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opencc-zeroJan 2022View details →

Long-distance dependencies in birdsong syntax

Songbird syntax is generally thought to be simple, lacking in particular long-distance dependencies in which one element affects choice of another occurring considerably later in the sequence. Here we test for long-distance dependencies in the sequences of songs produced by song sparrows (Melospiza melodia). Song sparrows sing with eventual variety, repeating each song type in a consecutive series termed a "bout." We show that in switching between song types, song sparrows follow a "cycling rule," cycling through their repertoires in close to the minimum possible number of bouts. Song sparrows do not cycle in a set order but rather vary the order of song types from cycle to cycle. Cycling in a variable order strongly implies long-distance dependencies: choice of the next type must depend on the song types sung over the past cycle, in the range of 9-10 bouts. Song sparrows also follow a "bout length rule," whereby the number of repetitions of a song type in a bout is positively associated with the length of the interval until that type recurs. This rule requires even longer-distance dependencies that cross one another; such dependencies are characteristic of more complex levels of syntax than previously attributed to non-human animals.

opencc-zeroJan 2022View details →

Cold winters have morph-specific effects on natal dispersal distance in a wild raptor

Dispersal is a key process with crucial implications in spatial distribution, density and genetic structure of species' populations. Dispersal strategies can vary according to both individual and environmental features, but putative phenotype-by-environment interactions have rarely been accounted for. Melanin-based color polymorphism is a phenotypic trait associated with specific behavioral and physiological profiles and is therefore a good candidate trait to study dispersal tactics in different environments. Here, using a 40 years dataset of a population of color polymorphic tawny owls (Strix aluco), we investigated natal dispersal distance of recruiting gray and pheomelanic reddish-brown (hereafter brown) color morphs in relation to post-fledging winter temperature and individual characteristics. Since morphs are differently sensitive to cold winters, we predicted that morphs' natal dispersal distances vary according to winter conditions. Winter temperature did not affect the proportion of brown (or gray) among recruits. We found that dispersal distances correlate with winter temperature in an opposite manner in the two morphs. While the gray morph undertakes larger movements in harsher conditions, likely because it copes better with winter severity, the brown morph disperses shorter distances when winters are harsher. We discuss this morph-specific natal dispersal pattern in a context of competition for territories between morphs and in terms of costs and benefits of these alternative strategies. Our results stress the importance of considering the interaction between phenotype and environment to fully disentangle dispersal movement patterns and provide further evidence that climate affects behavior and local distribution of this species.

opencc-zeroFeb 2022View details →

Empirical tests of habitat selection theory reveal that conspecific density and patch quality, but not habitat amount, drive long-distance immigration in a wild bird

Individuals that disperse long distances from their natal site must select breeding patches with no prior knowledge of patch suitability. Despite decades of theoretical studies examining which cues dispersing individuals should use to select breeding patches, few empirical studies have tested the predictions of these theories at spatial scales relevant to long-distance dispersal in wild animal populations. Here, we use a novel assignment model based on multiple intrinsic markers to quantify natal dispersal distances of Wood Thrush (Hylocichla mustelina) breeding in forest fragments. We show that long-distance natal dispersal in this species is more frequent than commonly assumed for songbirds and that habitat selection by these individuals is driven by density-dependence and patch quality but not the amount of habitat surrounding breeding patches. These results represent an important contribution to understanding habitat selection by dispersing individuals, especially with regards to long-distance dispersal.

opencc-by-4.0Mar 2022View details →

Southern Hemisphere coasts are biologically connected by frequent, long-distance rafting events

