The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species.

Bridging the gap between genetic variations, environmental determinants, and phenotypic outcomes is critical for supporting clinical diagnosis and understanding mechanisms of diseases. It requires integrating open data at a global scale. The Monarch Initiative advances these goals by developing open ontologies, semantic data models, and knowledge graphs for translational research. The Monarch App is an integrated platform combining data about genes, phenotypes, and diseases across species. Monarch's APIs enable access to carefully curated datasets and advanced analysis tools that support the understanding and diagnosis of disease for diverse applications such as variant prioritization, deep phenotyping, and patient profile-matching. We have migrated our system into a scalable, cloud-based infrastructure; simplified Monarch's data ingestion and knowledge graph integration systems; enhanced data mapping and integration standards; and developed a new user interface with novel search and graph navigation features. Furthermore, we advanced Monarch's analytic tools by developing a customized plugin for OpenAI's ChatGPT to increase the reliability of its responses about phenotypic data, allowing us to interrogate the knowledge in the Monarch graph using state-of-the-art Large Language Models. The resources of the Monarch Initiative can be found at monarchinitiative.org and its corresponding code repository at github.com/monarch-initiative/monarch-app.

Targeting Sagebrush (Artemisia Spp.) Restoration Following Wildfire with Greater Sage-Grouse (Centrocercus Urophasianus) Nest Selection and Survival Models.

Unprecedented conservation efforts for sagebrush (Artemisia spp.) ecosystems across the western United States have been catalyzed by risks from escalated wildfire activity that reduces habitat for sagebrush-obligate species such as Greater Sage-Grouse (Centrocercus urophasianus). However, post-fire restoration is challenged by spatial variation in ecosystem processes influencing resilience to disturbance and resistance to non-native invasive species, and spatial and temporal lags between slower sagebrush recovery processes and faster demographic responses of sage-grouse to loss of important habitat. Decision-support frameworks that account for these factors can help users strategically apply restoration efforts by predicting short and long-term ecological benefits of actions. Here, we developed a framework that strategically targets burned areas for restoration actions (e.g., seeding or planting sagebrush) that have the greatest potential to positively benefit sage-grouse populations through time. Specifically, we estimated sagebrush recovery following wildfire and risk of non-native annual grass invasion under four scenarios: passive recovery, grazing exclusion, active restoration with seeding, and active restoration with seedling transplants. We then applied spatial predictions of integrated nest site selection and survival models before wildfire, immediately following wildfire, and at 30 and 50 years post-wildfire based on each restoration scenario and measured changes in habitat. Application of this framework coupled with strategic planting designs aimed at developing patches of nesting habitat may help increase operational resilience for fire-impacted sagebrush ecosystems.

Wildfire and the ecological niche: Diminishing habitat suitability for an indicator species within semi-arid ecosystems.

Globally accelerating frequency and extent of wildfire threatens the persistence of specialist wildlife species through direct loss of habitat and indirect facilitation of exotic invasive species. Habitat specialists may be especially prone to rapidly changing environmental conditions because their ability to adapt lags behind the rate of habitat alteration. As a result, these populations may become increasingly susceptible to ecological traps by returning to suboptimal breeding habitats that were dramatically altered by disturbance. We demonstrate a multistage modeling approach that integrates habitat selection and survival during the key nesting life-stage of a bird species of high conservation concern, the greater sage-grouse (Centrocercus urophasianus; hereafter, sage-grouse). We applied these spatially explicit models to a spatiotemporally robust dataset of sage-grouse nest locations and fates across wildfire-altered sagebrush ecosystems of the Great Basin ecoregion, western United States. Female sage-grouse exhibited intricate habitat selection patterns that varied across regional gradients of ecological productivity among sagebrush communities, but often selected nest sites that disproportionately resulted in nest failure. For example, 23% of nests occurred in wildfire-affected habitats characterized by reduced sagebrush cover and greater composition of invasive annual grasses. We found survival of nests was negatively associated with wildfire-affected areas, but positively associated with higher elevations with increased ruggedness and overall shrub cover. Strong site fidelity likely drove sage-grouse to continue nesting in habitats degraded by wildfire. Hence, increasing frequency and extent of wildfire may contribute disproportionately to reduced reproductive success by creating ecological traps that act as population sinks. Identifying such habitat mismatches between selection and survival facilitates deeper understanding of the mechanisms driving reduced geographic niche space and population decline at broad spatiotemporal scales, while guiding management actions to areas that would be most beneficial to the species.

