Glacial refugia and recolonization pathways in the brown seaweed Fucus serratus

Population genomics of the white-beaked dolphin (Lagenorhynchus albirostris): Implications for conservation amid climate-driven range shifts

Climate change is rapidly affecting species distributions across the globe, particularly in the North Atlantic. For highly mobile and elusive cetaceans, the genetic data needed to understand population dynamics are often scarce. Cold-water obligate species such as the white-beaked dolphin (Lagenorhynchus albirostris) face pressures from habitat shifts due to rising sea surface temperatures in addition to other direct anthropogenic threats. Unravelling the genetic connectivity between white-beaked dolphins across their range is needed to understand the extent to which climate change and anthropogenic pressures may impact species-wide genetic diversity and identify ways to protect remaining habitat. We address this by performing a population genomic assessment of white-beaked dolphins using samples from much of their contemporary range. We show that the species displays significant population structure across the North Atlantic at multiple scales. Analysis of contemporary migration rates suggests a remarkably high connectivity between populations in the western North Atlantic, Iceland and the Barents Sea, while two regional populations in the North Sea and adjacent UK and Irish waters are highly differentiated from all other clades. Our results have important implications for the conservation of white-beaked dolphins by providing guidance for the delineation of more appropriate management units and highlighting the risk that local extirpation may have on species-wide genetic diversity. In a broader context, this study highlights the importance of understanding genetic structure of all species threatened with climate change-driven range shifts to assess the risk of loss of species-wide genetic diversity.

Rapid diversification of grey mangroves (Avicennia marina) driven by geographic isolation and extreme environmental conditions in the Arabian Peninsula

Biological systems occurring in ecologically heterogeneous and spatially discontinuous habitats provide an ideal opportunity to investigate the relative roles of neutral and selective factors in driving lineage diversification. The grey mangroves (Avicennia marina) of Arabia occur at the northern edge of the species' range and are subject to variable, often extreme, environmental conditions, as well as historic large fluctuations in habitat availability and connectivity resulting from Quaternary glacial cycles. Here, we analyse fully sequenced genomes sampled from 19 locations across the Red Sea, the Arabian Sea and the Persian/Arabian Gulf (PAG) to reconstruct the evolutionary history of the species in the region and to identify adaptive mechanisms of lineage diversification. Population structure and phylogenetic analyses revealed marked genetic structure correlating with geographic distance and highly supported clades among and within the seas surrounding the Arabian Peninsula. Demographic modelling showed times of divergence consistent with recent periods of geographic isolation and low marine connectivity during glaciations, suggesting the presence of (cryptic) glacial refugia in the Red Sea and the PAG. Significant migration was detected within the Red Sea and the PAG, and across the Strait of Hormuz to the Arabian Sea, suggesting gene flow upon secondary contact among populations. Genetic-environment association analyses revealed high levels of adaptive divergence and detected signs of multi-loci local adaptation driven by temperature extremes and hypersalinity. These results support a process of rapid diversification resulting from the combined effects of historical factors and ecological selection and reveal mangrove peripheral environments as relevant drivers of lineage diversity.

The molecular background of the aspartate aminotransferase polymorphism in Littorina snails maintained by strong selection on small spatial scales

Allozymes present several classical examples of divergent selection, including the variation in the cytosolic aspartate aminotransferase (AAT) in the intertidal snails Littorina saxatilis. AAT is a part of the asparate-malate shuttle, in the interidal molluscs involved in the anaerobic respiration during desiccation. Previous allozyme studies reported the sharp gradient in the frequencies of the AAT¹⁰⁰and the AAT¹²⁰ alleles between the low and high shores in the Northern Europe and the differences in their enzymatic activity, supporting the role of AAT in adaptation to desiccation. However, the populations in the Iberian Peninsula showed the opposite allele cline. Using the mRNA sequencing and the genome pool-seq analyses we characterize DNA sequences of the different AAT alleles, report the amino acid replacements behind the allozyme variation and show that same allozyme alleles in Northern and Southern populations have different protein sequences. Gene phylogeny reveals that the AAT¹⁰⁰ and the northern AAT¹²⁰ alleles represent the old polymorphism, shared among the closely related species of Littorina, while the southern AAT¹²⁰ allele is more recently derived from AAT¹⁰⁰. Further, we show that the Aat gene is expressed at constitutive level in different genotypes and conditions, supporting the role of structural variation in regulation of enzyme activity. Finally, we report the location and the structure of the gene in the L. saxatilis genome and the presence of two additional non-functional gene copies. Altogether, we provide a missing link between the classical allozyme studies and the genome scans and bring together the results produced over decades of the genetic research.

Evolutionary dynamics of sex-biased gene expression in a young XY system: insights from the brown alga genus Fucus

Sex-biased gene expression is considered to be an underlying cause of sexually dimorphic traits. Although the nature and degree of sex-biased expression have been well documented in several animal and plant systems, far less is known about the evolution of sex-biased genes in more distant eukaryotic groups. Here, we investigate sex-biased gene expression in two brown algal dioecious species, Fucus serratus and Fucus vesiculosus, where male heterogamety (XX/XY) has recently emerged. We find that in contrast to evolutionary distant plant and animal lineages, male-biased genes do not experience high turnover rates, but instead reveal remarkable conservation of bias and expression levels between the two species, suggesting their importance in sexual differentiation. Genes with consistent male bias were enriched in functions related to gamete production, along with sperm competition and include three flagellar proteins under positive selection. We present one of the first reports, outside of the animal kingdom, showing that male-biased genes display accelerated rates of coding sequence evolution compared with female-biased or unbiased genes. Our results imply that evolutionary forces affect male and female sex-biased genes differently on structural and regulatory levels, resulting in unique properties of differentially expressed transcripts during reproductive development in Fucus algae.

Climate change threatens unique evolutionary diversity in Australian kelp refugia

Climate change has driven contemporary decline and loss of kelp forests globally with an accompanying loss of their ecological and economic values. Kelp populations at equatorward-range edges are particularly vulnerable to climate change as these locations are undergoing warming at or beyond thermal tolerance thresholds. Concerningly, these range-edge populations may contain unique adaptive or evolutionary genetic diversity that is vulnerable to warming. We explore haplotype diversity by generating a Templeton-Crandall-Sing (TCS) network analysis of 119 Cytochrome C Oxidase (COI) sequences among four major population groupings for extant and putatively extinct populations only known from herbarium specimens of the dominant Laminarian kelp Ecklonia radiata in the south-western Pacific, a region warming at 2-4 times the global average. Six haplotypes occurred across the region with one being widespread across most populations. Three unique haplotypes were found in a deep-water range-edge population off Moreton Island, Queensland, which likely represents both a contemporary and historic refuge during periods of climatic change. Hindcasting E. radiata cover estimates using extant data, we reveal that this region likely supported the highest kelp cover in eastern Australia during the last glacial maximum. The equatorward range edge, deep-water kelp populations off Moreton Island represent a genetically diverse evolutionary refuge that is currently threatened by warming and requires prompt ex-situ conservation measures.

