INTERTIDAL MICROHABITAT AND SELECTION AT MPI: INTERLOCUS CONTRASTS IN THE NORTHERN ACORN BARNACLE, SEMIBALANUS BALANOIDES

Contamination acts as a genotype-dependent barrier to gene flow, causing genetic erosion and fine-grained population subdivision in Mussels from the Strait of Istanbul

This study provides evidence of fine-grained genetic structuring in Mediterranean mussels (Mytilus galloprovincialis) from the Strait of Istanbul, caused by barriers to gene flow via contaminant-mediated selection. In this study, mitochondrial D-loop sequences were analyzed in mussels from 8 localities, all less than 30 kilometers apart, with differing contaminant loads. The results were: 1) Intra-population genetic differentiation (ΦST) between sites with high and low contaminant loads was high (up to 0.459), even at distances of only a few kilometers. 2) Genetic diversity was negatively correlated with the contaminant load ("genetic erosion"). 3) There was evidence of selection, based on haplotype frequencies and neutrality tests (Tajima's D), with purifying selection at the most contaminated site and balancing selection at the least contaminated. 4) Genetic distance was not correlated with geographic distance (no isolation-by-distance), but was correlated with contaminant load at each site. 5) Population dendrograms and Bayesian estimators of migration indicated that gene flow between sites was affected by contamination. For the dendrograms of the sampling sites, the clades clustered according to contaminant load more than geographic distance. Overall, these results suggest that 1) contamination may serve as a genotype-dependent dispersal barrier (i.e., contamination may not affect total number of migrants, just the relative proportions of the haplotypes in the established immigrants), leading strong population differentiation over short distances, and 2) genetic erosion may occur by a combination of selection and altered patterns of haplotype-specific gene flow. These effects may be more pronounced in the Strait of Istanbul than in other locations because of the riverine nature and strong, uni-directional current of the strait.

From tides to nucleotides: Genomic signatures of adaptation to environmental heterogeneity in barnacles

The northern acorn barnacle (Semibalanus balanoides) is a robust system to study the genetic basis of adaptations to highly heterogeneous environments. Adult barnacles may be exposed to highly dissimilar levels of thermal stress depending on where they settle in the intertidal (i.e., closer to the upper or lower tidal boundary). For instance, barnacles near the upper tidal limit experience episodic summer temperatures above recorded heat coma levels. This differential stress at the microhabitat level is also dependent on the aspect of sun exposure. In the present study, we used pool-seq approaches to conduct a genome wide screen for loci responding to intertidal zonation across the North Atlantic basin (Maine, Rhode Island, and Norway). Our analysis discovered 382 genomic regions containing SNPs which are consistently zonated (i.e., SNPs whose frequencies vary depending on their position in the rocky intertidal) across all surveyed habitats. Notably, most zonated SNPs are young and private to the North Atlantic. These regions show high levels of genetic differentiation across ecologically extreme microhabitats concomitant with elevated levels of genetic variation and Tajima's D, suggesting the action of non-neutral processes. Overall, these findings support the hypothesis that spatially heterogeneous selection is a general and repeatable feature for this species, and that natural selection can maintain functional genetic variation in heterogeneous environments.

Ecological Load and Balancing Selection in Circumboreal Barnacles

Acorn barnacle adults experience environmental heterogeneity at various spatial scales of their circumboreal habitat, raising the question of how adaptation to high environmental variability is maintained in the face of strong juvenile dispersal and mortality. Here, we show that 4% of genes in the barnacle genome experience balancing selection across the entire range of the species. Many of these genes harbor mutations maintained across 2 My of evolution between the Pacific and Atlantic oceans. These genes are involved in ion regulation, pain reception, and heat tolerance, functions which are essential in highly variable ecosystems. The data also reveal complex population structure within and between basins, driven by the trans-Arctic interchange and the last glaciation. Divergence between Atlantic and Pacific populations is high, foreshadowing the onset of allopatric speciation, and suggesting that balancing selection is strong enough to maintain functional variation for millions of years in the face of complex demography.

