Find research datasets worth reusing

Figure 6 in Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus

Figure 6. rDNA tree of taxa with modified long loops. Best maximum-likelihood tree (GTR + invariant + gamma model) from RAxML with thorough bootstrap support (%), based on 2694 nucleotides of aligned sequences from SSU and LSU nuclear-encoded genes of 15 in-group and three rhynchonellide out-group taxa. Potentially misaligned and gapped sites (5%) were pruned by GBlocks. Several backbone nodes received very low bootstrap support and the tree has been redrawn by hand to remove them, leaving no effective resolution of relationships between the in-group superfamilies represented in this alignment. The sequence for Argyrotheca (JH97) was used with the permission of Dr J. Hoffman.

Figure 2. Case 2 in Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus

Figure 2. Case 2: Cancellothyridoid gene tree. Best maximum-likelihood tree (GTR + invariant + gamma model) from RAxML with thorough bootstrap support (%), based on 2810 nucleotides of aligned sequences from up to four genes (12S and 16S mitochondrial, and SSU and LSU nuclear) from 30 in-group and three rhynchonellide out-group taxa. Gblocks was used to prune potentially misaligned and gap sites (18% were discarded). In-group backbone nodes with no bootstrap support value attached are considered to be unsupported (may be collapsed; boostrap <50%). Four taxa, marked (LSU), are represented by LSU sequence data alone, and in each case this sequence clusters with the cognate multiple sequences, indicating that the LSU fragment alone can accurately place the taxon.

Figure 5 in Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus

Figure 5. Laqueoidea rDNA tree. Best maximum-likelihood tree (GTR + invariant + gamma model) from RAxML with thorough bootstrap support (%), based on 2882 nucleotides of aligned sequences from SSU and LSU nuclear-encoded genes of seven laqueoid in-group and six terebratulide out-group taxa. The small number of potentially misaligned and gap sites were not removed. The failure of the two Kingenoids to form a clade may be caused by limited sequence data rather than by misclassification.

Figure 9 in Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus

Figure 9. Ebiscothyris bellonensis gen. et sp. nov., cruise EBISCO, Coral Sea, South-West Pacific, SEM micrographs; A, B, ventral valve, station CP 2556, 741–791 m depth, IB-2013-7; A, transverse section of the entire shell showing the primary layer (pri) underlain by the fibrous secondary layer (sec), passing into the prismatic tertiary layer (ter); B, section of the shell showing primary (pri), secondary (sec), and tertiary (ter) layers; a puncta with a radiating brush is also visible; C, D, dorsal valve, CP 2557, 800–923 m depth, IB-2013-5; C, latero-oblique view of internal surface, showing the incurved valve margin built of densely arranged sheets of secondary fibres (left) and prisms of tertiary layer (right); D, internal surface showing discrete units of prisms and very small punctae (arrows). E, F, Kanakythyris pachyrhynchos Laurin, 1997, cruise NORFOLK 2, Norfolk Ridge, station DW 2136, 402–410 m depth; E, transverse section of the entire shell; F, internal surface with discrete units of prisms. Scale bars: A, C, D, E, F, 50 μm, B, 20 μm.

Figure 4. Laqueoidea cox1 in Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus

Figure 4. Laqueoidea cox1 tree. Best maximum-likelihood tree (GTR + invariant + gamma model) from RAxML with thorough bootstrap support (%), based on 1218 nucleotides of aligned sequences of the cox1 mitochondrial gene from 14 laqueoid in-group and six terebratulide out-group taxa. The sequences were aligned with no gaps. Nodes with no bootstrap support value attached are considered to be unsupported (bootstrap <50%) and may be collapsed.