Trans-Arctic vicariance in Strongylocentrotus sea urchins

The sea urchins Strongylocentotus pallidus and S. droebachiensis first invaded the Atlantic Ocean from the Pacific following the opening of the Bering seaway in the late Miocene. While trans-Arctic dispersal during the Pleistocene is thought to have maintained species' integrity, a recent genomic analysis identified a reproductively isolated cryptic species within S. droebachiensis. Based on previous studies, the distribution of one of these lineages (S. droebachiensis W) includes the shallow water habitats of the northwest Atlantic and Pacific, while the other (S. droebachiensis E) is found throughout the shallow habitat in the northeast but is mostly restricted to deep habitats (>65 m) in the northwest Atlantic. However, since genetic variation within S. droebachiensis has been largely unstudied in the north Pacific and Arctic oceans, the biogeography of the cryptic species is not well known, and it is difficult to identify the mechanisms driving population subdivision and speciation. Here we use population genetic analyses to characterize the distribution of each species, and to test hypotheses about the role of vicariance in the evolution of systematic and genomic divergence within the genus. We collected individuals of all three Strongylocentrotus species (n = 365) from 10 previously unsampled locations in the northeast Pacific and north Atlantic (Labrador Sea and Norway), and generated mtDNA sequence data for a 418 bp fragment of cytochrome c oxidase subunit I (COI). To assess the biogeography of all three species, we combined our alignment with five previously published data sets (total n = 789) and used statistical parsimony and maximum likelihood to identify species and characterize their distribution within and among oceans. Patterns of haplotype sharing, pairwise F _ST , and hierarchical analyses of molecular variance (AMOVA) identified trans-Arctic dispersal in S. pallidus and S. droebachiensis W, but other than 5 previously reported singletons we failed to detect additional mtDNA haplotypes of S. droebachiensis E in the north Pacific. Within the Atlantic, patterns of habitat segregation suggests that temperature may play a role in limiting the distribution of S. droebachiensis E, particularly throughout the warmer coastal waters along the coast of Nova Scotia. Our results are consistent with the cycles of trans-Arctic dispersal and vicariance in S. pallidus and S. droebachiensis W, but we suggest that the evolution of Atlantic populations of S. droebachiensis E has been driven by persistent trans-Arctic vicariance that may date to the initial invasion in the late Pliocene.

Geographical parthenogenesis in the brown alga Scytosiphon lomentaria (Scytosiphonaceae): Sexuals in warm waters and parthenogens in cold waters

Geographical parthenogenesis, a phenomenon where parthenogens and their close sexual relatives inhabit distinct geographical areas, has been considered an interesting topic in evolutionary biology. Reports of geographical parthenogenesis from land and freshwater are numerous, but this occurrence has been rarely reported from the sea. Brown algae are mostly marine and are thought to include numerous obligate parthenogens; still, little is known about the distribution, origin and evolution of parthenogens in this group. Here we report a novel pattern of geographical parthenogenesis in the isogamous brown alga Scytosiphon lomentaria. Sex ratio investigation demonstrated that, in Japan, sexual populations grew in the coast along warm ocean currents, whereas female-dominant parthenogenetic populations grew mainly in the coast along a cold ocean current. In the two localities where sexual and parthenogenetic populations were parapatric, parthenogens grew in more wave-exposed areas than sexuals. Population genetic and phylogenetic analyses, including those based on genome-wide single nucleotide polymorphism data, indicated that parthenogens have initially evolved at least twice and subsequent hybridizations between the parthenogens and sexuals have generated multiple new parthenogenetic lineages. The origin of the initial parthenogens is not clear, except that it would not be interspecies hybridization. Interestingly, we found that the production of sex pheromones, which attract male gametes, has been independently lost in the initial two parthenogenetic lineages. This parallel loss of the sexual trait may represent the direct origin of parthenogens, or the regressive evolution of a useless trait under asexuality.

Whole genome genotyping reveals discrete genetic diversity in north-east Atlantic maerl beds

Maerl beds are vital habitats for a diverse array of marine species across trophic levels, but they are increasingly threatened by human activities and climate change. Furthermore, little is known about the genetic diversity of maerl-forming species and the population structure of maerl beds, both of which are important for understanding the ability of these species to adapt to changing environments and for informing marine reserve planning. In this study, we used a whole genome genotyping approach to explore the population genomics of Phymatolithon calcareum, a maerl-forming red algal species, whose geographical distribution spans the north-east Atlantic, from Norway to Portugal. Our results, using 14,150 genome-wide SNPs (single nucleotide polymorphisms), showed that P. calcareum maerl beds across the north-east Atlantic are generally structured geographically, a pattern likely explained by low dispersal potential and limited connectivity between regions. Additionally, we found that P. calcareum from the Fal Estuary, south-west England, is genetically distinct from all other P. calcareum sampled, even from The Manacles, a site located only 13 km away. Further analysis revealed that this finding is not the result of introgression from two closely related species, Phymatolithon purpureum or Lithothamnion corallioides. Instead, this unique diversity may have been shaped over time by geographical isolation of the Fal Estuary maerl bed and a lack of gene flow with other P. calcareum populations. The genomic data presented in this study suggest that P. calcareum genetic diversity has accumulated over large temporal and spatial scales, the preservation of which will be important for maximizing the resilience of this species to changes in climate and the environment. Moreover, our findings underline the importance of managing the conservation of maerl beds across western Europe as distinct units, at a site-by-site level.

Evolution at two time frames: ancient structural variants involved in post-glacial divergence of the European plaice (Pleuronectes platessa)

Changing environmental conditions can lead to population diversification through differential selection on standing genetic variation. Structural variant (SV) polymorphisms provide examples of ancient alleles that in time become associated with novel environmental gradients. The European plaice (Pleuronectes platessa) is a marine flatfish showing large allele-frequency differences at two putative SVs associated with environmental variation. In this study, we explored the contribution of these SVs to population structure across the North East Atlantic. We compared genome-wide population structure using sets of RAD-sequencing SNPs with the spatial structure of the SVs. We found that in contrast to the rest of the genome, the SVs were only weakly associated with an isolation-by-distance pattern. Indeed, both SVs showed important variation in haplogroup frequencies, with the same haplogroup increasing both along the salinity gradient of the Baltic Sea, and found in high frequency in the northern-range margin of the Atlantic. Phylogenetic analyses suggested that the SV alleles are much older than the age of the Baltic Sea itself. These results suggest that the SVs are older than the age of the environmental gradients with which they currently co-vary. Altogether, our results suggest that the plaice SVs were shaped by evolutionary processes occurring at two time frames, firstly following their origin, ancient spread and maintenance in the ancestral populations, and secondly related to their current association with more recently formed environmental gradients such as those found in the North Sea-Baltic Sea transition zone.

Phylogeography in an "oyster" shell provides first insights into the genetic structure of an extinct Ostrea edulis population

The historical phylogeography of Ostrea edulis was successfully depicted in its native range for the first time using ancient DNA methods on dry shells from museum collections. This research reconstructed the historical population structure of the European flat oyster across Europe in the 1870s-including the now extinct population in the Wadden Sea. In total, four haplogroups were identified with one haplogroup having a patchy distribution from the North Sea to the Atlantic coast of France. This irregular distribution could be the result of translocations. The other three haplogroups are restricted to narrow geographic ranges, which may indicate adaptation to local environmental conditions or geographical barriers to gene flow. The phylogenetic reconstruction of the four haplogroups suggests the signatures of glacial refugia and postglacial expansion. The comparison with present-day O. edulis populations revealed a temporally stable population genetic pattern over the past 150 years despite large-scale translocations. This historical phylogeographic reconstruction was able to discover an autochthonous population in the German and Danish Wadden Sea in the late nineteenth century, where O. edulis is extinct today. The genetic distinctiveness of a now-extinct population hints at a connection between the genetic background of O. edulis in the Wadden Sea and for its absence until today.

Pleistocene Ice Ages Created New Evolutionary Lineages, but Limited Speciation in Northeast Pacific Winged Kelp

The extent that Pleistocene climate variability promoted speciation has been much debated. Here, we surveyed genetic markers in winged kelp Alaria in the Gulf of Alaska, Northeast Pacific Ocean to understand how paleoclimates may have influenced diversity in this kelp. The study included wide geographic sampling over 2800 km and large sample sizes compared to previous studies of this kelp. Mitochondrial 5'-COI (664 bp), plastid rbcL-3' (740 bp) and 8 microsatellite markers in 16 populations resolved 5 well-defined lineages. COI-rbcL haplotypes were distributed chaotically among populations around the Gulf of Alaska. Principal Coordinates Analysis of microsatellite genotypes grouped plants largely by organellar lineage instead of geography, indicating reproductive isolation among lineages. However, microsatellite markers detected hybrids at 3 sites where lineages co-occurred. Local adaptation on various time scales may be responsible for some genetic differences between populations located along wave-energy and salinity gradients, but the chaotic pattern of variability over hundreds of kilometers is likely due to isolations in northern refugia during Pleistocene ice ages. The range of divergences between populations indicates that episodic glaciations led to the creation of new lineages, but population turnover (local extinctions and recolonizations) limited the formation of new species in the Northeastern Pacific Ocean.

