Watershed boundaries and geographic isolation: patterns of diversification in cutthroat trout from western North America

<p>Abstract</p> <p>Background</p> <p>For wide-ranging species, intraspecific variation can occur as a result of reproductive isolation from local adaptive differences or from physical barriers to movement. Cutthroat trout (<it>Oncorhynchus clarkii</it>), a widely distributed fish species from North America, has been divided into numerous putative subspecies largely based on its isolation in different watersheds. In this study, we examined mtDNA sequence variation of cutthroat trout to determine the major phylogenetic lineages of this polytypic species. We use these data as a means of testing whether geographic isolation by watershed boundaries can be a primary factor organizing intraspecific diversification.</p> <p>Results</p> <p>We collected cutthroat trout from locations spanning almost the entire geographic range of this species and included samples from all major subspecies of cutthroat trout. Based on our analyses, we reveal eight major lineages of cutthroat trout, six of which correspond to subspecific taxonomy commonly used to describe intraspecific variation in this species. The Bonneville cutthroat trout (<it>O. c. utah</it>) and Yellowstone cutthroat trout (<it>O. c. bouvieri</it>) did not form separate monophyletic lineages, but instead formed an intermixed clade. We also document the geographic distribution of a Great Basin lineage of cutthroat trout; a group typically defined as Bonneville cutthroat trout, but it appears more closely related to the Colorado River lineage of cutthroat trout.</p> <p>Conclusion</p> <p>Our study indicates that watershed boundaries can be an organizing factor isolating genetic diversity in fishes; however, historical connections between watersheds can also influence the template of isolation. Widely distributed species, like cutthroat trout, offer an opportunity to assess where historic watershed connections may have existed, and help explain the current distribution of biological diversity across a landscape.</p

Optimization of DNA Extraction Methods for Sequencing of the NADH Dehydrogenase Subunit 2 (ND2) Gene in Rainbow Trout (\u3cem\u3eOncorhynchus mykiss\u3c/em\u3e)

Morphological, behavioral, and genetic variation due to broad geographic ranges is common in salmonid fishes. This variation can be attributed to the isolation of populations from natural phenomenon or human alteration to habitats, which affect gene flow and genetic drift. These changes may play a role in intraspecific genetic variation, potentially isolating them into separate subspecies or locally adapted populations. Rainbow Trout (Oncorhynchus mykiss) are one of the most widely distributed fish species in western North America but no study has identified the main evolutionary lineages from across its range. Identifying and comparing distinct evolutionary lineages can be achieved by comparing sequence data from mitochondrial genes but requires extraction of archived tissue samples of rainbow trout and amplification of selected genes. In this study, we compare different DNA extraction methods for rainbow trout tissue samples, some of which are more than 25 years old. DNA was extracted from tissue samples following a 5 or 15% Chelex method, or by following Zymo Research extraction kit instructions. Following extractions, polymerase chain reaction (PCR) for the highly conserved NADH dehydrogenase subunit 2 mtDNA gene (ND2) was completed using a BIO RAD thermal cycler and a gel electrophoresis is done to determine whether the ND2 gene was successfully amplified. Photographs of the agarose gels were taken using a ChemiDoc imaging system, and samples showing a band at 1050 base pairs are sent to the Molecular Research Core Facility at Idaho State University for sequencing. The genetic sequences are then compared and used to create a phylogeny and distribution for Rainbow trout subspecies. Sequencing of individual specimen and comparison across the species range will aid in the development of management and conservation strategies for rainbow trout across the species range

Assessment of acute myocardial infarction: current status and recommendations from the North American society for cardiovascular imaging and the European society of cardiac radiology

There are a number of imaging tests that are used in the setting of acute myocardial infarction and acute coronary syndrome. Each has their strengths and limitations. Experts from the European Society of Cardiac Radiology and the North American Society for Cardiovascular Imaging together with other prominent imagers reviewed the literature. It is clear that there is a definite role for imaging in these patients. While comparative accuracy, convenience and cost have largely guided test decisions in the past, the introduction of newer tests is being held to a higher standard which compares patient outcomes. Multicenter randomized comparative effectiveness trials with outcome measures are required

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Basic science232. Certolizumab pegol prevents pro-inflammatory alterations in endothelial cell function

