Combining genetic and demographic information to prioritize conservation efforts for anadromous alewife and blueback herring

Early detection and recovery of river herring spawning habitat use in response to a mainstem dam removal

Historical loss of river and stream habitats due to impassable dams has contributed to the severe decline of many fish species. Anadromous fishes that migrate from the sea to freshwater streams to spawn have been especially impacted as dams restrict these fish from accessing ancestral spawning grounds. In 2018, Bloede Dam was removed from the Patapsco River near Baltimore, Maryland, restoring approximately 100 km of potential habitat for migratory fish. We assessed the response of anadromous river herring, alewife (Alosa pseudoharengus) and blueback herring (Alosa aestivalis), to this dam removal by monitoring environmental DNA (eDNA) and eggs from 2015 to 2021 at locations upstream and downstream of the dam site during their spawning migrations. We additionally assessed the presence of fish by collecting electrofishing samples and tracked the movements of individual adult fish within the river using passive integrated transponder (PIT) tags. No adult river herring, eDNA, or eggs were detected upstream of Bloede Dam in the four years prior to its removal despite the presence of a fish ladder. Our results suggest initial habitat use recovery by spawning river herring in the first year post-removal, although a relatively small proportion of the population in the river used the newly accessible habitat. In the three years post-removal, the likelihood of detecting river herring eDNA upstream of the former dam site increased to 5% for alewife and 13% for blueback herring. Two adult fish were also collected in electrofishing samples upstream of the dam site in 2021. We found no evidence of changes in egg abundance and no tagged fish were detected upstream of the dam site post-removal. While long term monitoring is needed to assess population changes, this study highlights the value of integrating methods for comprehensive understanding of habitat use following dam removal.

North American diadromous fishes: Drivers of decline and potential for recovery in the Anthropocene

Diadromous fishes migrate between freshwater and marine habitats to complete their life cycle, a complexity that makes them vulnerable to the adverse effects of current and past human activities on land and in the oceans. Many North American species are critically endangered, and entire populations have been lost. Major factors driving declines include overfishing, pollution, water withdrawals, aquaculture, non-native species, habitat degradation, over-zealous application of hatcheries designed to mitigate effects of other factors, and effects of climate change. Perhaps, the most broadly tractable and effective factors affecting diadromous fishes are removals of the dams that prevent or hinder their migrations, alter their environment, and often favor non-native biotic communities. Future survival of many diadromous fish populations may depend on this.

Detection of fish movement patterns across management unit boundaries using age-structured Bayesian hierarchical models with tag-recovery data

Tagging studies have been widely conducted to investigate the movement pattern of wild fish populations. In this study, we present a set of length-based, age-structured Bayesian hierarchical models to explore variabilities and uncertainties in modeling tag-recovery data. These models fully incorporate uncertainties in age classifications of tagged fish based on length and uncertainties in estimated population structure. Results of a tagging experiment conducted by the Ontario Ministry of Natural Resources and Forestry (OMNRF) on yellow perch in Lake Erie was analyzed as a case study. A total of 13,694 yellow perch were tagged with PIT tags from 2009 to 2015; 322 of these were recaptured in the Ontario commercial gillnet fishery and recorded by OMNRF personnel. Different movement configurations modeling the tag-recovery data were compared, and all configurations revealed that yellow perch individuals in the western basin (MU1) exhibited relatively strong site fidelity, and individuals from the central basin (MU2 and MU3) moved within this basin, but their movements to the western basin (MU1) appeared small. Model with random effects of year and age on movement had the best performance, indicating variations in movement of yellow perch across the lake among years and age classes. This kind of model is applicable to other tagging studies to explore temporal and age-class variations while incorporating uncertainties in age classification.

