The role of reproductive timing as a driver of genetic differentiation in populations of Pacific herring

There is growing recognition that maintaining diversity in life history traits contributes to the sustainable management of wild populations. One important life history characteristic is reproductive phenology, and it has been shown that differences in the timing of reproduction can act as a barrier to gene flow between populations. If the difference in reproductive timing determines the level of connectivity, one would expect that genetic differentiation between populations would increase as a function of difference in reproductive date. This pattern, known as “isolation by time” (IBT), has been observed in wild populations of salmonids containing early and late runs. Pacific herring in the Salish Sea also exhibit a wide diversity of spawn times; some populations start reproducing as early as January and reproductive activity in the region continues through May. Here, we test whether these temporal differences in reproduction influence the genetic population structure of herring. We collected adult herring from seven different locations in the Salish Sea during active spawning events (N = 48 per site). Samples were sequenced using a restriction site-associated (RAD) approach and approximately 3,000 polymorphic loci were genotyped in each sample. We found a positive correlation between genetic differentiation and difference in spawn date, with evidence of migration between populations with similar spawn timing. Several loci exhibited exceptionally steep gradients in allele frequencies, including one locus linked to the photoperiodic regulation of reproduction. Our discovery of IBT in Pacific herring support the adaptive significance of spawn timing and underscore the importance of conserving spawning time diversity in Puget Sound herring

Environmental Symbiont Acquisition May Not Be the Solution to Warming Seas for Reef-Building Corals

BACKGROUND: Coral reefs worldwide are in decline. Much of the mortality can be attributed to coral bleaching (loss of the coral's intracellular photosynthetic algal symbiont) associated with global warming. How corals will respond to increasing oceanic temperatures has been an area of extensive study and debate. Recovery after a bleaching event is dependent on regaining symbionts, but the source of repopulating symbionts is poorly understood. Possibilities include recovery from the proliferation of endogenous symbionts or recovery by uptake of exogenous stress-tolerant symbionts. METHODOLOGY/PRINCIPAL FINDINGS: To test one of these possibilities, the ability of corals to acquire exogenous symbionts, bleached colonies of Porites divaricata were exposed to symbiont types not normally found within this coral and symbiont acquisition was monitored. After three weeks exposure to exogenous symbionts, these novel symbionts were detected in some of the recovering corals, providing the first experimental evidence that scleractinian corals are capable of temporarily acquiring symbionts from the water column after bleaching. However, the acquisition was transient, indicating that the new symbioses were unstable. Only those symbiont types present before bleaching were stable upon recovery, demonstrating that recovery was from the resident in situ symbiont populations. CONCLUSIONS/SIGNIFICANCE: These findings suggest that some corals do not have the ability to adjust to climate warming by acquiring and maintaining exogenous, more stress-tolerant symbionts. This has serious ramifications for the success of coral reefs and surrounding ecosystems and suggests that unless actions are taken to reverse it, climate change will lead to decreases in biodiversity and a loss of coral reefs

Unpublished Mediterranean and Black Sea records of marine alien, cryptogenic, and neonative species

To enrich spatio-temporal information on the distribution of alien, cryptogenic, and neonative species in the Mediterranean and the Black Sea, a collective effort by 173 marine scientists was made to provide unpublished records and make them open access to the scientific community. Through this effort, we collected and harmonized a dataset of 12,649 records. It includes 247 taxa, of which 217 are Animalia, 25 Plantae and 5 Chromista, from 23 countries surrounding the Mediterranean and the Black Sea. Chordata was the most abundant taxonomic group, followed by Arthropoda, Mollusca, and Annelida. In terms of species records, Siganus luridus, Siganus rivulatus, Saurida lessepsianus, Pterois miles, Upeneus moluccensis, Charybdis (Archias) longicollis, and Caulerpa cylindracea were the most numerous. The temporal distribution of the records ranges from 1973 to 2022, with 44% of the records in 2020–2021. Lethrinus borbonicus is reported for the first time in the Mediterranean Sea, while Pomatoschistus quagga, Caulerpa cylindracea, Grateloupia turuturu, and Misophria pallida are first records for the Black Sea; Kapraunia schneideri is recorded for the second time in the Mediterranean and for the first time in Israel; Prionospio depauperata and Pseudonereis anomala are reported for the first time from the Sea of Marmara. Many first country records are also included, namely: Amathia verticillata (Montenegro), Ampithoe valida (Italy), Antithamnion amphigeneum (Greece), Clavelina oblonga (Tunisia and Slovenia), Dendostrea cf. folium (Syria), Epinephelus fasciatus (Tunisia), Ganonema farinosum (Montenegro), Macrorhynchia philippina (Tunisia), Marenzelleria neglecta (Romania), Paratapes textilis (Tunisia), and Botrylloides diegensis (Tunisia).peer-reviewe

