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Anthropogenic-induced climate change is having profound impacts on aquatic ecosystems, and the resilience of fish populations will be determined by their response to these impacts. The northern Namibian coast is an ocean warming hotspot, with temperatures rising faster than the global average. The rapid warming in Namibia has had considerable impacts on marine fauna, such as the southern extension of the distribution of Argyrosomus coronus from southern Angola into northern Namibian waters, where it now overlaps and hybridizes with the closely related Namibian species, A. inodorus. Understanding how these species (and their hybrids) perform at current and future temperatures is vital to optimize adaptive management for Argyrosomus species. Intermittent flow-through respirometry was used to quantify standard and maximum metabolic rates for Argyrosomus individuals across a range of temperatures. The modelled aerobic scope (AS) of A. inodorus was notably higher at cooler temperatures (12, 15, 18 and 21°C) compared with that of A. coronus, whereas the AS was similar at 24°C. Although only five hybrids were detected and three modelled, their AS was in the upper bounds of the models at 15, 18 and 24°C. These findings suggest that the warming conditions in northern Namibia may increasingly favour A. coronus and promote the poleward movement of the leading edge of their southern distribution. In contrast, the poor aerobic performance of both species at cold temperatures (12°C) suggests that the cold water associated with the permanent Lüderitz Upwelling Cell in the south may constrain both species to central Namibia. This is most concerning for A. inodorus because it may be subjected to a considerable coastal squeeze.

Habitat loss and fragmentation due to urbanization can negatively affect metapopulation persistence when gene flow among populations is reduced and population sizes decrease. Inference of patterns and processes of population connectivity derived from spatial genetic analysis has proven invaluable for conservation and management. However, a more complete account of population dynamics may be obtained by combining spatial and temporal sampling. We, therefore, performed a genetic study on European stag beetle (Lucanus cervus L.) populations in a suburban context using samples collected in three locations and during the period 2002–2016. The sampling area has seen recent landscape changes which resulted in population declines. Through the use of a suite of F ST, clustering analysis, individual assignment, and relatedness analysis, we assessed fine scale spatiotemporal genetic variation within and among habitat patches using 283 individuals successfully genotyped at 17 microsatellites. Our findings suggested the three locations to hold demographically independent populations, at least over time scales of relevance to conservation, though with higher levels of gene flow in the past. Contrary to expectation from tagging studies, dispersal appeared to be mainly female‐biased. Although the life cycle of stag beetle suggests its generations to be discrete, no clear temporal structure was identified, which could be attributed to the varying duration of larval development. Since population bottlenecks were detected and estimates of effective number of breeders were low, conservation actions are eminent which should include the establishment of suitable dead wood for oviposition on both local and regional scales to increase (re)colonization success and connectivity among current populations., In this genetic study of suburban European stag beetle populations, we investigated the influence of recent habitat fragmentation using spatial and temporal samples. The results suggest the populations to be currently demographically independent, with dispersal being mainly female‐biased. Since recent bottlenecks were detected and estimates of effective number of breeders were low, conservation actions are eminent.

The Patagonian toothfish, Dissostichus eleginoides, is one of the largest predatory fishes inhabiting Southern Ocean waters spanning the Antarctic Polar Front (APF), a prominent biogeographic boundary restricting gene flow and driving species divergence between Antarctic and sub-Antarctic waters. In the light of emerging threats to toothfish conservation and sustainability, this study investigated genetic [mtDNA sequences and genome wide nuclear single nucleotide polymorphisms (SNPs)] and morphological data to critically evaluate the taxonomic status of toothfish north (Chile and Patagonian shelf) and south (South Georgia and South Sandwich Islands) of the APF. mtDNA revealed reciprocally monophyletic lineages on either side of the APF with coalescent analysis indicating these diverged during the Pleistocene. Integration with data from other sources suggests the Chilean/Patagonian lineage is endemic. SNP analysis confirmed restricted nuclear gene flow between both groups and revealed a consensus suite of positive outlier SNPs compatible with adaptive divergence between these groups. Finally, several morphological features permit unequivocal assignment of individuals to either of the clades. Based on the genetic, phenotypic and ecological divergence, the authors propose that toothfish on either side of the APF be recognised as distinct species, with the name D. eleginoides used for toothfish occurring in South American waters north of the APF and toothfish south of the APF being classified using the new name D. australis reflecting their southern distribution.

This study used RAD-seq-derived SNPs to explore population connectivity, local adaptation, and individual assignment in European sprat (Sprattus sprattus) and inform the alignment of management units with biological processes. FST, clustering, and outlier analyses support a genetically cohesive population spanning the Celtic Sea-English Channel-North Sea-Kattegat (NE Atlantic) region. The lack of structure among the NE Atlantic samples indicates connectivity across current management boundaries. However, the assumption of demographic panmixia is cautioned against unless verified by a multidisciplinary approach. The data confirm high genetic divergence of a Baltic population (average FST vs. NE Atlantic samples = 0.051) with signatures compatible with local adaptation in the form of outlier loci, some of which are shown to occur within exonic regions. The outliers permit diagnostic assignment of individuals between the NE Atlantic and Baltic populations and thus represent a “reduced panel” of markers for monitoring a potential mixed stock fishery within the western Baltic. Overall, this study provides information that may help refine spatial management boundaries of sprat and resources for genetic-assisted management.

