Ringed seal (Pusa hispida) seasonal movements,diving, and haul‐out behavior in the Beaufort,Chukchi, and Bering Seas (2011–2017)

Continued Arctic warming and sea‐ice loss will have important implications for the conservation of ringed seals, a highly ice‐dependent species. A better understanding of their spatial ecology will help characterize emerging ecological trends and inform management decisions. We deployed satellite transmitters on ringed seals in the summers of 2011, 2014, and 2016 near Utqia?vik (formerly Barrow), Alaska, to monitor their movements, diving, and haul‐out behavior. We present analyses of tracking and dive data provided by 17 seals that were tracked until at least January of the following year. Seals mostly ranged north of Utqia?vik in the Beaufort and Chukchi Seas during summer before moving into the southern Chukchi and Bering Seas during winter. In all seasons, ringed seals occupied a diversity of habitats and spatial distributions, from near shore and localized, to far offshore and wide‐ranging in drifting sea ice. Continental shelf waters were occupied for >96% of tracking days, during which repetitive diving (suggestive of foraging) primarily to the seafloor was the most frequent activity. From mid‐summer to early fall, 12 seals made ~1‐week forays off‐shelf to the deep Arctic Basin, most reaching the retreating pack‐ice, where they spent most of their time hauled out. Diel activity patterns suggested greater allocation of foraging efforts to midday hours. Haul‐out patterns were complementary, occurring mostly at night until April‐May when midday hours were preferred. Ringed seals captured in 2011—concurrent with an unusual mortality event that affected all ice‐seal species—differed morphologically and behaviorally from seals captured in other years. Speculations about the physiology of molting and its role in energetics, habitat use, and behavior are discussed; along with possible evidence of purported ringed seal ecotypes.     

Incidence of lamprey marks on Lake Sturgeon (Acipenser fulvescens Rafinesque, 1817) in the St. Clair – Detroit River System: Implications for Sea Lamprey (Petromyzon marinus Linnaeus, 1758) effects

Laurentian Great Lakes Lake Sturgeon (Acipenser fulvescens) are hosts to lamprey species, including native Silver Lamprey (Ichthyomyzon unicuspis) and invasive Sea Lamprey (Petromyzon marinus). Silver Lamprey coevolved with Lake Sturgeon and cause negligible mortality, but Sea Lamprey can negatively affect Lake Sturgeon populations. Sea Lamprey abundance in Lake Erie has been above targets set by resource managers, with the St. Clair – Detroit River System (SCDRS) suspected as a source of Sea Lamprey production into Lake Erie. This study summarizes lamprey marking on Lake Sturgeon captured during agency assessment surveys in the SCDRS since 1996 and provides insight on the potential for Sea Lamprey to negatively affect Lake Sturgeon in the SCDRS. Lamprey marks (any lamprey species) were noted on 48.2% of Lake Sturgeon (2.5 marks/fish) and 3.3% of Lake Sturgeon assumed to be susceptible to mortality by Sea Lamprey (<760 mm TL; 0.06 marks/fish). Silver Lamprey were the only lamprey species found attached to Lake Sturgeon and there was no difference between oral disc diameters of Silver Lamprey and marks measured on Lake Sturgeon in Lake St. Clair and the lower St. Clair River (p = .45). Based on logistic regression, probability of at least one lamprey mark increased with Lake Sturgeon total length and was highest in Lake St. Clair. The probability of observing at least one lamprey mark on a 760 mm Lake Sturgeon was 8.1% or less for each sampling location in the SCDRS aside from Lake St. Clair (28.1%). Results suggest that parasitism of Lake Sturgeon by Sea Lamprey in the SCDRS is rare, particularly for Lake Sturgeon <760 mm TL. Low incidence of lamprey marks on Lake Sturgeon assumed to be susceptible to mortality from Sea Lamprey parasitism and zero occurrence of Sea Lamprey being observed attached to a Lake Sturgeon suggest Sea Lamprey at their current abundance likely have little effect on the Lake Sturgeon population in the SCDRS. Caution should be taken when using mark size to assign marks to lamprey species as there is substantial overlap among species oral disc diameters, potentially inflating the perceived impact of Sea Lamprey on Lake Sturgeon in areas with native lampreys.     