Seascape genomics reveals population isolation in the reef-building honeycomb worm, Sabellaria alveolata (L.)

BACKGROUND

Under the threat of climate change populations can disperse, acclimatise or evolve in order to avoid fitness loss. In light of this, it is important to understand neutral gene flow patterns as a measure of dispersal potential, but also adaptive genetic variation as a measure of evolutionary potential. In order to assess genetic variation and how this relates to environment in the honeycomb worm (Sabellaria alveolata (L.)), a reef-building polychaete that supports high biodiversity, we carried out RAD sequencing using individuals from along its complete latitudinal range. Patterns of neutral population genetic structure were compared to larval dispersal as predicted by ocean circulation modelling, and outlier analyses and genotype-environment association tests were used to attempt to identify loci under selection in relation to local temperature data.

RESULTS

We genotyped 482 filtered SNPs, from 68 individuals across nine sites, 27 of which were identified as outliers using BAYESCAN and ARLEQUIN. All outlier loci were potentially under balancing selection, despite previous evidence of local adaptation in the system. Limited gene flow was observed among reef-sites (FST = 0.28 ± 0.10), in line with the low dispersal potential identified by the larval dispersal models. The North Atlantic reef emerged as a distinct population and this was linked to high local larval retention and the effect of the North Atlantic Current on dispersal.

CONCLUSIONS

As an isolated population, with limited potential for natural genetic or demographic augmentation from other reefs, the North Atlantic site warrants conservation attention in order to preserve not only this species, but above all the crucial functional ecological roles that are associated with their bioconstructions. Our study highlights the utility of using seascape genomics to identify populations of conservation concern.

Limited Genetic Connectivity Among Sargassum horneri (Phaeophyceae) Populations in the Chinese Marginal Seas Despite Their high Dispersal Capacity

Sargassum horneri is a habitat-forming species in the Northwest Pacific and an important contributor to seaweed rafts. In this study, 131 benthic samples and 156 floating samples were collected in the Yellow Sea and East China Sea (ECS) to test the effects of seaweed rafts on population structure and connectivity. Our results revealed high levels of genetic diversity in both benthic and floating samples based on concatenated mitochondrial markers (rpl5-rps3, rnl-atp9, and cob-cox2). Phylogenetic analyses consistently supported the existence of two lineages (lineages I and II), with divergence dating to c. 0.692 Mya (95% HPD: 0.255-1.841 Mya), indicating that long-term isolation may have occurred during the mid-Pleistocene (0.126-0.781 Mya). Extended Bayesian skyline plots demonstrated a constant population size over time in lineage I and slight demographic expansion in lineage II. Both lineages were found in each marginal sea (including both benthic and floating samples), but PCoA, FST , and AMOVA analyses consistently revealed deep genetic variation between regions. Highly structured phylogeographic pattern supports limited genetic connectivity between regions. IMA analyses demonstrated that asymmetric gene flow between benthic populations in the North Yellow Sea (NYS) and ECS was extremely low (ECS→NYS, 2Nm = 0.6), implying that high dispersal capacity cannot be assumed to lead to widespread population connectivity, even without dispersal barriers. In addition, there were only a few shared haplotypes between benthic and floating samples, suggesting the existence of hidden donors for the floating masses in the Chinese marginal seas.

Phylogeographic history of flat periwinkles, Littorina fabalis and L. obtusata

Background

The flat periwinkles, Littorina fabalis and L. obtusata, are two sister species widely distributed throughout the Northern Atlantic shores with high potential to inform us about the process of ecological speciation in the intertidal. However, whether gene flow has occurred during their divergence is still a matter of debate. A comprehensive assessment of the genetic diversity of these species is also lacking and their main glacial refugia and dispersal barriers remain largely unknown. In order to fill these gaps, we sequenced two mitochondrial genes and two nuclear fragments to perform a phylogeographic analysis of flat periwinkles across their distribution range.

Results

We identified two main clades largely composed by species-specific haplotypes corresponding to L. obtusata and L. fabalis, with moderate to strong support, respectively. Importantly, a model of divergence with gene flow between the two species (from L. obtusata to L. fabalis) was better supported, both in Iberia and in northern-central Europe. Three mitochondrial clades were detected within L. fabalis and two within L. obtusata, with strong divergence between Iberia and the remaining populations. The largest component of the genetic variance within each species was explained by differences between geographic regions associated with these clades. Our data suggests that overall intraspecific genetic diversity is similar between the two flat periwinkle species and that populations from Iberia tend to be less diverse than populations from northern-central Europe.

Conclusions

The phylogeographic analysis of this sister-species pair supports divergence with gene flow. This system thus provides us with the opportunity to study the contribution of gene flow and natural selection during diversification. The distribution of the different clades suggests the existence of glacial refugia in Iberia and northern-central Europe for both species, with a main phylogeographic break between these regions. Although the genetic diversity results are not fully conclusive, the lower diversity observed in Iberia could reflect marginal conditions at the southern limit of their distribution range during the current interglacial period.

The Biogeographic Importance of Buoyancy in Macroalgae: A Case Study of the Southern Bull-Kelp Genus Durvillaea (Phaeophyceae), Including Descriptions of Two New Species1

Long-distance dispersal plays a key role in evolution, facilitating allopatric divergence, range expansions, and species movement in response to environmental change. Even species that seem poorly suited to dispersal can sometimes travel long distances, for example via hitchhiking with other, more intrinsically dispersive species. In marine macroalgae, buoyancy can enable adults-and diverse hitchhikers-to drift long distances, but the evolution and role of this trait are poorly understood. The southern bull-kelp genus Durvillaea includes several non-buoyant and buoyant species, including some that have only recently been recognized. In revising the genus, we not only provide updated identification tools and describe two new species (D. incurvata comb. nov. from Chile and D. fenestrata sp. nov. from the Antipodes Islands), but also carry out biogeographic analyses to determine the evolutionary history of buoyancy in the genus. Although the ancestral state was resolved as non-buoyant, the distribution of species suggests that this trait has been both gained and lost, possibly more than once. We conclude that although buoyancy is a trait that can be useful for dispersal (creating evolutionary pressure for its gain), there is also evolutionary pressure for its loss as it restricts species to narrow environmental ranges (i.e., shallow depths).

Genetic and phylogenetic structure of Hynobius quelpaertensis, an endangered endemic salamander species on the Korean Peninsula

BACKGROUND

The Korean Peninsula is a small but unique area showing great endemic Hynobius diversity with H. quelpaertensis, H. yangi, H. unisacculus and three species candidates (HC1, HC3 and HC4). H. quelpaertensis is distributed in the southern part and in Jeju Island, while the remaining species have extremely narrow distributions.

OBJECTIVES

To examine the genetic structure of H. quelpaertensis and the phylogenetic placement in Hynobius.

METHODS

Three mitochondrial and six microsatellite loci were genotyped for 204 Hynobius quelpaertensis, three H. leechii, three H. yangi, three HC1, two H. unisacculus, three HC3, three HC4 and ten Japanses H. lichenatus.

RESULTS

A high level of mitochondrial diversity was found in H. quelpaertensis. Our mitochondrial data showed evidence of a historical link between inland and Jeju Island despite the signature of founder effect likely experienced by the early island populations. However, our microsatellite analysis showed the fairly clear signature of isolation history between in- and island populations. Upon phylogenetic analysis, H. quelpaertensis, H. unisacculus and HC1 formed a cluster, whereas H. yangi belonged to a separate cluster. HC3 and HC4 were clustered with either H. quelpaertensis or H. yangi depending on the locus used.

CONCLUSION

Our results show at least partially the historical imprints engraved by dispersal of Korean endemic Hynobius during Pleistocene, potentially providing a fundamental basis in determining the conservation units and finding management strategies for these species.