Transcriptome Expression of Biomineralization Genes in Littoraria flava Gastropod in Brazilian Rocky Shore Reveals Evidence of Local Adaptation

Understanding how selection shapes population differentiation and local adaptation in marine species remains one of the greatest challenges in the field of evolutionary biology. The selection of genes in response to environment-specific factors and microenvironmental variation often results in chaotic genetic patchiness, which is commonly observed in rocky shore organisms. To identify these genes, the expression profile of the marine gastropod Littoraria flava collected from four Southeast Brazilian locations in ten rocky shore sites was analyzed. In this first L. flava transcriptome, 250,641 unigenes were generated, and 24% returned hits after functional annotation. Independent paired comparisons between 1) transects, 2) sites within transects, and 3) sites from different transects were performed for differential expression, detecting 8,622 unique differentially expressed genes. Araçá (AR) and São João (SJ) transect comparisons showed the most divergent gene products. For local adaptation, fitness-related differentially expressed genes were chosen for selection tests. Nine and 24 genes under adaptative and purifying selection, respectively, were most related to biomineralization in AR and chaperones in SJ. The biomineralization-genes perlucin and gigasin-6 were positively selected exclusively in the site toward the open ocean in AR, with sequence variants leading to pronounced protein structure changes. Despite an intense gene flow among L. flava populations due to its planktonic larva, gene expression patterns within transects may be the result of selective pressures. Our findings represent the first step in understanding how microenvironmental genetic variation is maintained in rocky shore populations and the mechanisms underlying local adaptation in marine species.

Genetic and phenotypic variation exhibit both predictable and stochastic patterns across an intertidal fish metapopulation

Interactions among selection, gene flow, and drift affect the trajectory of adaptive evolution. In natural populations, the direction and magnitude of these processes can be variable across different spatial, temporal, or ontogenetic scales. Consequently, variability in evolutionary processes affects the predictability or stochasticity of microevolutionary outcomes. We studied an intertidal fish, Bathygobius cocosensis (Bleeker, 1854), to understand how space, time, and life stage structure genetic and phenotypic variation in a species with potentially extensive dispersal and a complex life cycle (larval dispersal preceding benthic recruitment). We sampled juvenile and adult life stages, at three sites, over three years. Genome-wide SNPs uncovered a pattern of chaotic genetic patchiness, that is, weak-but-significant patchy spatial genetic structure that was variable through time and between life stages. Outlier locus analyses suggested that targets of spatially divergent selection were mostly temporally variable, though a significant number of spatial outlier loci were shared between life stages. Head shape, a putatively ecologically responsive (adaptive) phenotype in B. cocosensis also exhibited high temporal variability within sites. However, consistent spatial relationships between sites indicated that environmental similarities among sites may generate predictable phenotype distributions across space. Our study highlights the complex microevolutionary dynamics of marine systems, where consideration of multiple ecological dimensions can reveal both predictable and stochastic patterns in the distributions of genetic and phenotypic variation. Such considerations probably apply to species that possess short, complex life cycles, have large dispersal potential and fecundities, and that inhabit heterogeneous environments.

Characterizing the cirri and gut microbiomes of the intertidal barnacle Semibalanus balanoides

BACKGROUND

Natural populations inhabiting the rocky intertidal experience multiple ecological stressors and provide an opportunity to investigate how environmental differences influence microbiomes over small geographical scales. However, very few microbiome studies focus on animals that inhabit the intertidal. In this study, we investigate the microbiome of the intertidal barnacle Semibalanus balanoides. We first describe the microbiome of two body tissues: the feeding appendages, or cirri, and the gut. Next, we examine whether there are differences between the microbiome of each body tissue of barnacles collected from the thermally extreme microhabitats of the rocky shores' upper and lower tidal zones.

RESULTS

Overall, the microbiome of S. balanoides consisted of 18 phyla from 408 genera. Our results showed that although cirri and gut microbiomes shared a portion of their amplicon sequence variants (ASVs), the microbiome of each body tissue was distinct. Over 80% of the ASVs found in the cirri were also found in the gut, and 44% of the ASVs found in the gut were also found in the cirri. Notably, the gut microbiome was not a subset of the cirri microbiome. Additionally, we identified that the cirri microbiome was responsive to microhabitat differences.

CONCLUSION

Results from this study indicate that S. balanoides maintains distinct microbiomes in its cirri and gut tissues, and that the gut microbiome is more stable than the cirri microbiome between the extremes of the intertidal.

Investigation of mechanisms underlying chaotic genetic patchiness in the intertidal marbled crab Pachygrapsus marmoratus (Brachyura: Grapsidae) across the Ligurian Sea

Background

Studies on marine community dynamics and population structures are limited by the lack of exhaustive knowledge on the larval dispersal component of connectivity. Genetic data represents a powerful tool in understanding such processes in the marine realm. When dealing with dispersion and connectivity in marine ecosystems, many evidences show patterns of genetic structure that cannot be explained by any clear geographic trend and may show temporal instability. This scenario is usually referred to as chaotic genetic patchiness, whose driving mechanisms are recognized to be selection, temporal shifts in local population dynamics, sweepstakes reproductive success and collective dispersal.