Territoriality drives preemptive habitat selection in recovering wolves: Implications for carnivore conservation.

According to the ideal-free distribution (IFD), individuals within a population are free to select habitats that maximize their chances of success. Assuming knowledge of habitat quality, the IFD predicts that average fitness will be approximately equal among individuals and between habitats, while density varies, implying that habitat selection will be density dependent. Populations are often assumed to follow an IFD, although this assumption is rarely tested with empirical data, and may be incorrect when territoriality indicates habitat selection tactics that deviate from the IFD (e.g. ideal-despotic distribution or ideal-preemptive distribution). When territoriality influences habitat selection, species' density will not directly reflect components of fitness such as reproductive success or survival. In such cases, assuming an IFD can lead to false conclusions about habitat quality. We tested theoretical models of density-dependent habitat selection on a species known to exhibit territorial behaviour in order to determine whether commonly applied habitat models are appropriate under these circumstances. We combined long-term radiotelemetry and census data from grey wolves Canis lupus in the Upper Peninsula of Michigan, USA to relate spatiotemporal variability in wolf density to underlying classifications of habitat within a hierarchical state-space modelling framework. We then iteratively applied isodar analysis to evaluate which distribution of habitat selection best described this recolonizing wolf population. The wolf population in our study expanded by >1,000% during our study (~50 to >600 individuals), and density-dependent habitat selection was most consistent with the ideal-preemptive distribution, as opposed to the ideal-free or ideal-despotic alternatives. Population density of terrestrial carnivores may not be positively correlated with the fitness value of their habitats, and density-dependent habitat selection patterns may help to explain complex predator-prey dynamics and cascading indirect effects. Source-sink population dynamics appear likely when species exhibit rapid growth and occupy interspersed habitats of contrasting quality. These conditions are likely and have implications for large carnivores in many systems, such as areas in North America and Europe where large predator species are currently recolonizing their former ranges.

Patterns of divergence across the geographic and genomic landscape of a butterfly hybrid zone associated with a climatic gradient.

Hybrid zones are a valuable tool for studying the process of speciation and for identifying the genomic regions undergoing divergence and the ecological (extrinsic) and nonecological (intrinsic) factors involved. Here, we explored the genomic and geographic landscape of divergence in a hybrid zone between Papilio glaucus and Papilio canadensis. Using a genome scan of 28,417 ddRAD SNPs, we identified genomic regions under possible selection and examined their distribution in the context of previously identified candidate genes for ecological adaptations. We showed that differentiation was genomewide, including multiple candidate genes for ecological adaptations, particularly those involved in seasonal adaptation and host plant detoxification. The Z chromosome and four autosomes showed a disproportionate amount of differentiation, suggesting genes on these chromosomes play a potential role in reproductive isolation. Cline analyses of significantly differentiated genomic SNPs, and of species-diagnostic genetic markers, showed a high degree of geographic coincidence (81%) and concordance (80%) and were associated with the geographic distribution of a climate-mediated developmental threshold (length of the growing season). A relatively large proportion (1.3%) of the outliers for divergent selection were not associated with candidate genes for ecological adaptations and may reflect the presence of previously unrecognized intrinsic barriers between these species. These results suggest that exogenous (climate-mediated) and endogenous (unknown) clines may have become coupled and act together to reinforce reproductive isolation. This approach of assessing divergence across both the genomic and geographic landscape can provide insight about the interplay between the genetic architecture of reproductive isolation and endogenous and exogenous selection.

Two Theobroma cacao genotypes with contrasting pathogen tolerance show aberrant transcriptional and ROS responses after salicylic acid treatment.

