An Assessment of the Biological Significance of a Visual Clutch Staging Scheme for Ovigerous Female American Lobster (Homarus americanus).

Qualitative visual clutch staging is a useful tool for rapidly and non-invasively assessing the developmental stage of American lobster, Homarus americanus, embryos. While such a scheme has been used in fisheries monitoring strategies in Canada since the 1980s, the biological relevance of its four visually distinguishable stages is poorly understood. We conducted a laboratory experiment in which 10 ovigerous females were housed and the development of their embryos regularly assessed, both qualitatively and quantitatively, from November until hatching in July/August. We confirmed the biological relevance of the qualitative staging scheme by showing clear quantitative differences in the duration and rate of embryonic development of stages 2-4 (stage 1 was not assessed as the precise spawning date was unknown). Stage 2 represents winter-spring "dormancy". Stage 3 represents a shorter period of rapid development preceding hatch. Stage 4 represents hatching. We also recommend some improvements to the qualitative staging scheme, specifically (1) adding criteria related to the portion of eggs that are occupied by yolk to increase the accuracy of staging, (2) slightly redefining stage 3 to ensure it encompasses the full period of rapid embryonic development pre-hatch, and (3) adding the presence of pre-zoeae as a key indicator of hatching to avoid the misclassification of clutches in the early stages of hatching or those that are completely spent but still have adhesive substance.

Landscape genomics of the American lobster (Homarus americanus).

In marine species experiencing intense fishing pressures, knowledge of genetic structure and local adaptation represent a critical information to assist sustainable management. In this study, we performed a landscape genomics analysis in the American lobster to investigate the issues pertaining to the consequences of making use of putative adaptive loci to reliably infer population structure and thus more rigorously delineating biological management units in marine exploited species. Toward this end, we genotyped 14,893 single nucleotide polymorphism (SNPs) in 4190 lobsters sampled across 96 sampling sites distributed along 1000 km in the northwest Atlantic in both Canada and the USA. As typical for most marine species, we observed a weak, albeit highly significant genetic structure. We also found that adaptive genetic variation allows detecting fine-scale population structure not resolved by neutral genetic variation alone. Using the recent genome assembly of the American lobster, we were able to map and annotate several SNPs located in functional genes potentially implicated in adaptive processes such as thermal stress response, salinity tolerance and growth metabolism pathways. Taken together, our study indicates that weak population structure in high gene flow systems can be resolved at various spatial scales, and that putatively adaptive genetic variation can substantially enhance the delineation of biological management units of marine exploited species.

An arithmetic correction for the effect of lipid on carbon stable isotope ratios in muscle and digestive glands of the American lobster (Homarus americanus).

RATIONALE: Lipid correction models use elemental carbon-to-nitrogen ratios to estimate the effect of lipids on δ13 C values and provide a fast and inexpensive alternative to chemically removing lipids. However, the performance of these models varies, especially in whole-body invertebrate samples. The generation of tissue-specific lipid correction models for American lobsters, both an ecologically and an economically important species in eastern North America, will aid ecological research of this species and our understanding of the function of these models in invertebrates. METHOD: We determined the δ13 C and δ15 N values before and after lipid extraction in muscle and digestive glands of juvenile and adult lobster. We assessed the performance of four commonly used models (nonlinear, linear, natural logarithm (LN) and generalized linear model (GLM)) at estimating lipid-free δ13 C values based on the non-lipid-extracted δ13 C values and elemental C:N ratios. The accuracy of model predictions was tested using paired t-tests, and the performance of the different models was compared using the Akaike information criterion score. RESULTS: Lipid correction models accurately estimated post-lipid-extraction δ13 C values in both tissues. The nonlinear model was the least accurate for both tissues. In muscle, the three other models performed well, and in digestive glands, the LN model provided the most accurate estimates throughout the range of C:N values. In both tissues, the GLM estimates were not independent of the post-lipid-extraction δ13 C values, thus reducing their transferability to other datasets. CONCLUSIONS: Whereas previous work found that whole-body models poorly estimated the effect of lipids in invertebrates, we show that tissue-specific lipid correction models can generate accurate and precise estimates of lipid-free δ13 C values in lobster. We suggest that the tissue-specific logarithmic models presented here are the preferred models for accounting for the effect of lipid on lobster isotope ratios.

Copy number variants outperform SNPs to reveal genotype-temperature association in a marine species.

