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Feeding habits influence species habitat associations at the landscape scale in a diverse clade of Neotropical fishes

Aim. A primary goal of community ecology is to understand the mechanisms that drive species' spatial distribution and habitat associations. Species' geographic distribution can be influenced by the distribution of their prey partly because consumers' behavior is oriented to optimal energy use during foraging. We analyzed how differences in dietary preferences influence the spatial distribution and habitat associations of species at the landscape scale. We hypothesized that differences in feeding guilds will lead to divergent habitat association patterns among species. Location. Amazon River drainage basin. Taxon. Characiform fishes in the family Serrasalmidae (piranhas and pacus). Methods. We used diet data to classify species into feeding guilds (frugivores, herbivores, piscivores, fin and scale feeders, and planktivores). We used three proxies of habitat association derived from satellite products: floodplain extent, landscape heterogeneity, and flood duration, in three distance buffers. We implemented Phylogenetic Generalized Least Squares models to evaluate the relationship between habitat association and feeding guilds. Results. Frugivores, piscivores, and fin and scale feeders presented similar patterns of habitat associations, with frugivores occupying wider areas of floodplain and greater landscape heterogeneity. Herbivores and planktivores were associated with smaller floodplain extents and lower landscape heterogeneity. All feeding guilds were associated with similar levels of flood duration. Main conclusions. Differences in resource distribution (assessed through feeding guilds) can influence habitat association. Considering the hydrological variability (i.e., floodplain extent) and landscape heterogeneity that characterize floodplains, the patterns of habitat association vary with the spatial scale considered. This work highlights the importance of understanding species habitat associations by fish as well as food resource dynamics and floodplain dependence. This realization is critical for assessing the impact of anthropogenic activities on freshwater ecosystems.

Scale-dependent environmental effects on phenotypic distributions in Heliconius butterflies

Examining how environmental factors influence phenotypic distribution might provide valuable information about local adaptation, divergence, and speciation. The red-yellow Müllerian mimicry ring of Heliconius butterflies displays a wide range of color patterns across the Neotropics and is involved in several hybrid zones, making it an excellent system to study color phenotypic distribution. Using a multiscale distribution strategy, we studied whether different phenotypes of the distantly related species H. erato and H. melpomene, belonging to the red-yellow mimetic ring, are associated with different environmental conditions. We show that environmental gradients (particularly heat and precipitation factors) drive Heliconius phenotypic distributions, but that phenotype and environmental correlations vary with spatial scale. While co-mimics are frequently found in similar environments at a broad scale, patterns at the local level are not necessarily consistent (different variables are the best predictors of phenotypic occurrence in different areas) or congruent (co-mimic pairs show distinct associations with the environment). Thus, large-scale analysis may help to identify how environmental heterogeneity influences broad mimic phenotypic distributions, but local studies are needed to understand the context-dependent biotic, abiotic, and historical mechanisms that drive finer-scale phenotypic shifts.

opencc-by-4.0Jun 2009View details →

Large-scale grid computing for content-based image retrieval

The author presents an approach in which a large distributed processing Grid has been used to apply a range of content-based image retrieval methods to a substantial number of images. By massively distributing the required computational task across thousands of Grid nodes, we have achieved very high throughput at relatively low overheads.

Quantifying nitrogen deposition inputs to cropland: A national scale dataset from 1961 to 2020

