Efficient species identification for Pacific salmon genetic monitoring programs.

Genetic monitoring of Pacific salmon in the Columbia River basin provides crucial information to fisheries managers that is otherwise challenging to obtain using traditional methods. Monitoring programs such as genetic stock identification (GSI) and parentage-based tagging (PBT) involve genotyping tens of thousands of individuals annually. Although rare, these large sample collections inevitably include misidentified species, which exhibit low genotyping success on species-specific Genotyping-in-Thousands by sequencing (GT-seq) panels. For laboratories involved in large-scale genotyping efforts, diagnosing non-target species and reassigning them to the appropriate monitoring program can be costly and time-consuming. To address this problem, we identified 19 primer pairs that exhibit consistent cross-species amplification among salmonids and contain 51 species informative variants. These genetic markers reliably discriminate among 11 salmonid species and two subspecies of Cutthroat Trout and have been included in species-specific GT-seq panels for Chinook Salmon, Coho Salmon, Sockeye Salmon, and Rainbow Trout commonly used for Pacific salmon genetic monitoring. The majority of species-informative amplicons (16) were newly identified from the four existing GT-seq panels, thus demonstrating a low-cost approach to species identification when using targeted sequencing methods. A species-calling script was developed that is tailored for routine GT-seq genotyping pipelines and automates the identification of non-target species. Following extensive testing with empirical and simulated data, we demonstrated that the genetic markers and accompanying script accurately identified species and are robust to missing genotypic data and low-frequency, shared polymorphisms among species. Finally, we used these tools to identify Coho Salmon incidentally caught in the Columbia River Chinook Salmon sport fishery and used PBT to determine their hatchery of origin. These molecular and computing resources provide a valuable tool for Pacific salmon conservation in the Columbia River basin and demonstrate a cost-effective approach to species identification for genetic monitoring programs.

Distance-dependent resonance energy transfer in alkyl-terminated Si nanocrystal solids.

Understanding and controlling the energy transfer between silicon nanocrystals is of significant importance for the design of efficient optoelectronic devices. However, previous studies on silicon nanocrystal energy transfer were limited because of the strict requirements to precisely control the inter-dot distance and to perform all measurements in air-free environments to preclude the effect of ambient oxygen. Here, we systematically investigate the distance-dependent resonance energy transfer in alkyl-terminated silicon nanocrystals for the first time. Silicon nanocrystal solids with inter-dot distances varying from 3 to 5 nm are fabricated by varying the length and surface coverage of alkyl ligands in solution-phase and gas-phase functionalized silicon nanocrystals. The inter-dot energy transfer rates are extracted from steady-state and time-resolved photoluminescence measurements, enabling a direct comparison to theoretical predictions. Our results reveal that the distance-dependent energy transfer rates in Si NCs decay faster than predicted by the Förster mechanism, suggesting higher-order multipole interactions.

The ecological causes and consequences of hard and soft selection.

Interactions between natural selection and population dynamics are central to both evolutionary-ecology and biological responses to anthropogenic change. Natural selection is often thought to incur a demographic cost that, at least temporarily, reduces population growth. However, hard and soft selection clarify that the influence of natural selection on population dynamics depends on ecological context. Under hard selection, an individual's fitness is independent of the population's phenotypic composition, and substantial population declines can occur when phenotypes are mismatched with the environment. In contrast, under soft selection, an individual's fitness is influenced by its phenotype relative to other interacting conspecifics. Soft selection generally influences which, but not how many, individuals survive and reproduce, resulting in little effect on population growth. Despite these important differences, the distinction between hard and soft selection is rarely considered in ecology. Here, we review and synthesize literature on hard and soft selection, explore their ecological causes and implications and highlight their conservation relevance to climate change, inbreeding depression, outbreeding depression and harvest. Overall, these concepts emphasise that natural selection and evolution may often have negligible or counterintuitive effects on population growth-underappreciated outcomes that have major implications in a rapidly changing world.

Highly versatile near-infrared emitters based on an atomically defined HgS interlayer embedded into a CdSe/CdS quantum dot.

The availability of colloidal quantum dots with highly efficient, fast and 'non-blinking' near-infrared emission would benefit numerous applications, from advanced optical communication and quantum networks to biomedical diagnostics. Here, we report high-quality near-infrared emitters that are based on well known CdSe/CdS heterostructures. By incorporating an HgS interlayer at the quantum dot core/shell interface, we convert normally visible emitters into highly efficient near-infrared fluorophores. Employing thermodynamically controlled sequential deposition of metal and chalcogen ions, we achieve atomic-level precision in defining the thickness of the HgS interlayer (H). This manifests in 'quantized' jumps of the photoluminescence spectrum when H changes in discrete, atomic steps. The synthesized structures show highly efficient photoluminescence, tunable from 700 to 1,370 nm, and fast radiative rates of ~1/60 ns-1. The emission from individual CdSe/HgS/CdS colloidal quantum dots is virtually blinking free and exhibits nearly perfect single-photon purity. In addition, when incorporated into a light-emitting-diode architecture, these quantum dots demonstrate strong electroluminescence with a sub-bandgap turn-on voltage.