Copy number variants (CNVs) are a major component of genotypic and phenotypic variation in genomes. To date, our knowledge of genotypic variation and evolution has largely been acquired by means of single nucleotide polymorphism (SNPs) analyses. Until recently, the adaptive role of structural variants (SVs) and particularly that of CNVs has been overlooked in wild populations, partly due to their challenging identification. Here, we document the usefulness of Rapture, a derived reduced-representation shotgun sequencing approach, to detect and investigate copy number variants (CNVs) alongside SNPs in American lobster (Homarus americanus) populations. We conducted a comparative study to examine the potential role of SNPs and CNVs in local adaptation by sequencing 1,141 lobsters from 21 sampling sites within the southern Gulf of St. Lawrence, which experiences the highest yearly thermal variance of the Canadian marine coastal waters. Our results demonstrated that CNVs account for higher genetic differentiation than SNP markers. Contrary to SNPs, for which no significant genetic-environment association was found, 48 CNV candidates were significantly associated with the annual variance of sea surface temperature, leading to the genetic clustering of sampling locations despite their geographic separation. Altogether, we provide a strong empirical case that CNVs putatively contribute to local adaptation in marine species and unveil stronger spatial signal of population structure than SNPs. Our study provides the means to study CNVs in nonmodel species and highlights the importance of considering structural variants alongside SNPs to enhance our understanding of ecological and evolutionary processes shaping adaptive population structure.

Comparing Pool-seq, Rapture, and GBS genotyping for inferring weak population structure: The American lobster (Homarus americanus) as a case study.

Unraveling genetic population structure is challenging in species potentially characterized by large population size and high dispersal rates, often resulting in weak genetic differentiation. Genotyping a large number of samples can improve the detection of subtle genetic structure, but this may substantially increase sequencing cost and downstream bioinformatics computational time. To overcome this challenge, alternative, cost-effective sequencing approaches, namely Pool-seq and Rapture, have been developed. We empirically measured the power of resolution and congruence of these two methods in documenting weak population structure in nonmodel species with high gene flow comparatively to a conventional genotyping-by-sequencing (GBS) approach. For this, we used the American lobster (Homarus americanus) as a case study. First, we found that GBS, Rapture, and Pool-seq approaches gave similar allele frequency estimates (i.e., correlation coefficient over 0.90) and all three revealed the same weak pattern of population structure. Yet, Pool-seq data showed F ST estimates three to five times higher than GBS and Rapture, while the latter two methods returned similar F ST estimates, indicating that individual-based approaches provided more congruent results than Pool-seq. We conclude that despite higher costs, GBS and Rapture are more convenient approaches to use in the case of species exhibiting very weak differentiation. While both GBS and Rapture approaches provided similar results with regard to estimates of population genetic parameters, GBS remains more cost-effective in project involving a relatively small numbers of genotyped individuals (e.g., <1,000). Overall, this study illustrates the complexity of estimating genetic differentiation and other summary statistics in complex biological systems characterized by large population size and migration rates.

Seascape genomics provides evidence for thermal adaptation and current-mediated population structure in American lobster (Homarus americanus).

Investigating how environmental features shape the genetic structure of populations is crucial for understanding how they are potentially adapted to their habitats, as well as for sound management. In this study, we assessed the relative importance of spatial distribution, ocean currents and sea surface temperature (SST) on patterns of putatively neutral and adaptive genetic variation among American lobster from 19 locations using population differentiation (PD) approaches combined with environmental association (EA) analyses. First, PD approaches (using bayescan, arlequin and outflank) found 28 outlier SNPs putatively under divergent selection and 9770 neutral SNPs in common. Redundancy analysis revealed that spatial distribution, ocean current-mediated larval connectivity and SST explained 31.7% of the neutral genetic differentiation, with ocean currents driving the majority of this relationship (21.0%). After removing the influence of spatial distribution, no SST were significant for putatively neutral genetic variation whereas minimum annual SST still had a significant impact and explained 8.1% of the putatively adaptive genetic variation. Second, EA analyses (using Pearson correlation tests, bayescenv and lfmm) jointly identified seven SNPs as candidates for thermal adaptation. Covariation at these SNPs was assessed with a spatial multivariate analysis that highlighted a significant temperature association, after accounting for the influence of spatial distribution. Among the 505 candidate SNPs detected by at least one of the three approaches, we discovered three polymorphisms located in genes previously shown to play a role in thermal adaptation. Our results have implications for the management of the American lobster and provide a foundation on which to predict how this species will cope with climate change.

RAD genotyping reveals fine-scale genetic structuring and provides powerful population assignment in a widely distributed marine species, the American lobster (Homarus americanus).