Globally, species distributions are shifting in response to environmental change, and those that cannot disperse risk extinction. Many taxa, including marine species, are showing poleward range shifts as the climate warms. In the Southern Hemisphere, however, circumpolar oceanic fronts can present formidable barriers to dispersal4. Although passive, southward movement of species across this barrier has been considered unlikely, the recent discovery of buoyant kelp rafts on beaches in Antarctica demonstrates that such journeys are possible. Rafting is a key process by which diverse taxa – including terrestrial and coastal marine species – can cross oceans. Kelp rafts can carry passengers, and thus can act as vectors for long-distance dispersal of coastal organisms. The small numbers of kelp rafts previously found in Antarctica do not, however, shed much light on the frequency of such dispersal events. We here use a combination of high-resolution phylogenomic analyses (>220,000 SNPs) and oceanographic modelling to show that long-distance biological dispersal events in the Southern Ocean are not rare. We document tens of kelp (Durvillaea antarctica) rafting events of thousands of kilometres each, over several decades (1950 – 2019), with many kelp rafts apparently still reproductively viable. Modelling of dispersal trajectories from genomically-inferred source locations shows that some distant landmasses are particularly well connected, for example South Georgia and New Zealand, and the Kerguelen Islands and Tasmania. Our findings illustrate the power of genomic approaches to track, and modelling to show frequencies, of long-distance dispersal events.

opencc-zeroMar 2022View details →

Do natural enemies mediate conspecific negative distance- and density-dependence of trees? A meta-analysis of exclusion experiments

Conspecific negative distance- and density-dependence is believed to be one of the most important mechanisms controlling forest community assembly and species diversity globally. Plant pathogens, and insect and mammalian herbivores, are the most common natural enemy types that have been implicated in this phenomenon, but their general effects at different plant life stages are still unclear. Here, we conduct a meta-analysis of studies that involved robust manipulative experiments, using fungicides, insecticides, or exclosures, to assess the contributions of different natural enemy types to distance- and density-dependent effects at seed and seedling stages. We found that conspecific negative distance- and density-dependence was more common at the seedling stage. Only 30% of studies showed significant conspecific negative distance- and density-dependence. Among those studies, applying fungicides significantly reduced the effect of conspecific negative distance -dependent mortality. Excluding large mammals reduced the effect of conspecifics, but with only marginal significance (p < 0.1). Our study confirms that plant pathogens have a significant impact on distance -dependent mortality and suggests that the impacts of herbivores on seedlings have been understudied. At the seed stage, large and small mammals, respectively, appear to weaken and enhance negative conspecific distance-dependent mortality. Future research should identify specific agents of mortality, investigate the interactions among different enemy types, and assess how global change may affect natural enemies and thus influence the strength of conspecific distance- and density-dependence.

opencc-zeroMar 2022View details →

Distance decay 2.0 – a global synthesis of taxonomic and functional decay in ecological communities

Datasets used in the analysis of the manuscript by Graco-Roza, C., Aarnio, S., Abrego, N., Acosta, A. T., Alahuhta, J., Altman, J., ... & Soininen, J. (2022). Distance decay 2.0–a global synthesis of taxonomic and functional turnover in ecological communities. Global Ecology and Biogeography.   raw_data.zip - Includes the raw datasets used in the analysis.  processed_data.xlsx - Includes the results from the distance decay analysis, specifically:  - Dataset : dataset code (same as in raw_data) - Beta_type: The component of beta diversity (i.e., total similarity, replacement, richness differences) - Level : Taxonomic (TAX) or functional (FUN) - Based: Occurrence (occ) or Abundance (abund) - Organism: Code used to describe organisms (see Appendix S1 of the paper) - Realm: Aquatic, Terrestrial, or Freshwaters - Body_size  - Dispersal_mode: Seeds, Passive or Active - Latitude: Mean latitude of the dataset (average of all data points) - Latitude_range Distance in kilometres between the two vertically most distant points. - Longitude_range:  Distance in kilometres between the two horizontally most distant points. - spa_min: minimum distance between sites (in kilometres)  - spa_mean: average distance between sites (in kilometres)  - spa_max: maximum distance between sites (in kilometres) - ext: area in kilometres covered by all sites in the dataset - n_sites: Number of sites in each dataset - n_var: Number of environmental variables in each dataset - gamma_spe: Number of species observed in each dataset - gamma_trait: Volume of the hypervolume constructed using the traits in each dataset - n_traits: Number of traits in each dataset - Intercept_spa:  Intercept of GLM including community similarity and spatial distances - Slope_Spa: Slope of GLM including community similarity and spatial distances - R2_spa: R² of GLM including community similarity and spatial distances - Intercept_env:   Intercept of GLM including community similarity and environmental distances - Slope_env:  Slope of GLM including community similarity and environmental distances - R2_env:  R² of GLM including community similarity and environmental distances - Mantel_spa: Mantel statistics of community similarity and spatial distances - spa_signif: Significance of Mantel statistics considering community similarity and spatial distances - Mantel_env: Mantel statistics considering community similarity and environmental distances - env_signif: Significance of Mantel statistics considering community similarity and environmental distances Null_models.zip - Includes the results from the null models for each dataset.

