Phenology and predictors of spring emergence for the Timber Rattlesnake (Crotalus horridus).

Many temperate reptiles survive winter by using subterranean refugia until external conditions become suitable for activity. Determining when to emerge from refugia relies on the ability to interpret when above-ground environmental conditions are survivable. If temperate reptiles rely on specific environmental cues such as temperature to initiate emergence, we should expect emergence phenologies to be predictable using local climatic data. However, specific predictors of emergence for many temperate reptiles, including the Timber Rattlesnake (Crotalus horridus), remain unclear, limiting our understanding of their overwintering phenology and restricting effective conservation and management. Our objectives were to identify environmental cues of spring emergence for C. horridus in Illinois to determine the species' emergence phenology, and to examine the applicability of identified cues in predicting emergence phenology across the species' range. We used wildlife cameras and weather station-derived environmental data to observe and predict the daily surface presence of C. horridus throughout the late winter and early spring at communal refugia in west-central and northern Illinois. The most parsimonious model for predicting surface presence included the additive effects of maximum daily temperature, accumulated degree days, and latitude. With a notable exception in the southeastern U.S., the model accurately predicted the average emergence day for eight other populations range wide, emphasizing the importance of temperature in influencing the phenological plasticity observed across the species' range. The apparent broad applicability of the model to other populations suggests it can be a valuable tool in predicting spring emergence phenology. Our results provide a foundation for further ecological enquiries and improved management and conservation strategies.

Integrating 3D genomic and epigenomic data to enhance target gene discovery and drug repurposing in transcriptome-wide association studies.

Transcriptome-wide association studies (TWAS) are popular approaches to test for association between imputed gene expression levels and traits of interest. Here, we propose an integrative method PUMICE (Prediction Using Models Informed by Chromatin conformations and Epigenomics) to integrate 3D genomic and epigenomic data with expression quantitative trait loci (eQTL) to more accurately predict gene expressions. PUMICE helps define and prioritize regions that harbor cis-regulatory variants, which outperforms competing methods. We further describe an extension to our method PUMICE +, which jointly combines TWAS results from single- and multi-tissue models. Across 79 traits, PUMICE + identifies 22% more independent novel genes and increases median chi-square statistics values at known loci by 35% compared to the second-best method, as well as achieves the narrowest credible interval size. Lastly, we perform computational drug repurposing and confirm that PUMICE + outperforms other TWAS methods.

Model-based assessment of replicability for genome-wide association meta-analysis.

Genome-wide association meta-analysis (GWAMA) is an effective approach to enlarge sample sizes and empower the discovery of novel associations between genotype and phenotype. Independent replication has been used as a gold-standard for validating genetic associations. However, as current GWAMA often seeks to aggregate all available datasets, it becomes impossible to find a large enough independent dataset to replicate new discoveries. Here we introduce a method, MAMBA (Meta-Analysis Model-based Assessment of replicability), for assessing the "posterior-probability-of-replicability" for identified associations by leveraging the strength and consistency of association signals between contributing studies. We demonstrate using simulations that MAMBA is more powerful and robust than existing methods, and produces more accurate genetic effects estimates. We apply MAMBA to a large-scale meta-analysis of addiction phenotypes with 1.2 million individuals. In addition to accurately identifying replicable common variant associations, MAMBA also pinpoints novel replicable rare variant associations from imputation-based GWAMA and hence greatly expands the set of analyzable variants.

Prioritizing genetic variants in GWAS with lasso using permutation-assisted tuning.

MOTIVATION: Large scale genome-wide association studies (GWAS) have resulted in the identification of a wide range of genetic variants related to a host of complex traits and disorders. Despite their success, the individual single-nucleotide polymorphism (SNP) analysis approach adopted in most current GWAS can be limited in that it is usually biologically simple to elucidate a comprehensive genetic architecture of phenotypes and statistically underpowered due to heavy multiple-testing correction burden. On the other hand, multiple-SNP analyses (e.g. gene-based or region-based SNP-set analysis) are usually more powerful to examine the joint effects of a set of SNPs on the phenotype of interest. However, current multiple-SNP approaches can only draw an overall conclusion at the SNP-set level and does not directly inform which SNPs in the SNP-set are driving the overall genotype-phenotype association. RESULTS: In this article, we propose a new permutation-assisted tuning procedure in lasso (plasso) to identify phenotype-associated SNPs in a joint multiple-SNP regression model in GWAS. The tuning parameter of lasso determines the amount of shrinkage and is essential to the performance of variable selection. In the proposed plasso procedure, we first generate permutations as pseudo-SNPs that are not associated with the phenotype. Then, the lasso tuning parameter is delicately chosen to separate true signal SNPs and non-informative pseudo-SNPs. We illustrate plasso using simulations to demonstrate its superior performance over existing methods, and application of plasso to a real GWAS dataset gains new additional insights into the genetic control of complex traits. AVAILABILITY AND IMPLEMENTATION: R codes to implement the proposed methodology is available at https://github.com/xyz5074/plasso. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Methods for the Analysis and Interpretation for Rare Variants Associated with Complex Traits.