In this study we focused on the marbled crab Pachygrapsus marmoratus that inhabits the rocky shores of the Mediterranean Sea, Black Sea and East Atlantic Ocean, and disperses through planktonic larvae for about 1 month. P. marmoratus exhibits unexpectedly low connectivity levels at local scale, although well-defined phylogeographic patterns across the species’ distribution range were described. This has been explained as an effect of subtle geographic barriers or due to sweepstake reproductive success. In order to verify a chaotic genetic patchiness scenario, and to explore mechanisms underlying it, we planned our investigation within the Ligurian Sea, an isolated basin of the western Mediterranean Sea, and we genotyped 321 individuals at 11 microsatellite loci.

Results

We recorded genetic heterogeneity among our Ligurian Sea samples with the occurrence of genetic clusters not matching the original populations and a slight inter-population divergence, with the geographically most distant populations being the genetically most similar ones. Moreover, individuals from each site were assigned to all the genetic clusters. We also recorded evidences of self-recruitment and a higher than expected within-site kinship.

Conclusions

Overall, our results suggest that the chaotic genetic patchiness we found in P. marmoratus Ligurian Sea populations is the result of a combination of differences in reproductive success, en masse larval dispersion and local larval retention. This study defines P. marmoratus as an example of marine spawner whose genetic pool is not homogenous at population level, but rather split in a chaotic mosaic of slightly differentiated genetic patches derived from complex and dynamic ecological processes.

Interactive effects of large- and local-scale environmental gradients on phenotypic differentiation

Intraspecific differentiation across a steep environmental gradient depends on the relative influences of evolutionary, organismal, and environmental processes. But steep environmental gradients may be nested within larger-scale, regional conditions that could influence these processes at the local scale. Therefore, we hypothesized that phenotypic differentiation along a steep environmental gradient would vary among regions. To test this hypothesis, we conducted a reciprocal transplant experiment on rocky intertidal shores, a habitat characterized by gradients in abiotic and biotic stress, in three regions of the Gulf of Maine. We used the ubiquitous and ecologically important rockweed species Fucus vesiculosus to quantify differentiation in growth, tissue nitrogen, and nitrogen productivity between upper and lower intertidal individuals. We found that phenotypic differentiation between tide heights varied among traits and regions. Although tissue nitrogen did not vary among any treatment combinations, growth and nitrogen productivity response were region specific. A strong effect of transplant height was found in all regions; however, an effect of home (source) height was only detectable in the central Gulf of Maine. Our study reveals that intraspecific responses to steep environmental gradients vary among populations, but the mechanisms underlying these patterns remain unknown. Given the roles that rockweeds play as food and habitat, these in situ patterns of growth and nitrogen productivity could have important community- and ecosystem-level consequences.

Effects of balancing selection and microhabitat temperature variations on heat tolerance of the intertidal black mussel Septifer virgatus

Realistic assessments of the impacts of global warming on population extinction risk are likely to require an integrated analysis of the roles of standing genetic variation, microhabitat thermal complexity, and the inter-individual variation of heat tolerance due to both genetic differences and seasonal acclimatization effects. Here, we examine whether balancing selection and microhabitat temperature heterogeneity can interact to enhance the population persistence to thermal stress for the black mussel Septifer virgatus. We deployed biomimetic data loggers on the shore to measure the microhabitat-specific thermal variation from June 2014 to April 2016. Thermal tolerance of specimens was indexed by measuring effects of temperature on heart rate. Genotyping of specimens was performed using double digestion restriction association RADSeq (ddRADseq). Our results show that inter-individual variations in thermal tolerance correlate significantly with genetic differences at some specific gene loci, and that heterozygotes have higher thermal tolerances than homozygotes. The observed seasonal changes in genotype frequency suggest that these loci are under balancing selection. The ability of thermally resistant heterozygotes to survive in sun-exposed microhabitats acts to balance the loss of homozygotes during summer and enable the persistence of genetic polymorphisms. Population persistence of the mussel is also facilitated by the micro-scale variation in temperature, which provides refugia from thermal stress. Our results emphasize that inter-individual variation in thermal tolerance and in microhabitat heterogeneity in temperature are important for the persistence of populations in rocky shore habitats.

Footprints of natural selection at the mannose-6-phosphate isomerase locus in barnacles

The rocky intertidal is a natural laboratory to study how natural selection acts on the genes and proteins responsible for organismal survival and reproduction. Alternative forms of enzymes that differ across the intertidal have been known for decades and have provided examples of selection, but the genetic basis of such enzyme variation is known in only a few cases. In this paper, we present molecular evidence of natural selection at the Mpi gene, a key enzyme in energy metabolism that alters survival of barnacles living across the stress gradient imposed by the intertidal. Our study demonstrates how natural selection can facilitate survival in highly heterogeneous environments through the maintenance of multiple molecular solutions to ecological stresses.

