexapetala plasticity during its rapid aquatic to terrestrial transition.

Integrating genetics, biophysical, and demographic insights identifies critical sites for seagrass conservation

The eelgrass Zostera marina is an important foundation species of coastal areas in the Northern Hemisphere, but is continuing to decline, despite management actions. The development of new management tools is therefore urgent in order to prioritize limited resources for protecting meadows most vulnerable to local extinctions and identifying most valuable present and historic meadows to protect and restore, respectively. We assessed 377 eelgrass meadows along the complex coastlines of two fjord regions on the Swedish west coast-one is currently healthy and the other is substantially degraded. Shoot dispersal for all meadows was assessed with Lagrangian biophysical modeling (scale: 100-1,000 m) and used for barrier analysis and clustering; a subset (n = 22) was also assessed with population genetic methods (20 microsatellites) including diversity, structure, and network connectivity. Both approaches were in very good agreement, resulting in seven subpopulation groupings or management units (MUs). The MUs correspond to a spatial scale appropriate for coastal management of "waterbodies" used in the European Water Framework Directive. Adding demographic modeling based on the genetic and biophysical data as a third approach, we are able to assess past, present, and future metapopulation dynamics to identify especially vulnerable and valuable meadows. In a further application, we show how the biophysical approach, using eigenvalue perturbation theory (EPT) and distribution records from the 1980s, can be used to identify lost meadows where restoration would best benefit the present metapopulation. The combination of methods, presented here as a toolbox, allows the assessment of different temporal and spatial scales at the same time, as well as ranking of specific meadows according to key genetic, demographic and ecological metrics. It could be applied to any species or region, and we exemplify its versatility as a management guide for eelgrass along the Swedish west coast.

Incorporating the Connectivity Timescale in Metapopulation Partitioning

The often complex spatial patterns of propagule dispersal across a metapopulation present a challenge for species management, motivating efforts to represent the connectivity in simpler but meaningful ways. The reduction of complexity may be achieved by partitioning the metapopulation into groups of highly connected patches called "subpopulations." To have relevance for management, these subunits must be defined from ecological or evolutionary principles. The probabilities of dispersal-mediated propagule interchange between sites, commonly organized into a connectivity matrix, entail a timescale that is usually ignored in subpopulation analyses, limiting their utility and possibly leading to misinterpretation and wrong management decisions. Recognition of the essentially dynamical role played by metapopulation connectivity naturally leads to the incorporation of the generational timescale into the partitioning analysis. An algorithm is proposed to determine the subpopulations-both their cardinality and their composition-as a function of the generational timescale and of a limiting probability of connection, illustrated with a novel empirical estimate of mesopelagic connectivity. The proposed framework allows the unambiguous determination of the timescales corresponding to dispersal barriers and the identification of effective ecological units across the spectrum of management-relevant time horizons.

Scaling of species distribution explains the vast potential marine prokaryote diversity

Global ocean expeditions have provided minimum estimates of ocean’s prokaryote diversity, supported by apparent asymptotes in the number of prokaryotes with sampling effort, of about 40,000 species, representing <1% of the species cataloged in the Earth Microbiome Project, despite being the largest habitat in the biosphere. Here we demonstrate that the abundance of prokaryote OTUs follows a scaling that can be represented by a power-law distribution, and as a consequence, we demonstrate, mathematically and through simulations, that the asymptote of rarefaction curves is an apparent one, which is only reached with sample sizes approaching the entire ecosystem. We experimentally confirm these findings using exhaustive repeated sampling of a prokaryote community in the Red Sea and the exploration of global assessments of prokaryote diversity in the ocean. Our findings indicate that, far from having achieved a thorough sampling of prokaryote species abundance in the ocean, global expeditions provide just a start for this quest as the richness in the global ocean is much larger than estimated.

