Regional differentiation and post-glacial expansion of the Atlantic silverside, Menidia menidia, an annual fish with high dispersal potential

The coastal marine environment of the Northwest Atlantic contains strong environmental gradients that create distinct marine biogeographic provinces by limiting dispersal, recruitment, and survival. This region has also been subjected to numerous Pleistocene glacial cycles, resulting in repeated extirpations and recolonizations in northern populations of marine organisms. In this study, we examined patterns of genetic structure and historical demography in the Atlantic silverside, Menidia menidia, an annual marine fish with high dispersal potential but with well-documented patterns of clinal phenotypic adaptation along the environmental gradients of the Northwest Atlantic. Contrary to previous studies indicating genetic homogeneity that should preclude regional adaptation, results demonstrate subtle but significant (F(ST) = 0.07; P < 0.0001) genetic structure among three phylogeographic regions that partially correspond with biogeographic provinces, suggesting regional limits to gene flow. Tests for non-equilibrium population dynamics and latitudinal patterns in genetic diversity indicate northward population expansion from a single southern refugium following the last glacial maximum, suggesting that phylogeographic and phenotypic patterns have relatively recent origins. The recovery of phylogeographic structure and the partial correspondence of these regions to recognized biogeographic provinces suggest that the environmental gradients that shape biogeographic patterns in the Northwest Atlantic may also limit gene flow in M. menidia, creating phylogeographic structure and contributing to the creation of latitudinal phenotypic clines in this species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00227-010-1577-3) contains supplementary material, which is available to authorized users

Transcriptional Analysis of Fracture Healing and the Induction of Embryonic Stem Cell–Related Genes

Fractures are among the most common human traumas. Fracture healing represents a unique temporarily definable post-natal process in which to study the complex interactions of multiple molecular events that regulate endochondral skeletal tissue formation. Because of the regenerative nature of fracture healing, it is hypothesized that large numbers of post-natal stem cells are recruited and contribute to formation of the multiple cell lineages that contribute to this process. Bayesian modeling was used to generate the temporal profiles of the transcriptome during fracture healing. The temporal relationships between ontologies that are associated with various biologic, metabolic, and regulatory pathways were identified and related to developmental processes associated with skeletogenesis, vasculogenesis, and neurogenesis. The complement of all the expressed BMPs, Wnts, FGFs, and their receptors were related to the subsets of transcription factors that were concurrently expressed during fracture healing. We further defined during fracture healing the temporal patterns of expression for 174 of the 193 genes known to be associated with human genetic skeletal disorders. In order to identify the common regulatory features that might be present in stem cells that are recruited during fracture healing to other types of stem cells, we queried the transcriptome of fracture healing against that seen in embryonic stem cells (ESCs) and mesenchymal stem cells (MSCs). Approximately 300 known genes that are preferentially expressed in ESCs and ∼350 of the known genes that are preferentially expressed in MSCs showed induction during fracture healing. Nanog, one of the central epigenetic regulators associated with ESC stem cell maintenance, was shown to be associated in multiple forms or bone repair as well as MSC differentiation. In summary, these data present the first temporal analysis of the transcriptome of an endochondral bone formation process that takes place during fracture healing. They show that neurogenesis as well as vasculogenesis are predominant components of skeletal tissue formation and suggest common pathways are shared between post-natal stem cells and those seen in ESCs

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms

Research on marine coastal impacts to promote ecosystem-based management : nonnative species in northeast Pacific estuaries

Ecosystem-based management (EBM) offers a holistic evaluation of tradeoffs between human activities, but this offer rests upon a foundation of science. In this thesis, I assessed and advanced the knowledge-base for EBM in five ways, focusing on nonnative species in estuarine ecosystems. In Chapter 2, I tested for the comprehensiveness of research that connects the impacts of anthropogenic activities to changes in ecosystem service production, employing a literature review of estuarine ecosystems. Research on these connections virtually never included the relationship of activities to ecosystem services production, presenting an impressive gap in research for evaluating tradeoffs using EBM. I addressed the sufficiency of existing information regarding nonnative species in eelgrass beds in Chapter 3. I tested the relationship of nonnative species in British Columbia’s (BC) eelgrass beds with arrival pathways and environmental selection factors. There were few (12) nonnatives in BC’s eelgrass; all associated most commonly with aquaculture facilities and warm temperatures. Existing reports included the majority of nonnatives: only one species, the bamboo worm Clymenella torquata, represented a new record, as I described in Chapter 4. Impacts of nonnatives are difficult to limit after invasion. In Chapter 5, I developed an approach for characterizing the potential economic impacts of nonnatives. I focused on European green crab, a nonnative species that has not yet arrived in Puget Sound, Washington. At a range of invasion densities and increasing calorie diets, I calculated a value-at-risk to shellfish harvest ranging from $1.6 -$41 million USD. Such calculations can aid in preparation for impending invasion by motivating prevention and mitigation efforts. Nonnative management is often based on the available understanding of the impacts on native species. In Chapter 6, I assessed available research on the impact of nonnative seagrass, Zostera japonica, in northeast Pacific estuaries. My results suggested existing studies that quantitatively test Z. japonica impacts are insufficient to comprehensively assess the effects of this invasion. My dissertation research highlights the need for research to determine the ecosystem role of nonnatives in their invaded range through analysis of quantitative studies across broad scales.Science, Faculty ofResources, Environment and Sustainability (IRES), Institute forGraduat

Human impacts and ecosystem services : insufficient research for trade-off evaluation

