Ecological connectivity of the marine protected area network in the Baltic Sea, Kattegat and Skagerrak: Current knowledge and management needs

Marine protected areas (MPAs) have become a key component of conservation and fisheries management to alleviate anthropogenic pressures. For MPA networks to efficiently promote persistence and recovery of populations, ecological connectivity, i.e. dispersal and movement of organisms and material across ecosystems, needs to be taken into account. To improve the ecological coherence of MPA networks, there is hence a need to evaluate the connectivity of species spreading through active migration and passive dispersal. We reviewed knowledge on ecological connectivity in the Baltic Sea, Kattegat and Skagerrak in the northeast Atlantic and present available information on species-specific dispersal and migration distances. Studies on genetic connectivity are summarised and discussed in relation to dispersal-based analyses. Threats to ecological connectivity, limiting dispersal of populations and lowering the resilience to environmental change, were examined. Additionally, a review of studies evaluating the ecological coherence of MPA networks in the Baltic Sea, Kattegat and Skagerrak was performed, and suggestions for future evaluations to meet management needs are presented.

Genetic Diversity of the Surubim-Do-Iguaçu, a Giant Catfish Species Threatened with Extinction: Recommendations for Species Conservation

Steindachneridion melanodermatum is the largest catfish of the Lower Iguaçu River and is endangered due to the habitat fragmentation caused by dams. Currently, the wild population’s last refuge is restricted to an area of 190 km. This study presents the first analysis of its genetic diversity and population structure, using microsatellite loci and mtDNA. The population has an adequate level of genetic diversity, but signs of a recent bottleneck were observed. The Baixo Iguaçu Hydroelectric Power Plant has recently fragmented the population and threatened it with extinction in a reduced area of nearly 30 km. Based on our results, we strongly advise against the stocking of breeding specimens below the Salto Caxias HPP to not compromise the integrity of the native gene pools at the receptor sites. In addition, we recommend manual fish transposition, trap-and-haul, to maintain the genetic connectivity of individuals upstream and downstream of the dam as a conservation strategy. Furthermore, studies on behavior and swimming capacities, and suitable fishways for this species must be developed. We strongly recommend that the Lower Iguaçu River and its tributaries be protected and preserved as free from additional barriers to prevent future habitat disruption for the benefit of S. melanodermatum and several other endemic and endangered species.

No Evidence of Low Genetic Diversity Despite High Levels of Inbreeding and Poor Genetic Connectivity Among Tetrastigma loheri (Vitaceae) Populations in Remaining Forest Areas in Cebu, Philippines

Abstract— Little is known about the effects of habitat fragmentation on the patterns of genetic diversity and genetic connectivity of species in the remaining tropical forests of Southeast Asia. This is particularly evident in Cebu, a Philippine island that has a long history of deforestation and has lost nearly all of its forest cover. To begin filling this gap, data from 13 microsatellite loci developed for Tetrastigma loheri (Vitaceae), a common vine species in Philippine forests, were used to study patterns of genetic diversity and genetic connectivity for the four largest of the remaining forest areas in Cebu. Evidence of relatively high levels of inbreeding was found in all four areas, despite no evidence of low genetic diversity. The four areas are genetically differentiated, suggesting low genetic connectivity. The presence of inbreeding and low genetic connectivity in a commonly encountered species such as T. loheri in Cebu suggests that the impact of habitat fragmentation is likely greater on rare plant species with more restricted distributions in Cebu. Conservation recommendations for the remaining forest areas in Cebu include the establishment of steppingstone corridors between nearby areas to improve the movement of pollinators and seed dispersers among them.

Kilometer-Scale Larval Dispersal Processes Predict Metapopulation Connectivity Pathways for Paramuricea biscaya in the Northern Gulf of Mexico

