Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

Estuarine and coastal transformation is as old as civilization yet has dramatically accelerated over the past 150 to 300 years. Reconstructed time lines, causes, and consequences of change in 12 once diverse and productive estuaries and coastal seas worldwide show similar patterns: Human impacts have depleted >90% of formerly important species, destroyed >65% of seagrass and wetland habitat, degraded water quality, and accelerated species invasions. Twentieth-century conservation efforts achieved partial recovery of upper trophic levels but have so far failed to restore former ecosystem structure and function. Our results provide detailed historical baselines and quantitative targets for ecosystem-based management and marine conservation.

/pdf/depletion-degradation-and-recovery-potential-of-estuaries-1hinljyave.pdf

Depletion, Degradation, and Recovery Potential of Estuaries and Coastal Seas

In the 12 years since Dudgeon et al. (2006) reviewed major pressures on freshwater ecosystems, the biodiversity crisis in
the world’s lakes, reservoirs, rivers, streams and wetlands has deepened. While lakes, reservoirs and rivers cover only
2.3% of the Earth’s surface, these ecosystems host at least 9.5% of the Earth’s described animal species. Furthermore,
using the World Wide Fund for Nature’s Living Planet Index, freshwater population declines (83% between 1970 and
2014) continue to outpace contemporaneous declines in marine or terrestrial systems. The Anthropocene has brought
multiple new and varied threats that disproportionately impact freshwater systems. We document 12 emerging threats
to freshwater biodiversity that are either entirely new since 2006 or have since intensified: (i) changing climates; (ii)
e-commerce and invasions; (iii) infectious diseases; (iv) harmful algal blooms; (v) expanding hydropower; (vi) emerging
contaminants; (vii) engineered nanomaterials; (viii) microplastic pollution; (ix) light and noise; (x) freshwater salinisation;
(xi) declining calcium; and (xii) cumulative stressors. Effects are evidenced for amphibians, fishes, invertebrates, microbes,
plants, turtles and waterbirds, with potential for ecosystem-level changes through bottom-up and top-down processes.
In our highly uncertain future, the net effects of these threats raise serious concerns for freshwater ecosystems. However,
we also highlight opportunities for conservation gains as a result of novel management tools (e.g. environmental flows,
environmental DNA) and specific conservation-oriented actions (e.g. dam removal, habitat protection policies,managed
relocation of species) that have been met with varying levels of success.Moving forward, we advocate hybrid approaches
that manage fresh waters as crucial ecosystems for human life support as well as essential hotspots of biodiversity and
ecological function. Efforts to reverse global trends in freshwater degradation now depend on bridging an immense gap
between the aspirations of conservation biologists and the accelerating rate of species endangerment.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/brv.12480

Emerging threats and persistent conservation challenges for freshwater biodiversity

http://auburn.edu/academic/agriculture/fisheries/genomics/FISH7660%202006/DNA%20marker%20review%20paper-Aquaculture.pdf

DNA marker technologies and their applications in aquaculture genetics.

Running waters are perhaps the most impacted ecosystem on the planet as they have been the focus for human settlement and are heavily exploited for water supplies, irrigation, electricity generation, and waste disposal. Lotic systems also have an intimate contact with their catchments and so land-use alterations affect them directly. Here long-term trends in the factors that currently impact running waters are reviewed with the aim of predicting what the main threats to rivers will be in the year 2025. The main ultimate factors forcing change in running waters (ecosystem destruction, physical habitat and water chemistry alteration, and the direct addition or removal of species) stem from proximate influences from urbanization, industry, land-use change and water-course alterations. Any one river is likely to be subjected to several types of impact, and the management of impacts on lotic systems is complicated by numerous links between different forms of anthropogenic effect. Long-term trends for different impacts vary. Concentrations of chemical pollutants such as toxins and nutrients have increased in rivers in developed countries over the past century, with recent reductions for some pollutants (e.g. metals, organic toxicants, acidification), and continued increases in others (e.g. nutrients); there are no long-term chemical data for developing countries. Dam construction increased rapidly during the twentieth century, peaking in the 1970s, and the number of reservoirs has stabilized since this time, whereas the transfer of exotic species between lotic systems continues to increase. Hence, there have been some success stories in the attempts to reduce the impacts from anthropogenic impacts in developed nations. Improvements in the pH status of running waters should continue with lower sulphurous emissions, although emissions of nitrous oxides are set to continue under current legislation and will continue to contribute to acidification and nutrient loadings. Climate change also will impact running waters through alterations in hydrology and thermal regimes, although precise predictions are problematic; effects are likely to vary between regions and to operate alongside rather than override those from other impacts. Effects from climate change may be more extreme over longer time scales (>50 years). The overriding pressure on running water ecosystems up to 2025 will stem from the predicted increase in the human population, with concomitant increases in urban development, industry, agricultural activities and water abstraction, diversion and damming. Future degradation could be substantial and rapid (c. 10 years) and will be concentrated in those areas of the world where resources for conservation are most limited and knowledge of lotic ecosystems most incomplete; damage will centre on lowland rivers, which are also relatively poorly studied. Changes in management practices and public awareness do appear to be benefiting running water ecosystems in developed countries, and could underpin conservation strategies in developing countries if they were implemented in a relevant way.