Single nucleotide polymorphisms reveal a genetic cline across the north-east Atlantic and enable powerful population assignment in the European lobster

Resolving stock structure is crucial for fisheries conservation to ensure that the spatial implementation of management is commensurate with that of biological population units. To address this in the economically important European lobster (Homarus gammarus), genetic structure was explored across the species' range using a small panel of single nucleotide polymorphisms (SNPs) previously isolated from restriction-site-associated DNA sequencing; these SNPs were selected to maximize differentiation at a range of both broad and fine scales. After quality control and filtering, 1,278 lobsters from 38 sampling sites were genotyped at 79 SNPs. The results revealed a pronounced phylogeographic break between the Atlantic and Mediterranean basins, while structure within the Mediterranean was also apparent, partitioned between lobsters from the central Mediterranean and the Aegean Sea. In addition, a genetic cline across the north-east Atlantic was revealed using both putatively neutral and outlier SNPs, but the precise driver(s) of this clinal pattern-isolation by distance, secondary contact, selection across an environmental gradient, or a combination of these factors-remains undetermined. Putatively neutral markers differentiated lobsters from Oosterschelde, an estuary on the Dutch coast, a finding likely explained by past bottlenecks and limited gene flow with adjacent North Sea populations. Building on the findings of our spatial genetic analysis, we were able to test the accuracy of assigning lobsters at various spatial scales, including to basin of origin (Atlantic or Mediterranean), region of origin and sampling location. The predictive model assembled using 79 SNPs correctly assigned 99.7% of lobsters not used to build the model to their basin of origin, but accuracy decreased to region of origin and again to sampling location. These results are of direct relevance to managers of lobster fisheries and hatcheries, and provide the basis for a genetic tool for tracing the origin of European lobsters in the food supply chain.

Global phylogeography of toxic cyanobacteria Moorea producens reveals distinct genetic partitioning influenced by Proterozoic glacial cycles

Lyngbya majuscula is a marine filamentous cyanobacteria belonging to the family Oscillatoriaceae. Recent phylogenetic analyses of L. majuscula have reclassified a subset of this species into various genera such as Moorea, Okeania and Dapis. From the genus Moorea, Moorea producens is a toxic invasive cyanobacterium that produces bioactive secondary metabolites that can cause severe inflammation and blistering. Despite the global distribution of M. producens, little information is available on their origin, patterns of dispersal and population structure. In this study, the spatial population structure of M. producens was investigated using near-complete 16S rRNA sequences. Analysis of the global population of M. producens by Isolation by Distance and STRUCTURE revealed two significantly distinct cosmopolitan populations that were separated by a genetic break. Lineage-specific divergence estimates of 147 cyanobacterial taxa, based on a relaxed molecular clock indicated the first global emergence of M. producens during the Mesoarchean and a subsequent global recolonization during the Mesoproterozoic period. We conclude that the genetic discontinuity between both cosmopolitan populations is attributed to refugia associated with Proterozoic glacial cycles.

Reproductive and dispersal strategies shape the diversity of mycobiont-photobiont association in Cladonia lichens

Ecological preferences, partner compatibility, or partner availability are known to be important factors shaping obligate and intimate lichen symbioses. We considered a complex of Cladonia species, traditionally differentiated by the extent of sexual reproduction and the type of vegetative propagules, to assess if the reproductive and dispersal strategies affect mycobiont-photobiont association patterns. In total 85 lichen thalli from 72 European localities were studied, two genetic markers for both Cladonia mycobionts and Asterochloris photobionts were analyzed. Variance partitioning analysis by multiple regression on distance matrices was performed to describe and partition variance in photobiont genetic diversity. Asexually reproducing Cladonia in our study were found to be strongly specific to their photobionts, associating with only two closely related Asterochloris species. In contrast, sexually reproducing lichens associated with seven unrelated Asterochloris lineages, thus being photobiont generalists. The reproductive mode had the largest explanatory power, explaining 44% of the total photobiont variability. Reproductive and dispersal strategies are the key factors shaping photobiont diversity in this group of Cladonia lichens. A strict photobiont specialisation observed in two studied species may steer both evolutionary flexibility and responses to ecological changes of these organisms, and considerably limit their distribution ranges.

Microbial Organic Matter Degradation Potential in Baltic Sea Sediments Is Influenced by Depositional Conditions and In Situ Geochemistry

Sediments sequester organic matter over geologic time scales and impact global climate regulation. Microbial communities in marine sediments drive organic matter degradation, but the factors controlling their assemblages and activities, which in turn impact their role in organic matter degradation, are not well understood. Hence, determining the role of microbial communities in carbon cycling in various sediment types is necessary for predicting future sediment carbon cycling. We examined microbial communities in Baltic Sea sediments, which were deposited across various climatic and geographical regimes to determine the relationship between microbial potential for breakdown of organic matter and abiotic factors, including geochemistry and sediment lithology. The findings from this study will contribute to our understanding of carbon cycling in the deep biosphere and how microbial communities live in deeply buried environments.

Globally, marine sediments are a vast repository of organic matter, which is degraded through various microbial pathways, including polymer hydrolysis and monomer fermentation. The sources, abundances, and quality (i.e., labile or recalcitrant) of the organic matter and the composition of the microbial assemblages vary between sediments. Here, we examine new and previously published sediment metagenomes from the Baltic Sea and the nearby Kattegat region to determine connections between geochemistry and the community potential to degrade organic carbon. Diverse organic matter hydrolysis encoding genes were present in sediments between 0.25 and 67 meters below seafloor and were in higher relative abundances in those sediments that contained more organic matter. New analysis of previously published metatranscriptomes demonstrated that many of these genes were transcribed in two organic-rich Holocene sediments. Some of the variation in deduced pathways in the metagenomes correlated with carbon content and depositional conditions. Fermentation-related genes were found in all samples and encoded multiple fermentation pathways. Notably, genes involved in alcohol metabolism were amongst the most abundant of these genes, indicating that this is an important but underappreciated aspect of sediment carbon cycling. This study is a step towards a more complete understanding of microbial food webs and the impacts of depositional facies on present sedimentary microbial communities.

IMPORTANCE Sediments sequester organic matter over geologic time scales and impact global climate regulation. Microbial communities in marine sediments drive organic matter degradation, but the factors controlling their assemblages and activities, which in turn impact their role in organic matter degradation, are not well understood. Hence, determining the role of microbial communities in carbon cycling in various sediment types is necessary for predicting future sediment carbon cycling. We examined microbial communities in Baltic Sea sediments, which were deposited across various climatic and geographical regimes to determine the relationship between microbial potential for breakdown of organic matter and abiotic factors, including geochemistry and sediment lithology. The findings from this study will contribute to our understanding of carbon cycling in the deep biosphere and how microbial communities live in deeply buried environments.

Phylogeography and genetic connectivity of the marine macro-alga Sargassum ilicifolium (Phaeophyceae, Ochrophyta) in the northwestern Pacific1

The evolutionary influences of historical and contemporary factors on the population connectivity and phylogeographic structure of a brown seaweed, Sargassum ilicifolium, were elucidated using the nuclear ITS2 and mitochondrial COI markers for the collections newly sampled within its distribution range in the northwestern Pacific (NWP). Significant genetic structure at variable levels was identified between populations (pairwise FST ) and among populations grouped by geographical proximity (ΦCT among regions). The adjacent groups of populations with moderate structure revealed from AMOVA appeared to have high genetic connectivity. However, a lack of genealogical concordance with the geographic distribution was uncovered for S. ilicifolium from the NWP. Such genetic homogeneity is interpreted as a result of the interaction between postglacial recolonization and dynamic oceanic current regimes in the region. Two separated glacial refugia, the South China Sea and the Okinawa Trough, in the marginal seas of east China were recognized based on the presence of endemic haplotypes and high haplotype diversity in the populations at southern China and northeast of Taiwan. Populations persisting in these refugia may have served as the source for recolonization in the NWP with the rise of sea level during the warmer interglacial periods. The role of oceanic currents in maintaining genetic connectivity of S. ilicifolium in the region was further corroborated by the coherence between the direction of oceanic currents and that of gene flow, especially along the eastern coast of Taiwan. This study underlines the interaction between historical postglacial recolonization and contemporary coastal hydrodynamics in contributing to population connectivity and distribution for this tropical seaweed in the NWP.