The mannose-6-phosphate isomerase (Mpi) locus in Semibalanus balanoides has been studied as a candidate gene for balancing selection for more than two decades. Previous work has shown that Mpi allozyme genotypes (fast and slow) have different frequencies across Atlantic intertidal zones due to selection on postsettlement survival (i.e., allele zonation). We present the complete gene sequence of the Mpi locus and quantify nucleotide polymorphism in S. balanoides, as well as divergence to its sister taxon Semibalanus cariosus. We show that the slow allozyme contains a derived charge-altering amino acid polymorphism, and both allozyme classes correspond to two haplogroups with multiple internal haplotypes. The locus shows several footprints of balancing selection around the fast/slow site: an enrichment of positive Tajima’s D for nonsynonymous mutations, an excess of polymorphism, and a spike in the levels of silent polymorphism relative to silent divergence, as well as a site frequency spectrum enriched for midfrequency mutations. We observe other departures from neutrality across the locus in both coding and noncoding regions. These include a nonsynonymous trans-species polymorphism and a recent mutation under selection within the fast haplogroup. The latter suggests ongoing allelic replacement of functionally relevant amino acid variants. Moreover, predicted models of Mpi protein structure provide insight into the functional significance of the putatively selected amino acid polymorphisms. While footprints of selection are widespread across the range of S. balanoides, our data show that intertidal zonation patterns are variable across both spatial and temporal scales. These data provide further evidence for heterogeneous selection on Mpi.

Non-reversible and Reversible Heat Tolerance Plasticity in Tropical Intertidal Animals: Responding to Habitat Temperature Heterogeneity

The theory for thermal plasticity of tropical ectotherms has centered on terrestrial and open-water marine animals which experience reduced variation in diurnal and seasonal temperatures, conditions constraining plasticity selection. Tropical marine intertidal animals, however, experience complex habitat thermal heterogeneity, circumstances encouraging thermal plasticity selection. Using the tropical rocky-intertidal gastropod, Echinolittorina malaccana, we investigated heat tolerance plasticity in terms of laboratory acclimation and natural acclimatization of populations from thermally-dissimilar nearby shorelines. Laboratory treatments yielded similar capacities of snails from either population to acclimate their lethal thermal limit (LT50 variation was ∼2°C). However, the populations differed in the temperature range over which acclimatory adjustments could be made; LT50 plasticity occurred over a higher temperature range in the warm-shore snails compared to the cool-shore snails, giving an overall acclimation capacity for the populations combined of 2.9°C. In addition to confirming significant heat tolerance plasticity in tropical intertidal animals, these findings reveal two plasticity forms, reversible (laboratory acclimation) and non-reversible (population or shoreline specific) plasticity. The plasticity forms should account for different spatiotemporal scales of the environmental temperature variation; reversible plasticity for daily and tidal variations in microhabitat temperature and non-reversible plasticity for lifelong, shoreline temperature conditions. Non-reversible heat tolerance plasticity, likely established after larvae settle on the shore, should be energetically beneficial in preventing heat shock protein overexpression, but also should facilitate widespread colonization of coasts that support thermally-diverse shorelines. This first demonstration of different plasticity forms in benthic intertidal animals supports the hypothesis that habitat heterogeneity (irrespective of latitude) drives thermal plasticity selection. It further suggests that studies not making reference to different spatial scales of thermal heterogeneity, nor seeking how these may drive different thermal plasticity forms, risk misinterpreting ectothermic responses to environmental warming.

Genomic signatures of environmental selection despite near-panmixia in summer flounder

Rapid environmental change is altering the selective pressures experienced by marine species. While adaptation to local environmental conditions depends on a balance between dispersal and natural selection across the seascape, the spatial scale of adaptation and the relative importance of mechanisms maintaining adaptation in the ocean are not well understood. Here, using population assignment tests, Approximate Bayesian Computation (ABC), and genome scans with double-digest restriction-site associated DNA sequencing data, we evaluated population structure and locus-environment associations in a commercially important species, summer flounder (Paralichthys dentatus), along the U.S. east coast. Based on 1,137 single nucleotide polymorphisms across 232 individuals spanning nearly 1,900 km, we found no indication of population structure across Cape Hatteras, North Carolina (F ST = 0.0014) or of isolation by distance along the coast using individual relatedness. ABC estimated the probability of dispersal across the biogeographic break at Cape Hatteras to be high (95% credible interval: 7%-50% migration). However, we found 15 loci whose allele frequencies were associated with at least one of four environmental variables. Of those, 11 were correlated with bottom temperature. For summer flounder, our results suggest continued fisheries management as a single population and identify likely response mechanisms to climate change. Broadly speaking, our findings suggest that spatial balancing selection can manifest in adaptive divergence on regional scales in marine fish despite high dispersal, and that these conditions likely result in the widespread distribution of adaptive alleles and a high potential for future genetic adaptation in response to changing environmental conditions. In the context of a rapidly changing world, a landscape genomics perspective offers a useful approach for understanding the causes and consequences of genetic differentiation.

