Genetic decline and recovery of a demographically rebuilt fishery species.

The demographic history of a population is important for conservation and evolution, but this history is unknown for many populations. Methods that use genomic data have been developed to infer demography, but they can be challenging to implement and interpret, particularly for large populations. Thus, understanding if and when genetic estimates of demography correspond to true population history is important for assessing the performance of these genetic methods. Here, we used double-digest restriction-site associated DNA (ddRAD) sequencing data from archived collections of larval summer flounder (Paralichthys dentatus, n = 279) from three cohorts (1994-1995, 1997-1998 and 2008-2009) along the U.S. East coast to examine how contemporary effective population size and genetic diversity responded to changes in abundance in a natural population. Despite little to no detectable change in genetic diversity, coalescent-based demographic modelling from site frequency spectra revealed that summer flounder effective population size declined dramatically in the early 1980s. The timing and direction of change corresponded well with the observed decline in spawning stock census abundance in the late 1980s from independent fish surveys. Census abundance subsequently recovered and achieved the prebottleneck size. Effective population size also grew following the bottleneck. Our results for summer flounder demonstrate that genetic sampling and site frequency spectra can be useful for detecting population dynamics, even in species with large effective sizes.

Using multiple natural tags provides evidence for extensive larval dispersal across space and through time in summer flounder.

Dispersal sets the fundamental scales of ecological and evolutionary dynamics and has important implications for population persistence. Patterns of marine dispersal remain poorly understood, partly because dispersal may vary through time and often homogenizes allele frequencies. However, combining multiple types of natural tags can provide more precise dispersal estimates, and biological collections can help to reconstruct dispersal patterns through time. We used single nucleotide polymorphism genotypes and otolith core microchemistry from archived collections of larval summer flounder (Paralichthys dentatus, n = 411) captured between 1989 and 2012 at five locations along the US East coast to reconstruct dispersal patterns through time. Neither genotypes nor otolith microchemistry alone were sufficient to identify the source of larval fish. However, microchemistry identified clusters of larvae (n = 3-33 larvae per cluster) that originated in the same location, and genetic assignment of clusters could be made with substantially more confidence. We found that most larvae probably originated near a biogeographical break (Cape Hatteras) and that larvae were transported in both directions across this break. Larval sources did not shift north through time, despite the northward shift of adult populations in recent decades. Our novel approach demonstrates that summer flounder dispersal is widespread throughout their range, on both intra- and intergenerational timescales, and may be a particularly important process for synchronizing population dynamics and maintaining genetic diversity during an era of rapid environmental change. Broadly, our results reveal the value of archived collections and of combining multiple natural tags to understand the magnitude and directionality of dispersal in species with extensive gene flow.

Correction: Change in larval fish assemblage in a USA east coast estuary estimated from twenty-six years of fixed weekly sampling.

[This corrects the article DOI: 10.1371/journal.pone.0224157.].

Change in larval fish assemblage in a USA east coast estuary estimated from twenty-six years of fixed weekly sampling.

Climate change is leading to significant alterations to ecosystems all over the world and some of the resulting impacts on fish and fisheries are now becoming apparent. Estuaries, which are highly susceptible to climate change because they are relatively shallow and in close proximity to anthropogenic stressors, provide habitat to many fish species at a critical time in the life history, after transport and just prior to settlement in nurseries. Despite this, the long-term impacts of climate change on larval fish at this critical location/stage in the life history are not well documented. The larval fish assemblage of a coastal estuary was sampled once per week for twenty-six years at a fixed location in southern New Jersey, USA. We used ordination and regression analysis to evaluate the whole assemblage, individual species/family occurrence, and trends in total density and diversity over that time. The larval fish assemblage changed significantly in response to warming water temperatures. In addition, approximately one quarter of the species/families in the assemblage exhibited a statistically significant trend in individual occurrence over time. Of these, all five of the five northern-affiliated species decreased in occurrence while 18 of 21 southern-affiliated species increased in occurrence. Finally, total fish density and species diversity increased over the course of the study. The non-uniform response of the species/families in this larval assemblage is similar to what has been documented in other studies that evaluated the temporal trend of open ocean juvenile and adult fish assemblages.

Is Exposure to Macondo Oil Reflected in the Otolith Chemistry of Marsh-Resident Fish?

Genomic and physiological responses in Gulf killifish (Fundulus grandis) in the northern Gulf of Mexico have confirmed oil exposure of resident marsh fish following the Macondo blowout in 2010. Using these same fish, we evaluated otolith microchemistry as a method for assessing oil exposure history. Laser-ablation inductively-coupled-plasma mass spectrometry was used to analyze the chemical composition of sagittal otoliths to assess whether a trace metal signature could be detected in the otoliths of F. grandis collected from a Macondo-oil impacted site in 2010, post-spill relative to pre-spill, as well as versus fish from areas not impacted by the spill. We found no evidence of increased concentrations of two elements associated with oil contamination (nickel and vanadium) in F. grandis otoliths regardless of Macondo oil exposure history. One potential explanation for this is that Macondo oil is relatively depleted of those metals compared to other crude oils globally. During and after the spill, however, elevated levels of barium, lead, and to a lesser degree, copper were detected in killifish otoliths at the oil-impacted collection site in coastal Louisiana. This may reflect oil contact or other environmental perturbations that occurred concomitant with oiling. For example, increases in barium in otoliths from oil-exposed fish followed (temporally) freshwater diversions in Louisiana in 2010. This implicates (but does not conclusively demonstrate) freshwater diversions from the Mississippi River (with previously recorded higher concentrations of lead and copper), designed to halt the ingress of oil, as a mechanism for elevated elemental uptake in otoliths of Louisiana marsh fishes. These results highlight the potentially complex and indirect effects of the Macondo oil spill and human responses to it on Gulf of Mexico ecosystems, and emphasize the need to consider the multiple stressors acting simultaneously on inshore fish communities.