Understanding the genetic basis of pathogen susceptibility in various crop plants is crucial to increasing the stability of food, feed, and fuel production. Varietal differences in defence responses provide insights into the mechanisms of resistance and are a key resource for plant breeders. To explore the role of salicylic acid in the regulation of defence in cacao, we demonstrated that SA treatment decreased susceptibility to a pod rot pathogen, Phytophthora tropicalis in two genotypes, Scavina 6 and Imperial College Selection 1, which differ in their resistance to several agriculturally important pathogens. Transient overexpression of TcNPR1, a major transcriptional regulator of the SA-dependent plant immune system, also increased pathogen tolerance in cacao leaves. To explore further the genetic basis of resistance in cacao, we used microarrays to measure gene expression profiles after salicylic acid (SA) treatment in these two cacao genotypes. The two genotypes displayed distinct transcriptional responses to SA. Unexpectedly, the expression profile of the susceptible genotype ICS1 included a larger number of pathogenesis-related genes that were induced by SA at 24h after treatment, whereas genes encoding many chloroplast and mitochondrial proteins implicated in reactive oxygen species production were up-regulated in the resistant genotype, Sca6. Sca6 accumulated significantly more superoxide at 24h after treatment of leaves with SA. These experiments revealed critical insights regarding the molecular differences between cacao varieties, which will allow a better understanding of defence mechanisms to help guide breeding programmes.

Gene expression in closely related species mirrors local adaptation: consequences for responses to a warming world.

Local adaptation of populations could preclude or slow range expansions in response to changing climate, particularly when dispersal is limited. To investigate the differential responses of populations to changing climatic conditions, we exposed poleward peripheral and central populations of two Lepidoptera to reciprocal, common-garden climatic conditions and compared their whole-transcriptome expression. We found evidence of simple population differentiation in both species, and in the species with previously identified population structure and phenotypic local adaptation, we found several hundred genes that responded in a synchronized and localized fashion. These genes were primarily involved in energy metabolism and oxidative stress, and expression levels were most divergent between populations in the same environment in which we previously detected divergence for metabolism. We found no localized genes in the species with less population structure and for which no local adaptation was previously detected. These results challenge the assumption that species are functionally similar across their ranges and poleward peripheral populations are preadapted to warmer conditions. Rather, some taxa deserve population-level consideration when predicting the effects of climate change because they respond in genetically based, distinctive ways to changing conditions.

A comparative study of ripening among berries of the grape cluster reveals an altered transcriptional programme and enhanced ripening rate in delayed berries.

Transcriptional studies in relation to fruit ripening generally aim to identify the transcriptional states associated with physiological ripening stages and the transcriptional changes between stages within the ripening programme. In non-climacteric fruits such as grape, all ripening-related genes involved in this programme have not been identified, mainly due to the lack of mutants for comparative transcriptomic studies. A feature in grape cluster ripening (Vitis vinifera cv. Pinot noir), where all berries do not initiate the ripening at the same time, was exploited to study their shifted ripening programmes in parallel. Berries that showed marked ripening state differences in a véraison-stage cluster (ripening onset) ultimately reached similar ripeness states toward maturity, indicating the flexibility of the ripening programme. The expression variance between these véraison-stage berry classes, where 11% of the genes were found to be differentially expressed, was reduced significantly toward maturity, resulting in the synchronization of their transcriptional states. Defined quantitative expression changes (transcriptional distances) not only existed between the véraison transitional stages, but also between the véraison to maturity stages, regardless of the berry class. It was observed that lagging berries complete their transcriptional programme in a shorter time through altered gene expressions and ripening-related hormone dynamics, and enhance the rate of physiological ripening progression. Finally, the reduction in expression variance of genes can identify new genes directly associated with ripening and also assess the relevance of gene activity to the phase of the ripening programme.

Harnessing Consumer Wearable Digital Biomarkers for Individualized Recognition of Postpartum Depression Using the All of Us Research Program Data Set: Cross-Sectional Study.

