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Figure 4. Selected skull features. A, B in The phylogeny of charadriiform birds (shorebirds and allies) - reassessing the conflict between morphology and molecules
Figure 4. Selected skull features. A, B, cranium (ventrolateral view) of A, Haematopus ostralegus (Haematopodidae) and B, Burhinus oedicnemus (Burhinidae). C, D, caudal section of orbita of C, H. ostralegus and D, Sterna paradisaea (Sternidae). E, cranium of Rostratula benghalensis (Rostratulidae) in ventral view. F–I, os lacrimale/os ectethmoidale complex of F, Sterna paradisaea (Sternidae); G, Larus fuscus (Laridae); H, Alca torda (Alcidae); and I, Pluvianus aegyptius (Pluvianidae). J–M, basicranial area (ventral view) of J, Sterna paradisaea (Sternidae); K, Chionis minor (Chionidae); L, Haematopus ostralegus (Haematopodidae); and M, Burhinus oedicnemus (Burhinidae). Abbreviations: bpt, processus basipterygoideus; ccv, concavity next to condylus medialis of quadratum; cdf, foramen caudal of foramen nervi maxillomandibularis; fnm, foramen nervi maxillomandibularis; for, foramen formed by duct of nasal gland; hlp, hook-like projection on os pterygoideum; mpA, maxillopalatine strut A; orb, processus orbitalis of os lacrimale; plp, processus lateralis parasphenoidalis; smt, processus suprameaticus; unc, os uncinatum; zyg, processus zygomaticus. Figures not to scale.
Figure 3 in The phylogeny of charadriiform birds (shorebirds and allies) - reassessing the conflict between morphology and molecules
Figure 3. Trees resulting from analyses of the character matrix in Appendix 2 with NONA 2.0 with different settings. A, Psophiidae as outgroup taxon, consensus of 12 most parsimonious trees [length = 118, consistency index (CI) = 0.44, retention index (RI) = 0.67]. B, Columbidae as outgroup taxon, consensus of 19 most parsimonious trees (length = 115, CI = 0.45, RI = 0.68). C, Columbidae as outgroup taxon and Turnicidae removed from analysis, consensus of six most parsimonious trees (length = 110, CI = 0.47, RI = 0.69). Bootstrap support values are listed above the nodes, characters and characters states next to the internodes (numbers refer to the character list in Appendix 1). Filled circles represent strict apomorphies, open circles homoplastic ones.
Untying the Gordian Knot of plastid phylogenomic conflict: a case from ferns
<p>Phylogenomic studies based on plastid genome have resolved the recalcitrant relationships among various plants, yet the phylogeny of Dennstaedtiaceae at the taxonomic level remains unresolved due to conflicting plastid genes, limited molecular data and incomplete taxon sampling of previous studies. The present study generated 31 new plastid genomes of Dennstaedtiaceae (9 genera, 30 species) and combined 41 publicly available sequences of plastid genome (including 24 families, 26 genera, 41 species) to solve and explore the evolution of Dennstaedtiaceae. In order to minimize the impact of systematic errors on the resolution of phylogenetic inference, we applied six strategies to generate 30 datasets based on CDS, Spacer, and All datasets, and two tree inference methods (maximum-likelihood, ML; and multispecies coalescent, MSC) to comprehensively analyze the plastome-scale data. Besides, the phylogenetic signal among all loci was quantified for the controversial node using the ML framework, and the phylogenetic hypotheses among all datasets were tested. In the species tree based on different data sets and methods, obvious conflicts were detected at the base of the polypod ferns. Meanwhile, the topology of the "CDS-codon-align-rm3" (CDS removed the third codon) matrix was selected as the primary reference or summary tree due to its analysis results are consistent, and similar to the topological structure of the amino-acid matrix. The final phylogenetic tree supported Dennstaedtiaceae as the sister group to eupolypods, and<em> Dennstaedtia</em> (sen. lat.) can divided into smaller genera, which was also supported by geographical distribution and plastid structure. This robust reconstructed phylogenetic backbone established a framework for future studies on Dennstaedtiaceae classification, evolution and diversification. The present study suggests considering plastid phylogenomic conflict when using plastid genomes. From our results, reducing saturated genes or sites can effectively mitigate the tree conflicts of distantly related taxa. Moreover, amino acid sequences may verify the accuracy of nucleotide-based phylogeny.</p>
Genetic basis of cytonuclear conflicts in citrus hybridization, domestication, and diversification
<p>184.cp.variations.map.vcf.zip--the chloroplast variation map of 184 samples<br> 184.mt.variations.map.vcf.zip----the mitochondrial variation map of 184 samples<br> aligment1.fa-- the group of grapefruit, sweet orange and sour orange for mitochondrial heteroplasmy analysis<br> aligment2.fa-- the group of lemon for mitochondrial heteroplasmy analysis<br> coverage depth of 184 short reads samples.zip -- the coverage depth of BAMs in mitochondrial variation map in 184 samples<br> Fortunella hindsii mitochondrial genome.gb -- the conservation proteins annotation of kumquat reference mitochondrial genome<br> GWAS-118.samples.input.phenotype.for GWAS.txt -- the inputfiles for GWAS <br> GWAS-LD.linked.input.gwas.vcf.gz -- the LD linked variations for GWAS<br> LD.purning.nuclear.variation.map.vcf.gz -- LD purning nuclear variations for demography analysis<br> normalization.RNA-seqs.txt -- the nomarlization data of expression of mitochondrial genome<br> nuclear.variation.map.vcf.gz -- the nuclaer variation map<br> ORFs annotation based on Augustus.gtf -- the annotation gene structure using Augustus <br> pan-genome and aligned mitochondrial genomes.zip -- the pan-genome(.fa and .gfa) and aligned mitochondrial genomes<br> scaffold-assemblies.zip -- the scaffolds of mitochondrial genomes</p>
