Ryan P. Kelly

Mitigating Local Causes of Ocean Acidification with Existing Laws

Even as global and national efforts struggle to mitigate CO2 emissions, local and state governments have policy tools to address “hot spots” of ocean acidification. As the level of atmospheric carbon dioxide (CO2) continues to rise, so too does the amount of CO2 in the ocean (1, 2), which increases the oceans acidity. This affects marine ecosystems on a global scale in ways we are only beginning to understand: for example, impairing the ability of organisms to form shells or skeletons, altering food webs, and negatively affecting economies dependent on services ranging from coral reef tourism to shellfish harvests to salmon fisheries (3–5). Although increasing anthropogenic inputs drive acidification at global scales, local acidification disproportionately affects coastal ecosystems and the communities that rely on them. We describe policy options by which local and state governments—as opposed to federal and international bodies—can reduce these local and regional “hot spots” of ocean acidification.

Harnessing DNA to improve environmental management

Genetic monitoring can help public agencies implement environmental laws Responsive environmental policy demands a constant stream of information about the living world, but biological monitoring is difficult and expensive. For many species and ecosystems—especially in aquatic and marine environments—practical monitoring methods are lacking; even where methods do exist, they may be inefficient, highly destructive, or dependent on diminishing taxonomic expertise.

SOUTHERN HOSPITALITY: A LATITUDINAL GRADIENT IN GENE FLOW IN THE MARINE ENVIRONMENT

Abstract In recent years population genetics and phylogeographic studies have become increasingly valuable tools for inferring both historical and present-day genetic patterns within marine species. Here, we take a comparative approach to population-level study, analyzing original mitochondrial DNA data from 969 individuals representing 28 chiton (Mollusca: Polyplacophora) species to uncover large-scale genetic patterns along the Pacific coast of North America. The data reveal a distinct latitudinal connectivity gradient among chitons: species that exist at lower latitudes tend to have more isolated populations. This trend appears to be a product of between-species differences; within species, no significant gradient in connectivity is observed. Lower average annual sea surface temperatures are hypothesized to contribute to longer larval duration (and by extension, greater connectivity) among lecithotrophic species, providing a mechanism for the observed positive correlation between gene flow and latitude. Because increased isolation among populations may lead to speciation, a latitudinal trend in gene flow may contribute to the increased species diversity observed at lower latitudes.

Embracing thresholds for better environmental management

Three decades of study have revealed dozens of examples in which natural systems have crossed biophysical thresholds (‘tipping points’)—nonlinear changes in ecosystem structure and function—as a result of human-induced stressors, dramatically altering ecosystem function and services. Environmental management that avoids such thresholds could prevent severe social, economic and environmental impacts. Here, we review management measures implemented in ecological systems that have thresholds. Using Ostroms social–ecological systems framework, we analysed key biophysical and institutional factors associated with 51 social–ecological systems and associated management regimes, and related these to management success defined by ecological outcomes. We categorized cases as instances of prospective or retrospective management, based upon whether management aimed to avoid a threshold or to restore systems that have crossed a threshold. We find that smaller systems are more amenable to threshold-based management, that routine monitoring is associated with successful avoidance of thresholds and recovery after thresholds have been crossed, and that success is associated with the explicit threshold-based management. These findings are powerful evidence for the policy relevance of information on ecological thresholds across a wide range of ecosystems.

A Method for Detecting Population Genetic Structure in Diverse, High Gene-Flow Species