Kelp are foundation species threatened by ongoing warming trends and increased harvesting pressure. This emphasizes the need to study genetic structure over various spatial scales to resolve demographic and genetic processes underpinning resilience. Here, we investigate the genetic diversity in the kelp, Laminaria digitata, in previously understudied southern (trailing-edge) and northern (range-centre) regions in the Northeastern Atlantic Ocean. There was strong hierarchical spatial structuring with significantly lower genetic variability and gene flow among southern populations. As these span the area of the Hurd’s deep Pleistocene glacial refuge, the current low variation likely reflects a fraction of previous levels that has been eroded at the species southern edge. Northern variability and private alleles also indicate contributions from cryptic northern glacial refugia. Contrary to expectations of a positive relationship between neutral genetic diversity and resilience, a previous study reported individuals from the same genetically impoverished southern populations to be better adapted to cope with thermal stress than northern individuals. This not only demonstrates that neutral genetic diversity may be a poor indicator of resilience to environmental stress but also confirms that extirpation of southern populations will result in the loss of evolved, not just potential, adaptations for resilience.

Two sister species of horse mackerel (Trachurus trachurus and T. capensis) are described that are intensively harvested in East Atlantic waters. To address long‐standing uncertainties as to their respective geographical ranges, overlap and intraspecific population structure this study combined genetic (mitochondrial DNA and microsatellite) analysis and targeted sampling of the hitherto understudied West African coast. mtDNA revealed two reciprocally monophyletic clades corresponding to each species with interspecies nuclear differentiation supported by F ST values. The T. trachurus clade was found across the north‐east Atlantic down to Ghana but was absent from Angolan and South African samples. The T. capensis clade was found only in South Africa, Angola and a single Ghanaian individual. This pattern suggests that both species may overlap in the waters around Ghana. The potential for cryptic hybridization and/or indiscriminate harvesting of both species in the region is discussed. For T. capensis mtDNA supports high gene flow across the Benguela upwelling system, which fits with the species' ecology. The data add to evidence of a lack of significant genetic structure throughout the range of T. trachurus though the assumption of demographic panmixia is cautioned against. For both species, resolution of stock recruitment heterogeneity relevant to fishery management, as well as potential hybridization, will require more powerful genomic analyses.

The Osprey (Pandion haliaetus) experienced severe declines in Europe over the past centuries, including extirpations from large parts of its range. After Ospreys began naturally recolonizing Wales, United Kingdom (UK), in 2004, the Dyfi Osprey Project initiated an extensive ecological (ringing, satellite tracking, and nest video recordings) and genetic (microsatellite genotyping) monitoring program alongside artificial nest platform construction. From 2004 to 2019 there were 40 reproductive events (i.e., eggs laid in a nest) across six nests, resulting in a total of 95 fledglings and a yearly average of 2.35 ± 0.8 (SD) fledglings per nest-with-eggs. Video recording at one nest documented high hatching success and survival to the fledging and dispersal phases, as well as mate- and nest-fidelity across multiple years. Collectively these breeding parameters suggest high productivity associated with artificial nest structures and limited density-dependent effects for the Welsh population due to its small size and low density at this stage of recovery. Satellite tracking of four migrating individuals revealed that Ospreys used a western European migratory flyway and wintered in sub-Saharan western Africa. Genetic analysis of nestlings from five nests indicated single paternity in all cases, in agreement with evidence of social monogamy. Genetic analysis of geographical outgroups (Scottish, Swedish, and Latvian) provided preliminary evidence of cryptic population structure among UK (Welsh and Scottish) populations. The novel combination of loci show Welsh Osprey retain high levels of variation and more broadly direct reconsideration of the hitherto inferred genetic poverty of the species compared to other raptors. We recommend implementation of similar long-term ecological and genetic monitoring programs for other populations.

Diseases of bivalve molluscs caused by paramyxid parasites of the genus Marteilia have been linked to mass mortalities and the collapse of commercially important shellfish populations. Until recently, no Marteilia spp. have been detected in common cockle (Cerastoderma edule) populations in the British Isles. Molecular screening of cockles from ten sites on the Welsh coast indicates that a Marteilia parasite is widespread in Welsh C. edule populations, including major fisheries. Phylogenetic analysis of ribosomal DNA (rDNA) gene sequences from this parasite indicates that it is a closely related but different species to Marteilia cochillia, a parasite linked to mass mortality of C. edule fisheries in Spain, and that both are related to Marteilia octospora, for which we provide new rDNA sequence data. Preliminary light and transmission electron microscope (TEM) observations support this conclusion, indicating that the parasite from Wales is located primarily within areas of inflammation in the gills and the connective tissue of the digestive gland, whereas M. cochillia is found mainly within the epithelium of the digestive gland. The impact of infection by the new species, here described as Marteilia cocosarum n. sp., upon Welsh fisheries is currently unknown.

Determining and predicting species' responses to climate change is a fundamental goal of contemporary ecology. When interpreting responses to warming species are often treated as a single physiological unit with a single species-wide thermal niche. This assumes that trailing edge populations are most vulnerable to warming, as it is here where a species' thermal niche will be exceeded first. Local adaptation can, however, result in narrower thermal tolerance limits for local populations, so that similar relative increases in temperature can exceed local niches throughout a species range. We used a combination of common garden temperature heat-shock experiments (8–32 °C) and population genetics (microsatellites) to identify thermal ecotypes of northeast Atlantic range centre and trailing edge populations of the habitat-forming kelp , Laminaria digitata . Using upregulation of hsp70 as an indicator of thermal stress, we found that trailing edge populations were better equipped to tolerate acute temperature shocks. This pattern was consistent across seasons, indicating that between-population variability is fixed. High genetic structuring was also observed, with range centre and trailing edge populations representing highly distinct clusters with little gene flow between regions. Taken together, this suggests the presence of distinct thermal ecotypes for L. digitata, which may mean responses to future warming are more complex than linear range contractions.