Data from: Parent-offspring conflict and its outcome under uni-and biparental care
<p>Conflicts over parental investment are predicted to be common among family members, especially between parents and their offspring. Parent–offspring conflict has been studied in many brood-caring organisms, but whether its outcome is closer to the parental or offspring optimum is usually unknown, as is whether the presence of a second parent, a caring male partner, can affect the outcome. Here, we manipulated the initial brood size of single and paired female burying beetles to examine how many offspring are necessary to maintain parental care in the current brood. We found that mothers continued to invest in small broods even if their reproductive output would have been higher if they had discontinued their care and produced a second brood instead. Consequently, our data suggests that the offspring have the upper hand in the conflict. However, our results further show that paired females laid a second egg clutch more often and produced more offspring than single females, suggesting that the presence of a male partner shifts the conflict outcome towards the parental optimum. This latter result not only is a novel aspect of parent–offspring theory, but also represents an additional factor that might explain the evolution of biparental care.</p>
Tests of search image and learning in the wild: insights from sexual conflict in damselflies
<p><a name="_Hlk52373699">Search image formation, a proximal mechanism to maintain genetic polymorphisms by negative frequency-dependent selection, has rarely been tested under natural conditions. Females of many non-territorial damselflies resemble either conspecific males or background vegetation. Mate-searching males are assumed to form search images of the majority female type, sexually harassing it at rates higher than expected from its frequency, thus selectively favoring the less common morph. We tested this and how morph coloration and behavior influenced male perception and intersexual encounters by following marked <i>Ischnura elegans</i> and noting their reactions<i> </i>to conspecifics. Contrary to search image formation and associative learning hypotheses, although males </a>encountered the minority, male-like morph more often, sexual harassment and clutch size were similar for both morphs. Prior mating attempts or copulas with morphs did not affect a male's subsequent reaction to them; males rarely attempted matings with immature females or males. Females mated early in the day, reducing the opportunity for males to learn their identity beforehand. Once encountered, the male-like morph was more readily noticed by males than the alternative morph, which, once noticed was more likely to receive mating attempts. Flexible behavior gave morphs considerable control over their apparency to males, influencing intersexual encounters. Results suggested a more subtle proximal mechanism than male learning maintains these color polymorphisms and call for inferences of learning to be validated by behavior of wild receivers and their signalers.</p>
Data set for FSE 2022 Submission Program Merge Conflict Resolution via Neural Transformers
<p>Data set for FSE 2022 Submission Program Merge Conflict Resolution via Neural Transformers</p>
Figures for "Towards Improved Satellite Monitoring of Armed Conflicts"
<p>Figure 1. From space, VHR imagery from Planet and Maxar reveals the landscape effects of Russia’s invasion of Ukraine. 1. Cars waiting at the Ukrainian-Hungarian border (Maxar technologies); 2. Active fires in Chernihiv (PlanetScope-2022/03/21); 3a. The North Crimean Channel without water pre-invasion (PlanetScope-2022/02/21); 3b. Filled with water post-invasion (PlanetScope-2022/03/24); 4. Burning apartment buildings in Mariupol (Maxar technologies). Maxar technologies images were obtained from https://www.maxar.com/ on April 5th, 2022. PlanetScope data were obtained under the University of Copenhagen license agreement PL-0030875_2021/2022. Because Maxar and Planetscope original images are commercial they can not be publicly shared but can be requested from the Maxar and Planet with the additional assistance of authors.</p> <p>Figure 2. A village and surrounding farmland in Ukraine’s Lviv Oblast are more difficult to discern in imagery from medium-resolution civilian Landsat-8 (USGS-2021/05/04) and Sentinel-2 (ESA-2021/05/11) satellites than in imagery from their commercial VHR counterparts (Dove/PlanetScope -2021/05/09 and SkySat-2021/05/09, both of which belong to Planet). Landsat-8 (USGS) and Sentinel-2 (ESA) are available via glovis.usgs.gov. PlanetScope data were obtained under the University of Copenhagen license agreement PL-0030875_2021/2022. SkySat imagery was obtained under special request from Planet. PlanetScope and SkySat original images are commercial they can not be publicly shared but can be requested from Planet with the additional assistance of authors.</p> <p> </p> <p> </p>