Fine-scale larval dispersal and connectivity processes are key to species survival, growth, recovery and adaptation under rapidly changing disturbances. Quantifying both are required to develop any effective management strategy. In the present work, we examine the dispersal pattern and potential connectivity of a common deep-water coral, Paramuricea biscaya, found in the northern Gulf of Mexico by evaluating predictions of physical models with estimates of genetic connectivity. While genetic approaches provide estimates of realized connectivity, they do not provide information on the dispersal process. Physical circulation models can now achieve kilometer-scale resolution sufficient to provide detailed insight into the pathways and scales of larval dispersal. A high-resolution regional ocean circulation model is integrated for 2015 and its advective pathways are compared with the outcome of the genetic connectivity estimates of corals collected at six locations over the continental slope at depths comprised between 1,000 and 3,000 m. Furthermore, the likely interannual variability is extrapolated using ocean hindcasts available for this basin. The general connectivity pattern exhibits a dispersal trend from east to west following 1,000 to 2,000-m isobaths, corresponding to the overall westward near-bottom circulation. The connectivity networks predicted by our model were mostly congruent with the estimated genetic connectivity patterns. Our results show that although dispersal distances of 100 km or less are common, depth differences between tens to a few hundred meters can effectively limit larval dispersal. A probabilistic graphic model suggests that stepping-stone dispersal mediated by intermediate sites provides a likely mechanism for long-distance connectivity between the populations separated by distances of 300 km or greater, such as those found in the DeSoto and Keathley canyons.

Patterns of population genetic structure and connectivity of squat lobsters associated with vulnerable marine ecosystems

<p>Vulnerable marine ecosystems (VMEs) are susceptible to the impact of intense or long-term anthropogenic activities (e.g., bottom trawling). Networks of marine protected areas (MPAs) can help facilitate the conservation and restoration of biodiversity and ecosystem function provided by VMEs. An understanding of the connectivity amongst populations of deep-sea organisms is crucial for informing the management of VMEs, by assessing the effectiveness of existing MPAs and informing the placement of new MPAs. Genetic evaluation of population structure is one of the most commonly used indirect approaches for interpreting connectivity. In contrast to corals or sponges, which are typically habitat-forming organisms as VME-indicator taxa, squat lobsters are often found in close association with VMEs and can be considered to be VME-associated taxa. Nowadays, population genetic studies of deep-sea fauna mainly focus on VME-indicator taxa, whilst relatively few studies have focussed on VME-associated taxa, such as squat lobsters, whose distribution is not exclusively limited to VMEs. In this study, three deep-sea squat lobster species, Munida isos Ahyong & Poore, 2004, Munida endeavourae Ahyong & Poore, 2004 and Munida gracilis Henderson, 1885, were selected based on their association with VMEs (e.g., cold-water coral reefs and seamounts), wide distributional ranges across the southwest Pacific Ocean, and sample availability. The overall aims of this research are to evaluate patterns of population structure and genetic connectivity of three squat lobster taxa in the southwest Pacific Ocean and consider how the acquired genetic information can contribute to the management and conservation of VMEs in the southwest Pacific Ocean. A general introduction of VMEs, MPAs, connectivity of deep-sea fauna, High-Throughput Sequencing (HTS), study area and study taxa are presented in Chapter 1. To provide background information for this research, a review was conducted of the molecular-based studies of the systematics, taxonomy and phylogenetics of marine squat lobster taxa (Chapter 2). Recent molecular-based studies have dramatically increased our understanding of squat lobster phylogenetics and systematics, and thereby the taxonomy of this diverse and challenging group, which provide a valuable starting point for evaluating hypotheses concerning speciation, biogeography, adaptation and co-evolution (e.g., squat lobsters and corals). Notably, accurate taxonomy is critical for population genetic studies and consequently supports the conservation efforts of VMEs. A range of molecular genetic markers, including the mitochondrial COI region, nuclear microsatellites and single nucleotide polymorphisms (SNPs), were utilised to evaluate the genetic connectivity amongst populations of three VME-associated taxa (Munida isos, M. endeavourae and M. gracilis). In addition to this, universal invertebrate primers were used to yield partial COI fragments of 649 bp (DNA barcoding) for the three Munida species to confirm the taxonomic identity and to exclude the possibility of cryptic species. Due to limited genetic information for the three Munida species, novel microsatellite loci were developed for M. isos based on the HiSeq 2500 sequencing platform and used for cross-species amplification in M. endeavourae and M. gracilis (Chapter 3). Additionally, a Genotyping by Sequencing (GBS) protocol and the Universal Network Enabled Analysis Kit (UNEAK) pipeline were employed to develop novel SNPs for M. isos samples from the southwest Pacific Ocean (Chapter 5). A spatially explicit hierarchical testing framework (Northern-Southern biogeographical provinces, North-Central-South regions, and individual geomorphic features) was employed for the evaluation of connectivity amongst populations of the three deep-sea squat lobster taxa across their distributional range in the southwest Pacific Ocean (Chapter 4). The level of genetic diversity was high as revealed by variation at the COI region, and moderate based on microsatellite markers across the three Munida species. With more than 96% of the variance being attributed to differences within populations in the three Munida species, based on both marker types, no genetic subdivision was detected in M. endeavourae, whilst little genetic differentiation was observed in M. isos and M. gracilis based on microsatellite variation. For M. isos, populations from the Tasmanian slope were potentially genetically different from all other populations and may act as source populations, whereas populations from the Kermadec Ridge may be sink populations. Robust evidence of recent demographic expansions was detected in the three Munida species, based on COI and microsatellite marker types. The estimated time of demographic expansions for the three Munida species was ca. 16.1 kya, 24.4 kya and 21.6 kya for the M. isos, M. endeavourae and M. gracilis, respectively, coinciding with the late Pleistocene. The results are discussed in the context of the distribution of existing MPAs, and contribute new information useful to the management of VMEs within national and international waters in the region. To further investigate patterns of connectivity in deep-sea squat lobster populations and provide valuable information for the design of management strategies to protect VMEs, newly developed SNPs were utilised (Chapter 5). The results showed that the Tasmanian slope and Macquarie Ridge populations were genetically different from all other populations, both within New Zealand’s exclusive economic zone (EEZ) and the high seas beyond, with little gene flow derived from Tasmanian slope populations to Macquarie Ridge populations. The results are discussed in the context of existing MPAs, and highlight the complexity of the endeavour to maintain population diversity and gene flow across multiple national jurisdictions as well as international waters, all of which employ different spatial protective measures. The findings of this research are summarised and discussed in relation to the usefulness of genetic studies to provide new and valuable information about the genetic diversity and connectivity of VME-associated species, and to highlight what additional genetic research is needed to assist in the management and conservation of VMEs in the southwest Pacific Ocean (Chapter 6).</p>