Figure 3. Case 3 in Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus

Figure 3. Case 3: Dyscolioid and Terebratuloid gene tree. Best maximum-likelihood tree (GTR + invariant + gamma model) from RAxML with thorough bootstrap support (%), based on 3427 nucleotides of aligned sequences from up to four genes (12S and 16S mitochondrial, and SSU and LSU nuclear) from 19 in-group and three rhynchonellide out-group taxa. Pruned of potentially misaligned and gap sites by hand (7% discarded). In-group backbone nodes with no bootstrap support value attached are considered to be unsupported (may be collapsed; boostrap <50%). Nine taxa, marked (LSU), are represented by LSU sequence data alone, and in each case this sequence clusters with the cognate multiple sequences, indicating that the LSU fragment alone can accurately place the taxon. These results validate the placement of Ebiscothyris, Dallithyris, and Dyscolia, each of which is represented by LSU alone.

opencc-by-4.0Nov 2022View details →

Dataset: Stimulus salience conflicts and colludes with endogenous goals during urgent choices

This dataset (packaged as the zip file 3CS_datashare.zip) accompanies the article titled "Stimulus salience conflicts and colludes with endogenous goals during urgent choices" by EE Oor, TR Stanford, and E Salinas, iScience  26:106253 (2023). The experimental results in the paper are based on behavioral data collected from three monkey subjects during performance of visuomotor tasks, as described in the article. This dataset contains the trial-by-trial results collected for each subject and upon which all subsequent analyses were based. In addition to the trial-wise data arrays (stored in three *.csv files), the dataset includes Matlab functions and scripts (*.m files) used to analyze the data and generate figures in the article. Instructions and specifics are detailed in the README file.

opencc-zeroDec 2022View details →

The dynamics of social cohesion in response to simulated intergroup conflict in banded mongooses

Intergroup conflict is widespread in nature and is proposed to have strong impacts on the evolution of social behaviour. The conflict-cohesion hypothesis predicts that exposure to intergroup conflict should lead to increased social cohesion to improve group success or resilience in future conflicts. There is evidence to support this prediction from studies of affiliative responses to outgroup threats in some animal societies. However, most of these studies have focused on behavioural changes over short time periods (minutes and hours after exposure to an outgroup), and hence very little is known about the dynamics and durability of responses to intergroup conflict over the longer term. We investigated this question by simulating intergroup encounters in wild banded mongooses (Mungos mungo) and measuring social behaviour before, during, and after these encounters over a five day period. We also ran control trials with non-threatening stimuli. Banded mongooses reacted immediately to intrusion stimuli by vocalising, grouping together and advancing on the stimulus. In the first five minutes after simulated intrusions, we saw an elevation in grooming levels, but in the hour after exposure grooming rates declined sharply, contrary to our expectation. In the two subsequent days grooming rates remained at this depressed rate. In control trials, the initial increase in grooming was not seen, but grooming declined compared in the longer term time periods. Grooming changed across time, but not in the same pattern as during intrusions, suggesting that intrusions had an impact above and beyond that of the experimental set-up. The dynamics of grooming responses were short-lived and more complex than we initially expected. We suggest this unexpected result may be linked to the frequency of aggressive intergroup encounters in this system. Our results indicate short-lived impacts of outgroup threat on measures of social cohesion in this species, but cannot confirm longer term changes.

opencc-by-4.0Dec 2022View details →

Shaking Legitimacy: The Impact of Earthquakes on Conflict in Historical China

Bai, Ying. 2022. Replication files for "Shaking Legitimacy: The Impact of Earthquakes on Conflict in Historical China". Economic Journal. Conditionally accepted.

opencc-by-4.0Apr 2023View details →

Producer Conflict Management Approaches in Online Peer Production Communities – Case Study of OpenStreetMap

These files are supplementary materials to a paper: Youjin Choe, Martin Tomko, and Mohsen Kalantari. 2023. Producer Conflict Management Approaches in Online Peer Production Communities – Case Study of OpenStreetMap. In Proceedings of the 2023 CHI Conference on Human Factors in Computing Systems (CHI ’23), April 23–28, 2023, Hamburg, Germany. ACM, New York, NY, USA, 19 pages. https://doi.org/10.1145/3544548.3581036: (1) finaldata_FILENAMES: Files that starts with "finaldata_" contain final data we used for the analysis in text file (binary data) with a codebook. It also contains the count data (with a codebook) that we initially used but failed to pass the linearity assumption. (2) LOGITM~1.R: It is R code that we used for logistic regression analysis. (3) osmcha-parser.py: This our Python code and the resulting files that extracted raw data from OSM Changeset Analyzer (OSM) website. (4) 20210920_AnnotatorsGuide.pdf: This file is the annotators guide that we shared with our two external annotators for introduction and training of our data annotation.