Background: Cardiovascular disease is a major comorbidity of rheumatoid arthritis (RA) and a leading cause of death. Chronic systemic inflammation involving tumour necrosis factor alpha (TNF) could contribute to endothelial activation and atherogenesis. A number of anti-TNF therapies are in current use for the treatment of RA, including certolizumab pegol (CZP), (Cimzia ®; UCB, Belgium). Anti-TNF therapy has been associated with reduced clinical cardiovascular disease risk and ameliorated vascular function in RA patients. However, the specific effects of TNF inhibitors on endothelial cell function are largely unknown. Our aim was to investigate the mechanisms underpinning CZP effects on TNF-activated human endothelial cells. Methods: Human aortic endothelial cells (HAoECs) were cultured in vitro and exposed to a) TNF alone, b) TNF plus CZP, or c) neither agent. Microarray analysis was used to examine the transcriptional profile of cells treated for 6 hrs and quantitative polymerase chain reaction (qPCR) analysed gene expression at 1, 3, 6 and 24 hrs. NF-κB localization and IκB degradation were investigated using immunocytochemistry, high content analysis and western blotting. Flow cytometry was conducted to detect microparticle release from HAoECs. Results: Transcriptional profiling revealed that while TNF alone had strong effects on endothelial gene expression, TNF and CZP in combination produced a global gene expression pattern similar to untreated control. The two most highly up-regulated genes in response to TNF treatment were adhesion molecules E-selectin and VCAM-1 (q 0.2 compared to control; p > 0.05 compared to TNF alone). The NF-κB pathway was confirmed as a downstream target of TNF-induced HAoEC activation, via nuclear translocation of NF-κB and degradation of IκB, effects which were abolished by treatment with CZP. In addition, flow cytometry detected an increased production of endothelial microparticles in TNF-activated HAoECs, which was prevented by treatment with CZP. Conclusions: We have found at a cellular level that a clinically available TNF inhibitor, CZP reduces the expression of adhesion molecule expression, and prevents TNF-induced activation of the NF-κB pathway. Furthermore, CZP prevents the production of microparticles by activated endothelial cells. This could be central to the prevention of inflammatory environments underlying these conditions and measurement of microparticles has potential as a novel prognostic marker for future cardiovascular events in this patient group. Disclosure statement: Y.A. received a research grant from UCB. I.B. received a research grant from UCB. S.H. received a research grant from UCB. All other authors have declared no conflicts of interes

Bioenergetic calculations evaluate changes to habitat quality for salmonid fishes in streams treated with salmon carcass analog

Nutrient supplementation in oligotrophic streams is proposed as a means of mitigating losses of marine-derived subsidies from declining or extirpated populations of anadromous fishes. One of the central predictions of nutrient addition is an increased production of fish through bottom-up increases in invertebrate abundance. Such changes in food availability may increase growth and production rates for stream fishes by increasing habitat quality. In this study we apply bioenergetic calculations to estimate changes to habitat quality based on predicted increases in net energy intake. We compared invertebrate drift abundance and estimated changes in energy availability in streams treated with salmon carcass analog versus untreated controls. Our results revealed a 2-3 fold increase in invertebrate drift abundance following the addition of salmon carcass analog; however, this effect appeared to be short-term. Measures of the energetic profitability of stream habitat for salmonid fishes revealed small, yet significant increases in net energy availability in streams that received analog additions, but only after controlling for differences in physical habitat features such as temperature and stream flow.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Cutthroat Trout Population Response to Instream Habitat Improvement Efforts

Salmonid fish populations in headwater streams are often limited by the amount and availability of suitable habitat. This limitation can be exacerbated by stressors that contribute to habitat degradation in and around streams. Intense livestock grazing in riparian areas adjacent to streams often reduces or removes streamside vegetation. This loss causes streams to become simplified and the abundance of pool habitat is reduced. In this study, we examined if the addition of instream habitat improvement structures improved the capacity for salmonid survival and recruitment in simplified streams. Four streams in Southeast Idaho, containing only native cutthroat trout, were treated with instream structures last August. Untreated control sections were established to compare the effectiveness of the structures at increasing fish abundance. Fish populations were sampled by two-pass electrofishing in July and October 2016 and will be resampled July 2017. During sampling, fish length and mass were recorded and fish greater than 80 mm in length were tagged to track growth. Using these data we will compare fish population structure in treatment and control sections. The aim of this study is to test the efficiency of woody additions at increasing fish densities in degraded streams

Some like it slow: a bioenergetic evaluation of habitat quality for juvenile Chinook salmon in the Lemhi River, Idaho

Management and conservation of freshwater habitat requires fine spatial resolution and watershed-scale and life-stage-specific methods due to complex linkages among land, climate, water uses, and aquatic organism necessities. In this study, we present a valley-scale microhabitat resolution, process-based bioenergetics approach that combines high-resolution topobathymetric LiDAR survey with two-dimensional hydrodynamic and bioenergetics modeling. We applied the model to investigate the role of lateral habitat, stream morphological complexity, water use, and temperature regimes on aquatic habitat quality distribution of juvenile Chinook salmon (Oncorhynchus tshawytscha) within the Lemhi River (eastern Idaho, USA). Modeling results showed two key aspects: (i) a reduction in diverted flows is not sufficient to improve habitat quality potentially because of a legacy of morphological simplification (directly due to straightening and wood removal and indirectly due to low in-channel flows) and (ii) morphological complexity and connectivity with side channels and margin areas, which are key and vital elements to support suitable habitats that meet or exceed energetic needs to sustain or promote growth of individuals and populations.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author