Range-wide genomic data synthesis reveals transatlantic vicariance and secondary contact in Atlantic cod

Recent advances in genetic and genomic analysis have greatly improved our understanding of spatial population structure in marine species. However, studies addressing phylogeographic patterns at oceanic spatial scales remain rare. In Atlantic cod (Gadus morhua), existing range-wide examinations suggest significant transatlantic divergence, although the fine-scale contemporary distribution of populations and potential for secondary contact are largely unresolved. Here, we explore transatlantic phylogeography in Atlantic cod using a data-synthesis approach, integrating multiple genome-wide single-nucleotide polymorphism (SNP) datasets representative of different regions to create a single range-wide dataset containing 1,494 individuals from 54 locations and genotyped at 796 common loci. Our analysis highlights significant transatlantic divergence and supports the hypothesis of westward post-glacial colonization of Greenland from the East Atlantic. Accordingly, our analysis suggests the presence of transatlantic secondary contact off eastern North America and supports existing perspectives on the phylogeographic history of Atlantic cod with an unprecedented combination of genetic and geographic resolution. Moreover, we demonstrate the utility of integrating distinct SNP databases of high comparability.

The evolutionary history of the goby Elacatinus puncticulatus in the tropical eastern pacific: Effects of habitat discontinuities and local environmental variability

Habitat discontinuities, temperature gradients, upwelling systems, and ocean currents, gyres and fronts, can affect distributions of species with narrow environmental tolerance or motility and influence the dispersal of pelagic larvae, with effects ranging from the isolation of adjacent populations to connections between them. The coast of the Tropical Eastern Pacific (TEP) is a highly dynamic environment, with various large gyres and upwelling systems, alternating currents and large rocky-habitat discontinuities, which may greatly influence the genetic connectivity of populations in different parts of the coast. Elacatinus puncticulatus is a cryptic, shallow-living goby that is distributed along the continental shore of virtually the entire TEP, which makes it a good model for testing the influence of these environmental characteristics in the molecular evolution of widespread species in this region. A multilocus phylogeny was used to evaluate the influence of habitat gaps, and oceanographic processes in the evolutionary history of E. puncticulatus throughout its geographical range in the TEP. Two well-supported allopatric clades (one with two allopatric subclades) were recovered, the geographic distribution of which does not correspond to any previously proposed major biogeographic provinces. These populations show strong genetic structure and substantial genetic distances between clades and sub-clades (cytb 0.8-7.3%), with divergence times between them ranging from 0.53 to 4.88 Mya, and recent population expansions dated at 170-130 Kya. The ancestral area of all populations appears to be the Gulf of Panama, while several isolation events have formed the phylogeographic patterns evident in this species. Local and regional oceanographic processes as well as habitat discontinuities have shaped the distribution patterns of the genetic lineages along the continental TEP. Large genetic distances, high genetic differentiation, and the results of species-tree and phylogenetic analyses indicate that E. puncticulatus comprises a complex of three allopatric species with an unusual geographic arrangement.

Meta-analysis of northeast Atlantic marine taxa shows contrasting phylogeographic patterns following post-LGM expansions

Background

Comparative phylogeography enables the study of historical and evolutionary processes that have contributed to shaping patterns of contemporary genetic diversity across co-distributed species. In this study, we explored genetic structure and historical demography in a range of coastal marine species across the northeast Atlantic to assess whether there are commonalities in phylogeographic patterns across taxa and to evaluate whether the timings of population expansions were linked to the Last Glacial Maximum (LGM).

Methods

A literature search was conducted using Web of Science. Search terms were chosen to maximise the inclusion of articles reporting on population structure and phylogeography from the northeast Atlantic; titles and abstracts were screened to identify suitable articles within the scope of this study. Given the proven utility of mtDNA in comparative phylogeography and the availability of these data in the public domain, a meta-analysis was conducted using published mtDNA gene sequences. A standardised methodology was implemented to ensure that the genealogy and demographic history of all mtDNA datasets were reanalysed in a consistent and directly comparable manner.

Results

Mitochondrial DNA datasets were built for 21 species. The meta-analysis revealed significant population differentiation in 16 species and four main types of haplotype network were found, with haplotypes in some species unique to specific geographical locations. A signal of rapid expansion was detected in 16 species, whereas five species showed evidence of a stable population size. Corrected mutation rates indicated that the majority of expansions were estimated to have occurred after the earliest estimate for the LGM (∼26.5 Kyr), while few expansions were estimated to have pre-dated the LGM.

Conclusion

This study suggests that post-LGM expansion appeared to be common in a range of marine taxa, supporting the concept of rapid expansions after the LGM as the ice sheets started to retreat. However, despite the commonality of expansion patterns in many of these taxa, phylogeographic patterns appear to differ in the species included in this study. This suggests that species-specific evolutionary processes, as well as historical events, have likely influenced the distribution of genetic diversity of marine taxa in the northeast Atlantic.

Natural history and molecular evolution of demersal Mediterranean sharks and skates inferred by comparative phylogeographic and demographic analyses

Background

The unique and complex paleoclimatic and paleogeographic events which affected the Mediterranean Sea since late Miocene deeply influenced the distribution and evolution of marine organisms and shaped their genetic structure. Following the Messinian salinity crisis and the sea-level fluctuations during the Pleistocene, several Mediterranean marine species developed deep genetic differentiation, and some underwent rapid radiation. Here, we consider two of the most prioritized groups for conservation in the light of their evolutionary history: sharks and rays (elasmobranchs). This paper deals with a comparative multispecies analysis of phylogeographic structure and historical demography in two pairs of sympatric, phylogenetically- and ecologically-related elasmobranchs, two scyliorhinid catsharks (Galeus melastomus, Scyliorhinus canicula) and two rajid skates (Raja clavata, Raja miraletus). Sampling and experimental analyses were designed to primarily test if the Sicilian Channel can be considered as effective eco-physiological barrier for Mediterranean demersal sympatric elasmobranchs.

Methods

The phylogeography and the historical demography of target species were inferred by analysing the nucleotide variation of three mitochondrial DNA markers (i.e., partial sequence of COI, NADH2 and CR) obtained from a total of 248 individuals sampled in the Western and Eastern Mediterranean Sea as well as in the adjacent northeastern Atlantic Ocean. Phylogeographic analysis was performed by haplotype networking and testing spatial genetic differentiation of samples (i.e., analysis of molecular variance and of principal components). Demographic history of Mediterranean populations was reconstructed using mismatch distribution and Bayesian Skyline Plot analyses.

Results

No spatial genetic differentiation was identified in either catshark species, while phylogeographic structure of lineages was identified in both skates, with R. miraletus more structured than R. clavata. However, such structuring of skate lineages was not consistent with the separation between Western and Eastern Mediterranean. Sudden demographic expansions occurred synchronously during the upper Pleistocene (40,000–60,000 years ago) in both skates and G. melastomus, likely related to optimal environmental conditions. In contrast, S. canicula experienced a slow and constant increase in population size over the last 350,000 years.

Discussion

The comparative analysis of phylogeographic and historical demographic patterns for the Mediterranean populations of these elasmobranchs reveals that historical phylogeographic breaks have not had a large impact on their microevolution. We hypothesize that interactions between environmental and ecological/physiological traits may have been the driving force in the microevolution of these demersal elasmobranch species in the Mediterranean rather than oceanographic barriers.

Intraspecific mitogenomics of three marine species-at-risk: Atlantic, spotted, and northern wolffish (Anarhichas spp.)