Sexual conflict does not maintain female colour polymorphism in a territorial damselfly
<div> <div> <div> <div> <p>Female-limited dimorphism is commonly hypothesized to be an adaptation resulting from male harassment or sexual conflict over female mating rate. We examined whether males discriminate be- tween female colour morphs of the beautiful Hawaiian damselfly, Megalagrion calliphya, in order to evaluate whether male harassment could explain the existence and/or maintenance of this dimorphism. Previous studies of this species suggest that spatially varying ecological selection maintains the dimorphism, but these hypotheses are not mutually exclusive. Here, we used a common method of measuring male behaviour towards secured females at mating sites under naturally occurring conditions, using five populations that range in male-like female morph frequency from 0 to 0.86. We found very low rates of interaction in a total of 64 one-hour trials, and male behaviour towards females did not differ significantly between colour morphs. By comparing the populations that vary in female morph fre- quency, we found no evidence of frequency-dependent sexual selection on colour, suggesting that this polymorphism is maintained by selective forces other than sexual conflict.</p> </div> </div> </div> </div>
Custom codes related to the publication "Mitigating transcription-replication conflicts: In early Drosophila embryos, rapid onset of transcription after mitosis depends on DNA replication"
<p>This dataset includes the custom codes related to the publication: Mitigating transcription-replication conflicts: In early Drosophila embryos, rapid onset of transcription after mitosis depends on DNA replication, Cell Reports 2022.</p> <p>The raw imaging data can be found at https://doi.org/10.5281/zenodo.7102432</p>
When is it safe to go home? Post-predation assessment of risk and safety when personal information conflicts with social cues
<p>Navigating the risk of predation is a major driver of behavioral decision-making in small fishes. Fish use personal information from olfactory and visual indicators of risk, and also rely upon social cues to inform behavioral trade-offs between risk avoidance and fitness-positive activities such as foraging. Here, fathead minnows (<em>Pimephales promelas</em>), were captured, clipped, and released at 48 field sites chemically labeled with either fathead minnow alarm cue (high risk) or water (low risk). We removed the chemical label after 2 h, then monitored area use by clipped and non-clipped fish. In addition, a shoal was placed in traps in half of the risky and half of the safe locations as a visual social cue of safety. We caught 2919 fish in the first sample, of which 594 were fathead minnows. These were clipped and released. The second sample caught 1500 fish, of which 164 were fathead minnows including 11 bearing marks from the first sample. Fathead minnows and northern redbelly dace in the general community, which lacked personal information about risk status associated with trap sites, avoided areas previously labeled with alarm cues for at least 2 h after the source of alarm cue was removed, unless an experimental shoal was present at the risky site, in which case they joined the shoal in the trap. Clipped fathead minnows with direct personal knowledge of risk showed a significant shift away from areas labeled with conspecific alarm cues and a significant attraction toward sites seeded with a shoal. Moreover, unlike fish in the general community, clipped fathead minnows were not influenced by experimental shoals at sites previously labeled as risky. These data indicate that the influence of social cues on safety depends on whether individual minnows have access to recent personal information about risk assessment.</p>
Partner retention as a mechanism to reduce sexual conflict over care in a seabird
<p><span>The costs of caring for offspring are predicted to lead to an evolutionary conflict between parents, where each parent benefits if the other provides the majority of care. However, in many biparental species, breeding partners remain together for multiple breeding attempts and their respective future reproductive fitness prospects are therefore intertwined. Since an increase in current care by a long-term partner reduces that partner's future investment and longevity, individuals do not automatically only benefit when their partner provides care. We test whether selection will favour individuals that reduce the burden of care falling on long-term partners, thus decreasing evolutionary conflict over parental care. Using a semi-natural, captive colony of black-headed gulls (<em>Chroicocephalus ridibundus</em>), we show that benefits of long-term partner retention can indeed reduce sexual conflict. Long-term partners have less intense courtships and are more behaviourally compatible, and individuals in long-term pairs spare each other's resources by increasing their own parental investment compared to those with new partners. Lastly, we demonstrate that high partner compatibility in newly-formed pairs can select for commitment to the pair bond. Our results highlight that compatibility benefits of long-term partnerships can increase selection for mate retention and increase parental investment.</span></p>
Data from: Evaluating diversionary feeding as a method to resolve conservation conflicts in a recovering ecosystem.