Network-based hierarchical population structure analysis for large genomic data sets

Analysis of population structure in natural populations using genetic data is a common practice in ecological and evolutionary studies. With large genomic data sets of populations now appearing more frequently across the taxonomic spectrum, it is becoming increasingly possible to reveal many hierarchical levels of structure, including fine-scale genetic clusters. To analyze these data sets, methods need to be appropriately suited to the challenges of extracting multilevel structure from whole-genome data. Here, we present a network-based approach for constructing population structure representations from genetic data. The use of community-detection algorithms from network theory generates a natural hierarchical perspective on the representation that the method produces. The method is computationally efficient, and it requires relatively few assumptions regarding the biological processes that underlie the data. We show the approach by analyzing population structure in the model plant species Arabidopsis thaliana and in human populations. These examples illustrate how network-based approaches for population structure analysis are well-suited to extracting valuable ecological and evolutionary information in the era of large genomic data sets.

Ecological networks: Pursuing the shortest path, however narrow and crooked

Representing data as networks cuts across all sub-disciplines in ecology and evolutionary biology. Besides providing a compact representation of the interconnections between agents, network analysis allows the identification of especially important nodes, according to various metrics that often rely on the calculation of the shortest paths connecting any two nodes. While the interpretation of a shortest paths is straightforward in binary, unweighted networks, whenever weights are reported, the calculation could yield unexpected results. We analyzed 129 studies of ecological networks published in the last decade that use shortest paths, and discovered a methodological inaccuracy related to the edge weights used to calculate shortest paths (and related centrality measures), particularly in interaction networks. Specifically, 49% of the studies do not report sufficient information on the calculation to allow their replication, and 61% of the studies on weighted networks may contain errors in how shortest paths are calculated. Using toy models and empirical ecological data, we show how to transform the data prior to calculation and illustrate the pitfalls that need to be avoided. We conclude by proposing a five-point check-list to foster best-practices in the calculation and reporting of centrality measures in ecology and evolution studies.

Coalescent Theory of Migration Network Motifs

Natural populations display a variety of spatial arrangements, each potentially with a distinctive impact on genetic diversity and genetic differentiation among subpopulations. Although the spatial arrangement of populations can lead to intricate migration networks, theoretical developments have focused mainly on a small subset of such networks, emphasizing the island-migration and stepping-stone models. In this study, we investigate all small network motifs: the set of all possible migration networks among populations subdivided into at most four subpopulations. For each motif, we use coalescent theory to derive expectations for three quantities that describe genetic variation: nucleotide diversity, F_ST, and half-time to equilibrium diversity. We describe the impact of network properties on these quantities, finding that motifs with a high mean node degree have the largest nucleotide diversity and the longest time to equilibrium, whereas motifs with low density have the largest F_ST. In addition, we show that the motifs whose pattern of variation is most strongly influenced by loss of a connection or a subpopulation are those that can be split easily into disconnected components. We illustrate our results using two example data sets—sky island birds of genus Sholicola and Indian tigers—identifying disturbance scenarios that produce the greatest reduction in genetic diversity; for tigers, we also compare the benefits of two assisted gene flow scenarios. Our results have consequences for understanding the effect of geography on genetic diversity, and they can assist in designing strategies to alter population migration networks toward maximizing genetic variation in the context of conservation of endangered species.

A network approach to identify bioregions in the distribution of Mediterranean amphipods associated with Posidonia oceanica meadows

Although amphipods are key components of the macro-fauna associated with Posidonia oceanica meadows, to date no studies focused on the structure and diversity of their assemblages across the whole Mediterranean Sea. Here, we applied a network approach based on modularity on a dataset mined from literature to identify biogeographic modules and to assess the biogeographic roles of associated localities. We also correlated the patterns evidenced with the biogeographic distribution of amphipod groups by means of a multivariate analysis. Modularity analysis highlighted four biogeographic modules bounded by the main Mediterranean biogeographic divides and evidenced a decrease in species diversity along a NW-SE gradient. Assemblages associated with Central-Western Mediterranean and, to a lesser extent, Tunisian modules showed the highest species richness and were identified as hubs, characterized by species with regional distributions that behave as source in a biogeographic context. The paleogeographic history of the host seagrass and the ecology of associated amphipods, both suggest the joint effect of species persistence and post-Last Glacial Maximum expansion in explaining the pattern of amphipod distribution in the Mediterranean Sea.

Evaluating the effects of landscape structure on the recovery of an invasive vertebrate after population control

CONTEXT

Effective landscape control of invasive species is context-dependent due to the interplay between the landscape structure, local population dynamics, and metapopulation processes. We use a modelling approach incorporating these three elements to explore the drivers of recovery of populations of invasive species after control.