BACKGROUND: Postpartum depression (PPD) poses a significant maternal health challenge. The current approach to detecting PPD relies on in-person postpartum visits, which contributes to underdiagnosis. Furthermore, recognizing PPD symptoms can be challenging. Therefore, we explored the potential of using digital biomarkers from consumer wearables for PPD recognition. OBJECTIVE: The main goal of this study was to showcase the viability of using machine learning (ML) and digital biomarkers related to heart rate, physical activity, and energy expenditure derived from consumer-grade wearables for the recognition of PPD. METHODS: Using the All of Us Research Program Registered Tier v6 data set, we performed computational phenotyping of women with and without PPD following childbirth. Intraindividual ML models were developed using digital biomarkers from Fitbit to discern between prepregnancy, pregnancy, postpartum without depression, and postpartum with depression (ie, PPD diagnosis) periods. Models were built using generalized linear models, random forest, support vector machine, and k-nearest neighbor algorithms and evaluated using the κ statistic and multiclass area under the receiver operating characteristic curve (mAUC) to determine the algorithm with the best performance. The specificity of our individualized ML approach was confirmed in a cohort of women who gave birth and did not experience PPD. Moreover, we assessed the impact of a previous history of depression on model performance. We determined the variable importance for predicting the PPD period using Shapley additive explanations and confirmed the results using a permutation approach. Finally, we compared our individualized ML methodology against a traditional cohort-based ML model for PPD recognition and compared model performance using sensitivity, specificity, precision, recall, and F1-score. RESULTS: Patient cohorts of women with valid Fitbit data who gave birth included <20 with PPD and 39 without PPD. Our results demonstrated that intraindividual models using digital biomarkers discerned among prepregnancy, pregnancy, postpartum without depression, and postpartum with depression (ie, PPD diagnosis) periods, with random forest (mAUC=0.85; κ=0.80) models outperforming generalized linear models (mAUC=0.82; κ=0.74), support vector machine (mAUC=0.75; κ=0.72), and k-nearest neighbor (mAUC=0.74; κ=0.62). Model performance decreased in women without PPD, illustrating the method's specificity. Previous depression history did not impact the efficacy of the model for PPD recognition. Moreover, we found that the most predictive biomarker of PPD was calories burned during the basal metabolic rate. Finally, individualized models surpassed the performance of a conventional cohort-based model for PPD detection. CONCLUSIONS: This research establishes consumer wearables as a promising tool for PPD identification and highlights personalized ML approaches, which could transform early disease detection strategies.

Linking resource selection to population performance spatially to identify species' habitat across broad scales: An example of greater sage-grouse in a distinct population segment.

Management decisions often focus on the habitat selection of marked individuals without considering the contribution to demographic performance in selected habitats. Because habitat selection is not always adaptive, understanding the spatial relationship between habitat selection and demographic performance is critical to management decisions. Mapping both habitat selection and demographic performance for species of conservation concern can help guide population-scale conservation efforts. We demonstrate a quantitative approach to differentiate areas supporting selection and survival at large spatial extents. As a case study, we applied this approach to greater sage-grouse (Centrocercus urophasianus; hereafter, sage-grouse), an indicator species for sagebrush ecosystems. We evaluated both habitat selection and survival across multiple reproductive life stages (nesting, brood-rearing) in the Bi-State Distinct Population Segment, a genetically distinct and geographically isolated population of sage-grouse on the southwestern edge of the species' range. Our approach allowed us to identify both mismatches between selection and survival and trade-offs between reproductive life stages. These findings suggest resource demands vary across time, with predation risk being a dominant driver of habitat selection during nesting and early brood-rearing periods when chicks are smaller and flightless, whereas access to forage resources becomes more important during late brood rearing when resources become increasingly limited. Moving beyond identifying and managing habitat solely based on species occupancy or use by incorporating demographic measures allows managers to tailor actions to their specific goals; for example, protections of areas that support high selection and high survival and restoration actions focused on increasing survival in areas of high selection and low survival.

Finding Long-COVID: Temporal Topic Modeling of Electronic Health Records from the N3C and RECOVER Programs.

Post-Acute Sequelae of SARS-CoV-2 infection (PASC), also known as Long-COVID, encompasses a variety of complex and varied outcomes following COVID-19 infection that are still poorly understood. We clustered over 600 million condition diagnoses from 14 million patients available through the National COVID Cohort Collaborative (N3C), generating hundreds of highly detailed clinical phenotypes. Assessing patient clinical trajectories using these clusters allowed us to identify individual conditions and phenotypes strongly increased after acute infection. We found many conditions increased in COVID-19 patients compared to controls, and using a novel method to associate patients with clusters over time, we additionally found phenotypes specific to patient sex, age, wave of infection, and PASC diagnosis status. While many of these results reflect known PASC symptoms, the resolution provided by this unprecedented data scale suggests avenues for improved diagnostics and mechanistic understanding of this multifaceted disease.

Finding Long-COVID: temporal topic modeling of electronic health records from the N3C and RECOVER programs.