Phylogeography of the oyster borer (Haustrum scobina)

<p>An effective investigation of the underlying ecological processes that shape genetic diversity and connectivity typically requires comparisons among phylogeographic studies of multiple species. Phylogeographic studies of New Zealand’s coastal marine benthos have historically relied on post hoc speculation rather than directed research questions to investigate ecological processes. There has also been a lack of studies on direct developing marine molluscs. Direct developers are expected to have a low potential for dispersal and thus show a pattern of genetic isolation by distance across their distributions. Recent research indicates that this assumption may frequently be violated by instances of long distance dispersal/translocation. The oyster borer (Haustrum scobina) is an endemic direct-developing marine mollusc found in high abundances at rocky intertidal environments across the entirety of New Zealand. This distribution and life history makes H. scobina an ideal target to study genetic connectivity in a species expected to show low realised dispersal and high population genetic structuring. This thesis research used 379 new DNA sequences from the mitochondrial gene cytochrome c oxidase subunit 1 (COI) to investigate the phylogeography of H. scobina across the southern North Island. In addition 16 new COI sequences were inadvertently sequenced from the morphologically similar congener Haustrum albomarginatum. Results from both species support the recently proposed division of H. scobina and H. albomarginatum as separate species. H. scobina populations show significant geographic structure and a lack of haplotype diversity across the south-eastern North Island concordant with results of another previous study of a direct developer. This finding suggests that ecological processes may be producing similar population genetic structures for direct developers generally. Contrast between high and low haplotype diversities in northern and southern H. scobina populations respectively, indicates that southern H. scobina populations may have originated via recolonisation from northern populations following a range contraction during the Last Glacial Maximum. Evidence of multiple long distance dispersal/translocation events was found indicating that long distance dispersal via rafting and/or inadvertent human-mediated translocations may have occurred frequently. Results are then discussed with a view to inform further research in to New Zealand direct developers.</p>

Patterns of population genetic structure and connectivity of squat lobsters associated with vulnerable marine ecosystems