Negative Frequency-Dependent Selection Is Frequently Confounding

Persistent genetic variation within populations presents an evolutionary problem, as natural selection and genetic drift tend to erode genetic diversity. Models of balancing selection were developed to account for the maintenance of genetic variation observed in natural populations. Negative frequency-dependent selection is a powerful type of balancing selection that maintains many natural polymorphisms, but it is also commonly misinterpreted. This review aims to clarify the processes underlying negative frequency-dependent selection, describe classes of polymorphisms that can and cannot result from these processes, and discuss the empirical data needed to accurately identify processes that generate or maintain diversity in nature. Finally, the importance of accurately describing the processes affecting genetic diversity within populations as it relates to research progress is considered.

Genetic and epigenetic variation in Spartina alterniflora following the Deepwater Horizon oil spill

Catastrophic events offer unique opportunities to study rapid population response to stress in natural settings. In concert with genetic variation, epigenetic mechanisms may allow populations to persist through severe environmental challenges. In 2010, the Deepwater Horizon oil spill devastated large portions of the coastline along the Gulf of Mexico. However, the foundational salt marsh grass, Spartina alterniflora, showed high resilience to this strong environmental disturbance. Following the spill, we simultaneously examined the genetic and epigenetic structure of recovering populations of S. alterniflora to oil exposure. We quantified genetic and DNA methylation variation using amplified fragment length polymorphism and methylation sensitive fragment length polymorphism (MS‐AFLP) to test the hypothesis that response to oil exposure in S. alterniflora resulted in genetically and epigenetically based population differentiation. We found high genetic and epigenetic variation within and among sites and found significant genetic differentiation between contaminated and uncontaminated sites, which may reflect nonrandom mortality in response to oil exposure. Additionally, despite a lack of genomewide patterns in DNA methylation between contaminated and uncontaminated sites, we found five MS‐AFLP loci (12% of polymorphic MS‐AFLP loci) that were correlated with oil exposure. Overall, our findings support genetically based differentiation correlated with exposure to the oil spill in this system, but also suggest a potential role for epigenetic mechanisms in population differentiation.

Current hypotheses to explain genetic chaos under the sea

Chaotic genetic patchiness (CGP) refers to surprising patterns of spatial and temporal genetic structure observed in some marine species at a scale where genetic variation should be efficiently homogenized by gene flow via larval dispersal. Here we review and discuss 4 mechanisms that could generate such unexpected patterns: selection, sweepstakes reproductive success, collective dispersal, and temporal shifts in local population dynamics. First, we review examples where genetic differentiation at specific loci was driven by diversifying selection, which was historically the first process invoked to explain CGP. Second, we turn to neutral demographic processes that may drive genome-wide effects, and whose effects on CGP may be enhanced when they act together. We discuss how sweepstakes reproductive success accelerates genetic drift and can thus generate genetic structure, provided that gene flow is not too strong. Collective dispersal is another mechanism whereby genetic structure can be maintained regardless of dispersal intensity, because it may prevent larval cohorts from becoming entirely mixed. Theoretical analyses of both the sweepstakes and the collective dispersal ideas are presented. Finally, we discuss an idea that has received less attention than the other ones just mentioned, namely temporal shifts in local population dynamics.