High-resolution mitogenomics of within-species relationships can answer such phylogeographic questions as how species survived the most recent glaciation, as well as identify contemporary factors such as physical barriers, isolation, and gene flow. We examined the mitogenomic population structure of three at-risk species of wolffish: Atlantic (Anarhichas lupus), spotted (A. minor), and northern (A. denticulatus). These species are extensively sympatric across the North Atlantic but exhibit very different life history strategies, a combination that results in concordant and discordant patterns of genetic variation and structure. Wolffish haplogroups were not structured geographically: Atlantic and spotted wolffish each comprised three shallow clades, whereas northern wolffish comprised two deeper but unstructured lineages. We suggest that wolffish species survived in isolation in multiple glacial refugia, either refugia within refugia (Atlantic and spotted wolffish) or more distant refugia (northern wolffish), followed by secondary admixture upon post-glacial recolonisation of the North Atlantic.

Decadal stability in genetic variation and structure in the intertidal seaweed Fucus serratus (Heterokontophyta: Fucaceae)

BACKGROUND

The spatial distribution of genetic diversity and structure has important implications for conservation as it reveals a species' strong and weak points with regard to stability and evolutionary capacity. Temporal genetic stability is rarely tested in marine species other than commercially important fishes, but is crucial for the utility of temporal snapshots in conservation management. High and stable diversity can help to mitigate the predicted northward range shift of seaweeds under the impact of climate change. Given the key ecological role of fucoid seaweeds along rocky shores, the positive effect of genetic diversity may reach beyond the species level to stabilize the entire intertidal ecosystem along the temperate North Atlantic. In this study, we estimated the effective population size, as well as temporal changes in genetic structure and diversity of the seaweed F. serratus using 22 microsatellite markers. Samples were taken across latitudes and a range of temperature regimes at seven locations with decadal sampling (2000 and 2010).

RESULTS

Across latitudes, genetic structure and diversity remained stable over 5-10 generations. Stable small-scale structure enhanced regional diversity throughout the species' range. In accordance with its biogeographic history, effective population size and diversity peaked in the species' mid-range in Brittany (France), and declined towards its leading and trailing edge to the north and south. At the species' southern edge, multi-locus-heterozygosity displayed a strong decline from 1999 to 2010.

CONCLUSION

Temporally stable genetic structure over small spatial scales is a potential driver for local adaptation and species radiation in the genus Fucus. Survival and adaptation of the low-diversity leading edge of F. serratus may be enhanced by regional gene flow and 'surfing' of favorable mutations or impaired by the accumulation of deleterious mutations. Our results have clear implications for the conservation of F. serratus at its genetically unique southern edge in Northwest Iberia, where increasing temperatures are likely the major cause for the decline not only of F. serratus, but also other intertidal and subtidal macroalgae. We expect that F. serratus will disappear from Northwest Iberia by 2100 if genetic rescue is not induced by the influx of genetic variation from Brittany.

Strong population structure but no equilibrium yet: Genetic connectivity and phylogeography in the kelp Saccharina latissima (Laminariales, Phaeophyta)

Kelp aquaculture is globally developing steadily as human food source, along with other applications. One of the newer crop species is Saccharina latissima, a northern hemisphere kelp inhabiting temperate to arctic rocky shores. To protect and document its natural genetic variation at the onset of this novel aquaculture, as well as increase knowledge on its taxonomy and phylogeography, we collected new genetic data, both nuclear and mitochondrial, and combined it with previous knowledge to estimate genetic connectivity and infer colonization history. Isolation‐with‐migration coalescent analyses demonstrate that gene flow among the sampled locations is virtually nonexistent. An updated scenario for the origin and colonization history of S. latissima is developed as follows: We propose that the species (or species complex) originated in the northwest Pacific, crossed to the northeast Pacific in the Miocene, and then crossed the Bering Strait after its opening ~5.5 Ma into the Arctic and northeast Atlantic. It subsequently crossed the Atlantic from east to west. During the Pleistocene, it was compressed in the south with evidence for northern refugia in Europe. Postglacial recolonization led to secondary contact in the Canadian Arctic. Saccharina cichorioides is shown to probably belong to the S. latissima species complex and to derive from ancestral populations in the Asian North Pacific. Our novel approach of comparing inferred gene flow based on coalescent analysis versus Wright's island model suggests that equilibrium levels of differentiation have not yet been reached in Europe and, hence, that genetic differentiation is expected to increase further if populations are left undisturbed.

Historical demography and colonization pathways of the widespread intertidal seaweed Hormosira banksii (Phaeophyceae) in southeastern Australia

The palaeoceanography of southern Australia has been characterized by fluctuating sea levels during glacial periods, changing temperature regimes and modified boundary currents. Previous studies on genetic structuring of species in southeastern Australia have focused mainly on the differentiation of eastern and western populations while the potential role of Bass Strait as a region of overlap for three biogeographic provinces (Peronia, Maugea, and Flindersia) has been largely ignored. This study aimed to explore the likely roles of historic and contemporary factors in determining divergence patterns in the habitat-forming intertidal seaweed Hormosira banksii in southeastern Australia with a special focus on postglacial dispersal into Bass Strait. We examined the genetic diversity of 475 Hormosira specimens collected from 19 sites around southern Australia using DNA sequence analysis of cytochrome oxidase 1. Three major haplotype groups were identified (western, centre and eastern) corresponding with the three existing biogeographical provinces in this region. Historic break points appeared to be retained and reinforced by modern day dispersal barriers. Phylogeographic grouping of Hormosira reflected a combination of historic and contemporary oceanography. As western and eastern group haplotypes were largely absent within Bass Strait, re-colonization after the last glacial maximum appeared to have originated from refuges within or near present day Bass Strait. Patterns of genetic structure for Hormosira are consistent with other marine species in this region and highlight the importance of biogeographical barriers in contributing to modern genetic structure.

Projected climate changes threaten ancient refugia of kelp forests in the North Atlantic

Intraspecific genetic variability is critical for species adaptation and evolution and yet it is generally overlooked in projections of the biological consequences of climate change. We ask whether ongoing climate changes can cause the loss of important gene pools from North Atlantic relict kelp forests that persisted over glacial-interglacial cycles. We use ecological niche modelling to predict genetic diversity hotspots for eight species of large brown algae with different thermal tolerances (Arctic to warm temperate), estimated as regions of persistence throughout the Last Glacial Maximum (20,000 YBP), the warmer Mid-Holocene (6,000 YBP), and the present. Changes in the genetic diversity within ancient refugia were projected for the future (year 2100) under two contrasting climate change scenarios (RCP2.6 and RCP8.5). Models predicted distributions that matched empirical distributions in cross-validation, and identified distinct refugia at the low latitude ranges, which largely coincide among species with similar ecological niches. Transferred models into the future projected polewards expansions and substantial range losses in lower latitudes, where richer gene pools are expected (in Nova Scotia and Iberia for cold affinity species and Gibraltar, Alboran, and Morocco for warm-temperate species). These effects were projected for both scenarios but were intensified under the extreme RCP8.5 scenario, with the complete borealization (circum-Arctic colonization) of kelp forests, the redistribution of the biogeographical transitional zones of the North Atlantic, and the erosion of global gene pools across all species. As the geographic distribution of genetic variability is unknown for most marine species, our results represent a baseline for identification of locations potentially rich in unique phylogeographic lineages that are also climatic relics in threat of disappearing.

Clonorchis sinensis and Clonorchiasis: The Relevance of Exploring Genetic Variation

Parasitic trematodes (flukes) cause substantial mortality and morbidity in humans. The Chinese liver fluke, Clonorchis sinensis, is one of the most destructive parasitic worms in humans in China, Vietnam, Korea and the Russian Far East. Although C. sinensis infection can be controlled relatively well using anthelmintics, the worm is carcinogenic, inducing cholangiocarcinoma and causing major suffering in ~15 million people in Asia. This chapter provides an account of C. sinensis and clonorchiasis research-covering aspects of biology, epidemiology, pathogenesis and immunity, diagnosis, treatment and control, genetics and genomics. It also describes progress in the area of molecular biology (genetics, genomics, transcriptomics and proteomics) and highlights challenges associated with comparative genomics and population genetics. It then reviews recent advances in the sequencing and characterisation of the mitochondrial and nuclear genomes for a Korean isolate of C. sinensis and summarises salient comparative genomic work and the implications thereof. The chapter concludes by considering how advances in genomic and informatics will enable research on the genetics of C. sinensis and related parasites, as well as the discovery of new fluke-specific intervention targets.