OBJECTIVES

We aim to improve our understanding of the factors influencing the landscape-level control of invasive species.

METHODS

We focus on the case study of invasive brushtail possum (Trichosurus vulpecula) control in New Zealand. We assess how 13 covariates describing the landscape, patch, and population features influence the time of population recovery to a management density threshold of two possums/ha. We demonstrate the effects of those covariates on population recovery under three scenarios of population growth: logistic growth, strong Allee effects, and weak Allee effects.

RESULTS

Recovery times were rapid regardless of the simulated population dynamics (average recovery time < 2 years), although populations experiencing Allee effects took longer to recover than those growing logistically. Our results indicate that habitat availability and patch area play a key role in reducing times to recovery after control, and this relationship is consistent across the three simulated scenarios.

CONCLUSIONS

The control of invasive possum populations in patchy landscapes would benefit from a patch-level management approach (considering each patch as an independent management unit), whereas simple landscapes would be better controlled by taking a landscape-level view (the landscape as the management unit). Future research should test the predictions of our models with empirical data to refine control operations.

Dramatic loss of seagrass habitat under projected climate change in the Mediterranean Sea

Although climate warming is affecting most marine ecosystems, the Mediterranean is showing earlier impacts. Foundation seagrasses are already experiencing a well-documented regression in the Mediterranean which could be aggravated by climate change. Here, we forecast distributions of two seagrasses and contrast predicted loss with discrete regions identified on the basis of extant genetic diversity. Under the worst-case scenario, Posidonia oceanica might lose 75% of suitable habitat by 2050 and is at risk of functional extinction by 2100, whereas Cymodocea nodosa would lose only 46.5% in that scenario as losses are compensated with gained and stable areas in the Atlantic. Besides, we predict that erosion of present genetic diversity and vicariant processes can happen, as all Mediterranean genetic regions could decrease considerably in extension in future warming scenarios. The functional extinction of Posidonia oceanica would have important ecological impacts and may also lead to the release of the massive carbon stocks these ecosystems stored over millennia.

Phylogeography and demographic history of the Chagas disease vector Rhodnius nasutus (Hemiptera: Reduviidae) in the Brazilian Caatinga biome

BACKGROUND

Rhodnius nasutus, a vector of the etiological agent Trypanosoma cruzi, is one of the epidemiologically most relevant triatomine species of the Brazilian Caatinga, where it often colonizes rural peridomestic structures such as chicken coops and occasionally invades houses. Historical colonization and determination of its genetic diversity and population structure may provide new information towards the improvement of vector control in the region. In this paper we present thoughtful analyses considering the phylogeography and demographic history of R. nasutus in the Caatinga.

METHODOLOGY/PRINCIPAL FINDINGS

A total of 157 R. nasutus specimens were collected from Copernicia prunifera palm trees in eight geographic localities within the Brazilian Caatinga biome, sequenced for 595-bp fragment of the mitochondrial cytochrome b gene (cyt b) and genotyped for eight microsatellite loci. Sixteen haplotypes were detected in the cyt b sequences, two of which were shared among different localities. Molecular diversity indices exhibited low diversity levels and a haplotype network revealed low divergence among R. nasutus sequences, with two central haplotypes shared by five of the eight populations analyzed. The demographic model that better represented R. nasutus population dynamics was the exponential growth model. Results of the microsatellite data analyses indicated that the entire population is comprised of four highly differentiated groups, with no obvious contemporary geographic barriers that could explain the population substructure detected. A complex pattern of migration was observed, in which a western Caatinga population seems to be the source of emigrants to the eastern populations.

CONCLUSIONS/SIGNIFICANCE

R. nasutus that inhabit C. prunifera palms do not comprise a species complex. The species went through a population expansion at 12-10 ka, during the Holocene, which coincides with end of the largest dry season in South America. It colonized the Caatinga in a process that occurred from west to east in the region. R. nasutus is presently facing an important ecological impact caused by the continuous deforestation of C. prunifera palms in northeast Brazil. We hypothesize that this ecological disturbance might contribute to an increase in the events of invasion and colonization of human habitations.