Nitrogen (N) deposition is one of the major inputs to cropland and consequently important for the estimation of N Use Efficiency (NUE) for crop production. However, the estimates for N deposition carry large uncertainty, and existing assessments of N budgets and NUE on agricultural land use different estimates of N deposition. To evaluate the uncertainties in existing methods for national scale N deposition estimation and assess their impacts on the resulting NUE estimation for countries around the world, we 1) reviewed existing methods and related data sources for quantifying N deposition inputs to crop production on a national scale; 2) identified the most up–to–date data sources and designed methods to quantify N deposition input to crop production on a national scale; 3) collected N deposition data from observation sites in major countries (e.g., UK, US, and China) to validate the estimated N deposition input; and 4) conducted sensitivity analysis to evaluate how the uncertainties in N deposition affect crop NUE assessment. As a result, we established four estimates for N deposition inputs on cropland for 251 countries around the world during 1961–2020 as combinations of two sets of N deposition maps (ACCMIP1 and Wang et al.2-4) and two sets of cropland maps (HYDE5 and LUH26). The four products (1. AH: ACCMIP and HYDE, 2. AL: ACCMIP and LUH2, 3. WH: Wang et al. and HYDE, and 4. WL: Wang et al. and LUH2) show good agreement in N deposition estimates for the majority of countries, but have large differences in several Asian countries (e.g., China, India, and Pakistan), and the differences are mostly caused by the use of different N deposition maps. According to the comparison with the observation records in China, the deposition estimates based on Wang et al. show a better agreement with the observations. Hence, the authors recommend using product #4 WL (Wang et al. and LUH2) as the reference dataset for N deposition in the global assessments of N budgets by countries. References: <ol> <li>Lamarque, J. F. et al. Multi-model mean nitrogen and sulfur deposition from the atmospheric chemistry and climate model intercomparison project (ACCMIP): Evaluation of historical and projected future changes. Atmos. Chem. Phys. 13, 7997–8018 (2013).</li> <li>Shang, Z. et al. Weakened growth of cropland-N2O emissions in China associated with nationwide policy interventions. Glob. Chang. Biol. 25, 3706–3719 (2019).</li> <li>Wang, Q. et al. Data-driven estimates of global nitrous oxide emissions from croplands. Natl. Sci. Rev. 7, 441–452 (2020).</li> <li>Wang, R. et al. Global forest carbon uptake due to nitrogen and phosphorus deposition from 1850 to 2100. Glob. Chang. Biol. 23, 4854–4872 (2017).</li> <li>Goldewijk, K. K., Beusen, A., Doelman, J. & Stehfest, E. Anthropogenic land use estimates for the Holocene - HYDE 3.2. Earth Syst. Sci. Data 9, 927–953 (2017).</li> <li>Hurtt, G. C. et al. Harmonization of global land use change and management for the period 850-2100 (LUH2) for CMIP6. Geoscientific Model Development 13, (2020).</li> </ol>

Grassland bird population declines at three Breeding Bird Survey spatial scales in contrast to a large native prairie

Grassland biomes in North America are threatened by agricultural intensification with implications for grassland associated bird populations via habitat loss, alteration, pesticide use and declining landscape heterogeneity. Despite decades of conservation concern, steep declines of North American grassland bird populations continue. Key to optimizing conservation effort is understanding how land-use practices, such as agriculture, across the annual cycle affects population status. Determining the relative influence of impacts on grassland bird declines is difficult given that the most robust estimates of population trends, the North American Breeding Bird Survey (BBS), are from surveys throughout agriculturally dominated regions. Our goal was to explore whether agriculture during the breeding season is a major driver of grassland bird declines. We derived trends for 16 grassland bird species spanning 23 years (1994-2016) at a large (459 km2), native prairie site, Suffield National Wildlife Area (SNWA) in Alberta, Canada. We compared those trends to the BBS across three spatial scales, a regional monitoring scheme with higher than average native grass cover (GBM), BCR 11 - Canada (Canada) and all of BCR 11 (BCR 11). Trends measured as annual percent change and credible interval varied greatly among species and survey strata. Across all species, declines were greatest for Canada (-1.3%, CI: -2.8, 0.0) and BCR 11 (-1.9%, CI: -3.2, -0.6). This contrasts with positive mean trends for GBM routes (1.0%, CI: -0.4, 2.3) and the SNWA data (1.7%, CI: 0.3, 3.3). Six of 16 species at SNWA were increasing with one decreasing. Five species increased at GBM and four declined. Canada had 10 species declines and three increases and BCR 11 had 10 declines and no increases. None of six grassland obligate species declined at SNWA, two declined at GBM, and all six declined over the two larger BBS strata. Our results showing fewer negative population trends at a large native grassland site compared to BBS at three spatial scales across the North American prairies support the prediction that agricultural intensification on breeding grounds is a major driver of declining populations and protection of remaining native grasslands should remain a key component of grassland bird conservation efforts.

High-density genomic data reveal fine-scale population structure and pronounced islands of adaptive divergence in lake whitefish (Coregonus clupeaformis) from Lake Michigan