Evaluating the outcomes of genetic rescue attempts.

Augmenting gene flow is a powerful tool for the conservation of small, isolated populations. However, genetic rescue attempts have largely been limited to populations at the brink of extinction, in part due to concerns over negative outcomes (e.g., outbreeding depression). Increasing habitat fragmentation may necessitate more proactive genetic management. Broader application of augmented gene flow will, in turn, require rigorous evaluation to increase confidence and identify pitfalls in this approach. To date, there has been no assessment of best monitoring practices for genetic rescue attempts. We used genomically explicit, individual-based simulations to examine the effectiveness of common approaches (i.e., tests for increases in fitness, migrant ancestry, heterozygosity, and abundance) for determining whether genetic rescue or outbreeding depression occurred. Statistical power to detect the effects of gene flow on fitness was high (≥0.8) when effect sizes were large, a finding consistent with those from previous studies on severely inbred populations. However, smaller effects of gene flow on fitness can appreciably affect persistence probability but current evaluation approaches fail to provide results from which reliable inferences can be drawn. The power of the metrics we examined to evaluate genetic rescue attempts depended on the time since gene flow and whether gene flow was beneficial or deleterious. Encouragingly, the use of multiple metrics provided nonredundant information and improved inference reliability, highlighting the importance of intensive monitoring efforts. Further development of best practices for evaluating genetic rescue attempts will be crucial for a responsible transition to increased use of translocations to decrease extinction risk.

Evaluación de los Resultados de los Intentos de Rescate Genético Resumen El aumento del flujo génico es una herramienta poderosa para la conservación de poblaciones pequeñas y aisladas. Sin embargo, los intentos de rescate genético en su mayoría se han limitado a las poblaciones que se encuentran al borde de la extinción, en parte debido a la preocupación que existe por los resultados negativos (es decir, la depresión exogámica). La creciente fragmentación del hábitat puede requerir un manejo genético más proactivo. La aplicación más extensa del flujo génico aumentado requerirá a su vez una evaluación rigurosa para incrementar la confianza e identificar las dificultades de esta estrategia. A la fecha, no ha habido una evaluación de las mejores prácticas de monitoreo para los intentos de rescate genético. Usamos simulaciones explícitas basadas en individuos para examinar la efectividad de las estrategias comunes (es decir, análisis del incremento en adaptabilidad, ascendencia migratoria, heterocigosidad y abundancia) para determinar si ocurrió el rescate genético o la depresión exogámica. El poder estadístico para detectar los efectos del flujo génico sobre la adaptabilidad fue elevado (≥0.8) cuando el tamaño de los efectos fue grande, un hallazgo consistente con aquellos realizados en estudios previos sobre poblaciones con una endogamia severa. Sin embargo, los efectos menores del flujo génico sobre la adaptabilidad pueden afectar de manera apreciable la probabilidad de persistencia, pero las estrategias actuales de evaluación no proporcionan resultados de los cuales se puedan hacer inferencias confiables. El poder de las medidas que examinamos para evaluar los intentos de rescate genético dependió del tiempo desde que inició el flujo génico y de si el flujo génico fue benéfico o perjudicial. De manera alentadora, el uso de múltiples medidas proporcionó información no redundante y mejoró la confiabilidad de la inferencia, resaltando así la importancia de los esfuerzos intensivos de monitoreo. El futuro desarrollo de mejores prácticas para la evaluación de los intentos de rescate genético será de suma importancia para la transición responsable hacia el mayor uso de reubicaciones para reducir el riesgo de extinción.

Metal-insulator transition in a semiconductor nanocrystal network.

Many envisioned applications of semiconductor nanocrystals (NCs), such as thermoelectric generators and transparent conductors, require metallic (nonactivated) charge transport across an NC network. Although encouraging signs of metallic or near-metallic transport have been reported, a thorough demonstration of nonzero conductivity, σ, in the 0 K limit has been elusive. Here, we examine the temperature dependence of σ of ZnO NC networks. Attaining both higher σ and lower temperature than in previous studies of ZnO NCs (T as low as 50 mK), we observe a clear transition from the variable-range hopping regime to the metallic regime. The critical point of the transition is distinctly marked by an unusual power law close to σ ∝ T 1/5. We analyze the critical conductivity data within a quantum critical scaling framework and estimate the metal-insulator transition (MIT) criterion in terms of the free electron density, n, and interparticle contact radius, ρ.