Population genetic structure of the Patagonian longfin squid Doryteuthis gahi was assessed across the Falkland Islands, central-southern Chile, and Peru. Microsatellite and mtDNA data partitioned samples into two groups: one consisting of the Peruvian samples, the other comprised the Chilean and Falklands samples, with no sub-structuring within either group. Recurrent demographic independence between groups can be linked to abrupt changes in continental shelf features between the Peruvian and central Chilean sites restricting adult dispersal. Phylogeographic analyses indicate a prolonged period of isolation between the Peruvian and Chilean–Falkland groups which may include divergence in allopatric glacial refugia. Both groups have experienced dissimilar historical population size dynamics with the Peruvian population exhibiting signals of size fluctuations, similar to other species in the area, that align with postglacial changes in the productivity of the Humboldt Current system. Genetic cohesion among central-southern Chilean and Falklands samples supports connectivity across current management boundaries and indicates that phenotypic differences between D. gahi from these areas reflect plastic responses to environmental heterogeneity. The study adds to evidence that loliginid squids typically display connected populations over large geographical areas unless specific oceanographic features restrict gene flow. Recognition of the Peruvian and Chilean–Falklands groups as distinct evolutionary significant units is recommended.

Background The Barotse floodplains of the upper Zambezi River and its tributaries are a highly dynamic environment, with seasonal flooding and transhumance presenting a shifting mosaic of potential larval habitat and human and livestock blood meals for malaria vector mosquitoes. However, limited entomological surveillance has been undertaken to characterize the vector community in these floodplains and their environs. Such information is necessary as, despite substantial deployment of insecticide-treated nets (ITNs) and indoor residual spraying (IRS) against Anopheles vectors, malaria transmission persists across Barotseland in Zambia’s Western Province. Methods Geographically extensive larval surveys were undertaken in two health districts along 102 km of transects, at fine spatial resolution, during a dry season and following the peak of the successive wet season. Larvae were sampled within typical Anopheles flight range of human settlements and identified through genetic sequencing of cytochrome c oxidase I and internal transcribed spacer two regions of mitochondrial and nuclear DNA. This facilitated detailed comparison of taxon-specific abundance patterns between ecological zones differentiated by hydrological controls. Results An unexpected paucity of primary vectors was revealed, with An. gambiae s.l. and An. funestus representing < 2% of 995 sequenced anophelines. Potential secondary vectors predominated in the vector community, primarily An. coustani group species and An. squamosus. While the distribution of An. gambiae s.l. in the study area was highly clustered, secondary vector species were ubiquitous across the landscape in both dry and wet seasons, with some taxon-specific relationships between abundance and ecological zones by season. Conclusions The diversity of candidate vector species and their high relative abundance observed across diverse hydro-ecosystems indicate a highly adaptable transmission system, resilient to environmental variation and, potentially, interventions that target only part of the vector community. Larval survey results imply that residual transmission of malaria in Barotseland is being mediated predominantly by secondary vector species, whose known tendencies for crepuscular and outdoor biting renders them largely insensitive to prevalent vector control methods. Graphical Abstract

Understanding demographic processes over multiple spatial scales is vital for the optimization of conservation/management strategies, particularly for commercially harvested taxa such as the brown crab (Cancer pagurusL). Brown crab population genetic structure was investigated at (i) a local scale within the Irish Sea, which included comparisons with the Lundy No Take Zone (NTZ) and (ii) across the NE Atlantic. The results indicate that the brown crab does not exhibit strong spatial structure either within the Irish Sea or at the regional level, suggesting high gene flow within and among the Irish Sea, English Channel and North Sea. Comparisons between the Lundy NTZ and harvested areas revealed similarly high levels of genetic diversity. An intriguing result was that the Lundy NTZ sample exhibited a degree of genetic patchiness (ephemeral geographically unpatterned differentiation) which may indicate elevated recruitment skews within the NTZ. Overall, the results support the view that brown crabs within the sampled area belong to a single genetically panmictic stock and that if breeding stock sizes are maintained genetic drift will not be strong enough to reduce neutral genetic diversity. The highly connected nature of this species requires international cooperation for sustainable management, an important component of which will be the application of more powerful population genomic approaches to assess finer scale aspects of stock structure as well drivers of genetic patchiness reported for the species. This is a timely consideration in light of potential future misalignments between biological and geopolitical stock boundaries in the Irish Sea following Brexit.

The genus Diplodus presents multiple cases of taxonomic conjecture. Among these the D. cervinus complex was previously described as comprising three subspecies that are now regarded as separate species: Diplodus cervinus, Diplodus hottentotus and Diplodus omanensis. Diplodus hottentotus exhibits a clear break in its distribution around the Benguela Current system, prompting speculation that Angolan and South African populations flanking this area may be isolated and warrant formal taxonomic distinction. This study reports the first integrated genetic [mitochondrial (mt)DNA and nuclear microsatellite] and morphological (morphometric, meristic and colouration) study to assess patterns of divergence between populations in the two regions. High levels of cytonuclear divergence between the populations support a prolonged period of genetic isolation, with the sharing of only one mtDNA haplotype (12 haplotypes were fully sorted between regions) attributed to retention of ancestral polymorphism. Fish from the two regions were significantly differentiated at a number of morphometric (69·5%) and meristic (46%) characters. In addition, Angolan and South African fish exhibited reciprocally diagnostic colouration patterns that were more similar to Mediterranean and Indian Ocean congeners, respectively. Based on the congruent genetic and phenotypic diversity we suggest that the use of hottentotus, whether for full species or subspecies status, should be restricted to South African D. cervinus to reflect their status as a distinct species-like unit, while the relationship between Angolan and Atlantic-Mediterranean D. cervinus will require further demo-genetic analysis. This study highlights the utility of integrated genetic and morphological approaches to assess taxonomic diversity within the biogeographically dynamic Benguela Current region.