With the advent of Next Generation Sequencing (NGS) technologies, whole genome and whole exome DNA sequencing has become affordable for routine genetic studies. Coupled with improved genotyping arrays and genotype imputation methodologies, it is increasingly feasible to obtain rare genetic variant information in large datasets. Such datasets allow researchers to gain a more complete understanding of the genetic architecture of complex traits caused by rare variants. State-of-the-art statistical methods for the statistical genetics analysis of sequence-based association, including efficient algorithms for association analysis in biobank-scale datasets, gene-association tests, meta-analysis, fine mapping methods that integrate functional genomic dataset, and phenome-wide association studies (PheWAS), are reviewed here. These methods are expected to be highly useful for next generation statistical genetics analysis in the era of precision medicine. © 2019 by John Wiley & Sons, Inc.

Variants on chromosome 4q21 near PKD2 and SIBLINGs are associated with dental caries.

A recent genome-wide association study (GWAS) for dental caries nominated the chromosomal region 4q21 near ABCG2, PKD2 and the SIBLING (small integrin-binding ligand N-linked glycoprotein) gene family. In this investigation, we followed up and fine-mapped this region using a tag-SNP (single-nucleotide polymorphism) approach in 13 age- and race-stratified samples from 6 independent studies (N=4089). Participants were assessed for dental caries via intraoral examination and 49 tag-SNPs were genotyped capturing much of the variation in the 4q21 locus. Linear models were used to test for genetic association, while adjusting for sex, age and components of ancestry. SNPs in and near PKD2 showed significant evidence of association in individual samples of black adults (rs17013735, P-value=0.0009) and white adults (rs11938025; P-value=0.0005; rs2725270, P-value=0.003). Meta-analyses across black adult samples recapitulated the association with rs17013735 (P-value=0.003), which occurs at low frequency in non-African populations, possibly explaining the race specificity of the effect. In addition to race-specific associations, we also observed evidence of gene-by-fluoride exposure interaction effects in white adults for SNP rs2725233 upstream of PKD2 (P=0.002). Our results show evidence of regional replication, though no single variant clearly accounted for the original GWAS signal. Therefore, while we interpret our results as strengthening the hypothesis that chromosome 4q21 may impact dental caries, additional work is needed.

Hearing in the Juvenile Green Sea Turtle (Chelonia mydas): A Comparison of Underwater and Aerial Hearing Using Auditory Evoked Potentials.

Sea turtles spend much of their life in aquatic environments, but critical portions of their life cycle, such as nesting and hatching, occur in terrestrial environments, suggesting that it may be important for them to detect sounds in both air and water. In this study we compared underwater and aerial hearing sensitivities in five juvenile green sea turtles (Chelonia mydas) by measuring auditory evoked potential responses to tone pip stimuli. Green sea turtles detected acoustic stimuli in both media, responding to underwater stimuli between 50 and 1600 Hz and aerial stimuli between 50 and 800 Hz, with maximum sensitivity between 200 and 400 Hz underwater and 300 and 400 Hz in air. When underwater and aerial hearing sensitivities were compared in terms of pressure, green sea turtle aerial sound pressure thresholds were lower than underwater thresholds, however they detected a wider range of frequencies underwater. When thresholds were compared in terms of sound intensity, green sea turtle sound intensity level thresholds were 2-39 dB lower underwater particularly at frequencies below 400 Hz. Acoustic stimuli may provide important environmental cues for sea turtles. Further research is needed to determine how sea turtles behaviorally and physiologically respond to sounds in their environment.

Sedation and anesthesia of hatchling leatherback sea turtles (Dermochelys coriacea) for auditory evoked potential measurement in air and in water.

