Southall Environmental Associates (United States)

Molecular data are widely used to resolve complex phylogenetic relationships between cryptic species, particularly in cases where morphological features are insufficient to confirm taxonomic distinctness. For benthic shallow-water octopuses, several successes and failures have been reported when attempting to delineate species using individual nuclear or mitochondrial markers. In this study, we investigated the potential of shallow random shotgun sequencing to assess the phylogenetic placement of an undescribed southern hemisphere lineage within the Octopus vulgaris species complex, which could not be conclusively delimited using single-marker approaches. A total of 338 nuclear loci, along with complete mitochondrial genomes, were generated for two specimens presently classified as Octopus vulgaris (Type III) that originated from the southeastern Atlantic coast of South Africa and Amsterdam Island in the southern Indian Ocean. Our combined phylogenomic approach reveals that this lineage is genetically distinct from O. vulgaris sensu stricto (ss) from the Mediterranean and the northeast Atlantic, as well as from the closely related O. sinensis from East Asia. A further separation of O. vulgaris (Type III) into distinct South African and Amsterdam Island lineages cannot be proven. These findings add to the growing body of evidence that supports O. vulgaris Type III as a genetically distinct lineage within the O. vulgaris species complex, and emphasise that the taxonomic classification of this southern hemisphere lineage warrants re-evaluation.

The design of experiments to investigate the combined effects of multiple stressors requires exposing target organisms to multiple combinations of stressor doses. Concurrent manipulation of stressors is often infeasible with wildlife, but long-lasting health effects allow individual health to be used as an integrator of prior stressor exposure. The population of bottlenose dolphins in Barataria Bay, Louisiana, experienced long-lasting health effects after exposure to oil from the Deepwater Horizon spill. We investigated whether compromised health status affects dolphins' ability to respond to other stressors, specifically vessel traffic, potentially leadingto increased collision risk. We used this case study to develop a hypothesis-driven experimental approach to assess the combined effects of multiple stressors in a large, long-lived vertebrate species. We conducted controlled vessel approaches to test whether the health status of targeted dolphins affected their behavioral responses. Our results highlighted some effects of health, suggesting that oil spills may exacerbate the effects of other stressors in coastal populations. For example, lung disease was associated with a delayed dive response, which could affect the ability to vertically avoid vessels and lead to increased collision risk. However, health effects on response probability were overall smaller than anticipated, and other contextual variables (e.g., sex, age, calf presence, prior experience, and exposure context) contributed to response variability. Our work demonstrated the value of formalizing stressor interactions as multidimensional dose-response functions and showed the feasibility of an experimental, multiple-stressor study in a wild system in which individual health status can be used as an integrator of prior stressor exposure. This approach has broad implications for other species that are difficult to handle experimentally. The quantification and management of the cumulative risk from multiple stressors on wildlife will require a combination of empirical and mechanistic approaches to inform long-term, population consequences.

Marine fauna are vulnerable to a variety of acute and chronic stressors that act across varying spatial and temporal scales. The evaluation of the effect of these stressors requires consideration of the key threats and impact pathways, and the cumulative effect of anthropogenic pressures from all aspects of a project in concert with projects and long-term environmental change. Migratory species, particularly those that migrate across jurisdictional boundaries, may be exposed to pressures that compromise the recovery or health of the population that are not manageable under any one country’s legislation. Thus, the evaluation of cumulative impacts in a meaningful manner requires careful consideration of pressures at biologically meaningful spatial and temporal scales. Complex models predicting the population consequence of disturbance are increasingly being used to understand the potential significance of anthropogenic pressures on populations. While incredibly valuable, information to parametrize these models are not available for many species and populations. This chapter presents a semi-quantitative framework for the prediction of cumulative impacts on migratory marine mammal populations, with examples of how this may be applied using the Australian legislative and environmental context.