Patella candei d’Orbigny is an exploited limpet endemic to the archipelagos of the Azores, Madeira, Selvagens and Canaries (Macaronesia). Marked declines reported for the species likely reflect overexploitation and inadequacy of current management measures with biodiversity further threatened by illegal harvesting and anthropogenic movement of limpets among archipelagos. Previous phylogeographic analyses of mtDNA COI sequence variation revealed that the (i) Azores, (ii) Madeira and (iii) Canaries and Selvagens represent three reciprocally monophyletic genetic stocks. The objective of this research was to identify diagnostic DNA sequence polymorphisms among the stocks that could be assayed by PCR-RFLP, thus permitting cost effective high throughput stock assignment. PCR-RFLP analysis of a COI fragment with two restriction enzymes (TaqI and AvaI) was sufficient to define diagnostic stock genotypes for the three stocks and permitted unambiguous stock assignment of a large sample of individuals (n = 952). This PCR-RFLP approach can be readily extended to discriminate other Patella stocks, through judicious selection of restriction enzymes and similar protocols and offers great potential for eco-certification associated practises.

This study initially aimed to investigate the genetic population/stock structuring of Lethrinus nebulosus in the Southwest Indian Ocean (SWIO) to inform management practices in light of emerging evidence of overharvesting of this species throughout its distribution. Adult samples were genotyped for 14 nuclear microsatellites and by sequencing fragments of the mtDNA control region and COI gene. A salient feature of the data was the congruent cyto-nuclear partitioning of samples into two high divergent, reciprocally monophyletic groups. This indicates that despite no a priori evidence, hitherto described L. nebulosus in the SWIO comprises two cryptic species that co-occur among southern samples. This intermingling indicates that, at least in southern samples, both species are being indiscriminately harvested, which may severely compromise sustainability. Limited microsatellite differentiation was detected within both species, though there was some evidence of isolation in the Mauritian population. In contrast, mtDNA revealed a pattern consistent with chaotic genetic patchiness, likely promoted by stochastic recruitment, which may necessitate a spatial bet-hedging approach to management to satisfy fishery management and conservation goals.

Climate change is driving the redistribution of species at a global scale and documenting and predicting species' responses to warming is a principal focus of contemporary ecology. When interpreting and predicting their responses to warming, species are generally treated as single homogenous physiological units. However, local adaptation and phenotypic plasticity can result in intraspecific differences in thermal niche. Therefore, population loss may also not only occur from trailing edges. In species with low dispersal capacity this will have profound impacts for the species as a whole, as local population loss will not be offset by immigration of warm tolerant individuals. Recent evidence from terrestrial forests has shown that incorporation of intraspecific variation in thermal niche is vital to accurately predicting species responses to warming. However, marine macrophytes (i.e. seagrasses and seaweeds) that form some of the world's most productive and diverse ecosystems have not been examined in the same context. We conducted a literature review to determine how common intraspecific variation in thermal physiology is in marine macrophytes. We find that 90% of studies identified (n = 42) found clear differences in thermal niche between geographically separated populations. Therefore, non-trailing edge populations may also be vulnerable to future warming trends and given their limited dispersal capacity, such population loss may not be offset by immigration. We also explore how next generation sequencing (NGS) is allowing unprecedented mechanistic insight into plasticity and adaptation. We conclude that in the ‘genomic era’ it may be possible to link understanding of plasticity and adaptation at the genetic level through to changes in populations providing novel insights on the redistribution of populations under future climate change.

Accurate species identification and biogeographic characterisation are fundamental for appropriate management of expanding cephalopod fisheries. This study addresses this topic within the common cuttlefish Sepia officinalis species complex (S. officinalis, S. hierredda and S. vermiculata), with an emphasis on occurrence in African waters. Tissue samples from the currently presumed distributions of S. vermiculata and S. hierredda (from South Africa and Ghana/Angola, respectively) were sequenced for the cytochrome c oxidase subunit I (COI) and the cytochrome b (cytb) genes of the mitochondrial genome and then compared to existing S. officinalis sequences. Three highly divergent and reciprocally monophyletic clades, corresponding to S. officinalis, S. hierredda and S. vermiculata, were resolved, representing the first molecular confirmation of the distinct species status of S. hierredda and S. vermiculata. The sequences also revealed that, contrary to expectations based on presently published information, al...

Southern blue whiting Micromesistus australis support a substantial commercial fishery in South America. There is growing evidence of a high level of demographic independence between stocks associated with the two main spawning grounds, one in the SW Atlantic (SWA) and one in the SE Pacific (SEP), but the potential genetic structuring of these stocks is unknown. In this study adults collected from sites throughout SWA and SEP waters were genotyped at hypervariable microsatellite markers to investigate genetic structuring between and within regions. Allele frequency-based analyses reported highly significant genetic differentiation between regions, indicating low levels of allo-recruitment. Ancillary data on migratory behaviours support natal homing as a prominent stock isolating mechanism. Genetic differentiation was also detected among samples from around the Falkland Islands: kinship analyses indicated that this was due to non-random genetic relatedness within samples. Despite a general pattern of genetic homogeneity among SEP samples, the northernmost sample exhibited significantly high mean relatedness. The data indicate the occurrence of a further level of structuring within both regions that prevents complete mixing, specifically that schools may be hierarchically structured (from putative subpopulations down to kin-containing groups) and exhibit some degree of ontogenetic cohesion, which may also be a component of homing. The importance of homing and group cohesion as factors influencing resilience to, and recovery from, overexploitation is discussed. This study represents an important baseline for future genetic monitoring and assessment of M. australis. The need for such studies is emphasised by the observation of significantly lower levels of genetic variation among SWA samples, which may reflect genetic erosion, and the subsequent collapse of the SWA stock.