Intraspecific trait variability shapes leaf trait response to altered fire regimes

Background and AimsUnderstanding impacts of altered disturbance regimes on community structure and function is a key goal for community ecology. Functional traits link species composition to ecosystem functioning. Changes in the distribution of functional traits at community scales in response to disturbance can be driven not only by shifts in species composition, but also by shifts in intraspecific trait values. Understanding the relative importance of these two processes has important implications for predicting community responses to altered disturbance regimes.MethodsWe experimentally manipulated fire return intervals in replicated blocks of a fire-adapted, longleaf pine (Pinus palustris) ecosystem in North Carolina, USA and measured specific leaf area (SLA), leaf dry matter content (LDMC) and compositional responses along a lowland to upland gradient over a 4 year period. Plots were burned between zero and four times. Using a trait-based approach, we simulate hypothetical scenarios which allow species presence, abundance or trait values to vary over time and compare these with observed traits to understand the relative contributions of each of these three processes to observed trait patterns at the study site. We addressed the following questions. (1) How do changes in the fire regime affect community composition, structure and community-level trait responses? (2) Are these effects consistent across a gradient of fire intensity? (3) What are the relative contributions of species turnover, changes in abundance and changes in intraspecific trait values to observed changes in community-weighted mean (CWM) traits in response to altered fire regime?Key ResultsWe found strong evidence that altered fire return interval impacted understorey plant communities. The number of fires a plot experienced significantly affected the magnitude of its compositional change and shifted the ecotone boundary separating shrub-dominated lowland areas from grass-dominated upland areas, with suppression sites (0 burns) experiencing an upland shift and annual burn sites a lowland shift. We found significant effects of burn regimes on the CWM of SLA, and that observed shifts in both SLA and LDMC were driven primarily by intraspecific changes in trait values.ConclusionsIn a fire-adapted ecosystem, increased fire frequency altered community composition and structure of the ecosystem through changes in the position of the shrub line. We also found that plant traits responded directionally to increased fire frequency, with SLA decreasing in response to fire frequency across the environmental gradient. For both SLA and LDMC, nearly all of the observed changes in CWM traits were driven by intraspecific variation.     

Freshwater fish functional and taxonomic diversity above and below Niagara Falls

The Niagara River, which connects two Great Lakes (Erie and Ontario) and forms a border between Canada and the United States, has experienced decades of abiotic and biotic disturbance as well as long-term restoration efforts. Given the iconic riverscape and importance as a binational fisheries resource, a biodiversity assessment of the mainstem Niagara River fish assemblage is overdue. Here, fish assemblage and habitat data from a standardized boat electrofishing program of the Niagara River were combined with species trait data related to substrate associations, diet preferences, reproductive strategies, and body size to quantify biodiversity patterns among river sections (sites above and below Niagara Falls), seasons (spring, summer, fall), and years (2015–2017). Sixty-five species were captured representing a variety of trait combinations. Significant differences in functional dispersion and divergence (i.e., functional diversity) were observed between river sections, seasons, and (or) years. The fish community captured in the lower river in spring 2015 had both the highest average functional dispersion (2.08?±?0.32 SD) and divergence (0.88?±?0.04 SD) compared to the other seasonal sampling efforts, but relatively few fishes were captured (n?=?686). Although non-native fishes represented a small portion of the catch over the 3 years (8.6% of catch), the seasonal presence (spring and fall) of mostly introduced large-bodied salmonids expanded functional trait space in the lower river during these periods. The importance of rare species on functional diversity metrics suggests further insight on local species detection probabilities is needed to understand if differences in functional diversity reflect ecological patterns or are driven by sampling design.

     

Measuring cortisol in fish scales to study stress in wild tropical tuna

Environmental Biology of Fishes - Cortisol is recognized as a physiological indicator of stress in fish. However, this hormone is typically measured in plasma samples. In this study, cortisol...     