ABSTRACTAimEucalypt species are known for their diversity of bark types and adaptation to fire and drought. Eucalypts with stringy bark and ribboning bark are notorious for accumulating large amounts of bark fuels compared to other tree species. In this study, we examined the fire regime (fire frequency and intensity) and bioclimatic distributions of 12 contrasting eucalypt bark types, and provided maps of eucalypt bark type distributions for use in fire behaviour modelling.LocationTreed regions of New South Wales, Australia.MethodsWe used machine learning techniques to model eucalypt bark type observations recorded in 5949 vegetation census plots. We used 79 environmental variables, and a novel fire regime categorisation to model the geographical distributions of 12 eucalypt bark types.ResultsSmooth‐bark eucalypts are associated with a range of fire intensities, while eucalypts with a combination of smooth and rough bark (‘smooth with stocking’ and ‘halfbark’) are most likely to occur where fires are low intensity and rare. Smooth with stocking and halfbark eucalypts also occur more frequently in hot, dry regions than most of the rough‐barked eucalypts examined. The most hazardous bark types to fire management personnel are restricted to more productive locations, defined by high water and soil nutrient availability. They are also most likely to occur where fires tend to be frequent and medium to high intensity, likely contributing to more extreme fire behaviour.ConclusionsThese results support growing evidence for bark type being a key indicator of pyro‐ecological strategies. Our results provide partial support for the theory that trade‐offs in investment between smooth and rough bark govern the spatial distributions of the smooth with stocking and halfbark eucalypts. However, these trade‐offs do not apply universally across all eucalypt bark types. Bark types that produce large quantities of bark fuels were limited to highly productive sites. We posit that site productivity may limit the distributions of these bark types due to constraints on trunk growth rates, as trunk growth rates likely play a role in determining rates of bark fuel production.

In many rural areas of arid and semi-arid regions, balancing agricultural and environmental water needs is a key challenge facing resource managers. This is complicated by the tendency for the water needs of cultivated crops to be better understood than those of aquatic ecosystems. In particular, the timing and magnitude of flow needed to sustain key ecological functions remain poorly quantified in many regions. This work aims to quantify hydrologic conditions that support persistence of key ecosystem species using a functional flows framework. We use the coho ( Oncorhynchus kisutch) and Chinook ( Oncorhynchus tshawytscha) salmon run in Scott Valley, a 2,109 km 2 undammed rural watershed in northern California, USA, as a case study. Taking advantage of a nearly two-decade ecological monitoring dataset and long-term stream gauge measurements, we used lasso regression to build predictive models of coho and Chinook salmon reproductive success based on hydrologic metrics. To control for cohort effects, we chose normalized ecological response metrics for coho and Chinook (number of outmigrating smolt per spawning adult or spawning adult female). For both species, we calculated optimal prediction models using a cross-validation bootstrapping approach to resample and test on unsampled observations. Lambda values, a key fitting parameter in the lasso models, were selected based on an average relative test error threshold of 1.0. Selected lambda values were used to calculate a final predictive model, or Hydrologic Benefit function, using the full dataset for each species. Hydrology could explain a greater degree of variance in relative coho reproduction than in Chinook. The hydrologic metrics that explain the greatest variance in coho reproduction values occur during the window of their parents’ spawning and, to a lesser extent, in the spring and fall of their year of rearing in freshwater. This supports an interpretation that spawning conditions may exert a significant influence on the mortality rates of the hatching juveniles. Robustness of the results indicate that this method for empirically deriving hydrologic metrics with the highest ecological benefit for a threatened species may be useful in other watersheds, where sufficient ecological data records are available, to evaluate trade-offs and support water management decisions in human-altered novel ecosystems.

Protected areas are typically managed as a network of sites exposed to varying anthropogenic conditions. Managing these networks benefits from monitoring of conditions across sites to help prioritize coordinated efforts. Monitoring marine vessel activity and related underwater radiated noise impacts across a network of protected areas, like the U.S. National Marine Sanctuary system, helps managers ensure the quality of habitats used by a wide range of marine species. Here, we use underwater acoustic detections of vessels to quantify different characteristics of vessel noise at 25 locations within eight marine sanctuaries including the Hawaiian Archipelago and the U.S. east and west coasts. Vessel noise metrics, including temporal presence and sound levels, were paired with Automatic Identification System (AIS) vessel tracking data to derive a suite of robust vessel noise indicators for use across the network of marine protected areas. Network-wide comparisons revealed a spectrum of vessel noise conditions that closely matched AIS vessel traffic composition. Shifts in vessel noise were correlated with the decrease in vessel activity early in the COVID-19 pandemic, and vessel speed reduction management initiatives. Improving our understanding of vessel noise conditions in these protected areas can help direct opportunities for reducing vessel noise, such as establishing and maintaining noise-free periods, enhancing port efficiency, engaging with regional and international vessel quieting initiatives, and leveraging co-benefits of management actions for reducing ocean noise.