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S0376892902000097

Threats to the running water ecosystems of the world

We examined the status of diadromous (migratory between saltwater and freshwater) fishes within the North Atlantic basin, a region of pronounced declines in fisheries for many obligate marine species. Data on these 24 diadromous (22 anadromous, 2 catadromous) species are sparse, except for a few high-value forms. For 35 time series, relative abundances had dropped to less than 98% of historic levels in 13, and to less than 90% in an additional 11. Most reached their lowest levels near the end of the observation period. Many populations persist at sharply reduced levels, but all species had suffered population extirpations, and many species are now classified as threatened or endangered. Habitat loss (especially damming), overfishing, pollution, and, increasingly, climate change, nonnative species, and aquaculture contributed to declines in this group. For those diadromous fishes for which data exist, we show that populations have declined dramatically from original baselines. We also discuss the consequen...

https://www.jstor.org/stable/10.1525/bio.2009.59.11.7

Dramatic Declines in North Atlantic Diadromous Fishes

An holistic approach to fish stock identification

Introduction Life History Traits Natural Marks-Morphological Analyses Natural Marks-Environmental Signals Natural Marks-Genetic Analyses Applied Marks Stock Identification Data Analysis Application of Stock Identification Data in Resource Management

Stock identification methods : applications in fishery science

...increased demand has recently driven the price of black market smoked sturgeon as high as $ 26 a kilogram. With poachers standing to gain roughly a third of this price [besides the much higher price of caviar], a large fish could be worth thousands of dollars. Gary Hamilton in Canadian Geographic, July/August 1996, p. 62

The threatened status of acipenseriform species: a summary

Fish from urban and industrialized estuaries are exposed among the highest levels of contaminants of any vertebrate populations. As a result, they serve as especially relevant models for determining the toxic effects and mechanisms through which environmental toxicants work. In controlled laboratory experiments, fish from highly contaminated locales sometimes exhibit resistance to contaminant-induced toxicity. Resistance may be due to genetic adaptation or physiological acclimations. Distinguishing between these possibilities is important in predicting the persistence of resistance and its potential costs to affected populations and communities. Along the Atlantic coast of North America, populations of two estuarine species, Atlantic killifish (mummichog) Fundulus heteroclitus and Atlantic tomcod Microgadus tomcod, exhibit phenotypes that are resistant to aromatic hydrocarbon (AH) contaminants, including polychlorinated biphenyls (PCBs), polychlorinated dibenzo-p-dioxins (PCDDs), and polycyclic aromatic hydrocarbons (PAHs). Populations of these species exhibit resistance to AH-induced lethality, early life-stage toxicities, and expression of cytochrome P4501A (CYP1A). However, some differences among populations in the occurrence and type (genetic or physiological) of AH-resistant phenotypes have been observed. In some instances, resistance was obviously genetic and resulted in its transmission to at least the F2 generation, in others, resistance had a physiological or yet to be identified epigenetic basis. In some cases, resistance was observed for all AH compounds tested, in others, it was seen only for halogenated AHs. As toxic responses to AHs are believed to be mediated by the aryl hydrocarbon receptor pathway (AHR), several studies compared the structure and expression of AHR pathway molecules between resistant and sensitive fish populations. However, no obvious differences in these molecular parameters were observed between resistant and sensitive populations at the transcriptional level. Further studies at the protein level are recommended to further evaluate the role of the AHR pathway in conferring resistance. Open-ended microarray and proteomic approaches may provide additional resolution in determining the molecular mechanisms of resistance. Also, studies that evaluate the prevalence and ecosystem cost of resistance are needed.

John R. Waldman

Papers

Dramatic Declines in North Atlantic Diadromous Fishes

An holistic approach to fish stock identification

Stock identification methods : applications in fishery science

The threatened status of acipenseriform species: a summary

Resistance to contaminants in North American fish populations