Post-Acute Sequelae of SARS-CoV-2 infection (PASC), also known as Long-COVID, encompasses a variety of complex and varied outcomes following COVID-19 infection that are still poorly understood. We clustered over 600 million condition diagnoses from 14 million patients available through the National COVID Cohort Collaborative (N3C), generating hundreds of highly detailed clinical phenotypes. Assessing patient clinical trajectories using these clusters allowed us to identify individual conditions and phenotypes strongly increased after acute infection. We found many conditions increased in COVID-19 patients compared to controls, and using a novel method to associate patients with clusters over time, we additionally found phenotypes specific to patient sex, age, wave of infection, and PASC diagnosis status. While many of these results reflect known PASC symptoms, the resolution provided by this unprecedented data scale suggests avenues for improved diagnostics and mechanistic understanding of this multifaceted disease.

Assessing De Novo transcriptome assembly metrics for consistency and utility.

BACKGROUND: Transcriptome sequencing and assembly represent a great resource for the study of non-model species, and many metrics have been used to evaluate and compare these assemblies. Unfortunately, it is still unclear which of these metrics accurately reflect assembly quality. RESULTS: We simulated sequencing transcripts of Drosophila melanogaster. By assembling these simulated reads using both a "perfect" and a modern transcriptome assembler while varying read length and sequencing depth, we evaluated quality metrics to determine whether they 1) revealed perfect assemblies to be of higher quality, and 2) revealed perfect assemblies to be more complete as data quantity increased.Several commonly used metrics were not consistent with these expectations, including average contig coverage and length, though they became consistent when singletons were included in the analysis. We found several annotation-based metrics to be consistent and informative, including contig reciprocal best hit count and contig unique annotation count. Finally, we evaluated a number of novel metrics such as reverse annotation count, contig collapse factor, and the ortholog hit ratio, discovering that each assess assembly quality in unique ways. CONCLUSIONS: Although much attention has been given to transcriptome assembly, little research has focused on determining how best to evaluate assemblies, particularly in light of the variety of options available for read length and sequencing depth. Our results provide an important review of these metrics and give researchers tools to produce the highest quality transcriptome assemblies.

A Bayesian multi-stage modelling framework to evaluate impacts of energy development on wildlife populations: an application to greater sage-grouse (Centrocercus urophasianus).

Increased demand for domestic production of renewable energy has led to expansion of energy infrastructure across western North America. Much of the western U.S. comprises remote landscapes that are home to a variety of vegetation communities and wildlife species, including the imperiled sagebrush ecosystem and indicator species such as greater sage-grouse (Centrocercus urophasianus). Geothermal sources in particular have potential for continued development across the western U.S. but impacts to greater sage-grouse and other species are unknown. To address this information gap, we describe a novel two-pronged methodology that analyzes impacts of geothermal energy production on pattern and process of greater sage-grouse populations using (a) before-after control-impact (BACI) measures of population growth and lek absence rates and (b) concurrent-to-operation evaluations of demographic rates. Growth and absence rate analyses utilized 14 years of lek survey data collected prior (2005-2011) and concurrent (2012-2018) to geothermal operations at two sites in Nevada, USA. Demographic analyses utilized relocation data, restricted inference to concurrent years, and incorporated 17 additional control sites. Demographic results were applied to >100 potential geothermal sites distributed across the study region to generate spatially explicit predictions of unrealized population-level impacts.•State-space and generalized linear models yield estimates of population growth and lek absence rates, respectively, before and after the onset of geothermal energy production; distances ranging from 2-30 km are evaluated as alternative control-impact footprint hypotheses; this provides inference about the spatial extent as well as the magnitude of impacts associated with geothermal development.•Estimation of important population demographic rates are implemented to investigate the processes by which geothermal energy development might reduce population growth; independent estimates of confounding, environmental effects from 17 control sites are made spatially explicit within 'impact' models to establish baseline conditions otherwise masked by collinearity.•Population matrix models are built using estimates from demographic analyses to provide landscape mapping of impacts associated with potential geothermal sites.

Harnessing consumer wearable digital biomarkers for individualized recognition of postpartum depression using the All of Us Research Program dataset.