Asymmetric migration decreases stability but increases resilience in a heterogeneous metapopulation

Many natural populations are spatially distributed, forming a network of subpopulations linked by migration. Migration patterns are often asymmetric and heterogeneous, with important consequences on the ecology and evolution of the species. Here we investigate experimentally how asymmetric migration and heterogeneous structure affect a simple metapopulation of budding yeast, formed by one strain that produces a public good and a non-producer strain that benefits from it. We study metapopulations with star topology and asymmetric migration, finding that all their subpopulations have a higher fraction of producers than isolated populations. Furthermore, the metapopulations have lower tolerance to challenging environments but higher resilience to transient perturbations. This apparent paradox occurs because tolerance to a constant challenge depends on the weakest subpopulations of the network, while resilience to a transient perturbation depends on the strongest ones.

Asymmetrical movement among patches could affect the stability of ecological metapopulations, but this is difficult to test empirically. Here, Limdi et al. use experimental yeast metapopulations to show that asymmetric migration decreases stability but increases resilience to transient shocks.

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 are 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 multigeneration 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.

Detecting hierarchical levels of connectivity in a population of Acacia tortilis at the northern edge of the species' global distribution: Combining classical population genetics and network analyses

Genetic diversity and structure of populations at the edge of the species' spatial distribution are important for potential adaptation to environmental changes and consequently, for the long-term survival of the species. Here, we combined classical population genetic methods with newly developed network analyses to gain complementary insights into the genetic structure and diversity of Acacia tortilis, a keystone desert tree, at the northern edge of its global distribution, where the population is under threat from climatic, ecological, and anthropogenic changes. We sampled A. tortilis from 14 sites along the Dead Sea region and the Arava Valley in Israel and in Jordan. In addition, we obtained samples from Egypt and Sudan, the hypothesized origin of the species. Samples from all sites were genotyped using six polymorphic microsatellite loci.Our results indicate a significant genetic structure in A. tortilis along the Arava Valley. This was detected at different hierarchical levels-from the basic unit of the subpopulation, corresponding to groups of trees within ephemeral rivers (wadis), to groups of subpopulations (communities) that are genetically more connected relative to others. The latter structure mostly corresponds to the partition of the major drainage basins in the area. Network analyses, combined with classical methods, allowed for the identification of key A. tortilis subpopulations in this region, characterized by their relatively high level of genetic diversity and centrality in maintaining gene flow in the population. Characterizing such key subpopulations may enable conservation managers to focus their efforts on certain subpopulations that might be particularly important for the population's long-term persistence, thus contributing to species conservation within its peripheral range.

On the calculation of betweenness centrality in marine connectivity studies using transfer probabilities

Betweenness has been used in a number of marine studies to identify portions of sea that sustain the connectivity of whole marine networks. Herein we highlight the need of methodological exactness in the calculation of betweenness when graph theory is applied to marine connectivity studies based on transfer probabilities. We show the inconsistency in calculating betweeness directly from transfer probabilities and propose a new metric for the node-to-node distance that solves it. Our argumentation is illustrated by both simple theoretical examples and the analysis of a literature data set.

Predicting genomic selection efficiency to optimize calibration set and to assess prediction accuracy in highly structured populations

KEY MESSAGE

We propose a criterion to predict genomic selection efficiency for structured populations. This criterion is useful to define optimal calibration set and to estimate prediction reliability for multiparental populations. Genomic selection refers to the use of genotypic information for predicting the performance of selection candidates. It has been shown that prediction accuracy depends on various parameters including the composition of the calibration set (CS). Assessing the level of accuracy of a given prediction scenario is of highest importance because it can be used to optimize CS sampling before collecting phenotypes, and once the breeding values are predicted it informs the breeders about the reliability of these predictions. Different criteria were proposed to optimize CS sampling in highly diverse panels, which can be useful to screen collections of genotypes. But plant breeders often work on structured material such as biparental or multiparental populations, for which these criteria are less adapted. We derived from the generalized coefficient of determination (CD) theory different criteria to optimize CS sampling and to assess the reliability associated to predictions in structured populations. These criteria were evaluated on two nested association mapping (NAM) populations and two highly diverse panels of maize. They were efficient to sample optimized CS in most situations. They could also estimate at least partly the reliability associated to predictions between NAM families, but they could not estimate differences in the reliability associated to the predictions of NAM families using the highly diverse panels as calibration sets. We illustrated that the CD criteria could be adapted to various prediction scenarios including inter and intra-family predictions, resulting in higher prediction accuracies.