Color pattern variation in Cichla temensis (Perciformes: Cichlidae): resolution based on morphological, molecular, and reproductive data

Morphological variants of Cichla temensis, readily differentiated by their striking color pattern differences, are found in several Amazon basin flood pulse river systems. The adult variants have at times been thought to represent different species or sexual dimorphism. A three part study was performed in two regions in Brazil (rio Igapó Açú and rio Caures) to elucidate the nature of the variants. In part one; selected diagnostic morphometric characters were compared intraspecifically among the variants and interspecifically with C. monoculus and C. orinocensis. All of the C. temensis variants were found to differ significantly from their sympatric congeners while not differing among each other. In part two, mitochondrial DNA samples were compared intraspecifically among the variants and interspecifically with their sympatric congeners. There were no diagnostic molecular synapomorphies that would unambiguously distinguish the variants and all C. temensis variants were clearly diagnosable and divergent from their sympatric congeners. In part three, color pattern variation in both sexes was compared to a gonadosomatic index (GSI). A significant correlation between color pattern variation and gonadosomatic index was found. The results of this study demonstrate that Cichla temensis variants are confirmed to be members of a single species and that the variation does not represent a sexual dimorphism. The color pattern variation is a cyclically occurring secondary sexual characteristic and is indicative of the specific degree of an individual's seasonal sexual maturation.

Variantes morfológicas de Cichla temensis, facilmente diferenciados por seus padrões de coloração marcantes, são encontrados em vários rios do sistema de inundação da várzea da bacia Amazônica. Variantes dos indivíduos adultos têm sido cogitados como pertencerem a uma diferente espécie ou apresentarem dimorfismo sexual. Um estudo em três etapas foi realizado em duas regiões no Brasil (rio Igapó Açú e rio Caures) para elucidar a natureza desta variação. Na primeira parte, caracteres morfométricos diagnósticos foram comparados intraespecificamente entre os variantes e interespecificamente com C. monoculus e C. orinocensis. Todos os variantes de C. temensis apresentaram diferenças significativas quando comparados com seus congêneres simpátricos enquanto não diferiram entre si. Na segunda parte, sequências de DNA mitocondrial foram comparadas intraespecificamente entre os variantes e interespeficamente com seus congêneres simpátricos. Não houve sinapomorfias moleculares diagnósticas para diferenciar inequivocamente os variantes e todos os variantes de C. temensis foram claramente divergentes de seus congêneres simpátricos. Na terceira parte, a variação no padrão de cor em ambos os sexos foi comparado ao índice gonadossomático (GSI). Foi encontrada uma correlação significativa entre a variação na coloração e o índice gonadossomático. Os resultados deste estudo demonstram que os variantes em Cichla temensis são membros de uma única espécie e que a variação não representa um dimorfismo sexual. A variação no padrão de cor é uma característica sexual secundária que ocorre em ciclos, sendo um indicativo do grau de maturação sexual sazonal dos indivíduos.

Practical proxies for tidal marsh ecosystem services: application to injury and restoration.

Tidal marshes are valued, protected and restored in recognition of their ecosystem services: (1) high productivity and habitat provision supporting the food web leading to fish and wildlife, (2) buffer against storm wave damage, (3) shoreline stabilization, (4) flood water storage, (5) water quality maintenance, (6) biodiversity preservation, (7) carbon storage and (8) socio-economic benefits. Under US law, federal and state governments have joint responsibility for facilitating restoration to compensate quantitatively for ecosystem services lost because of oil spills and other contaminant releases on tidal marshes. This responsibility is now met by choosing and employing metrics (proxies) for the suite of ecosystem services to quantify injury and scale restoration accordingly. Most injury assessments in tidal marshes are triggered by oil spills and are limited to: (1) documenting areas covered by heavy, moderate and light oiling; (2) estimating immediate above-ground production loss (based on stem density and height) of the dominant vascular plants within each oiling intensity category and (3) sampling sediments for chemical analyses and depth of contamination, followed by sediment toxicity assays if sediment contamination is high and likely to persist. The percentage of immediate loss of ecosystem services is then estimated along with the recovery trajectory. Here, we review potential metrics that might refine or replace present metrics for marsh injury assessment. Stratifying plant sampling by the more productive marsh edge versus the less accessible interior would improve resolution of injury and provide greater confidence that restoration is truly compensatory. Using microphytobenthos abundance, cotton-strip decomposition bioassays and other biogeochemical indicators, or sum of production across consumer trophic levels fails as a stand-alone substitute metric. Below-ground plant biomass holds promise as a potential proxy for resiliency but requires further testing. Under some conditions, like chronic contamination by organic pollutants that affect animals but not vascular plants, benthic infaunal density, toxicity testing, and tissue contamination, growth, reproduction and mortality of marsh vertebrates deserve inclusion in the assessment protocol. Additional metrics are sometimes justified to assay microphytobenthos, use by nekton, food and habitat for reptiles, birds and mammals, or support of plant diversity. Empirical research on recovery trajectories in previously injured marshes could reduce the largest source of uncertainty in quantifying cumulative service losses.