Levels of self-recruitment within and connectivity among populations are key factors influencing marine population persistence and stock sustainability, as well as the effectiveness of spatially explicit management strategies such as Marine Protected Areas (MPAs). In the United Kingdom (UK), Lundy Island in the Bristol Channel was designated a No-Take Zone (NTZ) in 2003 and became the UK’s first Marine Conservation Zone (MCZ) in 2009. This NTZ is expected to represent an additional resource for the sustainable management of the European lobster (Homarus gammarus) fishery. As the first step in a genetic monitoring program, this study aimed to investigate population genetic structure of lobster within and between the Irish Sea and Bristol Channel and in doing so to assess the functioning of the Lundy NTZ in the context of connectivity and other genetic parameters. Analysis of microsatellite data indicated that lobsters within the study area are genetically homogeneous and supports the view of a single panmictic population wherein the Lundy NTZ is highly connected. Levels of genetic variability were universally high with no evidence of differences for the NTZ. Furthermore, there was no evidence of recent genetic bottlenecks, and estimates of effective population sizes were infinitely large. The results suggest that if current management and breeding stock sizes are maintained genetic drift will not be strong enough to reduce neutral genetic diversity.

Two geographically nonoverlapping species are currently described within the sparid genus Spondyliosoma: Spondyliosoma cantharus (Black Seabream) occurring across Mediterranean and eastern Atlantic waters from NW Europe to Angola and S. emarginatum (Steentjie) considered endemic to southern Africa. To address prominent knowledge gaps this study investigated range-wide phylogeographic structure across both species. Mitochondrial DNA sequences revealed deep phylogeographic structuring with four regionally partitioned reciprocally monophyletic clades, a Mediterranean clade and three more closely related Atlantic clades [NE Atlantic, Angola and South Africa (corresponding to S. emarginatum)]. Divergence and distribution of the lineages reflects survival in, and expansion from, disjunct glacial refuge areas. Cytonuclear differentiation of S. emarginatum supports its validity as a distinct species endemic to South African waters. However, the results also indicate that S. cantharus may be a cryptic species complex wherein the various regional lineages represent established/incipient species. A robust multilocus genetic assessment combining morphological data and detailing interactions among lineages is needed to determine the full diversity within Spondyliosoma and the most adequate biological and taxonomic status.

Lucanus cervus (L.), the stag beetle, is a saproxylic beetle species distributed widely across Europe. Throughout its distribution the species has exhibited pronounced declines and is widely considered threatened. Conservation efforts may be hindered by the lack of population genetic data and understanding of the spatial scale of population connectivity. To address this knowledge gap this research details the first broad scale phylogeographic study of L. cervus based on mitochondrial DNA (mtDNA) sequencing and microsatellite analysis of samples collected from 121 localities across Europe. Genetic data were complemented by palaeo-distribution models of spatial occupancy during the Last Glacial Maximum to strengthen inferences of refugial areas. A salient feature of the mtDNA was the identification of two lineages. Lineage I was widespread across Europe while lineage II was confined to Greece. Microsatellites supported the differentiation of the Greek samples and alongside palaeo-distribution models indicated this area was a glacial refuge. The genetic endemism of the Greek samples, and demographic results compatible with no signatures of spatial expansion likely reflects restricted dispersal into and out of the area. Lineage I exhibited a shallow star like phylogeny compatible with rapid population expansion across Europe. Demographic analysis indicated such expansions occurred after the Last Glacial Maximum. Nuclear diversity and hindcast species distribution models indicated a central Italian refuge for lineage I. Palaeo-distribution modelling results also suggested a western refuge in northern Iberia and south-west France. In conclusion the results provide evidence of glacial divergence in stag beetle while also suggesting high, at least on evolutionary timescales, gene flow across most of Europe. The data also provide a neutral genetic framework against which patterns of phenotypic variation may be assessed.

The big blue octopus, Octopus cyanea, occurs on coral reefs throughout the Indo-Pacific region from East Africa to the Hawaiian Islands, wherein it is of great ecological and socio-economic importance. However, many components of its intraspecific biodiversity, such as population structure, are unresolved due to a lack of informative genetic markers. To address this issue, which may compromise conservation and sustainability efforts, the development and characterisation of the first species-specific microsatellite loci for O. cyanea are described here. The eight loci were characterised by the genotyping of 40 adults from Madagascar, which revealed an average of 13.5 alleles per locus (range 9-18). The observed and expected heterozygosity per locus ranged from 0.432 to 0.949 and from 0.481 to 0.989, respectively. No evidence of linkage disequilibrium was detected between pairs of loci. Genotype proportions at six loci conformed to Hardy-Weinberg equilibrium expectations, with two loci exhibiting significant heterozygote deficits. These loci are applicable to multiple areas of eco-evolutionary research and, thus, represent a valuable resource for future studies of O. cyanea.

The analysis of mitochondrial DNA (mtDNA) base composition, codon usage, and genome arrangement patterns can provide insight into metabolic pathways and evolutionary history. Here, we report on the...