Shifting baselines in Puget Sound: population abundance of Pacific herring and its use by Native Americans over the millennia

Healthy marine ecosystems have become a top priority for management and conservation bodies. However, the definition of ecosystem health is usually based on data from populations that have already been degraded by recent human impacts such as commercial resource extraction, climate change and habitat destruction. Unfortunately, this incremental degradation of natural ecosystems is linked directly to the erosion of social systems, especially among Indigenous peoples. Pacific herring (Clupea pallasi) might be an example of ‘shifting baselines’ in the marine environment, as intense commercial fishing in both Canada and the US predate recent biomass estimates. Furthermore, the predominance of herring bones in archaeological remains and the importance of herring in local oral history are often not matched by the limited number of tribal herring fisheries today. Here, we present the rationale of a Washington Sea Grant funded project to reconstruct pre-industrial levels of population diversity of Pacific herring in Puget Sound, and to gather traditional local knowledge on its past abundance and cultural importance to local tribes. The project draws from several disciplines including anthropology, archaeology, and genetics, and is nested within two larger programs, the Herring School (SFU, Canada) and the NSF IGERT Program on Ocean Change (UW, USA). Specifically, we will (i) synthesize traditional local knowledge about herring in Puget Sound, (ii) quantify extant genetic population diversity, (iii) compare pre-industrial genetic population diversity estimated from archaeological bones with that of extant herring, and (iv) carry out outreach activities with our tribal partners. We expect that the project will lead to a re-evaluation of recovery goals of Puget Sound herring and foster discussions about achievable and desirable management goals between tribal and other stakeholder groups

SNP Genotypes and geographic data collected from chum salmon populations in Alaska

This data file contains the following data: 1) SNP genotypes for each individual fish, 2) geographic and temporal information associated with each collection, 3) population genetic indices and citation data for each SNP genotyped, 4) waterway distance between each collection site, as calculated by a least-cost path analysis in ARC-GIS

The socio-ecological system of razor clams and the Quinault Indian Nation: modeling the potential impacts of ocean change on a steadfast fishery

On the outer coast of Washington state, cultural values and traditional lifestyles are closely entwined with the marine resources affected by ocean change. Our research explores how ongoing ocean change may challenge the social-ecological system surrounding the Quinault Indian Nation’s razor clam harvest. We conducted semi-structured interviews with Quinault tribal members, scientists, and resource managers to generate a conceptual model of the social-ecological system, which we use to 1) understand the emergent effects of changes in availability of razor clams and 2) explore how the tribal community might prepare for or adapt to these impacts. We find that razor clams are a staple food and key income source for the Quinault people due to their high abundance, low cost to harvest, and long season of availability relative to other natural resources. Low-income families experience disproportionate economic impacts during razor clam harvest closures, but less tangible social and cultural impacts are felt broadly throughout the community. Although razor clams have been abundant and safe for harvest in many recent years, the Quinault perceive many threats to the resource, including climate change, harmful algal blooms, pollution, and habitat damage. We will extend our initial conceptual model using formal analysis of interview responses, supplemented with expert interviews of western scientists, to craft a Bayesian belief network of the Quinault-razor clam system. This will enable the exploration of qualitative connections between ocean change, razor clam availability and community-level variables such as indigenous health and well-being, income, and social network composition. Uncertainty around human responses will be incorporated to the extent possible. This work is an ongoing effort from graduate students in natural resource policy and fisheries science as part of the IGERT Program on Ocean Change at the University of Washington

Coastwide analysis of Pacific herring population structure using traditional ecological knowledge

Pacific herring (Clupea pallasii) are distributed across coastal waters of the Pacific Northwest; however, different countries/states have very different harvest and management policies. In Washington State, current management strategies emphasize conservation and rebuilding of herring stocks. In contrast, the relatively larger biomass of herring in Canadian waters supports both commercial and subsistence fisheries, and management efforts are primarily focused on user conflicts and allocation issues. Another contrast between the two countries concerns the status of individual spawning aggregates, which are managed as separate stocks in Washington, but as a part of larger stock complexes in Canada, despite consistent claims of First Nations of the existence and depletion of local, non-migratory stocks. A coast-wide analysis of population structure informed by traditional ecological knowledge is important to resolve isolated herring stocks and predict the effect of management measures. To address this issue, we sampled twelve populations of herring from Washington State and British Columbia. We confirmed genetic differentiation among temporally isolated herring populations and discovered high-resolution DNA markers using next-generation sequencing. These markers will be used in future analyses of mixed fisheries and ancient population structure. In addition, we will use the newly-developed markers to test hypotheses based on traditional ecological knowledge of resident and migratory herring stocks