A river runs through it: The causes, consequences, and management of intraspecific diversity in river networks

Rivers are fascinating ecosystems in which the eco-evolutionary dynamics of organisms are constrained by particular features, and biologists have developed a wealth of knowledge about freshwater biodiversity patterns. Over the last 10 years, our group used a holistic approach to contribute to this knowledge by focusing on the causes and consequences of intraspecific diversity in rivers. We conducted empirical works on temperate permanent rivers from southern France, and we broadened the scope of our findings using experiments, meta-analyses, and simulations. We demonstrated that intraspecific (genetic) diversity follows a spatial pattern (downstream increase in diversity) that is repeatable across taxa (from plants to vertebrates) and river systems. This pattern can result from interactive processes that we teased apart using appropriate simulation approaches. We further experimentally showed that intraspecific diversity matters for the functioning of river ecosystems. It indeed affects not only community dynamics, but also key ecosystem functions such as litter degradation. This means that losing intraspecific diversity in rivers can yield major ecological effects. Our work on the impact of multiple human stressors on intraspecific diversity revealed that-in the studied river systems-stocking of domestic (fish) strains strongly and consistently alters natural spatial patterns of diversity. It also highlighted the need for specific analytical tools to tease apart spurious from actual relationships in the wild. Finally, we developed original conservation strategies at the basin scale based on the systematic conservation planning framework that appeared pertinent for preserving intraspecific diversity in rivers. We identified several important research avenues that should further facilitate our understanding of patterns of local adaptation in rivers, the identification of processes sustaining intraspecific biodiversity-ecosystem function relationships, and the setting of reliable conservation plans.

Restoration-mediated secondary contact leads to introgression of alewife ecotypes separated by a colonial-era dam

Secondary contact may have important implications for ecological and evolutionary processes; however, few studies have tracked the outcomes of secondary contact from its onset in natural ecosystems. We evaluated an anadromous alewife (Alosa pseudoharengus ) reintroduction project in Rogers Lake (Connecticut, USA), which contains a landlocked alewife population that was isolated as a result of colonial-era damming. After access to the ocean was restored, adult anadromous alewife were stocked into the lake. We assessed anadromous juvenile production, the magnitude and direction of introgression, and the potential for competition between ecotypes. We obtained fin clips from all adult alewife stocked into the lake during the restoration and a sample of juveniles produced in the lake two years after the stocking began. We assessed the ancestry of juveniles using categorical assignment and pedigree reconstruction with newly developed microhaplotype genetic markers. Anadromous alewives successfully spawned in the lake and hybridized with the landlocked population. Parentage assignments revealed that male and female anadromous fish contributed equally to juvenile F1 hybrids. The presence of landlocked backcrosses shows that some hybrids were produced within the first two years of secondary contact, matured in the lake, and reproduced. Therefore, introgression appears directional, from anadromous into landlocked, in the lake environment. Differences in estimated abundance of juveniles of different ecotypes in different habitats were also detected, which may reduce competition between ecotypes as the restoration continues. Our results illustrate the utility of restoration projects to study the outcomes of secondary contact in real ecosystems.

Transforming Ocean Conservation: Applying the Genetic Rescue Toolkit

Although oceans provide critical ecosystem services and support the most abundant populations on earth, the extent of damage impacting oceans and the diversity of strategies to protect them is disconcertingly, and disproportionately, understudied. While conventional modes of conservation have made strides in mitigating impacts of human activities on ocean ecosystems, those strategies alone cannot completely stem the tide of mounting threats. Biotechnology and genomic research should be harnessed and developed within conservation frameworks to foster the persistence of viable ocean ecosystems. This document distills the results of a targeted survey, the Ocean Genomics Horizon Scan, which assessed opportunities to bring novel genetic rescue tools to marine conservation. From this Horizon Scan, we have identified how novel approaches from synthetic biology and genomics can alleviate major marine threats. While ethical frameworks for biotechnological interventions are necessary for effective and responsible practice, here we primarily assessed technological and social factors directly affecting technical development and deployment of biotechnology interventions for marine conservation. Genetic insight can greatly enhance established conservation methods, but the severity of many threats may demand genomic intervention. While intervention is controversial, for many marine areas the cost of inaction is too high to allow controversy to be a barrier to conserving viable ecosystems. Here, we offer a set of recommendations for engagement and program development to deploy genetic rescue safely and responsibly.