opencc-by-4.0Apr 2022View details →

Dipolar EPR distance distribution libraries from a T4-lysozime and polypyrimidine-tract binding protein 1 (PTBP1) MMM simulations

These datasets are part of the Supplementary Information of Compactness regularization in the analysis of dipolar EPR spectroscopy data Luis Fábregas-Ibáñez, Gunnar Jeschke, Stefan Stoll Journal of Magnetic Resonance, 2022 The datasets contain libraries of distributions of distances between nitroxide labels in a T4-Lysozyme protein (2LZM) and the polypyrimidine-tract binding protein 1 (PTBP1) simulated with the MMM software package. The libraries are saved in .mat (MATLAB) format and contain a structure with the distance axis `r0` and distance distributions `P0` and other statistical quantities of the distance distributions.

opencc-by-4.0Feb 2022View details →

Isolation-by-distance and genetic parentage analysis provide similar larval dispersal estimates

An R studio project that includes original SNP data files used to quantify dispersal in Elacatinus lori via the isolation-by-distance (IBD) method. Associated R-code used to generate IBD regression slopes, calculate sigma, and construct dispersal kernels. Includes output from NeEstimator,  estimating effective population size.  Folders 1-3 contain the code/data needed to obtain the slope of the IBD relationship, effective population size, and the standard deviation (sigma) of the dispersal distribution, respectively. Folder 4 contains the R code needed to construct Laplacian dispersal kernels.

opencc-by-4.0May 2022View details →

Does the social distancing measures impact collaboration in software processes?

Context: Social distancing measures to reduce the impacts of the COVID-19 pandemic bring challenges for several organizations and their Information Systems (IS). Problem: Social distancing were suddenly implemented, with no adequate planning. Furthermore, there is not a clear understanding of the impacts of social distancing measures on the software development teams’ work. Solution: This study aims to identify the presence and impacts of social distancing on collaboration between people, as well as on activities and technologies used in software development, from the perspective of professionals who work in software development teams. IS Theory: The research was developed under the aegis of the Team Resilience Theory. Method: A field study was conducted based on structured interviews and qualitative analysis. Results: In general, it was observed no impact on the software processes activities, although their performance was affected. It was also observed that the impact on the collaboration dynamics in software development was perceived in different ways, by several team members. This study identified the most  common tools used by organizations, as well as the benefits and challenges of collaboration in software development after social distancing measures. Contribution: The impacts of social distancing on collaboration in software development were identified, reinforcing the Team Resilience Theory and similar study conducted in the beginning of the COVID-19 pandemic. This study contributes to the Grand Research Challenge "Systemic and Socially Aware Perspective for Information Systems".

opencc-zeroDec 2021View details →

Data and code to explore annual cycle schedule adjustments in a long distance migrant

Matching the timing of annual cycle events with the required resources can have crucial consequences for individual fitness. But as the annual cycle is comprised of sequential events, a delay at any point may be carried over to the subsequent stage (or more, in a domino effect) and negatively influence individual performance. To investigate how migratory animals navigate their annual schedule, and where and when it may be adjusted, we used full annual cycle data of 38 Icelandic whimbrels Numenius phaeopus islandicus tracked over 7 years – a subspecies that typically performs long-distance migrations to West Africa. We found that individuals apparently used the wintering sites to compensate for delays that mostly arose due to previous successful breeding, and a domino effect was observed from spring departure to laying date, with the potential to affect breeding output. However, the total time saved during all stationary periods is apparently enough to avoid interannual effects between breeding seasons. These findings highlight the importance of preserving good quality non-breeding sites in which individuals may adjust annual schedules and avoid potentially adverse effects of arriving late at the breeding grounds.