Information from genetic (microsatellites and mtDNA Control Region) and previously collected otolith (trace element fingerprinting of otolith core and edge) markers was jointly interpreted to describe dispersal and gene flow in the Patagonian hoki (Macruronus magellanicus), an intensively harvested marine fish with seasonal migrations between spawning and feeding grounds. Spawning adults from a Chilean (Pacific) spawning site and three feeding ground samples (one from Chile and two temporal samples from the Falkland Islands (Atlantic)) were analysed. The data indicated a high level of Atlantic/Pacific connectivity by means of non-natal homing of individuals to spawning aggregations. Against this background of regional connectivity however, genetic data support the existence of a reproductively isolated population within the overwintering stock. Otolith core results are compatible with reproductive isolation being effected by natal homing to an Atlantic spawning site and/or local adaptation. The discordance between geopolitically defined Atlantic and Pacific management stocks and underlying biocomplexity, and implications for sustainability, are discussed. The study highlights the importance of intraspecific variation in homing behaviours in shaping population structure and the merit of employing complementary analytical approaches.

Combined analysis of genetic and morphological variation can provide synergistic insights into eco-evolutionary forces shaping biodiversity, as well as tools for conservation and management. Macaronesian limpets are undergoing severe declines due to overexploitation which calls for an evaluation of the evolutionary significance and taxonomic status of populations. This study details the analysis of genetic (mtDNA sequencing) and morphological (geometric analysis of shell shape) variation among Macaronesian populations of Patella aspera, P. rustica, and P. candei. In the case of P. aspera and P. rustica, this also included analysis of mainland conspecifics. mtDNA revealed distinct phylogeographic patterns for the three species. For both P. aspera and P. rustica Macaronesian and continental samples were reciprocally monophyletic, with shallower, and distinct, phylogeographic structure within both clades. For P. candei, the Macaronesian endemic, three reciprocally monophyletic groups corresponding to (i) the Azores, (ii) Madeira and (iii) Selvagens and Canary Islands were resolved. The different patterns for each species are compatible with independent processes of colonization and demographic processes. Morphological differentiation matched the major phylogeographic groupings (i.e., Macaronesian v Continent for P. aspera and P. rustica; Azores/Madeira/Selvagens and Canary Islands for P. candei) compatible with such variation being shaped by genetic drift associated with distinct demographic histories of lineages as well as historical/recurrent selection pressures. The genetic/morphological congruence supports the formal recognition of at least three described P. candei subspecies. Moreover, the data prompt recommendation of the separate management of limpets from each archipelago. At present management efforts are hampered by illegal harvesting of limpets. From an applied viewpoint, this study confirms that morphology retains useful information on genetic status and thus represents a potentially cheap method applicable to limpet conservation.

The Atlantic rock crab Cancer irroratus is native along the east coast of North America. The species was first recorded in Iceland in 2006 and has since rapidly spread throughout the country's southwestern and western coastal waters. The transport of larvae in ballast water is the most probable route by which introduction into Iceland occurred. As this species is commercially valuable, it may be possible to establish a viable industry harvesting rock crabs in Iceland; however, to do this, more information on species-wide genetic diversity and demography is required. In this study, genetic variation at 7 microsatellite markers was analyzed in samples from Iceland and 5 sites in North America, capturing most of the known range of this species. Our results divided samples from the native range into 2 groups, divided by a previously proposed barrier to gene flow, compatible with local hydrographic factors restricting larval-mediated gene flow. The Icelandic population was markedly differentiated from all other samples, but exhibited comparable levels of genetic diversity with no evidence of small population effects or genetic bottlenecks. No single population could be identified as a source for the Icelandic population, though the likely origin could be attributed to the 'northern group' in the native range. Genetic data indicate that the number of founders of the Icelandic population was sufficient to retain genetic variation. As the Icelandic population shows evidence of self-recruitment and population expansion, it may represent a potential harvestable resource in Iceland.

The big blue octopus, Octopus cyanea, occurs on coral reefs throughout the Indo-Pacific region from East Africa to the Hawaiian Islands, wherein it is of great ecological and socio-economic importance. However, many components of its intraspecific biodiversity, such as population structure, are unresolved due to a lack of informative genetic markers. To address this issue, which may compromise conservation and sustainability efforts, the development and characterisation of the first species-specific microsatellite loci for O. cyanea are described here. The eight loci were characterised by the genotyping of 40 adults from Madagascar, which revealed an average of 13.5 alleles per locus (range 9–18). The observed and expected heterozygosity per locus ranged from 0.432 to 0.949 and from 0.481 to 0.989, respectively. No evidence of linkage disequilibrium was detected between pairs of loci. Genotype proportions at six loci conformed to Hardy–Weinberg equilibrium expectations, with two loci exhibiting significant heterozygote deficits. These loci are applicable to multiple areas of eco-evolutionary research and, thus, represent a valuable resource for future studies of O. cyanea.

The last glaciation was a dynamic period with strong impact on the demography of many species and populations. In recent years, mitochondrial DNA sequences retrieved from radiocarbon-dated remains have provided novel insights into the history of Late Pleistocene populations. However, genotyping of loci from the nuclear genome may provide enhanced resolution of population-level changes. Here, we use four autosomal microsatellite DNA markers to investigate the demographic history of woolly mammoths (Mammuthus primigenius) in north-eastern Siberia from before 60 000 years ago up until the species' final disappearance c.4000 years ago. We identified two genetic groups, implying a marked temporal genetic differentiation between samples with radiocarbon ages older than 12 thousand radiocarbon years before present (ka) and those younger than 9ka. Simulation-based analysis indicates that this dramatic change in genetic composition, which included a decrease in individual heterozygosity of approximately 30%, was due to a multifold reduction in effective population size. A corresponding reduction in genetic variation was also detected in the mitochondrial DNA, where about 65% of the diversity was lost. We observed no further loss in genetic variation during the Holocene, which suggests a rapid final extinction event.