Clam hunger and the changing ocean: characterizing social and ecological risks to the Quinault razor clam fishery using participatory modeling

On the outer coast of Washington state, traditional lifestyles are closely entwined with the marine resources affected by ocean change, e.g., ocean warming, ocean acidification, fishing, coastal development, etc. Our research explores how ongoing ocean change may challenge the social-ecological system surrounding the Quinault Indian Nation's razor clam (Siliqua patula) harvest. We conducted semistructured interviews with Quinault tribal members, scientists, and resource managers to build a conceptual model of the social-ecological system, which we use to (1) understand the emergent effects of changes in availability of razor clams and (2) explore how the tribal community might prepare for or adapt to these changes. Razor clams are a staple food and key source of income for the Quinault people because of their lasting abundance, low cost to harvest, and long season of availability relative to other natural resources. Lower income families experience disproportionate economic impacts during razor clam harvest closures, but less tangible social and cultural impacts are felt broadly throughout the community. Although razor clams have been, in general, available and safe for harvest in recent years, the Quinault people perceive many threats to the resource, including climate change, harmful algal blooms, pollution, and habitat loss. We used the perceived risks identified from the interview results, along with peer-reviewed scientific literature, to develop several ocean change scenarios. Using a stage-based population model of the Pacific razor clam, we explored the relative impacts of these scenarios on annual razor clam harvest over a 20-year period. The simulation of scenarios was developed into a user-friendly web-based application as a planning tool for the Quinault Indian Nation, to help them explore connections between ocean change and razor clam availability, and to support their efforts to plan for and adapt to the impacts of change

Data from: Intraspecific DNA contamination distorts subtle population structure in a marine fish: decontamination of herring samples before restriction-site associated (RAD) sequencing and its effects on population genetic statistics

Wild specimens are often collected in challenging field conditions, where samples may be contaminated with the DNA of conspecific individuals. This contamination can result in false genotype calls, which are difficult to detect, but may also cause inaccurate estimates of heterozygosity, allele frequencies, and genetic differentiation. Marine broadcast spawners are especially problematic, because population genetic differentiation is low and samples are often collected in bulk and sometimes from active spawning aggregations. Here, we used contaminated and clean Pacific herring (Clupea pallasi) samples to test (i) the efficacy of bleach decontamination, (ii) the effect of decontamination on RAD genotypes, and (iii) the consequences of contaminated samples on population genetic analyses. We collected fin tissue samples from actively spawning (and thus contaminated) wild herring and non-spawning (uncontaminated) herring. Samples were soaked for 10 minutes in bleach or left untreated, and extracted DNA was used to prepare DNA libraries using a restriction-site associated DNA (RAD) approach. Our results demonstrate that intraspecific DNA contamination affects patterns of individual and population variability, causes an excess of heterozygotes, and biases estimates of population structure. Bleach decontamination was effective at removing intraspecific DNA contamination and compatible with RAD sequencing, producing high-quality sequences, reproducible genotypes, and low levels of missing data. Although sperm contamination may be specific to broadcast spawners, intraspecific contamination of samples may be common and difficult to detect from high-throughput sequencing data, and can impact downstream analyses

Data from: Fine-scale sampling reveals distinct isolation by distance patterns in chum salmon (Oncorhynchus keta) populations occupying a glacially dynamic environment

Populations with spatially restricted gene flow are characterized by genetic differentiation that may be positively correlated with the geographic distance separating populations, a pattern known as isolation by distance (IBD). Here we examined the fine-scale genetic structure of 66 chum salmon (Oncorhynchus keta) populations spawning in Alaska waterways and explored patterns of IBD using 90 nuclear and 3 mitochondrial single nucleotide polymorphisms. Estimating population structure of chum salmon in Alaska is of increasing concern because of fluctuating census sizes and the uncertain effects of harvest on specific populations. We hypothesized that IBD would be present because chum salmon spawn in coastal rivers that are distributed along a linear array and gene flow is spatially restricted due to homing. Evidence of very weak IBD was found throughout the region (R2 = 0.06, p < 0.0001) but the strength of the IBD relationship varied greatly over different spatial scales and geographic regions. Decomposed pairwise regression analyses identified nine outlier populations to regional IBD patterns, suggesting that geographic distance is not the only factor influencing genetic differentiation in the region. Instead, population structure appears to be heavily influenced by glacial history of the region and the presence of a glacial refugium on Kodiak Island