Genomic evidence for ecological divergence against a background of population homogeneity in the marine snail Chlorostoma funebralis

The balance between natural selection, gene flow and genetic drift is difficult to resolve in marine invertebrates with extensive dispersal and fluctuating population sizes. The intertidal snail Chlorostoma funebralis has planktonic larvae and previous work using mtDNA polymorphism reported no genetic population structure. Nevertheless, recent studies have documented differences in thermal tolerance and transcriptomic responses to heat stress between northern and southern California, USA, populations. To gain insight into the dynamics influencing adaptive divergence, we used double-digest restriction site-associated DNA (ddRAD) sequencing to identify 1861 genomewide, quality-filtered single-nucleotide polymorphism (SNP) loci for C. funebralis collected from three northern and three southern California sites (15 individuals per population). Considering all SNPs, there was no evidence for genetic differentiation among populations or regions (average FST  = 0.0042). However, outlier tests revealed 34 loci putatively under divergent selection between northern and southern populations, and structure and SNP tree analyses based on these outliers show clear genetic differentiation between geographic regions. Three of these outliers are known or hypothesized to be involved in stress granule formation, a response to environmental stress such as heat. Combined with previous work that found thermally tolerant southern populations show high baseline expression of stress response genes, these results further suggest that thermal stress is a strong selective pressure across C. funebralis populations. Overall, this study increases our understanding of the factors constraining local adaptation in marine organisms, while suggesting that ecologically driven, strong differentiation can occur at relevant loci in a species with planktonic larvae.

Genetic and epigenetic differences associated with environmental gradients in replicate populations of two salt marsh perennials

While traits and trait plasticity are partly genetically based, investigating epigenetic mechanisms may provide more nuanced understanding of the mechanisms underlying response to environment. Using AFLP and methylation-sensitive AFLP, we tested the hypothesis that differentiation to habitats along natural salt marsh environmental gradients occurs at epigenetic, but not genetic loci in two salt marsh perennials. We detected significant genetic and epigenetic structure among populations and among subpopulations, but we found multilocus patterns of differentiation to habitat type only in epigenetic variation for both species. In addition, more epigenetic than genetic loci were correlated with habitat in both species. When we analysed genetic and epigenetic variation simultaneously with partial Mantel, we found no correlation between genetic variation and habitat and a significant correlation between epigenetic variation and habitat in Spartina alterniflora. In Borrichia frutescens, we found significant correlations between epigenetic and/or genetic variation and habitat in four of five populations when populations were analysed individually, but there was no significant correlation between genetic or epigenetic variation and habitat when analysed jointly across the five populations. These analyses suggest that epigenetic mechanisms are involved in the response to salt marsh habitats, but also that the relationships among genetic and epigenetic variation and habitat vary by species. Site-specific conditions may also cloud our ability to detect response in replicate populations with similar environmental gradients. Future studies analysing sequence data and the correlation between genetic variation and DNA methylation will be powerful to identify the contributions of genetic and epigenetic response to environmental gradients.

Host-specific phenotypic plasticity of the turtle barnacle Chelonibia testudinaria: a widespread generalist rather than a specialist

Turtle barnacles are common epibionts on marine organisms. Chelonibia testudinaria is specific on marine turtles whereas C. patula is a host generalist, but rarely found on turtles. It has been questioned why C. patula, being abundant on a variety of live substrata, is almost absent from turtles. We evaluated the genetic (mitochondrial COI, 16S and 12S rRNA, and amplified fragment length polymorphism (AFLP)) and morphological differentiation of C. testudinaia and C. patula from different hosts, to determine the mode of adaptation exhibited by Chelonibia species on different hosts. The two taxa demonstrate clear differences in shell morphology and length of 4-6(th) cirri, but very similar in arthropodal characters. Moreover, we detected no genetic differentiation in mitochondrial DNA and AFLP analyses. Outlier detection infers insignificant selection across loci investigated. Based on combined morphological and molecular evidence, we proposed that C. testudinaria and C. patula are conspecific, and the two morphs with contrasting shell morphologies and cirral length found on different host are predominantly shaped by developmental plasticity in response to environmental setting on different hosts. Chelonibia testudinaria is, thus, a successful general epibiotic fouler and the phenotypic responses postulated can increase the fitness of the animals when they attach on hosts with contrasting life-styles.

Longitudinal trends in climate drive flowering time clines in North American Arabidopsis thaliana

Introduced species frequently show geographic differentiation, and when differentiation mirrors the ancestral range, it is often taken as evidence of adaptive evolution. The mouse-ear cress (Arabidopsis thaliana) was introduced to North America from Eurasia 150–200 years ago, providing an opportunity to study parallel adaptation in a genetic model organism. Here, we test for clinal variation in flowering time using 199 North American (NA) accessions of A. thaliana, and evaluate the contributions of major flowering time genes FRI, FLC, and PHYC as well as potential ecological mechanisms underlying differentiation. We find evidence for substantial within population genetic variation in quantitative traits and flowering time, and putatively adaptive longitudinal differentiation, despite low levels of variation at FRI, FLC, and PHYC and genome-wide reductions in population structure relative to Eurasian (EA) samples. The observed longitudinal cline in flowering time in North America is parallel to an EA cline, robust to the effects of population structure, and associated with geographic variation in winter precipitation and temperature. We detected major effects of FRI on quantitative traits associated with reproductive fitness, although the haplotype associated with higher fitness remains rare in North America. Collectively, our results suggest the evolution of parallel flowering time clines through novel genetic mechanisms.