In order to perform a science-based evaluation of ecosystem service tradeoffs, research is needed on the impacts to ecosystem services from multiple human activities and their associated stressors ('impact-pathways'). Whereas research frameworks and models abound, the evidence-base detailing these pathways for trade-off evaluation has not been well characterized. Toward this end, we review the evidence for impact-pathways using estuaries as a case study, focusing on seagrass and shellfish. Keyword searches of peer-reviewed literature revealed 2379 studies for a broad suite of impact-pathways, but closer inspection demonstrated that the vast majority of these made connections only rhetorically, and only 4.6% (based on a subset of 250 studies) actually evaluated impacts of stressors on ecosystem services. Furthermore, none of the reviewed studies tested pathways based on metrics of ecosystem services value that are most relevant to beneficiaries. Multi-activity tradeoff evaluation and management will require a concerted effort to structure ecosystem-based research around impact-pathways.Science, Faculty ofNon UBCResources, Environment and Sustainability (IRES), Institute forUnreviewedFacultyPostdoctora

Regional differentiation and post-glacial expansion of the Atlantic silverside, Menidia menidia, an annual fish with high dispersal potential.

The coastal marine environment of the Northwest Atlantic contains strong environmental gradients that create distinct marine biogeographic provinces by limiting dispersal, recruitment, and survival. This region has also been subjected to numerous Pleistocene glacial cycles, resulting in repeated extirpations and recolonizations in northern populations of marine organisms. In this study, we examined patterns of genetic structure and historical demography in the Atlantic silverside, Menidia menidia, an annual marine fish with high dispersal potential but with well-documented patterns of clinal phenotypic adaptation along the environmental gradients of the Northwest Atlantic. Contrary to previous studies indicating genetic homogeneity that should preclude regional adaptation, results demonstrate subtle but significant (FST&nbsp;=&nbsp;0.07; P&nbsp;&lt;&nbsp;0.0001) genetic structure among three phylogeographic regions that partially correspond with biogeographic provinces, suggesting regional limits to gene flow. Tests for non-equilibrium population dynamics and latitudinal patterns in genetic diversity indicate northward population expansion from a single southern refugium following the last glacial maximum, suggesting that phylogeographic and phenotypic patterns have relatively recent origins. The recovery of phylogeographic structure and the partial correspondence of these regions to recognized biogeographic provinces suggest that the environmental gradients that shape biogeographic patterns in the Northwest Atlantic may also limit gene flow in M. menidia, creating phylogeographic structure and contributing to the creation of latitudinal phenotypic clines in this species

A More Social Science: Barriers and Incentives for Scientists Engaging in Policy

Scientists are increasingly called upon to engage in policy formulation, but the literature on engagement is strong on speculation and weak on evidence. Using a survey administered at several broadly “ecological” conferences, we investigated: (1) the extent to which respondents engage in policy‐related activities (including reporting scientific results, interpreting science for policy makers, integrating science into decision making, taking a position on a policy issue, and acting as a decision maker); (2) what factors best explain these types of engagement; and (3) whether respondents\u27 activity levels match their stated beliefs on such activities. Different factors explain different forms of participation. Past negative experience was identified as a barrier to taking part in policy, while self‐perceived competence in navigating the science–policy interface was consistently important in explaining activity across all engagement types, highlighting the importance of training programs linking scientists to policy. Many respondents believed that scientists should interpret, integrate, and advocate, which contrasts with previous research and relatively low levels of self‐reported participation in policy

The Insignificance of Thresholds in Environmental Impact Assessment : An illustrative case study in Canada

Environmental assessment is the process that decision-makers rely on to predict, evaluate and prevent biophysical, social and economic impacts of potential project developments. The determination of significance in environmental assessment is central to environmental management in many nations. We reviewed ten recent environmental impact assessments from British Columbia, Canada and systematically reviewed and scored significance determination and the approaches used by assessors, the use of thresholds in significance determination, threshold exceedances and the outcomes. Findings of significant impacts were exceedingly rare and practitioners used a combination of significance determination approaches, most commonly relying upon reasoned argumentation. Quantitative thresholds were rarely employed, with less than 10% of the valued components evaluated using thresholds. Even where quantitative thresholds for significance were exceeded, in every case practitioners used a variety of rationales to demote negative impacts to non-significance. These reasons include combinations of scale (temporal and spatial) of impacts, an already exceeded baseline, model uncertainty and/or substituting less stringent thresholds. Governments and agencies can better protect resources by requiring clear and defensible significance determinations, by making government-defined thresholds legally enforceable and accountable, and by requiring or encouraging significance determination through inclusive and collaborative approaches.Forestry, Faculty ofScience, Faculty ofNon UBCResources, Environment and Sustainability (IRES), Institute forReviewedFacultyResearcherPostdoctoralGraduat

Supporting Risk Assessment: Accounting for Indirect Risk to Ecosystem Components

<div><p>The multi-scalar complexity of social-ecological systems makes it challenging to quantify impacts from human activities on ecosystems, inspiring risk-based approaches to assessments of potential effects of human activities on valued ecosystem components. Risk assessments do not commonly include the risk from indirect effects as mediated via habitat and prey. In this case study from British Columbia, Canada, we illustrate how such “indirect risks” can be incorporated into risk assessments for seventeen ecosystem components. We ask whether (i) the addition of indirect risk changes the at-risk ranking of the seventeen ecosystem components and if (ii) risk scores correlate with trophic prey and habitat linkages in the food web. Even with conservative assumptions about the transfer of impacts or risks from prey species and habitats, the addition of indirect risks in the cumulative risk score changes the ranking of priorities for management. In particular, resident orca, Steller sea lion, and Pacific herring all increase in relative risk, more closely aligning these species with their “at-risk status” designations. Risk assessments are not a replacement for impact assessments, but—by considering the potential for indirect risks as we demonstrate here—they offer a crucial complementary perspective for the management of ecosystems and the organisms within.</p></div