opencc-zeroJun 2022View details →

Community science reveals links between migration arrival timing advance, migration distance, and wing shape

Substantial global data show that many taxa are shifting their phenologies in response to climate change. For birds, migration arrival dates in breeding regions have been shifting earlier, and there is evidence that both evolutionary adaptation and behavioural flexibility influence these shifts. As more efficient flyers may be able to demonstrate more flexibility to respond to changing conditions during migratory flight, we hypothesize that differences among passerine species in flight efficiency, as reflected by morphology, may be associated with the magnitude of shifts in arrival date in response to climate warming. We applied a logistic model to eighteen years of eBird data to estimate mean arrival date for 44 common passerines migrating to northeast North America. We then used linear mixed-effects models to estimate changes in mean arrival date and compared these changes to morphological proxies for flight efficiency and migratory distance using phylogenetic generalized least squares models. On average, passerine species shifted their arrival dates 0.120 days earlier each year, with 27 of the 44 species shifting to significantly earlier arrival times, and two shifting to significantly later ones. Of the 15 species with non-significant shifts, 13 trended toward earlier arrivals. Longer migration distances and higher wing aspect ratios were associated with greater shifts towards earlier arrivals. Migration distance and aspect ratio were also significantly correlated to each other. This suggests that changes in arrival date are affected by factors pertaining to migratory flight over long distances namely, flight efficiency and migration distance. These traits may be able predict the magnitude of arrival date shift, and by extension identify species that are most at risk to climate change due to inflexible arrival timing.

opencc-zeroJun 2022View details →

Deep structure, long-distance migration and admixture in the colour polymorphic land snail Cepaea nemoralis

While snails of the genus Cepaea have historically been important in studying colour polymorphism an ongoing issue is that there is a lack of knowledge of the underlying genetics of the polymorphism, as well as an absence of genomic data to put findings in context. We therefore used phylogenomic methods to begin to investigate the post-glacial history of Cepaea nemoralis, with a long-term aim to understand the roles that selection and drift have in determining both European-wide and local patterns of colour polymorphism. By combining prior and new mitochondrial DNA data from over 1500 individuals with ddRAD genomic data from representative individuals across Europe, we show that patterns of differentiation are primarily due to multiple deeply diverged populations of snails. Minimally, there is a widespread Central European population and additional diverged groups in Northern Spain, the Pyrenees, as well as likely Italy and South Eastern Europe. The genomic analysis showed that the present-day snails in Ireland and possibly some other locations are likely descendants of admixture between snails from the Pyrenees and the Central European group, an observation that is consistent with prior inferences from mtDNA alone. The interpretation is that C. nemoralis may have arrived in Ireland via long-distance migration from the Pyrenean region, subsequently admixing with arrivals from elsewhere. This work therefore provides a baseline expectation for future studies on the genetics of the colour polymorphism, as well as providing a comparator for similar species.

opencc-by-4.0Jun 2022View details →

Prediction of inter-chain distance maps of protein complexes with 2D attention-based deep neural networks

Benchmark data sets of CDPred as described in Prediction of inter-chain distance maps of protein complexes with 2D attention-based deep neural networks Zhiye Guo1, Jian Liu1, Jeffrey Skolnick2, Jianlin Cheng1* 1 Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211 2 School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332-2000 *Corresponding author (chengji@missouri.edu) There is four test dataset in this package, each test dataset contains four different folders and one list file. The afpred_pdb includes all the corresponding monomer structures predicted by alphafold. The cdpred_output includes the prediction results of our tool CDPred for each dataset. The pre_gen_a3m includes the multiple sequence alignments file used by CDPred to generate prediction results. And the true_pdb includes the fasta file for the test dataset and its heavy atom distance map (h_dist) and carbon alpha distance map (real_dist) that extract from the native structure. HomoTest1: The homodimer test dataset contains 28 targets collect from CASP_CAPRI 10-13 HomoTest2: The homodimer test dataset contains 23 targets collect from CASP_CAPRI 13-14 HeteroTest1: The heterodimer test dataset contains 9 targets collect from CASP_CAPRI13-14 HeteroTest2: The heterodimer test dataset contains 55 targets collect from PDB bank 09-2021 to 11-2021

