Rémy Rochette

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.

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.

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.

Structurally complex cobble seafloor protects against predators, and is generally assumed to be the only meaningful habitat for settlement and benthic recruitment of American lobsters (Homarus americanus H. Milne Edwards, 1837). Accordingly, historical surveys on featureless substrates such as mud have found few and only older juveniles. Mud, however, is far more common than cobble across the lobster’s range, and may be of increasing importance in regions where the lobster population has been growing over the past few decades. As a first step to determining whether mud seafloor serves as meaningful recruitment habitat for juvenile lobsters, we deployed artificial habitats (bio-collectors) at five locations varying from 100% mud to mostly cobble, in Maces Bay, Bay of Fundy, NB, Canada, to capture young lobsters. A broad size range of lobsters, from new settlers up to adolescents, colonized bio-collectors in all locations, suggesting that lobsters settle and spend at least some of their juvenile life on mud. Differences in body condition (length-standardized mass) of lobsters sampled from the different locations suggest that some individuals must reside on mud for at least months to years, long enough to show differential growth between habitats. The greater relative abundance of adolescents in bio-collectors on mud also suggests their net movement from densely populated cobble beds into mud habitat. We propose that mud seafloor may be a more important habitat for settlement and early survival of American lobsters than is currently appreciated, especially given the current potential saturation of scarce cobble nursery habitat by growing lobster populations and, in some regions, reduced predation on mud seafloor due to overfishing of groundfish.

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.

The long-range dispersal of pelagic larvae is often assumed to be the dominant force behind connectivity in the marine environment, with little consideration given to benthic movements. We analyzed data from an American lobster (Homarus americanus) tagging study (1980–1996) in the Gulf of St. Lawrence during which 37 579 adults from 14 locations were tagged and 6296 were recaptured after 1–6 years at large. The 10th percentile greatest distance moved by tagged lobsters after 1 year at large contributed to demographic connectivity between neighbouring statistical districts, fishing ports, and (in one location) management areas. Considering the incremental dispersal of lobsters after 2 versus 1 year at large, we estimated that the 10th percentile greatest benthic dispersal distances after 1, 2, and 5 years at large represented, respectively, 7%, 14%, and 35% of larval dispersal in the “downstream” direction and 75%, 111%, and 220% of larval dispersal in the “upstream” direction (similar results obtained based on mean dispersal values). We conclude that more attention should be given to benthic movements in estimating connectivity and stock structure in American lobster.

Previous studies have documented female American lobster, Homarus americanus, carrying “abnormal clutches”, i.e. with eggs covering less than half of their abdomen. From 2011 to 2014, we worked alongside harvesters to quantify spatio-temporal patterns and reproductive costs of abnormal clutches among 138 738 egg-bearing female lobsters sampled from 193 homeports spread across eastern Canada. Females with abnormal clutches were ubiquitous, being found in 90% of homeports. Their incidence was, however, relatively low, averaging 6% across sampling times and locations. The incidence decreased between spawning and 7–9 months after spawning, potentially due to cases of complete brood failure caused by sperm limitation, and it then increased toward the end of the brooding period, potentially due to repeated catch and release of ovigerous females during the fishery. In most regions, small females were more likely to carry abnormal clutches than larger females. We estimated population-level egg loss between late oogenesis and hatching of embryos at 47–51%, with approximately half being associated with normal clutches and half with abnormal clutches and complete brood failure.

Changes in the environment and fishing have been shown to affect life-history characteristics, such as size or age of maturation, in a number of finfish and invertebrates. The American lobster (Homarus americanus) supports Canada’s most valuable fishery and exploitation rates are high. Female size-at-maturity (SM) is an important parameter in management of this species, as it is used in establishing minimum legal size regulations. In this study, we show with historical and recent data that SM of female American lobsters has declined across most of Canada, in some areas by as much as 30%, over the past 10–80 years. The spatial patterns of these declines are inconsistent with patterns of rising ocean temperature and lobster abundance (density). They are, however, strongly correlated to the strength of size-based fishery selection, and egg-per-recruit modeling indicates a gain in lifetime egg production associated with observed SM declines under a range of realistic harvesting scenarios. These findings suggest that the marked decrease we document in SM of female American lobsters in Canada over the past century represents an evolutionary response to intense exploitation.