Opening the tap: Increased riverine connectivity strengthens marine food web pathways

Reduction of ecosystem connectivity has long-lasting impacts on food webs. Anadromous fish, which migrate from marine to freshwater ecosystems to complete reproduction, have seen their historically larger ecosystem role undercut by widespread riverine habitat fragmentation and other impacts mainly derived from anthropogenic sources. The result has been extensive extirpations and increased susceptibility to a suite of environmental factors that currently impede recovery. Under this present-day context of reduced productivity and connectivity, aggressive management actions and enforcement of catch limits including bycatch caps and complete moratoria on harvest have followed. What remains less understood are the implications of changes to food webs that co-occurred. What benefits restoration could provide in terms of ecosystem functioning in relation to economic costs associated with dam removal and remediation is unknown and can limit the scope and value of restoration activities. Here we employ, historical landscape-based biomass estimates of anadromous alosine for the first time in an ecosystem modeling of the Northeast US large marine ecosystem (LME), to evaluate the value of improving connectivity by measuring the increase in energy flow and population productivity. We compared a restored alosine model to a contemporary model, analyzing the impacts of the potential increase of connectivity between riverine and oceanic systems. There was the potential for a moderate biomass increase of piscivorous species with high economic value, including Atlantic cod, and for a major increase for species of conservation concern such as pelagic sharks, seabirds and marine mammals. Our study highlights the benefits of increased connectivity between freshwater and ocean ecosystems. We demonstrate the significant role anadromous forage fish could play in improving specific fisheries and overall ecosystem functioning, mainly through the diversification of species capable of transferring primary production to upper trophic levels, adding to benefits associated with their restoration.

Environmental DNA analysis of river herring in Chesapeake Bay: A powerful tool for monitoring threatened keystone species

Environmental DNA (eDNA) sampling has emerged as a powerful tool to detect and quantify species abundance in aquatic environments. However, relatively few studies have compared the performance of eDNA-based abundance estimates to traditional catch or survey approaches in the field. Here, we have developed and field-tested a qPCR assay to detect eDNA from alewife and blueback herring (collectively known as ‘river herring’), comparing eDNA-based presence and abundance data to traditional methods of quantification (ichthyoplankton sampling and adult observations). Overall, the qPCR assay showed very high target specificity in lab trials, and was successful in detecting river herring for 11/12 Chesapeake Bay tributaries in spring 2015 and 2016, with 106 out of 445 samples exhibiting positive eDNA hits. We found a strong correlation between eDNA abundance and ichthyoplankton count data (Spearman’s Rho = 0.52), and Phi-tests (correlation of presence/absence data) showed higher correlation between eDNA and ichthyoplankton data (Phi = 0.45) than adult data (Phi = 0.35). Detection probability was significantly lower on western vs. eastern shore tributaries of Chesapeake Bay, and blueback herring and alewife were more likely detected on the western and eastern shores, respectively. Temporal patterns of eDNA abundance over the spring spawning season revealed that alewife were present in high abundances weeks ahead of blueback herring, which aligns with known differences in spawning behavior of the species. In summary, the eDNA abundance data corresponded well to other field methods and has great potential to assist future monitoring efforts of river herring abundance and habitat use.