Historical isolation and contemporary gene flow drive population diversity of the brown alga Sargassum thunbergii along the coast of China

BACKGROUND

Long-term survival in isolated marginal seas of the China coast during the late Pleistocene ice ages is widely believed to be an important historical factor contributing to population genetic structure in coastal marine species. Whether or not contemporary factors (e.g. long-distance dispersal via coastal currents) continue to shape diversity gradients in marine organisms with high dispersal capability remains poorly understood. Our aim was to explore how historical and contemporary factors influenced the genetic diversity and distribution of the brown alga Sargassum thunbergii, which can drift on surface water, leading to long-distance dispersal.

RESULTS

We used 11 microsatellites and the plastid RuBisCo spacer to evaluate the genetic diversity of 22 Sargassum thunbergii populations sampled along the China coast. Population structure and differentiation was inferred based on genotype clustering and pairwise F ST and allele-frequency analyses. Integrated genetic analyses revealed two genetic clusters in S. thunbergii that dominated in the Yellow-Bohai Sea (YBS) and East China Sea (ECS) respectively. Higher levels of genetic diversity and variation were detected among populations in the YBS than in the ECS. Bayesian coalescent theory was used to estimate contemporary and historical gene flow. High levels of contemporary gene flow were detected from the YBS (north) to the ECS (south), whereas low levels of historical gene flow occurred between the two regions.

CONCLUSIONS

Our results suggest that the deep genetic divergence in S. thunbergii along the China coast may result from long-term geographic isolation during glacial periods. The dispersal of S. thunbergii driven by coastal currents may facilitate the admixture between southern and northern regimes. Our findings exemplify how both historical and contemporary forces are needed to understand phylogeographical patterns in coastal marine species with long-distance dispersal.

Parallel Mitogenome Sequencing Alleviates Random Rooting Effect in Phylogeography

Reliably rooted phylogenetic trees play irreplaceable roles in clarifying diversification in the patterns of species and populations. However, such trees are often unavailable in phylogeographic studies, particularly when the focus is on rapidly expanded populations that exhibit star-like trees. A fundamental bottleneck is known as the random rooting effect, where a distant outgroup tends to root an unrooted tree "randomly." We investigated whether parallel mitochondrial genome (mitogenome) sequencing alleviates this effect in phylogeography using a case study on the Sea of Japan lineage of the intertidal goby Chaenogobius annularis Eighty-three C. annularis individuals were collected and their mitogenomes were determined by high-throughput and low-cost parallel sequencing. Phylogenetic analysis of these mitogenome sequences was conducted to root the Sea of Japan lineage, which has a star-like phylogeny and had not been reliably rooted. The topologies of the bootstrap trees were investigated to determine whether the use of mitogenomes alleviated the random rooting effect. The mitogenome data successfully rooted the Sea of Japan lineage by alleviating the effect, which hindered phylogenetic analysis that used specific gene sequences. The reliable rooting of the lineage led to the discovery of a novel, northern lineage that expanded during an interglacial period with high bootstrap support. Furthermore, the finding of this lineage suggested the existence of additional glacial refugia and provided a new recent calibration point that revised the divergence time estimation between the Sea of Japan and Pacific Ocean lineages. This study illustrates the effectiveness of parallel mitogenome sequencing for solving the random rooting problem in phylogeographic studies.

Resolving taxonomic uncertainty in vulnerable elasmobranchs: are the Madeira skate (Raja maderensis) and the thornback ray (Raja clavata) distinct species?

Skates and rays constitute the most speciose group of chondrichthyan fishes, yet are characterised by remarkable levels of morphological and ecological conservatism. They can be challenging to identify, which makes monitoring species compositions for fisheries management purposes problematic. Owing to their slow growth and low fecundity, skates are vulnerable to exploitation and species exhibiting endemism or limited ranges are considered to be the most at risk. The Madeira skate Raja maderensis is endemic and classified as ‘Data Deficient’ by the IUCN, yet its taxonomic distinctiveness from the morphologically similar and more wide-ranging thornback ray Raja clavata is unresolved. This study evaluated the sequence divergence of both the variable control region and cytochrome oxidase I ‘DNA barcode’ gene of the mitochondrial genome to elucidate the genetic differentiation of specimens identified as R. maderensis and R. clavata collected across much of their geographic ranges. Genetic evidence was insufficient to support the different species designations. However regardless of putative species identification, individuals occupying waters around the Azores and North African Seamounts represent an evolutionarily significant unit worthy of special consideration for conservation management.

Future climate change is predicted to shift long-term persistence zones in the cold-temperate kelp Laminaria hyperborea

Global climate change is shifting species distributions worldwide. At rear edges (warmer, low latitude range margins), the consequences of small variations in environmental conditions can be magnified, producing large negative effects on species ranges. A major outcome of shifts in distributions that only recently received attention is the potential to reduce the levels of intra-specific diversity and consequently the global evolutionary and adaptive capacity of species to face novel disturbances. This is particularly important for low dispersal marine species, such as kelps, that generally retain high and unique genetic diversity at rear ranges resulting from long-term persistence, while ranges shifts during climatic glacial/interglacial cycles. Using ecological niche modelling, we (1) infer the major environmental forces shaping the distribution of a cold-temperate kelp, Laminaria hyperborea (Gunnerus) Foslie, and we (2) predict the effect of past climate changes in shaping regions of long-term persistence (i.e., climatic refugia), where this species might hypothetically harbour higher genetic diversity given the absence of bottlenecks and local extinctions over the long term. We further (3) assessed the consequences of future climate for the fate of L. hyperborea using different scenarios of greenhouse gas emissions (RCP 2.6 and RCP 8.5). Results show NW Iberia, SW Ireland and W English Channel, Faroe Islands and S Iceland, as regions where L. hyperborea may have persisted during past climate extremes until present day. All predictions for the future showed expansions to northern territories coupled with the significant loss of suitable habitats at low latitude range margins, where long-term persistence was inferred (e.g., NW Iberia). This pattern was particularly evident in the most agressive scenario of climate change (RCP 8.5), likely driving major biodiversity loss, changes in ecosystem functioning and the impoverishment of the global gene pool of L. hyperborea. Because no genetic baseline is currently available for this species, our results may represent a first step in informing conservation and mitigation strategies.

Genetic diversity of the NE Atlantic sea urchin Strongylocentrotus droebachiensis unveils chaotic genetic patchiness possibly linked to local selective pressure

We compared the genetic differentiation in the green sea urchin Strongylocentrotus droebachiensis from discrete populations on the NE Atlantic coast. By using eight recently developed microsatellite markers, genetic structure was compared between populations from the Danish Strait in the south to the Barents Sea in the north (56-79°N). Urchins are spread by pelagic larvae and may be transported long distances by northwards-going ocean currents. Two main superimposed patterns were identified. The first showed a subtle but significant genetic differentiation from the southernmost to the northernmost of the studied populations and could be explained by an isolation by distance model. The second pattern included two coastal populations in mid-Norway (65°N), NH and NS, as well as the northernmost population of continental Norway (71°N) FV. They showed a high degree of differentiation from all other populations. The explanation to the second pattern is most likely chaotic genetic patchiness caused by introgression from another species, S. pallidus, into S. droebachiensis resulting from selective pressure. Ongoing sea urchin collapse and kelp forests recovery are observed in the area of NH, NS and FV populations. High gene flow between populations spanning more than 22° in latitude suggests a high risk of new grazing events to occur rapidly in the future if conditions for sea urchins are favourable. On the other hand, the possibility of hybridization in association with collapsing populations may be used as an early warning indicator for monitoring purposes.