Evidence for rangewide panmixia despite multiple barriers to dispersal in a marine mussel

Oceanographic features shape the distributional and genetic patterns of marine species by interrupting or promoting connections among populations. Although general patterns commonly arise, distributional ranges and genetic structure are species-specific and do not always comply with the expected trends. By applying a multimarker genetic approach combined with Lagrangian particle simulations (LPS) we tested the hypothesis that oceanographic features along northeastern Atlantic and Mediterranean shores influence dispersal potential and genetic structure of the intertidal mussel Perna perna. Additionally, by performing environmental niche modelling we assessed the potential and realized niche of P. perna along its entire native distributional range and the environmental factors that best explain its realized distribution. Perna perna showed evidence of panmixia across >4,000 km despite several oceanographic breaking points detected by LPS. This is probably the result of a combination of life history traits, continuous habitat availability and stepping-stone dynamics. Moreover, the niche modelling framework depicted minimum sea surface temperatures (SST) as the major factor shaping P. perna distributional range limits along its native areas. Forthcoming warming SST is expected to further change these limits and allow the species to expand its range polewards though this may be accompanied by retreat from warmer areas.

Palaeoclimatic conditions in the Mediterranean explain genetic diversity of Posidonia oceanica seagrass meadows

Past environmental conditions in the Mediterranean Sea have been proposed as main drivers of the current patterns of distribution of genetic structure of the seagrass Posidonia oceanica, the foundation species of one of the most important ecosystems in the Mediterranean Sea. Yet, the location of cold climate refugia (persistence regions) for this species during the Last Glacial Maximum (LGM) is not clear, precluding the understanding of its biogeographical history. We used Ecological Niche Modelling together with existing phylogeographic data to locate Pleistocene refugia in the Mediterranean Sea and to develop a hypothetical past biogeographical distribution able to explain the genetic diversity presently found in P. oceanica meadows. To do that, we used an ensemble approach of six predictive algorithms and two Ocean General Circulation Models. The minimum SST in winter and the maximum SST in summer allowed us to hindcast the species range during the LGM. We found separate glacial refugia in each Mediterranean basin and in the Central region. Altogether, the results suggest that the Central region of the Mediterranean Sea was the most relevant cold climate refugium, supporting the hypothesis that long-term persistence there allowed the region to develop and retain its presently high proportion of the global genetic diversity of P. oceanica.

Sex-specific graphs: Relating group-specific topology to demographic and landscape data

Sex-specific genetic structure is a commonly observed pattern among vertebrate species. Facing differential selective pressures, individuals may adopt sex-specific life history traits that ultimately shape genetic variation among populations. Although differential dispersal dynamics are commonly detected in the literature, few studies have used genetic structure to investigate sex-specific functional connectivity. The recent use of graph theoretic approaches in landscape genetics has demonstrated network capacities to describe complex system behaviours where network topology represents genetic interaction among subunits. Here, we partition the overall genetic structure into sex-specific graphs, revealing different male and female dispersal dynamics of a fisher (Pekania [Martes] pennanti) metapopulation in southern Ontario. Our analyses based on network topologies supported the hypothesis of male-biased dispersal. Furthermore, we demonstrated that the effect of the landscape, identified at the population level, could be partitioned among sex-specific strata. We found that female connectivity was negatively correlated with snow depth, whereas connectivity among males was not. Our findings underscore the potential of conducting sex-specific analysis by identifying landscape elements or configuration that differentially promotes or impedes functional connectivity between sexes, revealing processes that may otherwise remain cryptic. We propose that the sex-specific graph approach would be applicable to other vagile species where differential sex-specific processes are expected to occur.

