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.
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.
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.
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.
see also the Perspective by Anna Tigano.
•American lobsters (Homarus americanus) were tracked during a seasonal migration.•First use of a Pop-up Satellite Archival Tag (PSAT) on an American lobster.•Individual based model was created to ...test mechanisms and thermal outcomes of seasonal migrations.•Seasonal migrations increased the thermal environment for ovigerous lobster.
Ovigerous American lobsters, Homarus americanus, in the Bay of Fundy undertake seasonal migrations, which are thought to improve the thermal conditions experienced by their embryos. However, the complete thermal and bathymetric history of such females has never been characterized. To this end, we deployed pop-up satellite archival tags on two ovigerous females (160 mm carapace length) in the Bay of Fundy between September 2013 and July 2014. Tagged lobsters traveled from the release location (Grand Manan, New Brunswick) to points near Beaver Harbour, New Brunswick, and Port George, Nova Scotia, representing linear displacements of 33 and 123 km, respectively. Recorded depth and temperature for both lobsters confirm shallow-to-deep migrations in the fall and deep-to-shallow migrations in the spring. The high-resolution, nearly continuous data generated by the satellite tags indicated that local changes in temperature may be the proximate trigger for fall movements, but do not cue movements in spring. We then developed an individual-based model to investigate the mechanisms and thermal outcomes of seasonal migrations, where lobster movements were allowed to vary according to bottom temperature, an individual's level of preference for warmer waters and its scope for movement. This modeling work, combined with the fine-scale thermal and depth history of our tagged lobsters, indicated that the movements our lobster undertook clearly increased, but did not maximize, the temperature their embryos experienced, relative to lobsters moving randomly or not at all. The novel data and modeling approach used in this study shed new light on the nature, trigger and function of seasonal migrations displayed by American lobsters in the Bay of Fundy.
The detection and measurement of annual growth bands preserved in calcified structures underlies the assessment and management of exploited fish populations around the world. However, the estimation ...of growth, mortality, and other age-structured processes in crustaceans has been severely limited by the apparent absence of permanent growth structures. Here, we report the detection of growth bands in calcified regions of the eyestalk or gastric mill in shrimps, crabs, and lobsters. Comparison of growth band counts with reliable, independent estimates of age strongly suggests that the bands form annually, thus providing a direct and accurate method of age determination in all of the species examined. Chemical tags in the lobster cuticle were retained through one or two molts that occurred over the duration of an experiment, as apparently was the mesocardiac ossicle containing the growth bands in the gastric mill. Growth bands are not the previously documented lamellae of the endocuticle, and their formation was not associated with molting. Sex-specific growth curves were readily developed from growth band examination in multiple species, suggesting that routine measurement of growth and mortality in decapod crustaceans may now be possible.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Rationale
Lipid correction models use elemental carbon‐to‐nitrogen ratios to estimate the effect of lipids on δ13C 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 δ13C and δ15N 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 δ13C values based on the non‐lipid‐extracted δ13C 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 δ13C 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 δ13C 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 δ13C 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.
In this study, the activity and movements of juvenile, adolescent, and adult American lobsters (Homarus americanus) were simultaneously quantified for the first time, using two complementary ...ultrasonic telemetry tracking systems. Fourteen lobsters measuring 28 to 80.5 mm in carapace length were first tracked for two blocks of 14 days starting in late summer 2011 on a shallow nursery ground in Anse-Bleue, southern Gulf of St. Lawrence, Canada. Tagged lobsters were simultaneously tracked at a fine scale (≈5000 m2) using a VEMCO VRAP ultrasonic telemetry system, and at a larger scale (≈2.5 km2) using an array of 38 VEMCO VR2 receivers. Subsequent monitoring of individuals continued for an additional 58 days (72 total) within the larger VR2 array. Juvenile, adolescent and adult lobsters displayed diurnal activity rhythms, being significantly more active at night than during the day, and they behaved as “central place foragers”, undergoing excursions from and to a “central” shelter area. These behaviours were not found to be affected by body size. In contrast, average daily home range increased gradually with increasing body size, and study-length displacements showed a dichotomy between juveniles and adolescents/adults. Most (7/8) adolescent and adult lobsters moved to deeper water as water temperature decreased in the fall, whereas the juveniles (6/6) stayed in shallow water near the VRAP triangle for the duration of the study. This study provides rare empirical data concerning the movement and behavioural ecology of American lobsters on shallow nursery grounds, and it reveals ontogenetic changes in daily and seasonal movements over the juvenile, adolescent and adult life stages.
•Quantified movements of juvenile, adolescent, and adult American lobsters•Juveniles remained in shallow water, larger lobsters moved deeper as water cooled in the fall.•Average daily home range increased gradually with body size.•Dichotomy between juveniles & adolescents/adults in study-length displacements•All lobsters, irrespective of size, behaved as central place foragers
The way in which the effect of temperature on the development rate of crustacean larvae is simulated in larval dispersal models potentially impacts the inferences made about population recruitment ...and connectivity. In this study, we contrasted dispersal and connectivity predictions made by a large‐scale dispersal model of American lobster (Homarus americanus H. Milne Edwards, 1837) larvae using three temperature‐dependent larval development functions proposed in the literature: (1) “warm‐source lab”, (2) “warm‐source field”, and (3) “cold‐source lab”. Differences in predictions using each function were contrasted in the northern (colder) and southern (warmer) portions of the species' range. Using these different development functions resulted in significant and marked differences (61.3–162.4 km in the north and 30.9–81.9 km in the south) in the distances dispersed by larvae from hatch to settlement. In general, predicted self‐seeding, retention, and local connectivity were increased, and predicted connectivity among distant locations was decreased, when a function predicting faster development was used. The field‐derived function predicted much less connectivity and decreased dispersal overall than both lab‐derived functions. The cold‐source lab function predicted more retention in northern regions, but less in southern regions, than the warm‐source lab function. Our findings indicate the need for more studies to quantify the rate at which lobster larvae develop in nature, including how this may vary over space and time.
Abstract
Increasing ocean temperatures may affect life cycles of organisms whose biological processes are temperature-dependent. Our objective was to determine whether hatching time of American ...lobster (Homarus americanus), which has a 2-year reproductive cycle, has advanced in the southern Gulf of St Lawrence, Canada, in response to rising temperature. We investigated temporal trends in hatching time 1989–2014 using fisheries monitoring data. We considered two metrics: the first week of the year when ovigerous females with prehatch or hatching clutches were observed onset-of-hatching (OH) and the rate of change in the ratio of females with prehatch/hatching vs. developing clutches each spring fishing season rate of clutch development (RCD). OH advanced by 5 weeks and RCD increased by 40% on average. Comparisons of OH and RCD to cumulative degree-days going back 2 years prior to hatching suggested an effect of higher fall temperatures during early ovarian and embryonic development. The advancement of hatching time in response to environmental conditions 6–18 months before hatching occurs could lead to a mismatch with larval prey species with shorter life cycles. These findings highlight the importance of monitoring phenology of fished species and the need for further research into potential impacts of phenological changes.
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