Feeding en route: Prey availability and traits influence prey selection by an avian predator on migration.

During animal migration, ephemeral communities of taxa at all trophic levels co-occur over space and time. The interactions between predators and prey along migration corridors are ecologically and evolutionarily significant. However, these interactions remain understudied in terrestrial systems and warrant further investigations using novel approaches. We investigated the predator-prey interactions between a migrating avivorous predator and ephemeral avian prey community in the fall migration season. We tested for associations between avian traits and prey selection and hypothesized that prey traits (i.e. relative size, flocking behaviour, habitat, migration tendency and availability) would influence prey selection by a sexually dimorphic raptor on migration. To document prey consumption, we sampled trace prey DNA from beaks and talons of migrating sharp-shinned hawks Accipiter striatus (n = 588). We determined prey availability in the ephemeral avian community by extracting weekly abundance indices from eBird Status and Trends data. We used discrete choice models to assess prey selection and visualized the frequency of prey in diet and availability on the landscape over the fall migration season. Using eDNA metabarcoding, we detected prey species on 94.1% of the hawks sampled (n = 525/588) comprising 1396 prey species detections from 65 prey species. Prey frequency in diet and eBird relative abundance of prey species were correlated over the migration season for top-selected prey species, suggesting prey availability is an important component of raptor-songbird interactions during fall. Prey size, flocking behaviour and non-breeding habitat association were prey traits that significantly influenced predator choice. We found differences between female and male hawk prey selection, suggesting that sexual size dimorphism has led to distinct foraging strategies on migration. This research integrated field data collected by a volunteer-powered raptor migration monitoring station and public-generated data from eBird to reveal elusive predator-prey dynamics occurring in an ephemeral raptor-songbird community during fall migration. Understanding dynamic raptor-songbird interactions along migration routes remains a relatively unexplored frontier in animal ecology and is necessary for the conservation and management efforts of migratory and resident communities.

Durante la migración animal, las comunidades efímeras de taxones de todos los niveles tróficos coexisten en el espacio y el tiempo. Las interacciones entre depredadores y presas a lo largo de los corredores migratorios son significativas desde el punto de vista ecológica y evolutivo. Sin embargo, estas interacciones siguen siendo poco estudiadas en los sistemas terrestres y justifican más investigaciones utilizando enfoques novedosos. Investigamos las interacciones depredador­presa entre un depredador avívoro migratorio y una comunidad de presas aviares efímeras en la temporada migratoria otoñal. Probamos las asociaciones entre los rasgos de las aves y la selección de presas y planteamos la hipótesis de que los rasgos de las presas (tamaño relativo, comportamiento de bandada, hábitat, tendencia migratoria y disponibilidad) influirían en la selección de presas por parte de una rapaz sexualmente dimórfica durante la migración. Para documentar el consumo de presas, recogimos rastros de ADN de presas de picos y garras de Gavilán Americano Accipiter striatus (n = 588) migratorios. Determinamos la disponibilidad de presas en la comunidad de aves efímeras extrayendo índices de abundancia semanales de los datos de eBird Estado y Tendencias. Utilizamos modelos de elección discreta para evaluar la selección de presas y visualizamos la frecuencia de las presas en la dieta y la disponibilidad en el paisaje durante la temporada migratoria otoñal. Utilizando el metacódigo de barras del ADN ambiental, detectamos especies de presas en el 94,1% de los halcones muestreados (n = 525/588), comprendiendo 1396 detecciones de 65 especies de presas. La frecuencia de presas en la dieta y la abundancia relativa de especies de presas en eBird se correlacionaron a lo largo de la temporada de migración para las principales especies de presas seleccionadas, lo que sugiere que la disponibilidad de presas es un componente importante de las interacciones entre aves rapaces y aves canoras durante el otoño. El tamaño de las presas, el comportamiento de las bandadas y la asociación con el hábitat no reproductivo fueron rasgos de presa que influyeron significativamente en la elección de los depredadores. Encontramos diferencias entre la selección de presas de gavilán hembra y macho, lo que sugiere que el dimorfismo sexual de tamaño ha conducido a distintas estrategias de alimentación durante la migración. Esta investigación integró datos de campo recopilados por una estación de monitoreo de migración de rapaces impulsada por voluntarios y datos generados públicamente por eBird para revelar la esquiva dinámica depredador­presa que ocurre en una comunidad efímera de rapaces y aves canoras durante la migración otoñal. Comprender las interacciones dinámicas entre rapaces y aves canoras a lo largo de las rutas migratorias sigue siendo una frontera relativamente inexplorada en la ecología animal y es necesaria para los esfuerzos de conservación y gestión de las comunidades migratorias y residentes.

Rapid CRISPR-Cas13a genetic identification enables new opportunities for listed Chinook salmon management.