<p>Vulnerable marine ecosystems (VMEs) are susceptible to the impact of intense or long-term anthropogenic activities (e.g., bottom trawling). Networks of marine protected areas (MPAs) can help facilitate the conservation and restoration of biodiversity and ecosystem function provided by VMEs. An understanding of the connectivity amongst populations of deep-sea organisms is crucial for informing the management of VMEs, by assessing the effectiveness of existing MPAs and informing the placement of new MPAs. Genetic evaluation of population structure is one of the most commonly used indirect approaches for interpreting connectivity. In contrast to corals or sponges, which are typically habitat-forming organisms as VME-indicator taxa, squat lobsters are often found in close association with VMEs and can be considered to be VME-associated taxa. Nowadays, population genetic studies of deep-sea fauna mainly focus on VME-indicator taxa, whilst relatively few studies have focussed on VME-associated taxa, such as squat lobsters, whose distribution is not exclusively limited to VMEs. In this study, three deep-sea squat lobster species, Munida isos Ahyong & Poore, 2004, Munida endeavourae Ahyong & Poore, 2004 and Munida gracilis Henderson, 1885, were selected based on their association with VMEs (e.g., cold-water coral reefs and seamounts), wide distributional ranges across the southwest Pacific Ocean, and sample availability. The overall aims of this research are to evaluate patterns of population structure and genetic connectivity of three squat lobster taxa in the southwest Pacific Ocean and consider how the acquired genetic information can contribute to the management and conservation of VMEs in the southwest Pacific Ocean. A general introduction of VMEs, MPAs, connectivity of deep-sea fauna, High-Throughput Sequencing (HTS), study area and study taxa are presented in Chapter 1. To provide background information for this research, a review was conducted of the molecular-based studies of the systematics, taxonomy and phylogenetics of marine squat lobster taxa (Chapter 2). Recent molecular-based studies have dramatically increased our understanding of squat lobster phylogenetics and systematics, and thereby the taxonomy of this diverse and challenging group, which provide a valuable starting point for evaluating hypotheses concerning speciation, biogeography, adaptation and co-evolution (e.g., squat lobsters and corals). Notably, accurate taxonomy is critical for population genetic studies and consequently supports the conservation efforts of VMEs. A range of molecular genetic markers, including the mitochondrial COI region, nuclear microsatellites and single nucleotide polymorphisms (SNPs), were utilised to evaluate the genetic connectivity amongst populations of three VME-associated taxa (Munida isos, M. endeavourae and M. gracilis). In addition to this, universal invertebrate primers were used to yield partial COI fragments of 649 bp (DNA barcoding) for the three Munida species to confirm the taxonomic identity and to exclude the possibility of cryptic species. Due to limited genetic information for the three Munida species, novel microsatellite loci were developed for M. isos based on the HiSeq 2500 sequencing platform and used for cross-species amplification in M. endeavourae and M. gracilis (Chapter 3). Additionally, a Genotyping by Sequencing (GBS) protocol and the Universal Network Enabled Analysis Kit (UNEAK) pipeline were employed to develop novel SNPs for M. isos samples from the southwest Pacific Ocean (Chapter 5). A spatially explicit hierarchical testing framework (Northern-Southern biogeographical provinces, North-Central-South regions, and individual geomorphic features) was employed for the evaluation of connectivity amongst populations of the three deep-sea squat lobster taxa across their distributional range in the southwest Pacific Ocean (Chapter 4). The level of genetic diversity was high as revealed by variation at the COI region, and moderate based on microsatellite markers across the three Munida species. With more than 96% of the variance being attributed to differences within populations in the three Munida species, based on both marker types, no genetic subdivision was detected in M. endeavourae, whilst little genetic differentiation was observed in M. isos and M. gracilis based on microsatellite variation. For M. isos, populations from the Tasmanian slope were potentially genetically different from all other populations and may act as source populations, whereas populations from the Kermadec Ridge may be sink populations. Robust evidence of recent demographic expansions was detected in the three Munida species, based on COI and microsatellite marker types. The estimated time of demographic expansions for the three Munida species was ca. 16.1 kya, 24.4 kya and 21.6 kya for the M. isos, M. endeavourae and M. gracilis, respectively, coinciding with the late Pleistocene. The results are discussed in the context of the distribution of existing MPAs, and contribute new information useful to the management of VMEs within national and international waters in the region. To further investigate patterns of connectivity in deep-sea squat lobster populations and provide valuable information for the design of management strategies to protect VMEs, newly developed SNPs were utilised (Chapter 5). The results showed that the Tasmanian slope and Macquarie Ridge populations were genetically different from all other populations, both within New Zealand’s exclusive economic zone (EEZ) and the high seas beyond, with little gene flow derived from Tasmanian slope populations to Macquarie Ridge populations. The results are discussed in the context of existing MPAs, and highlight the complexity of the endeavour to maintain population diversity and gene flow across multiple national jurisdictions as well as international waters, all of which employ different spatial protective measures. The findings of this research are summarised and discussed in relation to the usefulness of genetic studies to provide new and valuable information about the genetic diversity and connectivity of VME-associated species, and to highlight what additional genetic research is needed to assist in the management and conservation of VMEs in the southwest Pacific Ocean (Chapter 6).</p>