Genetic variation in the acorn barnacle from allozymes to population genomics

Understanding the patterns of genetic variation within and among populations is a central problem in population and evolutionary genetics. We examine this question in the acorn barnacle, Semibalanus balanoides, in which the allozyme loci Mpi and Gpi have been implicated in balancing selection due to varying selective pressures at different spatial scales. We review the patterns of genetic variation at the Mpi locus, compare this to levels of population differentiation at mtDNA and microsatellites, and place these data in the context of genome-wide variation from high-throughput sequencing of population samples spanning the North Atlantic. Despite considerable geographic variation in the patterns of selection at the Mpi allozyme, this locus shows rather low levels of population differentiation at ecological and trans-oceanic scales (F(ST) ~ 5%). Pooled population sequencing was performed on samples from Rhode Island (RI), Maine (ME), and Southwold, England (UK). Analysis of more than 650 million reads identified approximately 335,000 high-quality SNPs in 19 million base pairs of the S. balanoides genome. Much variation is shared across the Atlantic, but there are significant examples of strong population differentiation among samples from RI, ME, and UK. An F(ST) outlier screen of more than 22,000 contigs provided a genome-wide context for interpretation of earlier studies on allozymes, mtDNA, and microsatellites. F(ST) values for allozymes, mtDNA and microsatellites are close to the genome-wide average for random SNPs, with the exception of the trans-Atlantic F(ST) for mtDNA. The majority of F(ST) outliers were unique between individual pairs of populations, but some genes show shared patterns of excess differentiation. These data indicate that gene flow is high, that selection is strong on a subset of genes, and that a variety of genes are experiencing diversifying selection at large spatial scales. This survey of polymorphism in S. balanoides provides a number of genomic tools that promise to make this a powerful model for ecological genomics of the rocky intertidal.

Phylogeography study of Ammodytes personatus in Northwestern Pacific: Pleistocene isolation, temperature and current conducted secondary contact

To assess the role of historical process and contemporary factors in shaping population structures in Northwestern Pacific, mitochondrial control region sequences were analyzed to characterize the phylogeography and population structure of the Japanese sand lance Ammodytes personatus. A total of 429 individuals sampled from 17 populations through the species' range are sequenced. Two distinct lineages are detected, which might have been divergent in the Sea of Japan and Pacific costal waters of Japanese Island, during the low sea level. Significant genetic structure is revealed between the Kuroshio and Oyashio Currents. However, significant genetic structure is also detected in the Sea of Japan, contracting expected homogenization hypothesis in Tsushima Current. The haplotype frequency of lineages in both sides of Japanese Island and significant genetic structure between north and south groups revealed that the distribution of lineage B and north group were highly limited by the annual sea temperature. The lack of lineage B in Qingdao population with low sea temperature reflects the sea temperature barrier. Lack of genetic structure in the south group and north group populations indicated that ocean currents within groups facilitated the dispersal of A. personatus.

Genetic structure and the North American postglacial expansion of the barnacle, Semibalanus balanoides

Population genetic characteristics are shaped by the life-history traits of organisms and the geologic history of their habitat. This study provides a neutral framework for understanding the population dynamics and opportunities for selection in Semibalanus balanoides, a species that figures prominently in ecological and evolutionary studies in the Atlantic intertidal. We used mitochondrial DNA (mtDNA) control region (N = 131) and microsatellite markers (∼40 individuals/site/locus) to survey populations of the broadly dispersing acorn barnacle from 8 sites spanning 800 km of North American coast and 1 site in Europe. Patterns of mtDNA sequence evolution were consistent with larger population sizes in Europe and population expansion at the conclusion of the last ice age, approximately 20 000 years ago, in North America. A significant portion of mitochondrial diversity was partitioned between the continents (ϕ(ST) = 0.281), but there was only weak structure observed from mtDNA within North America. Microsatellites showed significant structuring between the continents (F(ST) = 0.021) as well as within North America (F(ST) = 0.013). Isolation by distance in North America was largely driven by a split between populations south of Cape Cod and all others (P < 10(-4)). The glacial events responsible for generating allelic diversity at mtDNA and microsatellites may also be responsible for generating selectable variation at metabolic enzymes in S. balanoides.