Phylogeographic data revealed shallow genetic structure in the kelp Saccharina japonica (Laminariales, Phaeophyta)

BACKGROUND

Population structure and genetic diversity of marine organisms in the Northwestern Pacific Ocean exhibited complex patterns. Saccharina japonica is a commercially and ecologically important kelp species widely distributed along the coast of Japan Sea. However, it is still poorly known about population genetics and phylogeographic patterns of wild S. japonica populations on a large geographic scale, which is an important contribution to breeding and conservation of this marine crop.

RESULTS

We collected 612 mitochondrial COI and trnW-trnL sequences. Diversity indices suggested that S. japonica populations along the coast of Hokkaido exhibited the highest genetic diversity. Bayesian Analysis of Population Structure (BAPS) revealed four clusters in the kelp species (cluster 1: Hokkaido and South Korea; cluster 2: northwestern Hokkaido; cluster 3: Far Eastern Russia; cluster 4: China). The network inferred from concatenated data exhibited two shallow genealogies corresponding to two BAPS groups (cluster 2 and cluster 3). We did not detect gene flow between the two shallow genealogies, but populations within genealogy have asymmetric gene exchange. Bayesian skyline plots and neutrality tests suggested that S. japonica experienced postglacial expansion around 10.45 ka.

CONCLUSIONS

The coast of Hokkaido might be the origin and diversification center of S. japonica. Gene exchange among S. japonica populations could be caused by anthropogenic interference and oceanographic regimes. Postglacial expansions and gene exchange apparently led to more shared haplotypes and less differentiation that in turn led to the present shallow phylogeographical patterns in S. japonica.

Population genetic structure and colonization history of short ninespine sticklebacks (Pungitius kaibarae)

The contemporary distribution and genetic structure of a freshwater fish provide insight into its historical geodispersal and geographical isolation following Quaternary climate changes. The short ninespine stickleback, Pungitius kaibarae, is a small gasterosteid fish occurring in freshwater systems on the Korean Peninsula and in southeast Russia. On the Korean Peninsula, P. kaibarae populations are distributed in three geographically separated regions: the NE (northeast coast), SE (southeast coast), and a limited area in the ND (Nakdong River). In this study, we used mitochondrial loci and microsatellites to investigate the evolutionary history of P. kaibarae populations by assessing their pattern of genetic structure. Our analyses revealed a marked level of divergence among three regional populations, suggesting a long history of isolation following colonization, although ND individuals showed relatively higher genetic affinity to populations from SE than those from NE. The populations from NE showed a great degree of interpopulation differentiation, whereas populations from SE exhibited only weak genetic structuring. Upon robust phylogenetic analysis, P. kaibarae formed a monophyletic group with Russian P. sinensis and P. tymensis with strong node confidence values, indicating that P. kaibarae populations on the Korean Peninsula originated from the southward migration of its ancestral lineage around the middle Pleistocene.

The phylogeographic structure of Hydrilla verticillata (Hydrocharitaceae) in China and its implications for the biogeographic history of this worldwide-distributed submerged macrophyte

BACKGROUND

Aquatic vascular plants are a distinctive group, differing from terrestrial plants in their growth forms and habitats. Among the various aquatic plant life forms, the evolutionary processes of freshwater submerged species are most likely distinct due to their exclusive occurrence in the discrete and patchy aquatic habitats. Using the chloroplast trnL-F region sequence data, we investigated the phylogeographic structure of a submerged macrophyte, Hydrilla verticillata, the single species in the genus Hydrilla, throughout China, in addition to combined sample data from other countries to reveal the colonisation and diversification processes of this species throughout the world.

RESULTS

We sequenced 681 individuals from 123 sampling locations throughout China and identified a significant phylogeographic structure (NST > GST, p < 0.01), in which four distinct lineages occurred in different areas. A high level of genetic differentiation among populations (global FST = 0.820) was detected. The divergence of Hydrilla was estimated to have occurred in the late Miocene, and the diversification of various clades was dated to the Pleistocene epoch. Biogeographic analyses suggested an East Asian origin of Hydrilla and its subsequent dispersal throughout the world.

CONCLUSIONS

The presence of all four clades in China indicates that China is most likely the centre of Hydrilla genetic diversity. The worldwide distribution of Hydrilla is due to recent vicariance and dispersal events that occurred in different clades during the Pleistocene. Our findings also provide useful information for the management of invasive Hydrilla in North America.

Pre-zygotic isolation in the macroalgal genus Fucus from four contact zones spanning 100-10 000 years: a tale of reinforcement?

Hybrid zones provide an ideal natural experiment to study the selective forces driving evolution of reproductive barriers and speciation. If hybrid offspring are less fit than the parental species, pre-zygotic isolating barriers can evolve and strengthen in response to selection against the hybrids (reinforcement). Four contact zones between the intertidal macroalgae Fucus serratus (Fs) and Fucus distichus (Fd), characterized by varying times of sympatry and order of species introduction provide an opportunity to investigate reinforcement. We examined patterns of hybridization and reproductive isolation between Fs and Fd in: (i) northern Norway (consisting of two natural sites, 10 000 years old), (ii) the Kattegat near Denmark (Fd introduced, nineteenth century) and (iii) Iceland (Fs introduced, nineteenth century). Using 10 microsatellites and chloroplast DNA, we showed that hybridization and introgression decreased with increasing duration of sympatry. The two younger contact zones revealed 13 and 24% hybrids and several F 1 individuals, in contrast to the older contact zone with 2-3% hybrids and an absence of F 1s. Cross-fertilization experiments revealed that the reduction in hybridization in the oldest zone is consistent with increased gametic incompatibility.

Contemporary population structure and post-glacial genetic demography in a migratory marine species, the blacknose shark, Carcharhinus acronotus

Patterns of population structure and historical genetic demography of blacknose sharks in the western North Atlantic Ocean were assessed using variation in nuclear-encoded microsatellites and sequences of mitochondrial (mt)DNA. Significant heterogeneity and/or inferred barriers to gene flow, based on microsatellites and/or mtDNA, revealed the occurrence of five genetic populations localized to five geographic regions: the southeastern U.S Atlantic coast, the eastern Gulf of Mexico, the western Gulf of Mexico, Bay of Campeche in the southern Gulf of Mexico and the Bahamas. Pairwise estimates of genetic divergence between sharks in the Bahamas and those in all other localities were more than an order of magnitude higher than between pairwise comparisons involving the other localities. Demographic modelling indicated that sharks in all five regions diverged after the last glacial maximum and, except for the Bahamas, experienced post-glacial, population expansion. The patterns of genetic variation also suggest that the southern Gulf of Mexico may have served as a glacial refuge and source for the expansion. Results of the study demonstrate that barriers to gene flow and historical genetic demography contributed to contemporary patterns of population structure in a coastal migratory species living in an otherwise continuous marine habitat. The results also indicate that for many marine species, failure to properly characterize barriers in terms of levels of contemporary gene flow could in part be due to inferences based solely on equilibrium assumptions. This could lead to erroneous conclusions regarding levels of connectivity in species of conservation concern.

A tale of two seas: contrasting patterns of population structure in the small-spotted catshark across Europe

Elasmobranchs represent important components of marine ecosystems, but they can be vulnerable to overexploitation. This has driven investigations into the population genetic structure of large-bodied pelagic sharks, but relatively little is known of population structure in smaller demersal taxa, which are perhaps more representative of the biodiversity of the group. This study explores spatial population genetic structure of the small-spotted catshark (Scyliorhinus canicula), across European seas. The results show significant genetic differences among most of the Mediterranean sample collections, but no significant structure among Atlantic shelf areas. The data suggest the Mediterranean populations are likely to have persisted in a stable and structured environment during Pleistocene sea-level changes. Conversely, the Northeast Atlantic populations would have experienced major changes in habitat availability during glacial cycles, driving patterns of population reduction and expansion. The data also provide evidence of male-biased dispersal and female philopatry over large spatial scales, implying complex sex-determined differences in the behaviour of elasmobranchs. On the basis of this evidence, we suggest that patterns of connectivity are determined by trends of past habitat stability that provides opportunity for local adaptation in species exhibiting philopatric behaviour, implying that resilience of populations to fisheries and other stressors may differ across the range of species.