Discovery and characterization of single nucleotide polymorphisms in two anadromous alosine fishes of conservation concern

Freshwater habitat alteration and marine fisheries can affect anadromous fish species, and populations fluctuating in size elicit conservation concern and coordinated management. We describe the development and characterization of two sets of 96 single nucleotide polymorphism (SNP) assays for two species of anadromous alosine fishes, alewife and blueback herring (collectively known as river herring), that are native to the Atlantic coast of North America. We used data from high-throughput DNA sequencing to discover SNPs and then developed molecular genetic assays for genotyping sets of 96 individual loci in each species. The two sets of assays were validated with multiple populations that encompass both the geographic range and the known regional genetic stocks of both species. The SNP panels developed herein accurately resolved the genetic stock structure for alewife and blueback herring that was previously identified using microsatellites and assigned individuals to regional stock of origin with high accuracy. These genetic markers, which generate data that are easily shared and combined, will greatly facilitate ongoing conservation and management of river herring including genetic assignment of marine caught individuals to stock of origin.

Eco-evolution in size-structured ecosystems: simulation case study of rapid morphological changes in alewife

BACKGROUND

Over the last 300 years, interactions between alewives and zooplankton communities in several lakes in the U.S. have caused the alewives' morphology to transition rapidly from anadromous to landlocked. Lakes with landlocked alewives contain smaller-bodied zooplankton than those without alewives. Landlocked adult alewives display smaller body sizes, narrower gapes, smaller inter-gill-raker spacings, reach maturity at an earlier age, and are less fecund than anadromous alewives. Additionally, landlocked alewives consume pelagic prey exclusively throughout their lives whereas anadromous alewives make an ontogenetic transition from pelagic to littoral prey. These rapid, well-documented changes in the alewives' morphology provide important insights into the morphological evolution of fish. Predicting the morphological evolution of fish is crucial for fisheries and ecosystem management, but the involvement of multiple trophic interactions make predictions difficult. To obtain an improved understanding of rapid morphological change in fish, we developed an individual-based model that simulated rapid changes in the body size and gill-raker count of a fish species in a hypothetical, size-structured prey community. Model parameter values were based mainly on data from empirical studies on alewives. We adopted a functional trait approach; consequently, the model explicitly describes the relationships between prey body size, alewife body size, and alewife gill-raker count. We sought to answer two questions: (1) How does the impact of alewife populations on prey feed back to impact alewife size and gill raker number under several alternative scenarios? (2) Will the trajectory of the landlocked alewives' morphological evolution change after 150-300 years in freshwater?

RESULTS

Over the first 250 years, the alewives' numbers of gill-rakers only increased when reductions in their body size substantially improved their ability to forage for small prey. Additionally, alewives' gill-raker counts increased more rapidly as the adverse effects of narrow gill-raker spacings on foraging for large prey were made less severe. For the first 150-250 years, alewives' growth decreased monotonically, and their gill-raker number increased monotonically. After the first 150-250 years, however, the alewives exhibited multiple evolutionary morphological trajectories in different trophic settings. In several of these settings, their evolutionary trajectories even reversed after the first 150-250 years.

CONCLUSIONS

Alewives affected the abundance and morphology of their prey, which in turn changed the abundance and morphology of the alewives. Complex low-trophic-level interactions can alter the abundance and characteristics of alewives. This study suggests that the current morphology of recently (∼300 years)-landlocked alewives may not represent an evolutionarily stable state.

Tambora and the mackerel year: Phenology and fisheries during an extreme climate event

Global warming has increased the frequency of extreme climate events, yet responses of biological and human communities are poorly understood, particularly for aquatic ecosystems and fisheries. Retrospective analysis of known outcomes may provide insights into the nature of adaptations and trajectory of subsequent conditions. We consider the 1815 eruption of the Indonesian volcano Tambora and its impact on Gulf of Maine (GoM) coastal and riparian fisheries in 1816. Applying complex adaptive systems theory with historical methods, we analyzed fish export data and contemporary climate records to disclose human and piscine responses to Tambora's extreme weather at different spatial and temporal scales while also considering sociopolitical influences. Results identified a tipping point in GoM fisheries induced by concatenating social and biological responses to extreme weather. Abnormal daily temperatures selectively affected targeted fish species-alewives, shad, herring, and mackerel-according to their migration and spawning phenologies and temperature tolerances. First to arrive, alewives suffered the worst. Crop failure and incipient famine intensified fishing pressure, especially in heavily settled regions where dams already compromised watersheds. Insufficient alewife runs led fishers to target mackerel, the next species appearing in abundance along the coast; thus, 1816 became the "mackerel year." Critically, the shift from riparian to marine fisheries persisted and expanded after temperatures moderated and alewives recovered. We conclude that contingent human adaptations to extraordinary weather permanently altered this complex system. Understanding how adaptive responses to extreme events can trigger unintended consequences may advance long-term planning for resilience in an uncertain future.