Sedation or anesthesia of hatchling leatherback sea turtles was employed to acquire auditory evoked potential (AEP) measurements in air and in water to assess their hearing sensitivity in relation to potential consequences from anthropogenic noise. To reduce artifacts in AEP collection caused by muscle movement, hatchlings were sedated with midazolam 2 or 3 mg/kg i.v. for in-air (n = 7) or in-water (n = 11) AEP measurements; hatchlings (n = 5) were anesthetized with ketamine 6 mg/kg and dexmedetomidine 30 microg/kg i.v. reversed with atipamezole 300 microg/kg, half i.m. and half i.v. for in-air AEP measurements. Midazolam-sedated turtles were also physically restrained with a light elastic wrap. For in-water AEP measurements, sedated turtles were brought to the surface every 45-60 sec, or whenever they showed intention signs for breathing, and not submerged again until they took a breath. Postprocedure temperature-corrected venous blood pH, pCO2, pO2, and HCO3- did not differ among groups, although for the midazolam-sedated in-water group, pCO2 trended lower, and in the ketamine-dexmedetomidine anesthetized group there was one turtle considered clinically acidotic (temperature-corrected pH = 7.117). Venous blood lactate was greater for hatchlings recently emerged from the nest than for turtles sedated with midazolam in air, with the other two groups falling intermediate between, but not differing significantly from the high and low lactate groups. Disruptive movements were less frequent with anesthesia than with sedation in the in-air group. Both sedation with midazolam and anesthesia with ketamine-dexmedetomidine were successful for allowing AEP measurements in hatchling leatherback sea turtles. Sedation allowed the turtle to protect its airway voluntarily while limiting flipper movement. Midazolam or ketamine-dexmedetomidine (and reversal with atipamezole) would be useful for other procedures requiring minor or major restraint in leatherback sea turtle hatchlings and other sea turtles, although variable susceptibilities may require dose adjustments.

Predicting bycatch hotspots for endangered leatherback turtles on longlines in the Pacific Ocean.

Fisheries bycatch is a critical source of mortality for rapidly declining populations of leatherback turtles, Dermochelys coriacea. We integrated use-intensity distributions for 135 satellite-tracked adult turtles with longline fishing effort to estimate predicted bycatch risk over space and time in the Pacific Ocean. Areas of predicted bycatch risk did not overlap for eastern and western Pacific nesting populations, warranting their consideration as distinct management units with respect to fisheries bycatch. For western Pacific nesting populations, we identified several areas of high risk in the north and central Pacific, but greatest risk was adjacent to primary nesting beaches in tropical seas of Indo-Pacific islands, largely confined to several exclusive economic zones under the jurisdiction of national authorities. For eastern Pacific nesting populations, we identified moderate risk associated with migrations to nesting beaches, but the greatest risk was in the South Pacific Gyre, a broad pelagic zone outside national waters where management is currently lacking and may prove difficult to implement. Efforts should focus on these predicted hotspots to develop more targeted management approaches to alleviate leatherback bycatch.

Identification of distinct movement patterns in Pacific leatherback turtle populations influenced by ocean conditions.

Interactions with fisheries are believed to be a major cause of mortality for adult leatherback turtles (Dermochelys coriacea), which is of particular concern in the Pacific Ocean, where they have been rapidly declining. In order to identify where these interactions are occurring and how they may be reduced, it is essential first to understand the movements and behavior of leatherback turtles. There are two regional nesting populations in the East Pacific (EP) and West Pacific (WP), comprising multiple nesting sites. We synthesized tracking data from the two populations and compared their movement patterns. A switching state-space model was applied to 135 Argos satellite tracks to account for observation error, and to distinguish between migratory and area-restricted search behaviors. The tracking data, from the largest leatherback data set ever assembled, indicated that there was a high degree of spatial segregation between EP and WP leatherbacks. Area-restricted search behavior mainly occurred in the southeast Pacific for the EP leatherbacks, whereas the WP leatherbacks had several different search areas in the California Current, central North Pacific, South China Sea, off eastern Indonesia, and off southeastern Australia. We also extracted remotely sensed oceanographic data and applied a generalized linear mixed model to determine if leatherbacks exhibited different behavior in relation to environmental variables. For the WP population, the probability of area-restricted search behavior was positively correlated with chlorophyll-a concentration. This response was less strong in the EP population, but these turtles had a higher probability of search behavior where there was greater Ekman upwelling, which may increase the transport of nutrients and consequently prey availability. These divergent responses to oceanographic conditions have implications for leatherback vulnerability to fisheries interactions and to the effects of climate change. The occurrence of leatherback turtles within both coastal and pelagic areas means they have a high risk of exposure to many different fisheries, which may be very distant from their nesting sites. The EP leatherbacks have more limited foraging grounds than the WP leatherbacks, which could make them more susceptible to any temperature or prey changes that occur in response to climate change.