Mitochondrial DNA variation in the caramote prawn Penaeus (Melicertus) kerathurus across a transition zone in the Mediterranean Sea

In this study we analysed mitochondrial DNA variation in Penaeus kerathurus prawns collected from seven locations along a transect across the Siculo-Tunisian region in order to verify if any population structuring exists over a limited geographical scale and to delineate the putative transition zone with sufficient accuracy. Partial DNA sequences of COI and 16S genes were analysed. In contrast to the highly conservative 16S gene, the COI sequences exhibited sufficient diversity for population analysis. The COI gene revealed low levels of haplotype and nucleotide diversities. The size of the annual landings of this commercial species suggests large population sizes. Hence, the low genetic diversity detected in this study could indicate a possible reduction in effective population sizes in the past. We detected significant genetic differentiation between eastern and western populations likely due to restricted gene flow across the Siculo-Tunisian boundary. We discuss the different evolutionary forces that may have shaped the genetic variation and suggest that the genetic divide is probably maintained by present-day dispersal limitation.

Direct selection on allozymes is not required to explain heterogeneity among marker loci across a Mytilus hybrid zone

Unequal differentiation between two types of loci (allozyme and DNA markers) across a Mytilus hybrid zone has recently been claimed as evidence for direct selection on some allozyme loci. We provide here a counter-example: a noncoding DNA locus that exhibits as much differentiation as the incriminated allozymes do. The levels of genetic differentiation varied widely among both allozymes and noncoding DNA markers and no clear difference emerged between the two types of markers. This suggests that the strong interlocus variance in genetic differentiation has been confounded with a discrepancy between marker types as a result of an insufficient and unbalanced locus sampling. Heterogeneity in differentiation among neutral loci can be created by stochastic variance during the allopatric divergence preceding a secondary contact. In hybrid zones, a further source of variance is differential introgression among chromosomal regions after the secondary contact owing to the local influence of selected genes on more or less distant markers. However, the degree of differentiation alone gives no way to distinguish indirect pseudo-selection (a regular and ubiquitous feature of hybrid zones) from direct selection. More generally, we suggest that comparative neutrality tests based on discrepancies among marker types have to be applied with caution when the presence of semi-permeable genetic barriers to gene exchange is suspected.

The effects of diet and physiological stress on the evolutionary dynamics of an enzyme polymorphism

In the northern acorn barnacle Semibalanus balanoides, polymorphism at the mannose-6-phosphate isomerase (Mpi) locus appears to be maintained by distinct selection regimes that vary between intertidal microhabitats. The goal of the present experiment was to elucidate the mechanism of selection at the Mpi locus by examining the relationship between genotype and fitness-related life-history traits in laboratory manipulations. When barnacles were cultured on a mannose-supplemented diet and exposed to thermal stress, different Mpi genotypes exhibited differences in the rate of growth that predicted survivorship. In contrast, no such relationship was observed in control or fructose-supplemented dietary treatments either in the presence or in the absence of stress. Similarly, the phenotype and survivorship of genotypes at another allozyme locus and a presumably neutral mitochondrial DNA marker were homogeneous across all treatments and unaffected by experimental manipulations. These results suggest that the differential survivorship of Mpi genotypes in the field and laboratory results from a differential ability to process mannose-6-phosphate through glycolysis. The widespread polymorphism at Mpi observed in marine taxa may reflect the interaction between dietary composition and environmental heterogeneity in intertidal habitats.

Environmental heterogeneity and balancing selection in the acorn barnacle Semibalanus balanoides

The northern acorn barnacle Semibalans banlanoides occupies several intertidal microhabitats which vary greatly in their degree of physical stress. This environmental heterogeneity creates distinct selection regimes which can maintain genetic variation in natural populations. Despite considerable attention placed on the link between spatial variation in fitness and balancing selection at specific loci, experimental manipulations and fitness estimates for molecular polymorphisms have rarely been conducted in the wild. The aim of this transplant experiment was to manipulate the level of physical stress experienced by a cohort of barnacles in the field and then investigate the spatial variation in fitness for genotypes at three loci: two candidate allozymes and the mitochondrial DNA control region. The viability of mannose-6-phosphate isomerase (Mpi) genotypes was dependent on the level of physical stress experienced in the various treatments; alternative homozygotes were favoured in alternative high stress-low stress environments. In contrast, the fitness of genotypes at other loci was equivalent among treatments and unaffected by the manipulation. Evaluated in the light of balancing selection models, these data indicate that the presence of multiple environmental niches is sufficient to promote a stable Mpi polymorphism in barnacle populations and that allelic variation at this locus reflects the process of adaptation to the heterogeneous intertidal landscape.