Genomic population structure of freshwater-resident and anadromous ide (Leuciscus idus) in north-western Europe

Climate change experts largely agree that future climate change and associated rises in oceanic water levels over the upcoming decades, will affect marine salinity levels. The subsequent effects on fish communities in estuarine ecosystems however, are less clear. One species that is likely to become increasingly affected by changes in salinity is the ide (Leuciscus idus). The ide is a stenohaline freshwater fish that primarily inhabits rivers, with frequent anadromous behavior when sea salinity does not exceed 15%. Unlike most other anadromous Baltic Sea fish species, the ide has yet to be subjected to large-scale stocking programs, and thus provides an excellent opportunity for studying the natural population structure across the current salinity gradient in the Danish Belts. To explore this, we used Genotyping-by-Sequencing to determine genomic population structure of both freshwater resident and anadromous ide populations in the western Baltic Sea region, and relate the results to the current salinity gradient and the demographic history of ide in the region. The sample sites separate into four clusters, with all anadromous populations in one cluster and the freshwater resident populations in the remaining three. Results demonstrate high level of differentiation between sites hosting freshwater resident populations, but little differentiation among anadromous populations. Thus ide exhibit the genomic population structure of both a typical freshwater species, and a typical anadromous species. In addition to providing a first insight into the population structure of north-western European ide, our data also (1) provide indications of a single illegal introduction by man; (2) suggest limited genetic effects of heavy pollution in the past; and (3) indicate possible historical anadromous behavior in a now isolated freshwater population.

Morphological and genomic comparisons of Hawaiian and Japanese Black-footed Albatrosses (Phoebastria nigripes) using double digest RADseq: implications for conservation

Evaluating the genetic and demographic independence of populations of threatened species is important for determining appropriate conservation measures, but different technologies can yield different conclusions. Despite multiple studies, the taxonomic status and extent of gene flow between the main breeding populations of Black-footed Albatross (Phoebastria nigripes), a Near-Threatened philopatric seabird, are still controversial. Here, we employ double digest RADseq to quantify the extent of genomewide divergence and gene flow in this species. Our genomewide data set of 9760 loci containing 3455 single nucleotide polymorphisms yielded estimates of genetic diversity and gene flow that were generally robust across seven different filtering and sampling protocols and suggest a low level of genomic variation (θ per site = ∼0.00002-0.00028), with estimates of effective population size (N e = ∼500-15 881) falling far below current census size. Genetic differentiation was small but detectable between Japan and Hawaii (F ST ≈ 0.038-0.049), with no F ST outliers. Additionally, using museum specimens, we found that effect sizes of morphological differences by sex or population rarely exceeded 4%. These patterns suggest that the Hawaiian and Japanese populations exhibit small but significant differences and should be considered separate management units, although the evolutionary and adaptive consequences of this differentiation remain to be identified.