Entangled fates of holobiont genomes during invasion: nested bacterial and host diversities in Caulerpa taxifolia

Successful prevention and mitigation of biological invasions requires retracing the initial steps of introduction, as well as understanding key elements enhancing the adaptability of invasive species. We studied the genetic diversity of the green alga Caulerpa taxifolia and its associated bacterial communities in several areas around the world. The striking congruence of α and β diversity of the algal genome and endophytic communities reveals a tight association, supporting the holobiont concept as best describing the unit of spreading and invasion. Both genomic compartments support the hypotheses of a unique accidental introduction in the Mediterranean and of multiple invasion events in southern Australia. In addition to helping with tracing the origin of invasion, bacterial communities exhibit metabolic functions that can potentially enhance adaptability and competitiveness of the consortium they form with their host. We thus hypothesize that low genetic diversities of both host and symbiont communities may contribute to the recent regression in the Mediterranean, in contrast with the persistence of highly diverse assemblages in southern Australia. This study supports the importance of scaling up from the host to the holobiont for a comprehensive understanding of invasions.

Genetic structure of native ant supercolonies varies in space and time

Ant supercolonies are the largest cooperative units known in nature. They consist of networks of interconnected nests with hundreds of reproductive queens, where individuals move freely between nests, cooperate across nest boundaries and show little aggression towards non-nestmates. The combination of high queen numbers and free mixing of workers, queens and brood between nests results in extremely low nestmate relatedness. In such low-relatedness societies, cooperative worker behaviour appears maladaptive because it may aid random individuals instead of relatives. Here, we provide a comprehensive picture of genetic substructure in supercolonies of the native wood ant Formica aquilonia using traditional population genetic as well as network analysis methods. Specifically, we test for spatial and temporal variation in genetic structure of different classes of individuals within supercolonies and analyse the role of worker movement in determining supercolony genetic networks. We find that relatedness within supercolonies is low but positive when viewed on a population level, which may be due to limited dispersal of individuals and/or ecological factors such as nest site limitation and competition against conspecifics. Genetic structure of supercolonies varied with both sample class and sampling time point, which indicates that mobility of individuals varies according to both caste and season and suggests that generalizing has to be carried out with caution in studies of supercolonial species. Overall, our analysis provides novel evidence that native wood ant supercolonies exhibit fine-scale genetic substructure, which may explain the maintenance of cooperation in these low-relatedness societies.

Network Analysis Shows Asymmetrical Flows within a Bird Metapopulation

How the spatial expansion of a species changes at a human time scale is a process difficult to determine. We studied the dispersal pattern of the French white stork population, using a 21-year ringing/resighting dataset. We used the graph-theory to investigate the strength of links between 5 populations (North-East, North-West, Centre, West, and South) and to determine factors important for the birds’ movements. Two clusters of populations were identified within the metapopulation, with most frequent movements of individuals between North-Eastern and Centre populations, and between North-Western and Western populations. Exchanges of individuals between populations were asymmetrical, where North-Eastern and North-Western populations provided more emigrants than they received immigrants. Neither the geographical distance between populations, nor the difference in densities influenced the number of individuals exchanging between populations. The graph-theory approach provides a dynamic view of individual movements within a metapopulation and might be useful for future population studies in the context of conservation.

How individual links affect network stability in a large-scale, heterogeneous metacommunity

Elucidating how dispersal and landscape connectivity influence metacommunity stability will shed light on natural processes structuring ecosystems and help prioritize conservation actions in an increasingly fragmented world. Much of the theoretical and mathematical development of the metacommunity concept has been based on simplified experimental systems or simulated data. We still have limited understanding of how variation in the habitat matrix and species-specific differences in dispersal ability contribute to metacommunity dynamics in heterogeneous landscapes. We model a metacommunity of rainforest mammals in Borneo, a tropical biodiversity hotspot, where protected areas are increasingly isolated by ongoing habitat disturbance and loss. We employ a combination of hierarchical models of local abundance, circuit-theory-based dispersal analysis, and metapopulation models. Our goal was to understand which landscape links were the most important to metapopulation persistence and metacommunity stability. Links were particularly important if they were short and connected two large patches. This was partly because only the very shortest links could be traversed by poorly dispersing species, including small herbivores such as chevrotains (Tragulus spp.) and porcupines. Links that join large patches into a "super-patch" may also promote island-mainland rather than Levins-type metapopulation dynamics for good dispersers, particularly large carnivores such as clouded leopards (Neofelis diardi) and sun bears (Helarctos malayanus), reducing metapopulation extinction risk and thereby enhancing metacommunity stability. Link importance to metacommunity stability was highly correlated between heterogeneous and homogeneous landscapes. But link importance to metapopulation capacity varied strongly across species, and the correlation between heterogeneous and homogeneous landscape matrix scenarios was low for poorly dispersing taxa. This suggests that the environmental conditions in the area between habitat patches, the landscape matrix, is important for assessing certain individual species but less so for understanding the stability of the entire metacommunity.