The common cuttlefish, Sepia officinalis, represents a model mobile marine species for studies of evolutionary processes occurring across a range of spatial and temporal scales. Such studies are relevant to sustainable fishery management and biodiversity conservation as the species is intensely exploited and an important component of inshore marine ecosystems. The isolation and preliminary characterisation of 10 dinucleotide repeat microsatellite loci is described. Genotyping of 48 adults from Agon Coutainville (France) revealed polymorphism at 9 of the loci. Among the polymorphic loci there was an average of 8.8 alleles per locus (range 3–14) with observed and expected heterozygosity per locus ranging from 0.104 to 0.792 and from 0.101 to 0.806, respectively. No evidence of linkage disequilibrium was detected between any locus pair. The loci described here represent a valuable addition to the suite of genetic markers applicable to S. officinalis research.

Shaw, P. W., Hendrickson, L., McKeown, N., Stonier, T., Naud, M. . J., Sauer, W. H. H. (2010). Discrete spawning aggregations of loliginid squid do not represent genetically distinct populations. Marine Ecology Progress Series, 408, 117-127.

The phylogeographical structure of brown trout Salmo trutta in Britain and Ireland was studied using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of four mitochondrial DNA segments (16S/ND1, ND5/6, COXIII/ND5 and ND5/12S). Analysis of 3636 individuals from 83 sites-morphotypes revealed a total of 25 haplotypes. These haplotypes were nested in seven two-step clades. Although there was a clear geographical patterning to the occurrence of derived clades, admixture among ancestral clades was extensive throughout the studied area. A relevant feature of the data was that some populations contained mixtures of highly divergent clades. This type II phylogeographic pattern is uncommon in nature. Clade intermixing is likely to have taken place during earlier interglacials as well as since the Last Glacial Maximum. The anadromous life history of many S. trutta populations has probably also contributed to clade mixing. Based on the data presented here and published data, postglacial colonization of Britain and Ireland most likely involved S. trutta from at least five potential glacial refuges. Probable locations for such refugia were: south of England-western France, east of the Baltic Sea, western Ireland, Celtic Sea and North Sea. Ferox S. trutta, as defined by their longevity, late maturation and piscivory, exhibited a strong association with a particular clade indicating that they share a common ancestor. Current evidence indicates that the Lough Melvin gillaroo S. trutta and sonaghen S. trutta sympatric types diverged prior to colonization of Lough Melvin and, although limited gene flow has occurred since secondary contact, they have remained largely reproductively isolated due to inlet and outlet river spawning segregation. Gillaroo S. trutta may reflect descendents of a previously more widespread lineage that has declined due to habitat alterations particularly affecting outlet rivers. The mosaic-like distribution of mtDNA lineages means that conservation prioritization in Britain and Ireland should be based on the biological characteristics of local populations rather than solely on evolutionary lineages.

Ungfors, A., McKeown, N. J., Shaw, P. W., and André, C. 2009. Lack of spatial genetic variation in the edible crab (Cancer pagurus) in the Kattegat–Skagerrak area. – ICES Journal of Marine Science, 66: 462–469. The stock structure of the edible crab (Cancer pagurus L.) in the Kattegat and Skagerrak was investigated using eight microsatellite DNA loci. Replicate samples, collected 4–6 years apart, were derived from the Kattegat (Grove Bank, 57°N) and the Skagerrak (Lunneviken, 59°N), plus a geographical outgroup sample from the Norwegian Sea (Midsund, 62°N). Genetic differentiation among samples, estimated as global FST = 0.002, was significant (p = 0.03) when the statistical test was based on allele frequencies, but not when based on genotype frequencies. Moreover, all single- and multilocus pairwise tests between samples were non-significant. An analysis of molecular variance, AMOVA, did not reveal significant differentiation between spatial (Kattegat vs. Skagerrak) or temporal (2001/2002 vs. 2006/2007) groups of samples. Power analysis suggested that the loci and sample sizes employed conferred a power of >90% of detecting even low (true FST = 0.002) levels of population structure. Low spatial and temporal genetic structure might be explained by either or both of (i) high levels of contemporary gene flow in the area attributable to adult migration or larval dispersal or both factors taken together, and (ii) patterns of historical gene flow persisting among recently founded large populations.

Declining population sizes reported for a number of marine species have emphasised the need for information on mating systems to be incorporated into conservation and management strategies, particularly for exploited species. The brown crab Cancer pagurus L. supports a major fishery; however, many aspects of the species' mating system, such as paternity patterns, are unre- solved. In this study, 3 microsatellite loci conferring a high degree of statistical power were used to determine whether broods from 18 ovigerous females collected from the English Channel had been fertilised by multiple males. Despite the capacity of this species for long-term storage of sperm and the suspected potential for females to use sperm from multiple males simultaneously, no evidence of multiple paternity was detected. Hypotheses as to the predominant processes leading to single pater- nity are discussed. In systems where females exhibit genetic monogamy the effective population size is constrained by the number of females. Such systems may be particularly susceptible to declines if females are removed. This has important implications for management of C. pagurus populations, as fishery data indicate that females are more heavily harvested than males.

International audience; As cephalopods fulfil important roles in marine ecosystems and may be especially susceptible to overfish-ing the predicted expansion of cephalopod fisheries will require improved assessment and management of stocks to ensure ecosystem compatible exploitation. Genetic markers facilitating high throughput accurate species identification, particularly for early life history stages, would considerably benefit cephalopod fisheries research. Reported here is the development of a PCR-RFLP assay for identification of four squid species (Loligo vulgaris, Loligo forbesi, Alloteuthis media and Alloteuthis subulata) of growing interest as fisheries resources. The assay was used to type morphologically indistinguishable paralarvae collected from Seine Bay and revealed 99% to be A. media despite a priori expectations that L. vulgaris (present at 1%) would predominate. As the method can be applied to various life history stages and tissue types it offers considerable potential for use in studies of life history, stock structure, reproduction, recruitment and abundance that are necessary for sustainable management.