Combining genetic and demographic data for the conservation of a Mediterranean marine habitat-forming species

The integration of ecological and evolutionary data is highly valuable for conservation planning. However, it has been rarely used in the marine realm, where the adequate design of marine protected areas (MPAs) is urgently needed. Here, we examined the interacting processes underlying the patterns of genetic structure and demographic strucuture of a highly vulnerable Mediterranean habitat-forming species (i.e. Paramuricea clavata (Risso, 1826)), with particular emphasis on the processes of contemporary dispersal, genetic drift, and colonization of a new population. Isolation by distance and genetic discontinuities were found, and three genetic clusters were detected; each submitted to variations in the relative impact of drift and gene flow. No founder effect was found in the new population. The interplay of ecology and evolution revealed that drift is strongly impacting the smallest, most isolated populations, where partial mortality of individuals was highest. Moreover, the eco-evolutionary analyses entailed important conservation implications for P. clavata. Our study supports the inclusion of habitat-forming organisms in the design of MPAs and highlights the need to account for genetic drift in the development of MPAs. Moreover, it reinforces the importance of integrating genetic and demographic data in marine conservation.

Intestinal coccidiosis of anadromous and landlocked alewives, Alosa pseudoharengus, caused by Goussia ameliae n. sp. and G. alosii n. sp. (Apicomplexa: Eimeriidae)

•

Intestinal coccidiosis was described in anadromous and landlocked alewife populations.

•

The same coccidian species, Goussia ameliae, was found in both population types.

•

Sporulation dynamics and morphology of G. ameliae differed from the two populations.

•

Goussia alosii was described in posterior intestine of landlocked populations.

Anadromous alewives, Alosa pseudoharengus, have experienced significant population level declines caused by factors including habitat destruction. Alewives occur in two different life histories, anadromous and landlocked forms. The landlocked alewife evolved from ancestral anadromous populations, resulting in an exclusively freshwater and phenotypically unique form. The occurrence of parasites in a host is linked to the environment, making alewives an ideal model to compare parasitology within a single species with contrasting life histories. Currently, little information exists on the presence and impacts of parasites in these fish populations; the present study sets out to better understand coccidiosis in the threatened anadromous populations and to understand how coccidian parasites compare in both life history forms. The intestinal coccidian, Goussia ameliae n. sp., was described infecting the pyloric cecum of 76% and 86% of young-of-the-year and adult anadromous alewives, respectively, from the Maurice River, New Jersey, USA. The coccidian was found in landlocked alewife populations with a prevalence of 92% and 34% in YOY and adult fish, respectively. An analysis of the small subunit 18S ribosomal RNA gene of G. ameliae from both life history forms demonstrated that the coccidian had 100% sequence identity, confirming the same parasite species in both forms. Though genetic analysis demonstrated G. ameliae to be identical, some differences were observed in sporulation and morphology of the parasite within the two populations. The sporocysts in anadromous populations were shorter and wider, and sporulation timing differed from that of landlocked fish. These differences may either be attributed to differences in the host type or to the sporulation environment. Lastly, alewives from landlocked populations were frequently co-infected with a second coccidian species in the posterior intestine, which occurred at a lower prevalence. This species, G. alosii n. sp., was described based on morphological characters of the sporulated oocysts in fresh parasitological preparations.

Why evolutionary biologists should get seriously involved in ecological monitoring and applied biodiversity assessment programs

While ecological monitoring and biodiversity assessment programs are widely implemented and relatively well developed to survey and monitor the structure and dynamics of populations and communities in many ecosystems, quantitative assessment and monitoring of genetic and phenotypic diversity that is important to understand evolutionary dynamics is only rarely integrated. As a consequence, monitoring programs often fail to detect changes in these key components of biodiversity until after major loss of diversity has occurred. The extensive efforts in ecological monitoring have generated large data sets of unique value to macro-scale and long-term ecological research, but the insights gained from such data sets could be multiplied by the inclusion of evolutionary biological approaches. We argue that the lack of process-based evolutionary thinking in ecological monitoring means a significant loss of opportunity for research and conservation. Assessment of genetic and phenotypic variation within and between species needs to be fully integrated to safeguard biodiversity and the ecological and evolutionary dynamics in natural ecosystems. We illustrate our case with examples from fishes and conclude with examples of ongoing monitoring programs and provide suggestions on how to improve future quantitative diversity surveys.