Detecting small amounts of genetic subdivision across geographic space remains a persistent challenge. Often a failure to detect genetic structure is mistaken for evidence of panmixia, when more powerful statistical tests may uncover evidence for subtle geographic differentiation. Such slight subdivision can be demographically and evolutionarily important as well as being critical for management decisions. We introduce here a method, called spatial analysis of shared alleles (SAShA), that detects geographically restricted alleles by comparing the spatial arrangement of allelic co-occurrences with the expectation under panmixia. The approach is allele-based and spatially explicit, eliminating the loss of statistical power that can occur with user-defined populations and statistical averaging within populations. Using simulated data sets generated under a stepping-stone model of gene flow, we show that this method outperforms spatial autocorrelation (SA) and Phi(ST) under common real-world conditions: at relatively high migration rates when diversity is moderate or high, especially when sampling is poor. We then use this method to show clear differences in the genetic patterns of 2 nearshore Pacific mollusks, Tegula funebralis (= Chlorostoma funebralis) and Katharina tunicata, whose overall patterns of within-species differentiation are similar according to traditional population genetics analyses. SAShA meaningfully complements Phi(ST)/F(ST), SA, and other existing geographic genetic analyses and is especially appropriate for evaluating species with high gene flow and subtle genetic differentiation.

Taking Action Against Ocean Acidification: A Review of Management and Policy Options

Ocean acidification has emerged over the last two decades as one of the largest threats to marine organisms and ecosystems. However, most research efforts on ocean acidification have so far neglected management and related policy issues to focus instead on understanding its ecological and biogeochemical implications. This shortfall is addressed here with a systematic, international and critical review of management and policy options. In particular, we investigate the assumption that fighting acidification is mainly, but not only, about reducing CO2 emissions, and explore the leeway that this emerging problem may open in old environmental issues. We review nine types of management responses, initially grouped under four categories: preventing ocean acidification; strengthening ecosystem resilience; adapting human activities; and repairing damages. Connecting and comparing options leads to classifying them, in a qualitative way, according to their potential and feasibility. While reducing CO2 emissions is confirmed as the key action that must be taken against acidification, some of the other options appear to have the potential to buy time, e.g. by relieving the pressure of other stressors, and help marine life face unavoidable acidification. Although the existing legal basis to take action shows few gaps, policy challenges are significant: tackling them will mean succeeding in various areas of environmental management where we failed to a large extent so far.

Reconstructing a radiation: the chiton genus Mopalia in the north Pacific

The chiton genus Mopalia Gray, 1847 is highly speciose despite showing little morphological differentiation. Many of the 24 extant species are conspicuous, large-bodied and ecologically important today, but pre-Pleistocene fossils for the genus are rare. Here, we use a combined analysis of four gene regions (16S and COI mtDNA, 18S and 28S rDNA) to estimate the phylogenetic relationships for Mopalia species and use the inferred phylogeny to analyse the groups biogeography and patterns of speciation. We then use these molecular data to distinguish between two alternative inter- pretations of the fossil record, as there is a large temporal gap between the oldest fossils tentatively identified as Mopalia and the ne xt oldest fossils (Miocene versus Plio-Pleistocene). Based on the estimated substitution rates from a wide variety of other marine animals, we conclude that the observed rates in Mopalia are consistent with a Miocene origin for the genus. Given this age for the group and assuming a molecular clock, most speciation events in Mopalia are inferred to have occurred on average ~5 Mya. The phylogenetic results indicate that most of the speciation events leading to extant species must have occurred along the western North American coast, though there appear to have been multiple spreading events across the Pacific. When considered along with results for the many other near-shore taxa that have similar distributions to Mopalia, our findings suggest the emergence of a coherent historical biogeography of the northern Pacific.

General-use polymerase chain reaction primers for amplification and direct sequencing of enolase, a single-copy nuclear gene, from different animal phyla.

In contrast to mitochondrial DNA, remarkably few general‐use primer sets are available for single‐copy nuclear genes across animal phyla. Here, we present a primer set that yields a c. 364‐bp coding fragment of the metabolic gene enolase, which includes an intron in some taxa. In species where introns are absent or have few insertions/deletions, the amplified fragment can be sequenced directly for phylogenetic or population analysis. Between‐species variation in the coding region occurs widely at third codon positions, even between closely related taxa, making the fragment useful for species‐level systematics. In low gene‐flow species, the primers may also be of use for population genetics, as intraspecific polymorphisms occur at several silent positions in the taxa examined.