opencc-zeroFeb 2023View details →

The geometry of evolutionary conflict

Conflicts of interest abound not only in human affairs but also in the biological realm. Evolutionary conflict occurs over multiple scales of biological organization, from genetic outlawry within genomes, to sibling rivalry within nuclear families, to collective-action disputes within societies. However, achieving a general understanding of the dynamics and consequences of evolutionary conflict remains an outstanding challenge. Here, we show that a development of R. A. Fisher's classic "geometric model" of adaptation yields novel and surprising insights into the dynamics of evolutionary conflict and resulting maladaptation, including the discoveries that: (1) conflict can drive evolving traits arbitrarily far away from all parties' optima and, indeed, if all mutations are equally likely then contested traits are more often than not driven outwith the zone of actual conflict (hyper-maladaptation); (2) evolutionary conflicts drive persistent maladaptation of orthogonal, non-contested traits (para-maladaptation); and (3) modular design greatly ameliorates conflict-driven maladaptation, thereby facilitating major transitions in individuality.

opennotspecifiedFeb 2023View details →

FIGURE 1 in Improved modelling of compositional heterogeneity reconciles phylogenomic conflicts among lacewings

FIGURE 1. Phylogram of Neuropterida relationships based on the CAT-GTR+G4 analysis of anchored hybrid enrichment (AHE) amino acid data. All branches have a support value of ≥ 0.93 Bayesian posterior probability (BPP) except those indicated by red dots (BPP <0.9). Abbreviations: Conio., Coniopterygoidea; Dilar., Dilaroidea; Ithon., Ithonoidea; Megal., Megaloptera; Psych., Psychopsoidea; Raphi., Raphidioptera. Superfamilial classification is adapted from Engel et al. (2018).

opennotspecifiedFeb 2023View details →

FIGURE 2 in Improved modelling of compositional heterogeneity reconciles phylogenomic conflicts among lacewings

FIGURE 2. Congruent interfamilial relationships of Neuropterida inferred from transcriptomic (left) and AHE (right) amino acid data respectively under the site-heterogeneous CAT-GTR+G4 model. All branches have a strong support (BPP> 0.93), except for the monophyly of Myrmeleontidae (only weakly supported in AHE nucleotide data under the CAT-GTR+G4 model). Note that the transcriptomic dataset has fewer and sparser familial sampling than the AHE data.

opencc-by-4.0Mar 2023View details →

Replication package of: 'When information conflicts with obligations: the role of motivated cognition' ECONOMIC JOURNAL

Final_Ramadan_Survey.dta is the dataset from the survey experiment described in the paper. Final_Ramadan_Admin.dta is the dataset that includes exam takers’ score in the College Entrance Exam.

opennotspecifiedFeb 2017View details →

Fig. 4 in Adaptive use of nonlethal strategies for minimizing wolf-sheep conflict in Idaho

Fig. 4.—Killing of sheep (Ovis aries) by wolves (Canis lupus) in Protected and Nonprotected Areas in public grazing allotments in Blaine County, Idaho, as shown by cumulative weighted number of sheep killed in each year of the study. Lines indicate regression of killings on year.

opennotspecifiedFeb 2017View details →

Fig. 2 in Adaptive use of nonlethal strategies for minimizing wolf-sheep conflict in Idaho

Fig. 2.—State of Idaho (inset), showing Blaine County (light gray) and National Forest Service land (dark gray). Northern portion of Blaine County is enlarged to show grazing allotments where Wood River Wolf Project was carried out during Phase 1 (darker gray) and Phase 2 (lighter gray and darker gray).

opencc-by-4.0Apr 2023View details →

Quality of life among Romanian Emergency Medicine Personnel during the COVID-19 Pandemic and the Russian–Ukrainian Armed Conflict