The Exciting Potential and Remaining Uncertainties of Genetic Rescue.

Restoring gene flow into small, isolated populations can alleviate genetic load and decrease extinction risk (i.e., genetic rescue), yet gene flow is rarely augmented as a conservation strategy. Due to this discrepancy between opportunity and action, a recent call was made for widespread genetic rescue attempts. However, several aspects of augmenting gene flow are poorly understood, including the magnitude and duration of beneficial effects and when deleterious effects are likely to occur. We discuss the remaining uncertainties of genetic rescue in order to promote and direct future research and to hasten progress toward implementing this potentially powerful conservation strategy on a broader scale.

Tuning Nanocrystal Surface Depletion by Controlling Dopant Distribution as a Route Toward Enhanced Film Conductivity.

Electron conduction through bare metal oxide nanocrystal (NC) films is hindered by surface depletion regions resulting from the presence of surface states. We control the radial dopant distribution in tin-doped indium oxide (ITO) NCs as a means to manipulate the NC depletion width. We find in films of ITO NCs of equal overall dopant concentration that those with dopant-enriched surfaces show decreased depletion width and increased conductivity. Variable temperature conductivity data show electron localization length increases and associated depletion width decreases monotonically with increased density of dopants near the NC surface. We calculate band profiles for NCs of differing radial dopant distributions and in agreement with variable temperature conductivity fits find NCs with dopant-enriched surfaces have narrower depletion widths and longer localization lengths than those with dopant-enriched cores. Following amelioration of NC surface depletion by atomic layer deposition of alumina, all films of equal overall dopant concentration have similar conductivity. Variable temperature conductivity measurements on alumina-capped films indicate all films behave as granular metals. Herein, we conclude that dopant-enriched surfaces decrease the near-surface depletion region, which directly increases the electron localization length and conductivity of NC films.

ZnO Nanocrystal Networks Near the Insulator-Metal Transition: Tuning Contact Radius and Electron Density with Intense Pulsed Light.

Networks of ligand-free semiconductor nanocrystals (NCs) offer a valuable combination of high carrier mobility and optoelectronic properties tunable via quantum confinement. In principle, maximizing carrier mobility entails crossing the insulator-metal transition (IMT), where carriers become delocalized. A recent theoretical study predicted that this transition occurs at nρ3 ≈ 0.3, where n is the carrier density and ρ is the interparticle contact radius. In this work, we satisfy this criterion in networks of plasma-synthesized ZnO NCs by using intense pulsed light (IPL) annealing to tune n and ρ independently. IPL applied to as-deposited NCs increases ρ by inducing sintering, and IPL applied after the NCs are coated with Al2O3 by atomic layer deposition increases n by removing electron-trapping surface hydroxyls. This procedure does not substantially alter NC size or composition and is potentially applicable to a wide variety of nanomaterials. As we increase nρ3 to at least twice the predicted critical value, we observe conductivity scaling consistent with arrival at the critical region of a continuous quantum phase transition. This allows us to determine the critical behavior of the dielectric constant and electron localization length at the IMT. However, our samples remain on the insulating side of the critical region, which suggests that the critical value of nρ3 may in fact be significantly higher than 0.3.

Experimental test of genetic rescue in isolated populations of brook trout.

Genetic rescue is an increasingly considered conservation measure to address genetic erosion associated with habitat loss and fragmentation. The resulting gene flow from facilitating migration may improve fitness and adaptive potential, but is not without risks (e.g., outbreeding depression). Here, we conducted a test of genetic rescue by translocating ten (five of each sex) brook trout (Salvelinus fontinalis) from a single source to four nearby and isolated stream populations. To control for the demographic contribution of translocated individuals, ten resident individuals (five of each sex) were removed from each recipient population. Prior to the introduction of translocated individuals, the two smallest above-barrier populations had substantially lower genetic diversity, and all populations had reduced effective number of breeders relative to adjacent below-barrier populations. In the first reproductive bout following translocation, 31 of 40 (78%) translocated individuals reproduced successfully. Translocated individuals contributed to more families than expected under random mating and generally produced larger full-sibling families. We observed relatively high (>20%) introgression in three of the four recipient populations. The translocations increased genetic diversity of recipient populations by 45% in allelic richness and 25% in expected heterozygosity. Additionally, strong evidence of hybrid vigour was observed through significantly larger body sizes of hybrid offspring relative to resident offspring in all recipient populations. Continued monitoring of these populations will test for negative fitness effects beyond the first generation. However, these results provide much-needed experimental data to inform the potential effectiveness of genetic rescue-motivated translocations.