Connecting science, policy, and implementation for landscape-scale habitat connectivity

We examined the links between the science and policy of habitat corridors to better understand how corridors can be implemented effectively. As a case study, we focused on a suite of landscape-scale connectivity plans in tropical and subtropical Asia (Malaysia, Singapore, and Bhutan). The process of corridor designation may be more efficient if the scientific determination of optimal corridor locations and arrangement is synchronized in time with political buy-in and establishment of policies to create corridors. Land tenure and the intactness of existing habitat in the region are also important to consider because optimal connectivity strategies may be very different if there are few, versus many, political jurisdictions (including commercial and traditional land tenures) and intact versus degraded habitat between patches. Novel financing mechanisms for corridors include bed taxes, payments for ecosystem services, and strategic forest certifications. Gaps in knowledge of effective corridor design include an understanding of how corridors, particularly those managed by local communities, can be protected from degradation and unsustainable hunting. There is a critical need for quantitative, data-driven models that can be used to prioritize potential corridors or multicorridor networks based on their relative contributions to long-term metacommunity persistence.

Investigation of population structure in Gulf of Mexico Seepiophila jonesi (Polychaeta, Siboglinidae) using cross-amplified microsatellite loci

BACKGROUND

Vestimentiferan tubeworms are some of the most recognizable fauna found at deep-sea cold seeps, isolated environments where hydrocarbon rich fluids fuel biological communities. Several studies have investigated tubeworm population structure; however, much is still unknown about larval dispersal patterns at Gulf of Mexico (GoM) seeps. As such, researchers have applied microsatellite markers as a measure for documenting the transport of vestimentiferan individuals. In the present study, we investigate the utility of microsatellites to be cross-amplified within the escarpiid clade of seep vestimentiferans, by determining if loci originally developed for Escarpia spp. could be amplified in the GoM seep tubeworm, Seepiophila jonesi. Additionally, we determine if cross-amplified loci can reliably uncover the same signatures of high gene flow seen in a previous investigation of S. jonesi.

METHODS

Seventy-seven S. jonesi individuals were collected from eight seep sites across the upper Louisiana slope (<1,000 m) in the GoM. Forty-eight microsatellite loci that were originally developed for Escarpia laminata (18 loci) and Escarpia southwardae (30 loci) were tested to determine if they were homologous and polymorphic in S. jonesi. Loci found to be both polymorphic and of high quality were used to test for significant population structuring in S. jonesi.

RESULTS

Microsatellite pre-screening identified 13 (27%) of the Escarpia loci were homologous and polymorphic in S. jonesi, revealing that microsatellites can be amplified within the escarpiid clade of vestimentiferans. Our findings uncovered low levels of heterozygosity and a lack of genetic differentiation amongst S. jonesi from various sites and regions, in line with previous investigations that employed species-specific polymorphic loci on S. jonesi individuals retrieved from both the same and different seep sites. The lack of genetic structure identified from these populations supports the presence of significant gene flow via larval dispersal in mixed oceanic currents.

DISCUSSION

The ability to develop "universal" microsatellites reduces the costs associated with these analyses and allows researchers to track and investigate a wider array of taxa, which is particularly useful for organisms living at inaccessible locations such as the deep sea. Our study highlights that non-species specific microsatellites can be amplified across large evolutionary distances and still yield similar findings as species-specific loci. Further, these results show that S. jonesi collected from various localities in the GoM represents a single panmictic population, suggesting that dispersal of lecithotrophic larvae by deep sea currents is sufficient to homogenize populations. These data are consistent with the high levels of gene flow seen in Escarpia spp., which advocates that differences in microhabitats of seep localities lead to variation in biogeography of separate species.