Deciphering genetic structure and inferring connectivity in marine species have been challenging due to weak genetic differentiation and limited resolution offered by traditional genotypic methods. The main goal of this study was to assess how a population genomics framework could help delineate the genetic structure of the American lobster (Homarus americanus) throughout much of the species' range and increase the assignment success of individuals to their location of origin. We genotyped 10 156 filtered SNPs using RAD sequencing to delineate genetic structure and perform population assignment for 586 American lobsters collected in 17 locations distributed across a large portion of the species' natural distribution range. Our results revealed the existence of a hierarchical genetic structure, first separating lobsters from the northern and southern part of the range (FCT  = 0.0011; P-value = 0.0002) and then revealing a total of 11 genetically distinguishable populations (mean FST  = 0.00185; CI: 0.0007-0.0021, P-value < 0.0002), providing strong evidence for weak, albeit fine-scale population structuring within each region. A resampling procedure showed that assignment success was highest with a subset of 3000 SNPs having the highest FST . Applying Anderson's (Molecular Ecology Resources, 2010, 10, 701) method to avoid 'high-grading bias', 94.2% and 80.8% of individuals were correctly assigned to their region and location of origin, respectively. Lastly, we showed that assignment success was positively associated with sample size. These results demonstrate that using a large number of SNPs improves fine-scale population structure delineation and population assignment success in a context of weak genetic structure. We discuss the implications of these findings for the conservation and management of highly connected marine species, particularly regarding the geographic scale of demographic independence.

Differential snail predation by an exotic crab and the geography of shell-claw covariance in the Northwest Atlantic.

Here we investigate if predation by the European green crab (Carcinus maenas) differs between two congeneric snails in the northwest Atlantic (Littorina littorea and L. obtusata), and ask if differential predation can help explain the geography of claw and shell forms among geographically separated populations. First, correlations between crusher-claw size and shell mass -- tested across a wide size range of animals -- were highly significant among populations of C. maenas and L. obtusata, whereas only a small number of significant correlations were found between C. maenas and L. littorea, and these were limited to the smaller size classes of snails and crabs. Moreover, among populations, L. obtusata shells were more frequently scarred than those of L. littorea, and L. obtusata were attacked and killed more frequently than L. littorea during field- and laboratory-predation experiments. Combined, results suggest L. obtusata is currently under greater selection by C. maenas than L. littorea for more crab-resistant shell forms. One possible explanation for these patterns is that L. littorea may have interacted with green crabs for centuries (in Europe) prior to their reintroduction to green crabs in America, thus predator-resistance may had already evolved.

Mechanism of a plastic phenotypic response: predator-induced shell thickening in the intertidal gastropod Littorina obtusata.

Phenotypic plasticity has been the object of considerable interest over the past several decades, but in few cases are mechanisms underlying plastic responses well understood. For example, it is unclear whether predator-induced changes in gastropod shell morphology represent an active physiological response or a by-product of reduced feeding. We address this question by manipulating feeding and growth of intertidal snails, Littorina obtusata, using two approaches: (i) exposure to predation cues from green crabs Carcinus maenas and (ii) reduced food availability, and quantifying growth in shell length, shell mass, and body mass, as well as production of faecal material and shell micro-structural characteristics (mineralogy and organic fraction) after 96 days. We demonstrate that L. obtusata actively increases calcification rate in response to predation threat, and that this response entails energetic and developmental costs. That this induced response is not strictly tied to the animal's behaviour should enhance its evolutionary potential.

Aggregation of whelks, Buccinum undatum, near feeding predators: the role of reproductive requirements.

In the Mingan Islands, northern Gulf of St Lawrence (eastern Canada), the whelk Buccinum undatum displays a strong escape response to its predator, the asteroid Leptasterias polaris, nevertheless large sexually mature individuals occasionally approach feeding L. polaris to obtain food. In this study, we investigated the hypothesis that reproductive requirements increase the tendency of sexually mature whelks to approach feeding asteroids. Prior to egg laying, females (which invest more energy than males into the production of reproductive structures) represented 72% of the adult whelks that approached feeding L. polaris, but only 36% of the adults randomly collected from the study area. Furthermore, females that were attracted to feeding asteroids had smaller reproductive organs (after accounting for body size) than females randomly collected from the study area. Similarly, prior to egg laying, females fed longer and ingested more food than males when tested in the presence of L. polaris in the laboratory. After egg laying, however, females and males displayed a similar tendency to feed in the presence of a predator, both in the field and in the laboratory. Predator-impact indices, computed by contrasting the feeding activity of whelks in the absence and presence of a predator, indicated that females (but not males) responded more boldly to predators prior to than after egg laying, despite a general decrease in feeding activity at that period. Taken together, our observations indicate that the tendency of adult whelks to approach feeding predators is influenced by potential reproductive gains. Because such gains are presumably more directly linked to a given feeding opportunity in sexually active individuals, whelks may be selected to display increased levels of boldness towards predators with the onset of sexual maturity. Thus, potential reproductive benefits may partly explain the size-dependent tendency of whelks to approach feeding asteroids. Copyright 2001 The Association for the Study of Animal Behaviour.