Understanding patterns of genetic structure and adaptive variation in natural populations is crucial for informing conservation and management. Past genetic research using 11 microsatellite loci identified six genetic stocks of lake whitefish (Coregonus clupeaformis) within Lake Michigan, USA. However, ambiguity in genetic stock assignments suggested those neutral microsatellite markers did not provide adequate power for delineating lake whitefish stocks in this system, prompting calls for a genomics approach to investigate stock structure. Here, we generated a dense genomic dataset to characterize population structure and investigate patterns of neutral and adaptive genetic diversity among lake whitefish populations in Lake Michigan. Using Rapture sequencing, we genotyped 829 individuals collected from 17 baseline populations at 197,588 SNP markers after quality filtering. Although the overall pattern of genetic structure was similar to the previous microsatellite study, our genomic data provided several novel insights. Our results indicated a large genetic break between the northwestern and eastern sides of Lake Michigan, and we found a much greater level of population structure on the eastern side compared to the northwestern side. Collectively, we observed five genomic islands of adaptive divergence on five different chromosomes. Each island displayed a different pattern of population structure, suggesting that combinations of genotypes at these adaptive regions are facilitating local adaptation to spatially heterogenous selection pressures. Additionally, we identified a large linkage disequilibrium block of ~8.5 Mb on chromosome 20 that is suggestive of a putative inversion but with a low frequency of the minor haplotype. Our study provides a comprehensive assessment of population structure and adaptive variation that can help inform management of Lake Michigan's lake whitefish fishery and highlights the utility of incorporating adaptive loci into fisheries management.

opencc-by-4.0Jun 2022View details →

The June 2012 North American Derecho: A testbed for evaluating regional and global climate modeling systems at cloud-resolving scales

This is the companion data for the manuscript titled 'The June 2012 North American Derecho: A testbed for evaluating regional and global climate modeling systems at cloud-resolving scales', submitted to the Journal of Advances in Modeling Earth Systems in September 2022. derecho_simulation_result: this folder contains part of the SCREAM RRM outputs I ran on NERSC Cori in 2021-2022 corresponding to the simulation in Table 1 of the manuscript. wrf_simulation_result: this folder contains part of the WRF outputs run by Jianfeng Li from PNNL (jianfeng.li@pnnl.gov) in 2022 corresponding to the simulations in Table 4 of the manuscript. plot_script: this folder includes python scripts to plot figures shown in the manuscript. ASOS_station: this txt file contains the processed ASOS station wind speed used in the manuscript. Unfortunately, all model outputs are large (~ 3.8 TB for SCREAM RRM and 3.1 TB for WRF). Therefore, I only provide the variables (i.e., OLR, precipitation, composite radar reflectivity, and 10-m wind speed) used directly to generate figures in this repository. All model outputs are archived on tape at NERSC. For more details, refer to the manuscript, or contact me (wrliu@ucdavis.edu).

Environmental drivers of local abundance-mass scaling in soil animal communities

The relationship between species' body masses and densities is strongly conserved around a three-quarter power law when pooling data across communities. However, studies of local within-community relationships have revealed major deviations from this general pattern, which has profound implications for their stability and functioning. Despite multiple contributions of soil communities to people, there is limited knowledge on the drivers of body mass-abundance relationships in these communities. We compiled a dataset comprising 155 soil-animal communities across four countries (Canada, Germany, Indonesia, USA), all sampled using the same methodology. We tested if variation in local climatic and edaphic conditions drives differences in local body mass-abundance scaling relationships. We found substantial variation in the slopes of this power-law relationship across local communities. Structural equation modeling showed that soil temperature and water content have a positive and negative net effect, respectively, on soil communities. These effects are mediated by changes in local edaphic conditions (soil pH and carbon content) and the body-mass range of the communities. These results highlight ways in which alterations of soil climatic and edaphic conditions interactively impact the distribution of abundance between populations of small and large animals. These quantitative mechanistic relationships facilitate our understanding of how global changes in environmental conditions, such as temperature and precipitation, will affect community-abundance distributions and thus the stability and functioning of soil-animal communities.

Large scale eDNA monitoring of multiple aquatic pathogens as a tool to provide risk maps for wildlife diseases

Multiple parasites and pathogens cause disease in aquatic wildlife and in aquaculture species, generating a need for monitoring and management. Conventional disease monitoring methods involve laborious, costly and invasive capture and examination of host species, and require specialised expertise for every host and pathogen of interest. These restrictions could be alleviated by using pathogen detection techniques based on environmental DNA that provide simultaneous surveys of multiple aquatic pathogens across different host taxa. This would also be valuable for approaches employing parasite diversity as bioindicators of ecosystem disturbance, which suffer from similar restrictions. Here, we tested the potential for simultaneous detection of four wildlife pathogens in water samples from 280, mainly riverine, sites across Switzerland. We targeted the crayfish pathogen Aphanomyces astaci, the amphibian pathogen Batrachochytrium dendrobatidis, and the fish pathogens Saprolegnia parasitica and Tetracapsuloides bryosalmonae. The eDNA detection showed a widespread distribution of A. astaci, S. parasitica and T. bryosalmonae, although A. astaci and T. bryosalmonae were not detected in some alpine river catchments. B. dendrobatidis was detected only rarely, which was expected since the sampling did not target amphibian breeding sites. Co-detection rates were higher in rivers than in lakes, likely reflecting the habitat preferences and distributions of the host species. We discuss the advantages and limitations of eDNA-based pathogen monitoring and list a set of recommendations for managers. Our study illustrates how eDNA-based techniques can monitor several pathogen species concurrently, thus facilitating more comprehensive disease monitoring schemes. Combined with metabarcoding approaches in the future, eDNA based sampling and detection can facilitate the incorporation of parasite and pathogen occurrence and diversity as an indicator for aquatic ecosystem health, and for revealing the hidden biodiversity and structure of parasite communities.