Distance Education and related terms

Distance Education a broader term than digital education and online learning.

Distance matrix for UNITE sequences

Flattened and compressed version of 2 pairwise distance matrices corresponding to <a href="https://doi.org/10.15156/BIO/1264708">this</a> UNITE release. Can be imported in a pipeline for building an overarching fungal phylogeny for UNITE (<a href="https://github.com/luukromeijn/MDDB-phylogeny">Github source code</a>).  Importing might take up to an hour, but this is still much quicker than the 36-hours pairwise distance calculation.  The 6-mer Google distance is way more accurate than the w-metric, so we highly recommend using the 6-mer Google distance. More documentation can be found <a href="https://github.com/luukromeijn/MDDB-phylogeny#readme">here</a>.

opencc-zeroJul 2022View details →

Environmentally associated variation in dispersal distance affects inbreeding risk in a stream salamander

Avoiding inbreeding is considered a key driver of dispersal evolution, and dispersal distances should be especially important in mediating inbreeding risk because the likelihood of mating with relatives decreases with dispersal distance. However, a lack of direct data on dispersal distances has limited empirical tests of this prediction, particularly in the context of the multiple selective forces that can influence dispersal. Using a headwater salamander system, we tested whether spatial variation in environmental conditions leads to differences in dispersal distances, resulting in spatial variation in the effect of dispersal on inbreeding risk. Using capture-recapture and population genomic data from 5 streams, we found that dispersal distances were greater in downstream reaches than upstream reaches. Inbreeding risk was lower for dispersers than non-dispersers in downstream reaches, but not in upstream reaches. Furthermore, stream reaches did not differ in spatial patterns of individual relatedness, indicating that variation in inbreeding risk was in fact due to differences in dispersal distances. These results demonstrate that environmentally associated variation in dispersal distances can cause the inbreeding consequences of dispersal to vary at fine spatial scales. They also show that selective pressures other than inbreeding avoidance maintain phenotypic variation in dispersal, underscoring the importance of addressing alternative hypotheses in dispersal research.

Data and scripts for: Satellite-tracking reveals sex-specific migration distance in green turtles (Chelonia mydas)

Data derivates and analysis scripts (in R) used for the paper "Satellite-tracking reveals sex-specific migration distance in green turtles (Chelonia mydas)", published in Biology Letters, on analyzing male and female green turtle movements in West Africa.

opencc-by-4.0Aug 2022View details →

Supplementary material for "Sounding Obstacles for Social Distance Sonification".

Supplementary material for the paper "Sounding Obstacles for social distance Sonification": Three videos (FmodI, FmodD, and NoFS) demonstrating three experimental conditions and 16 simulated videos (DD 01 - SS 06) presenting scenarios used in the experiment.

Data for Functional Group Pair Distance Based Descriptor for Isomerisation in Porous Molecular Framework Materials

This is a dataset of isomer structure files for pore topology: Tri2Di3, Tri4Di6, Tri4-2Di6,Tri6Di9, Tet2Di4, Tet3Di3, Tet4-4Di8, Tet5Di10, and Tet6Di12.  All.tar.bz2 contains all pore topologies, the total disk space after unzipping the bundle is 1.8 Gb. The total disk space for pore Tet6Di12 alone is 1.5Gb. The base structure of all pore topologies are constructed using a metal node of radius ~5 (represented by a Zirconium atom) and a benzene linker, while the functional group is represented by a Nitrogen atom.