Phylogeography of the oyster borer (Haustrum scobina)

<p>An effective investigation of the underlying ecological processes that shape genetic diversity and connectivity typically requires comparisons among phylogeographic studies of multiple species. Phylogeographic studies of New Zealand’s coastal marine benthos have historically relied on post hoc speculation rather than directed research questions to investigate ecological processes. There has also been a lack of studies on direct developing marine molluscs. Direct developers are expected to have a low potential for dispersal and thus show a pattern of genetic isolation by distance across their distributions. Recent research indicates that this assumption may frequently be violated by instances of long distance dispersal/translocation. The oyster borer (Haustrum scobina) is an endemic direct-developing marine mollusc found in high abundances at rocky intertidal environments across the entirety of New Zealand. This distribution and life history makes H. scobina an ideal target to study genetic connectivity in a species expected to show low realised dispersal and high population genetic structuring. This thesis research used 379 new DNA sequences from the mitochondrial gene cytochrome c oxidase subunit 1 (COI) to investigate the phylogeography of H. scobina across the southern North Island. In addition 16 new COI sequences were inadvertently sequenced from the morphologically similar congener Haustrum albomarginatum. Results from both species support the recently proposed division of H. scobina and H. albomarginatum as separate species. H. scobina populations show significant geographic structure and a lack of haplotype diversity across the south-eastern North Island concordant with results of another previous study of a direct developer. This finding suggests that ecological processes may be producing similar population genetic structures for direct developers generally. Contrast between high and low haplotype diversities in northern and southern H. scobina populations respectively, indicates that southern H. scobina populations may have originated via recolonisation from northern populations following a range contraction during the Last Glacial Maximum. Evidence of multiple long distance dispersal/translocation events was found indicating that long distance dispersal via rafting and/or inadvertent human-mediated translocations may have occurred frequently. Results are then discussed with a view to inform further research in to New Zealand direct developers.</p>

Barrier mitigation measures trigger the rapid recovery of genetic connectivity in five freshwater fish species

ABSTRACTRivers are heavily fragmented by man-made instream barriers such as dams and weirs. This hyper-fragmentation is a major threat to freshwater biodiversity and restoration policies are now adopted worldwide to mitigate these impacts. However, there is surprisingly little feedback on the efficiency of barrier mitigation measures in restoring riverine connectivity, notably for non-migratory fish species. Here, we implemented a “before-after genetic monitoring” of the restoration of 11 weirs in France using a dedicated genetic index of fragmentation (the FINDEX), with a focus on five fish species from two genera. We found that most obstacles actually had a significant impact on connectivity before restoration, especially the highest and steepest ones, with an overall barrier effect of about 51% of the maximal theoretical impact. Most importantly, we demonstrated for the first time that mitigation measures such as dam removal or fish pass creation significantly and rapidly improved connectivity, with –for some barriers-a complete recovery of the genetic connectivity in less than twelve months. Our study provides a unique and strong proof-of-concept that barrier removal is an efficient strategy to restore riverine connectivity and that molecular tools can provide accurate measures of restoration efficiency within a few months.Graphical Abstract

Landscape Genetics of the Yellow-Bellied Toad (Bombina variegata) in the Northern Weser Hills of Germany

Anthropogenic influences such as deforestation, increased infrastructure, and general urbanization has led to a continuous loss in biodiversity. Amphibians are especially affected by these landscape changes. This study focuses on the population genetics of the endangered yellow-bellied toad (Bombina variegata) in the northern Weser Hills of Germany. Additionally, a landscape genetic analysis was conducted to evaluate the impact of eight different landscape elements on the genetic connectivity of the subpopulations in this area. Multiple individuals from 15 study sites were genotyped using 10 highly polymorphic species-specific microsatellites. Four genetic clusters were detected, with only two of them having considerable genetic exchange. The average genetic differentiation between populations was moderate (global FST = 0.1). The analyzed landscape elements showed significant correlations with the migration rates and genetic distances between populations. Overall, anthropogenic structures had the greatest negative impact on gene flow, whereas wetlands, grasslands, and forests imposed minimal barriers in the landscape. The most remarkable finding was the positive impact of the underpasses of the motorway A2. This element seems to be the reason why some study sites on either site of the A2 showed little genetic distance even though their habitat has been separated by a strong dispersal barrier.