Postpartum depression (PPD), afflicting one in seven women, poses a major challenge in maternal health. Existing approaches to detect PPD heavily depend on in-person postpartum visits, leading to cases of the condition being overlooked and untreated. We explored the potential of consumer wearable-derived digital biomarkers for PPD recognition to address this gap. Our study demonstrated that intra-individual machine learning (ML) models developed using these digital biomarkers can discern between pre-pregnancy, pregnancy, postpartum without depression, and postpartum with depression time periods (i.e., PPD diagnosis). When evaluating variable importance, calories burned from the basal metabolic rate (calories BMR) emerged as the digital biomarker most predictive of PPD. To confirm the specificity of our method, we demonstrated that models developed in women without PPD could not accurately classify the PPD-equivalent phase. Prior depression history did not alter model efficacy for PPD recognition. Furthermore, the individualized models demonstrated superior performance compared to a conventional cohort-based model for the detection of PPD, underscoring the effectiveness of our individualized ML approach. This work establishes consumer wearables as a promising avenue for PPD identification. More importantly, it also emphasizes the utility of individualized ML model methodology, potentially transforming early disease detection strategies.

Haplotype and minimum-chimerism consensus determination using short sequence data.

BACKGROUND: Assembling haplotypes given sequence data derived from a single individual is a well studied problem, but only recently has haplotype assembly been considered for population-sampled data. We discuss a software tool called Hapler, which is designed specifically for low-diversity, low-coverage data such as ecological samples derived from natural populations. Because such data may contain error as well as ambiguous haplotype information, we developed methods that increase confidence in these assemblies. Hapler also reconstructs full consensus sequences while minimizing and identifying possible chimeric points. RESULTS: Experiments on simulated data indicate that Hapler is effective at assembling haplotypes from gene-sized alignments of short reads. Further, in our tests Hapler-generated consensus sequences are less chimeric than the alternative consensus approaches of majority vote and viral quasispecies estimation regardless of error rate, read length, or population haplotype bias. CONCLUSIONS: The analysis of genetically diverse sequence data is increasingly common, particularly in the field of ecoinformatics where transcriptome sequencing of natural populations is a cost effective alternative to genome sequencing. For such studies, it is important to consider and identify haplotype diversity. Hapler provides robust haplotype information and identifies possible phasing errors in consensus sequences, providing valuable information for population studies and downstream usage of resulting assemblies.

Post-recovery COVID-19 and incident heart failure in the National COVID Cohort Collaborative (N3C) study.

Cardiac involvement has been noted in COVID-19 infection. However, the relationship between post-recovery COVID-19 and development of de novo heart failure has not been investigated in a large, nationally representative population. We examined post-recovery outcomes of 587,330 patients hospitalized in the United States (257,075 with COVID-19 and 330,255 without), using data from the National COVID Cohort Collaborative study. Patients hospitalized with COVID-19 were older (51 vs. 46 years), more often male (49% vs. 42%), and less often White (61% vs. 69%). Over a median follow up of 367 days, 10,979 incident heart failure events occurred. After adjustments, COVID-19 hospitalization was associated with a 45% higher hazard of incident heart failure (hazard ratio = 1.45; 95% confidence interval: 1.39-1.51), with more pronounced associations among patients who were younger (P-interaction = 0.003), White (P-interaction = 0.005), or who had established cardiovascular disease (P-interaction = 0.005). In conclusion, COVID-19 hospitalization is associated with increased risk of incident heart failure.

Nesting, brood rearing, and summer habitat selection by translocated greater sage-grouse in North Dakota, USA.

Human enterprise has led to large-scale changes in landscapes and altered wildlife population distribution and abundance, necessitating efficient and effective conservation strategies for impacted species. Greater sage-grouse (Centrocercus urophasianus; hereafter sage-grouse) are a widespread sagebrush (Artemisia spp.) obligate species that has experienced population declines since the mid-1900s resulting from habitat loss and expansion of anthropogenic features into sagebrush ecosystems. Habitat loss is especially evident in North Dakota, USA, on the northeastern fringe of sage-grouse' distribution, where a remnant population remains despite recent development of energy-related infrastructure. Resource managers in this region have determined a need to augment sage-grouse populations using translocation techniques that can be important management tools for countering species decline from range contraction. Although translocations are a common tool for wildlife management, very little research has evaluated habitat following translocation, to track individual behaviors such as habitat selection and fidelity to the release site, which can help inform habitat requirements to guide selection of future release sites. We provide an example where locations from previously released radio-marked sage-grouse are used in a resource selection function framework to evaluate habitat selection following translocation and identify areas of seasonal habitat to inform habitat management and potential restoration needs. We also evaluated possible changes in seasonal habitat since the late 1980s using spatial data provided by the Rangeland Analysis Platform coupled with resource selection modeling results. Our results serve as critical baseline information for habitat used by translocated individuals across life stages in this study area, and will inform future evaluations of population performance and potential for long-term recovery.