Persistent leatherback turtle migrations present opportunities for conservation.

Effective transboundary conservation of highly migratory marine animals requires international management cooperation as well as clear scientific information about habitat use by these species. Populations of leatherback turtles (Dermochelys coriacea) in the eastern Pacific have declined by >90% during the past two decades, primarily due to unsustainable egg harvest and fisheries bycatch mortality. While research and conservation efforts on nesting beaches are ongoing, relatively little is known about this population of leatherbacks' oceanic habitat use and migration pathways. We present the largest multi-year (2004-2005, 2005-2006, and 2007) satellite tracking dataset (12,095 cumulative satellite tracking days) collected for leatherback turtles. Forty-six females were electronically tagged during three field seasons at Playa Grande, Costa Rica, the largest extant nesting colony in the eastern Pacific. After completing nesting, the turtles headed southward, traversing the dynamic equatorial currents with rapid, directed movements. In contrast to the highly varied dispersal patterns seen in many other sea turtle populations, leatherbacks from Playa Grande traveled within a persistent migration corridor from Costa Rica, past the equator, and into the South Pacific Gyre, a vast, low-energy, low-productivity region. We describe the predictable effects of ocean currents on a leatherback migration corridor and characterize long-distance movements by the turtles in the eastern South Pacific. These data from high seas habitats will also elucidate potential areas for mitigating fisheries bycatch interactions. These findings directly inform existing multinational conservation frameworks and provide immediate regions in the migration corridor where conservation can be implemented. We identify high seas locations for focusing future conservation efforts within the leatherback dispersal zone in the South Pacific Gyre.

Modeling loggerhead turtle movement in the Mediterranean: importance of body size and oceanography.

Adapting state-space models (SSMs) to telemetry data has been helpful for dealing with location error and for modeling animal movements. We used a combination of two hierarchical Bayesian SSMs to estimate movement pathways from Argos satellite-tag data for 15 juvenile loggerhead turtles (Caretta caretta) in the western Mediterranean Sea, and to probabilistically assign locations to one of two behavioral movement types and relate those behaviors to environmental features. A Monte Carlo procedure helped propagate location uncertainty from the first SSM into the estimation of behavioral states and environment--behavior relationships in the second SSM. Turtles using oceanic habitats of the Balearic Sea (n = 9 turtles) within the western Mediterranean were more likely to exhibit "intensive search" behavior as might occur during foraging, but only larger turtles responded to variations in sea-surface height. This suggests that they were better able than smaller turtles to cue on environmental features that concentrate prey resources or were more dependent on high-quality feeding areas. These findings stress the importance of individual heterogeneity in the analysis of movement behavior and, taken in concert with descriptive studies of Pacific loggerheads, suggest that directed movements toward patchy ephemeral resources may be a general property of larger juvenile loggerheads in different populations. We discovered size-based variation in loggerhead distribution and documented use of the western Mediterranean Sea by turtles larger than previously thought to occur there. With one exception, only individuals > 57 cm curved carapace length used the most westerly basin in the Mediterranean (western Alborán Sea). These observations shed new light on loggerhead migration phenology.

Swim speed and movement patterns of gravid leatherback sea turtles (Dermochelys coriacea) at St Croix, US Virgin Islands.

Swim speed, dive behavior and movements were recorded for seven female leatherback sea turtles (Dermochelys coriacea Vandelli 1761) during a single internesting interval near St Croix in the US Virgin Islands. Modal speeds ranged from 0.56 to 0.84 m s(-1), maximum speed range 1.9-2.8 m s(-1). Turtles swam continuously throughout the day and night. There were two swim-speed patterns; the most common was slightly U-shaped, with high speeds at the initiation and conclusion of the dive, and the less common was continuous high-speed swimming. The U-shaped speed patterns were coincident with vertical diving by the turtles, while the second pattern occurred most frequently during the daytime, with the turtle swimming within 2 m of the surface. This latter swim behavior appeared to be designed to maximize efficiency for long-distance travel. The hypothesis that leatherbacks rest or bask at midday during their internesting interval is refuted by this study.