Accurate taxonomic identification is foundational for effective species monitoring and management. When visual identifications are infeasible or inaccurate, genetic approaches provide a reliable alternative. However, these approaches are sometimes less viable (e.g., need for near real-time results, remote locations, funding concerns, molecular inexperience). In these situations, CRISPR-based genetic tools can fill an unoccupied niche between real-time, inexpensive, but error-prone visual identification and more expensive or time-consuming, but accurate genetic identification for taxonomic units that are difficult or impossible to visually identify. Herein, we use genomic data to develop CRISPR-based SHERLOCK assays capable of rapidly (<1 h), accurately (94%-98% concordance between phenotypic and genotypic assignments), and sensitively (detects 1-10 DNA copies/reaction) distinguishing ESA-listed Chinook salmon runs (winter- and spring-run) from each other and from unlisted runs (fall- and late fall-run) in California's Central Valley. The assays can be field deployable with minimally invasive mucus swabbing negating the need for DNA extraction (decreasing costs and labour), minimal and inexpensive equipment needs, and minimal training to conduct following assay development. This study provides a powerful genetic approach for a species of conservation concern that benefits from near real-time management decision-making but also serves as a precedent for transforming how conservation scientists and managers view genetic identification going forward. Once developed, CRISPR-based tools can provide accurate, sensitive, and rapid results, potentially without the prohibitive need for expensive specialty equipment or extensive molecular training. Further adoption of this technology will have widespread value for the monitoring and protection of our natural resources.

Polygenic discrimination of migratory phenotypes in an estuarine forage fish.

Migration is a complex phenotypic trait with some species containing migratory and nonmigratory individuals. Such life history variation may be attributed in part to plasticity, epigenetics, or genetics. Although considered semianadromous, recent studies using otolith geochemistry have revealed life history variation within the critically endangered Delta Smelt. Broadly categorizable as migratory or freshwater residents, we examined Restriction site Associated DNA sequencing data to test for a relationship between genetic variation and migratory behaviors. As previously shown, we found no evidence for neutral population genetic structure within Delta Smelt; however, we found significant evidence for associations between genetic variants and life history phenotypes. Furthermore, discriminant analysis of principal components, hierarchical clustering, and machine learning resulted in accurate assignment of fish into the freshwater resident or migratory classes based on their genotypes. These results suggest the presence of adaptive genetic variants relating to life history variation within a panmictic population. Mechanisms that may lead to this observation are genotype dependent habitat choice and spatially variable selection, both of which could operate each generation and are not exclusive. Given that the population of cultured Delta Smelt are being used as a refugial population for conservation, as a supply for wild population supplementation, and currently represent the majority of all living individuals of this species, we recommend that the hatchery management strategy consider the frequencies of life history-associated alleles and how to maintain this important aspect of Delta Smelt biological variation while under captive propagation.

Rapid and accurate species identification for ecological studies and monitoring using CRISPR-based SHERLOCK.

One of the most fundamental aspects of ecological research and monitoring is accurate species identification, but cryptic speciation and observer error can confound phenotype-based identification. The CRISPR-Cas toolkit has facilitated remarkable advances in many scientific disciplines, but the fields of ecology and conservation biology have yet to fully embrace this powerful technology. The recently developed CRISPR-Cas13a platform SHERLOCK (Specific High-sensitivity Enzymatic Reporter unLOCKing) enables highly accurate taxonomic identification and has all the characteristics needed to transition to ecological and environmental disciplines. Here we conducted a series of "proof of principle" experiments to characterize SHERLOCK's ability to accurately, sensitively and rapidly distinguish three fish species of management interest co-occurring in the San Francisco Estuary that are easily misidentified in the field. We improved SHERLOCK's ease of field deployment by combining the previously demonstrated rapid isothermal amplification and CRISPR genetic identification with a minimally invasive and extraction-free DNA collection protocol, as well as the option of instrument-free lateral flow detection. This approach opens the door for redefining how, where and by whom genetic identifications occur in the future.

Migration-related phenotypic divergence is associated with epigenetic modifications in rainbow trout.

Migration is essential for the reproduction and survival of many animals, yet little is understood about its underlying molecular mechanisms. We used the salmonid Oncorhynchus mykiss to gain mechanistic insight into smoltification, which is a morphological, physiological and behavioural transition undertaken by juveniles in preparation for seaward migration. O. mykiss is experimentally tractable and displays intra- and interpopulation variation in migration propensity. Migratory individuals can produce nonmigratory progeny and vice versa, indicating a high degree of phenotypic plasticity. One potential way that phenotypic plasticity might be linked to variation in migration-related life history tactics is through epigenetic regulation of gene expression. To explore this, we quantitatively measured genome-scale DNA methylation in fin tissue using reduced representation bisulphite sequencing of F2 siblings produced from a cross between steelhead (migratory) and rainbow trout (nonmigratory) lines. We identified 57 differentially methylated regions (DMRs) between smolt and resident O. mykiss juveniles. DMRs were high in magnitude, with up to 62% differential methylation between life history types, and over half of the gene-associated DMRs were in transcriptional regulatory regions. Many of the DMRs encode proteins with activity relevant to migration-related transitions (e.g. circadian rhythm pathway, nervous system development, protein kinase activity). This study provides the first evidence of a relationship between epigenetic variation and life history divergence associated with migration-related traits in any species.