Population-level transcriptome sequencing of nonmodel organisms Erynnis propertius and Papilio zelicaon.

BACKGROUND: Several recent studies have demonstrated the use of Roche 454 sequencing technology for de novo transcriptome analysis. Low error rates and high coverage also allow for effective SNP discovery and genetic diversity estimates. However, genetically diverse datasets, such as those sourced from natural populations, pose challenges for assembly programs and subsequent analysis. Further, estimating the effectiveness of transcript discovery using Roche 454 transcriptome data is still a difficult task. RESULTS: Using the Roche 454 FLX Titanium platform, we sequenced and assembled larval transcriptomes for two butterfly species: the Propertius duskywing, Erynnis propertius (Lepidoptera: Hesperiidae) and the Anise swallowtail, Papilio zelicaon (Lepidoptera: Papilionidae). The Expressed Sequence Tags (ESTs) generated represent a diverse sample drawn from multiple populations, developmental stages, and stress treatments. Despite this diversity, > 95% of the ESTs assembled into long (> 714 bp on average) and highly covered (> 9.6x on average) contigs. To estimate the effectiveness of transcript discovery, we compared the number of bases in the hit region of unigenes (contigs and singletons) to the length of the best match silkworm (Bombyx mori) protein--this "ortholog hit ratio" gives a close estimate on the amount of the transcript discovered relative to a model lepidopteran genome. For each species, we tested two assembly programs and two parameter sets; although CAP3 is commonly used for such data, the assemblies produced by Celera Assembler with modified parameters were chosen over those produced by CAP3 based on contig and singleton counts as well as ortholog hit ratio analysis. In the final assemblies, 1,413 E. propertius and 1,940 P. zelicaon unigenes had a ratio > 0.8; 2,866 E. propertius and 4,015 P. zelicaon unigenes had a ratio > 0.5. CONCLUSIONS: Ultimately, these assemblies and SNP data will be used to generate microarrays for ecoinformatics examining climate change tolerance of different natural populations. These studies will benefit from high quality assemblies with few singletons (less than 26% of bases for each assembled transcriptome are present in unassembled singleton ESTs) and effective transcript discovery (over 6,500 of our putative orthologs cover at least 50% of the corresponding model silkworm gene).

Territorial landscapes: incorporating density-dependence into wolf habitat selection studies.

Habitat selection is a process that spans space, time and individual life histories. Ecological analyses of animal distributions and preferences are most accurate when they account for inherent dynamics of the habitat selection process. Strong territoriality can constrain perception of habitat availability by individual animals or groups attempting to colonize or establish new territory. Because habitat selection is a function of habitat availability, broad-scale changes in habitat availability or occupancy can drive density-dependent habitat functional responses. We investigated density-dependent habitat selection over a 19-year period of grey wolf (Canis lupus) recovery in Michigan, USA, using a generalized linear mixed model framework to develop a resource selection probability function (RSPF) with habitat coefficients conditioned on random effects for wolf packs and random year intercepts. In addition, we allowed habitat coefficients to vary as interactions with increasing wolf density over space and time. Results indicated that pack presence was driven by factors representing topography, human development, winter prey availability, forest structure, roads, streams and snow. Importantly, responses to many of these predictors were density-dependent. Spatio-temporal dynamics and population changes can cause considerable variation in wildlife-habitat relationships, possibly confounding interpretation of conventional habitat selection models. By incorporating territoriality into an RSPF analysis, we determined that wolves' habitat use in Michigan shifted over time, for example, exhibiting declining responses to winter prey indices and switching from positive to negative responses with respect to stream densities. We consider this an important example of a habitat functional response in wolves, driven by colonization, density-dependence and changes in occupancy during a time period of range expansion and population increase.