Ten polymorphic microsatellite DNA loci were isolated from Mexican four-eyed octopus Octopus maya, by construction of an enriched genomic library. Genotyping of 35 individuals from Sabancuy Campeche, Mexico, revealed variable levels of locus polymorphism with an average of 9.2 alleles. The observed and expected heterozygosity per locus ranged from 0.53 to 0.93 and from 0.48 to 0.87, respectively. No evidence of linkage disequilibrium was detected between pairs of loci and genotype proportions at all loci conformed to Hardy–Weinberg equilibrium expectations. The microsatellite loci developed constitute a suite of genetic markers applicable to sustainable fishery management for O. maya.

Octopus vulgaris, Octopus cyanea and Callistoctopus ornatus may co-occur in near-shore shallow reef habitats across the Southwestern Indian Ocean. All three species are harvested, both by small vessels and individual spearfishers and are of considerable socio-economic importance. Phenotypic-based discrimination of the three species is unreliable and at present species-specific catch data are not collected, preventing evaluation of species specific fisheries effects. In light of increasing exploitation rates the development of an unambiguous means of species discrimination is required for sustainable management and conservation of species and intraspecific stocks. In this study, a simple, cost effective, molecular technique to differentiate the three species is described.

Gerlach et al. (2012; Mar Ecol Prog Ser 450:281�283) argue that temporal instability in patterns of cryptic genetic differentiation in Doryteuthis pealeii, resulting from sampling of family groups, is the most likely explanation for differences in patterns of genetic differentiation presented in Buresch et al. (2006) and Shaw et al. (2010). We agree that temporal genetic patchi- ness might be an explanation, but disagree that cohesive and genetically differentiated family groups are the cause. We conclude that currently there is not enough evidence for temporally sta- ble population differentiation, explained by a feasible biological/physical mechanism, to support management of the species as anything other than single genetic stocks across large geographical regions of the NW Atlantic. Further study of this species is warranted to understand the factors generating temporal genetic changes.

Geelbeck (Atractoscion aequidens) represents a valuable fishery resource in the Benguela Current region in southwestern Africa. Due to overexploitation the species is considered depleted in South Africa, and little information is available for the rest of its distribution in the region. Genetic studies of the species are essential to inform management plans for sustainable harvesting and conservation. To facilitate such studies 12 polymorphic microsatellite DNA loci were isolated from an enriched genomic library. Genotyping of 41 individuals revealed an average of 17.75 alleles per locus (range 2–37), and observed/expected heterozygosity per locus of 0.024–0.951 and 0.024–0.962, respectively. These loci constitute the first microsatellite markers isolated for geelbeck and are applicable to multiple areas of research on this species.

Twelve polymorphic microsatellite DNA loci were isolated from the brown crab, Cancer pagurus L., by construction of microsatellite-enriched genomic libraries. Genotyping of 40 individuals from Norfolk (UK) revealed variable levels of locus polymorphism with an average of 7.75 alleles per locus (range 2-22). The observed and expected heterozygosities per locus ranged from 0.025 to 0.868 and from 0.025 to 0.947, respectively. No evidence of linkage disequilibrium was detected between pairs of loci and genotype proportions at all loci conformed to Hardy-Weinberg equilibrium expectations. The microsatellite loci developed constitute a suite of genetic markers applicable to numerous areas of C. pagurus research.

The taxonomy of stag beetles (Coleoptera: Lucanidae) remains challenging, mainly due to the sexual dimorphism and the strong allometry in males. Such conjecture confounds taxonomic based conservation efforts that are urgently needed due to numerous threats to stag beetle biodiversity. Molecular tools could help solve the problem of identification of the different recognized taxa in the “Lucanus cervus complex” and in some related Palaearctic species. We investigated the potential use of a 670 bp region at the 3’ end of the mitochondrial cytochrome c oxidase subunit 1 gene (COI) for barcoding purposes (different from the standard COI barcoding region). Well resolved species and subspecies were L. tetraodon, L. cervus akbesianus, L. c. laticornis, as well as the two eastern Asian outgroup taxa L. formosanus and L. hermani. Conversely, certain taxa could not be distinguished from each other based on K2P distances and tree topologies: L. c. fabiani / L. (P.) barbarossa, L. c. judaicus / an unknown Lucanus species, L. c. cervus / L. c. turcicus / L. c. pentaphyllus / L. (P.) macrophyllus / L. ibericus. The relative roles of phenotypic plasticity, recurrent hybridisation and incomplete lineage sorting underlying taxonomic and phylogenetic discordances are discussed.

The last glaciation was a dynamic period with strong impact on the demography of many species and populations. In recent years, mitochondrial DNA sequences retrieved from radiocarbon-dated remains have provided novel insights into the history of Late Pleistocene populations. However, genotyping of loci from the nuclear genome may provide enhanced resolution of population-level changes. Here, we use four autosomal microsatellite DNA markers to investigate the demographic history of woolly mammoths (Mammuthus primigenius) in north-eastern Siberia from before 60 000 years ago up until the species' final disappearance c.4000 years ago. We identified two genetic groups, implying a marked temporal genetic differentiation between samples with radiocarbon ages older than 12 thousand radiocarbon years before present (ka) and those younger than 9ka. Simulation-based analysis indicates that this dramatic change in genetic composition, which included a decrease in individual heterozygosity of approximately 30%, was due to a multifold reduction in effective population size. A corresponding reduction in genetic variation was also detected in the mitochondrial DNA, where about 65% of the diversity was lost. We observed no further loss in genetic variation during the Holocene, which suggests a rapid final extinction event.