Do large-scale associations in birds imply biotic interactions or environmental filtering?

Aim: There has been a wide interest in the effect of biotic interactions on species' occurrences and abundances at large spatial scales, coupled with a vast development of the statistical methods to study them. Still, the evidence whether the effects of within-trophic level biotic interactions (e.g. competition and heterospecific attraction) are discernible beyond local scales remains inconsistent. Here, we present a novel hypothesis-testing framework based on joint dynamic species distribution models (JDSDMs) and functional trait similarity to dissect between environmental filtering and biotic interactions. Location: France and Finland. Taxon: Birds. Methods: We estimated species-to-species associations within a trophic level, independent of the main environmental variables (mean temperature and total precipitation) for common species at large spatial scale with joint dynamic species distribution models (VAST). We created hypotheses based on species' functionality (morphological and/or diet dissimilarity) and habitat preferences about the sign and strength of the pairwise spatio-temporal associations to estimate the extent to which they result from biotic interactions (competition, heterospecific attraction) and/or environmental filtering. Results: Spatio-temporal associations were mostly positive (80%), followed by random (15%), and only 5% were negative. Negative spatio-temporal associations in different communities were due to a few species when they existed. The relationship between spatio-temporal association and functional dissimilarity among species was negative, which fulfills the predictions of both environmental filtering and heterospecific attraction. Main conclusions: We showed that processes leading to species aggregation (mixture between environmental filtering and heterospecific attraction) seem to dominate assembly rules, and we did not find evidence for competition. Altogether, hypothesis-testing framework based on joint dynamic species distribution models and functional trait similarity is beneficial in ecological interpretation of species-to-species associations from the long-term large-scale data.

opencc-by-4.0Jul 2022View details →

Fine-scale subpopulation detection via SNP-based unsupervised method: A case study on the 1000 Genomes Project Resources

Here are the supplementary files to the paper "Fine-scale subpopulation detection via SNP-based unsupervised method: A case study on the 1000 Genomes Project Resources". The repository is organized as: <ol> <li>Supplementary information: the additional detailed information for the experiments in the paper <ul> <li>Supplementary_information_IPCAPS_Chaichoompu_v1.pdf</li> </ul> </li> <li>Real-life dataset: the 1000 genome dataset, which is referred to in the paper and is filtered with the parameters explained in the paper. Reference: https://www.internationalgenome.org/ <ul> <li>1000genomes_with_filtering.zip</li> </ul> </li> </ol>

opencc-zeroOct 2022View details →

A chromosomal-scale reference genome of the New World Screwworm, Cochliomyia hominivorax

The New World Screwworm, Cochliomyia hominivorax (Calliphoridae), is the most important myiasis-causing species in America. Screwworm myiasis is a zoonosis that can cause severe lesions in livestock, domesticated and wild animals, and occasionally in people. Beyond the sanitary problems associated with this species, these infestations negatively impact economic sectors, such as the cattle industry. Here, we present a chromosome-scale assembly of C. hominivorax's genome, organized in 6 chromosome-length and 515 unplaced scaffolds spanning 534 Mb. There was a clear correspondence between the D. melanogaster linkage groups A-E and the chromosomal-scale scaffolds. Chromosome Quotient (CQ) analysis identified a single scaffold from the X chromosome that contains most of the orthologs of genes that are on the D. melanogaster fourth chromosome (linkage group F or dot chromosome). CQ analysis also identified potential X and Y unplaced scaffolds and genes. Y-linkage for selected regions was confirmed by PCR with male and female DNA. Some of the long chromosome-scale scaffolds include Y-linked sequences, suggesting misassembly of these regions. These resources will provide a basis for future studies aiming at understanding the biology and evolution of this devastating obligate parasite.