Mitonuclear Coevolution,but not Nuclear Compensation,Drives Evolution of OXPHOS Complexes in Bivalves

In Metazoa, four out of five complexes involved in oxidative phosphorylation (OXPHOS) are formed by subunits encoded by both the mitochondrial (mtDNA) and nuclear (nuDNA) genomes, leading to the expectation of mitonuclear coevolution. Previous studies have supported coadaptation of mitochondria-encoded (mtOXPHOS) and nuclear-encoded OXPHOS (nuOXPHOS) subunits, often specifically interpreted with regard to the “nuclear compensation hypothesis,” a specific form of mitonuclear coevolution where nuclear genes compensate for deleterious mitochondrial mutations due to less efficient mitochondrial selection. In this study, we analyzed patterns of sequence evolution of 79 OXPHOS subunits in 31 bivalve species, a taxon showing extraordinary mtDNA variability and including species with “doubly uniparental” mtDNA inheritance. Our data showed strong and clear signals of mitonuclear coevolution. NuOXPHOS subunits had concordant topologies with mtOXPHOS subunits, contrary to previous phylogenies based on nuclear genes lacking mt interactions. Evolutionary rates between mt and nuOXPHOS subunits were also highly correlated compared with non-OXPHO-interacting nuclear genes. Nuclear subunits of chimeric OXPHOS complexes (I, III, IV, and V) also had higher dN/dS ratios than Complex II, which is formed exclusively by nuDNA-encoded subunits. However, we did not find evidence of nuclear compensation: mitochondria-encoded subunits showed similar dN/dS ratios compared with nuclear-encoded subunits, contrary to most previously studied bilaterian animals. Moreover, no site-specific signals of compensatory positive selection were detected in nuOXPHOS genes. Our analyses extend the evidence for mitonuclear coevolution to a new taxonomic group, but we propose a reconsideration of the nuclear compensation hypothesis.     

Characterization of modeled inhibitory binding sites on isoform one of the Na+/H+ exchanger

Mammalian Na⁺/H⁺ exchanger isoform one (NHE1) is a plasma membrane protein responsible for pH regulation in mammalian cells. Excess activity of the protein promotes heart disease and is a trigger of metastasis in cancer. Inhibitors of the protein exist but problems in specificity have delayed their clinical application. Here we examined amino acids involved in two modeled inhibitor binding sites (A, B) in human NHE1. Twelve mutations (Asp159, Phe348, Ser351, Tyr381, Phe413, Leu465, Gly466, Tyr467, Leu468, His473, Met476, Leu481) were made and characterized. Mutants S351A, F413A, Y467A, L468A, M476A and L481A had 40–70% of wild type expression levels, while G466A and H473A expressed 22% ~ 30% of the wild type levels. Most mutants, were targeted to the cell surface at levels similar to wild type NHE1, approximately 50–70%, except for F413A and G466A, which had very low surface targeting. Most of the mutants had measurable activity except for D159A, F413A and G466A. Resistance to inhibition by EMD87580 was elevated in mutants F438A, L465A and L468A and reduced in mutants S351A, Y381A, H473A, M476A and L481A. All mutants with large alterations in inhibitory properties showed reduced Na⁺ affinity. The greatest changes in activity and inhibitor sensitivity were in mutants present in binding site B which is more closely associated with TM4 and C terminal of extracellular loop 5, and is situated between the putative scaffolding domain and transport domain. The results help define the inhibitor binding domain of the NHE1 protein and identify new amino acids involved in inhibitor binding.     

Benchmarking and optimization of a high-throughput sequencing based method for transgene sequence variant analysis in biotherapeutic cell line development

In recent years, High-Throughput Sequencing (HTS) based methods to detect mutations in biotherapeutic transgene products have become a key quality step deployed during the development of manufacturing cell line clones. Previously we reported on a higher throughput, rapid mutation detection method based on amplicon sequencing (targeting transgene RNA) and detailed its implementation to facilitate cell line clone selection. By gaining experience with our assay in a diverse set of cell line development programs, we improved the computational analysis as well as experimental protocols. Here we report on these improvements as well as on a comprehensive benchmarking of our assay. We evaluated assay performance by mixing amplicon samples of a verified mutated antibody clone with a non-mutated antibody clone to generate spike-in mutations from ∼60% down to ∼0.3% frequencies. We subsequently tested the effect of 16 different sample and HTS library preparation protocols on the assay's ability to quantify mutations and on the occurrence of false-positive background error mutations (artifacts). Our evaluation confirmed assay robustness, established a high confidence limit of detection of ∼0.6%, and identified protocols that reduce error levels thereby significantly reducing a source of false positives that bottlenecked the identification of low-level true mutations.