The aim of the present study was to investigate the relationship between threat perception and professional quality of life in a sample of Emergency Medicine Personnel, during the COVID-19 pandemic and during the outbreak of the Russian-Ukrainian Armed Conflict. Two types of threats were investigated (war threat and pandemic threat) and three indicators of professional quality of life (i.e., secondary traumatic stress, burnout, and compassion satisfaction). The mediating role of worries in the relationship between threat perception and quality of life was also assessed.

opencc-zeroJul 2023View details →

Data for: Lack of intergenerational reproductive conflict, rather than lack of inclusive fitness benefits, likely explains absence of post-reproductive lifespan in long-finned pilot whales

Life history theory suggests that individuals should reproduce until death, yet females of a small number of mammals live for a significant period after ceasing reproduction, a phenomenon known as post-reproductive lifespan. It is thought that the evolution of this trait is facilitated by increasing local relatedness throughout a female's lifetime. This allows older females to gain inclusive fitness through helping their offspring (known as a mother effect) and/or grandoffspring (known as a grandmother effect), rather than gaining direct fitness through reproducing. However, older females may only benefit from stopping reproducing when their direct offspring compete with those of their daughters. Here, we investigate whether a lack of post-reproductive lifespan in long-finned pilot whales (Globicephala melas) results from minimal benefits incurred from the presence of older females, or from a lack of costs resulting from mother-daughter co-reproduction. Using microsatellite data, we conducted parentage analysis on individuals from 25 pods and find that younger females were more likely to have offspring if their mother was present in their pod, indicating that mothers may assist inexperienced daughters to reproduce. However, we found no evidence of reproductive conflict between co-reproducing mothers and daughters, indicating that females may be able to reproduce into old age whilst simultaneously aiding their daughters in reproduction. This highlights the importance of reproductive conflict in the evolution of a post-reproductive lifespan and demonstrates that mother and grandmother effects alone do not result in the evolution of a post-reproductive lifespan.

opencc-zeroAug 2023View details →

SAMC Model Inputs from: Predicting dispersal and conflict risk for wolf recolonization in Colorado

The colonization of suitable yet unoccupied habitat due to natural dispersal or human introduction can benefit recovery of threatened species. Predicting habitat suitability and conflict potential of colonization areas can facilitate conservation planning. Planning for reintroduction of gray wolves (Canis lupus) to the U.S. state of Colorado is underway. Assessing which occupancy sites minimize the likelihood of human-wolf conflict during dispersal events and seasonal movements is critical to the success of this initiative. We used a spatial absorbing Markov chain (SAMC) framework, which extends random walk theory and probabilistically accounts for both movement behavior and mortality risk, to compare the viability of potential occupancy sites (public lands >500 km2 to minimally meet wolf pack range area). The SAMC framework produced spatially explicit predictions of wolf dispersal, philopatry, and conflict risk ahead of recolonization prior to reintroduction efforts. Our SAMC model included: 1) movement resistance based on terrain, roads, and housing density; 2) mortality risk and potential conflict (absorption) based on livestock presence, social tolerance, land ownership, and state boundaries; and 3) site fidelity based on habitat quality. Using this model, we compared 21 public land units by deriving predictions of: A) relative survival time outside each site, B) intensity of use and retention time within each site, and C) the probability of use on adjacent public lands. We also predicted and mapped potential conflict hotspots associated with each site. Among the units assessed, a complex of USFS Wilderness areas near Aspen, chiefly the Hunter-Fryingpan and Collegiate Peaks Wilderness areas, had the best overall rankings when comparing predictions of each metric. The area balances high-quality, well-connected habitat with relatively low livestock density and high social tolerance. Synthesis and applications: Our findings highlight the utility of the SAMC framework for assessing colonization areas and the capacity to identify locations for effective proactive management, especially of conflict-prone species. The flexibility of the SAMC framework enables predicting likely areas of philopatry and human-wildlife conflict using spatially-explicit metrics which can improve the success of conservation translocations and management of species with changing geographic extents.