Combined effects of stream hydrology and land use on basin-scale hyporheic zone denitrification in the Columbia River Basin

This data includes inputs and outputs of a coupled carbon-nitrogen river corridor model (RCM) for the Columbia River Basin and sensitivity results with varying substrate concentrations, and random forest model results with key model inputs/watershed/stream variables. The detailed descriptions of the individual files are included in the readme.txt file.

opencc-by-4.0Dec 2021View details →

Text-fig. 13. Paramblypterus sp. Locality Otovice "Chmelnice", P 64668, scale bar 10 mm. in Actinopterygians Of The Broumov Formation (Permian) In The Czech Part Of The Intra-Sudetic Basin (The Czech Republic)

Text-fig. 13. Paramblypterus sp. Locality Otovice "Chmelnice", P 64668, scale bar 10 mm.

opencc-by-4.0Dec 2021View details →

Text-fig. 5. Pyracantha coccinea M.ROEM. (Cottbus, herbarium Striegler). Scale bar 10 mm. in New Leaf Species From The Upper Miocene Flora Of The Leaf-Bearing Wischgrund Clay (Lower Lusatia, Brandenburg, Germany)

Text-fig. 5. Pyracantha coccinea M.ROEM. (Cottbus, herbarium Striegler). Scale bar 10 mm.

Revisiting GeV-scale annihilating dark matter with the AMS-02 positron fraction

We include our dark matter fluxes in their pre-fitted format for the entire set. That is in connection to our paper titled "Revisiting GeV-scale annihilating dark matter with the AMS-02 positron fraction"

Beta carotene apparent retention dataset, Likert scale dataset, and preference ranking scale dataset

the datasets attached contains data on (1) beta carotene retention levels in various provitamin A maize products (dry maize flour, pre germinated maize flour, fermented maize beverage, maize beverage and maize meal, (2) Likert scale which shows the degree of likeness of provitamin A maize porridge by children aged 6 to 24 months old, (3) Preference ranking scale which shows the degree of likeness of the provitamin A products by the children's caregivers

Data to reproduce the results presented in Lake et al. 2022. Hydrological processes, https://doi.org/10.1002/hyp.14726 ("Using particle size distributions to fingerprint suspended sediment sources – evaluation at laboratory and catchment scales")

This repository contains data on particle size distribution data obtained from the laboratory and field experiments as described in Lake et al., 2022.  The data contains the input files as needed for the modelling: - In the excel files the particle size distribution data for the target SS - In the text file the particle size distribution data from the sources.   Furthermore, the data contains the resulting output files.

opencc-zeroOct 2022View details →

Landscape-scale drivers of liana load across a Southeast Asian forest canopy differ to the Neotropics

Lianas (woody vines) are a key component of tropical forests, known to reduce forest carbon storage and sequestration and to be increasing in abundance. Analysing how and why lianas are distributed in forest canopies at landscape scales will help us determine the mechanisms driving changes in lianas over time. This will improve our understanding of liana ecology and projections of tropical forest carbon storage now and into the future. Despite competing hypotheses on the mechanisms driving spatial patterning of lianas, few studies have integrated multiple tree-level biotic and abiotic factors in an analytical framework. None have done so in the Palaeotropics, which are biogeographically and evolutionarily distinct from the Neotropics, where most research on lianas has been conducted. We used an unoccupied aerial system (UAS; drone) to assess liana load in 50-ha of Palaeotropical forest canopy in Southeast Asia. We obtained data on hypothesised drivers of liana spatial distribution in the forest canopy, including disturbance, tree characteristics, soil chemistry, and topography, from the UAS, from airborne LiDAR, and from ground surveys. We integrated these in a comprehensive analytical framework to extract variables at an individual-tree level and evaluated the relative strengths of the hypothesised drivers and their ability to predict liana distributions through boosted regression tree (BRT) modeling. Tree height and distance to canopy gaps were the two most important predictors of liana load, with relative contribution values in BRT models of 34.60% 45.39% and 7.93% - 10.19%, respectively. Our results suggest that taller trees were less often and less heavily infested by lianas than shorter trees, opposite to Neotropical findings. Lianas also occurred more often, and to a greater extent, in tree crowns close to canopy gaps and to neighbouring trees with lianas in their crown. Synthesis: Despite their known importance and prevalence in tropical forests, lianas are not well understood, particularly in the Palaeotropics. Examining 2,428 trees across 50-ha of Palaeotropical forest canopy in Southeast Asia, we find support for the hypothesis that canopy gaps promote liana infestation. Our finding that liana presence and load declined with tree height, opposite to well-established Neotropical findings, suggests a fundamental difference between Neotropical and Southeast Asian forests. Considering that most liana literature has focused on the Neotropics, this highlights the need for additional studies in other biogeographic regions to clarify potential differences and enable us to better understand liana impacts on tropical forest ecology, carbon storage and sequestration.