<p>Contains R-project code, and dataset for Multinomial analysis presented in the paper: Evaluating diversionary feeding as a method to resolve conservation conflicts in a recovering ecosystem. Accepted for Publication in the Journal of Applied Ecology 30.04.2024. </p> <p> </p> <p> </p>
Minimizing habitat conflicts in meeting net-zero energy targets in the western United States
<p>This dataset contains spatial and non-spatial input and output data generated for and from the <a href="https://www.nature.org/en-us/what-we-do/our-priorities/tackle-climate-change/climate-change-stories/power-of-place/">Power of Place West</a> study, published in the Proceedings of the National Academy of Science (PNAS). See readme pdf for more details. </p>
Survey Conflict Psychological Safety and Project Success
Open the record for dataset details and reuse information.
Data from: Human wildlife conflict in bardia banke complex data
<p>The data is about the human-wildlife conflict in Bardia - Banke Complex, Nepal. This research was undertaken to investigate the patterns and conflict-causing factors of human killing and injury by large mammals especially by Asian elephant (<em>Elephas maximus</em>), Common leopard (<em>Panthera pardus</em>), and Bengal tiger (<em>Panthera tigris)</em> in the Bardia-Banke Complex of western Nepal. We collected human death records and injuries caused by wildlife between 2019 and (March) 2023, from the regular monitoring record database.</p>
Post-conflict Behaviors of Wild Gelada Monkeys (Theropithecus gelada) at Guassa, Ethiopia
<p>Post-conflict behaviors are a crucial component of primate sociality, yet are difficult to study in the wild. We evaluated the presence and timing of reconciliation, victim-solicited and unsolicited third-party affiliation, and secondary and redirected aggression following observed agonistic interactions among 38 wild gelada monkeys (<em>Theropithecus gelada</em>) in eight one-male, multi-female units at Guassa, Ethiopia, from April to August 2018. We also report background rates of aggression and patterns of agonistic interactions and post-conflict behaviours among wild geladas relative to possible mediating factors for each conflict, including social rank disparity, kinship type, sex, age class, conflict intensity, and conflict decidedness. Across 55 post-conflict and 55 subsequent matched-control focal follows, we found no evidence for post-conflict reconciliation, third-party affiliation, secondary aggression, or redirected aggression. These findings contrast with previous studies of captive geladas, which find that individuals often reconcile after fights and frequently exhibit unsolicited third-party affiliation when reconciliation does not occur. Our results from wild geladas point to possible populational differences in behavioral tendencies arising from variable space, time, social grouping, and/or food availability constraints. Our findings also reveal potential limitations in applying identical data collection protocols across environmental contexts and underscore the importance of creating generalizable cross-context metrics to better understand, and contextualize, the diversity of post-conflict behavioral mechanisms underpinning primate sociality in geladas and other group-living primates</p>
Supplementary material 1 from: Chakona A, Kadye WT, Bere T, Mazungula DN, Vreven E (2018) Evidence of hidden diversity and taxonomic conflicts in five stream fishes from the Eastern Zimbabwe Highlands freshwater ecoregion. ZooKeys 768: 69-95. https://doi.org/10.3897/zookeys.768.21944
Evidence of hidden diversity and taxonomic conflicts in five stream fishes from the Eastern Zimbabwe Highlands freshwater ecoregion : Explanation note: Locality information, sample size, BOLD and GenBank accession numbers for mitochondrial COI sequences, and the candidate species identified in Amphilius natalensis, A. uranoscopus, Chiloglanis neumanni, Hippopotamyrus ansorgii and Zaireichthys monomotapa from the Eastern Zimbabwe Highlands freshwater ecoregion.
FIGURE 6 in Resolving the conflictive phylogenetic relationships of Oceanites (Oceanitidae: Procellariiformes) with the description of a new species
FIGURE 6. Live individual of Oceanites barrosi sp. nov. captured by Rodrigo Barros in Río Blanco, Los Andes province, Valparaíso Region, Chile (latitude 32°54'S, longitude 70°18'W, elevation 1,400 m), on 9 January 2022.
FIGURE 5 in Resolving the conflictive phylogenetic relationships of Oceanites (Oceanitidae: Procellariiformes) with the description of a new species
FIGURE 5. Type specimen of O. barrosi, specimen no. LACM 25182, Natural History Museum of Los Angeles County USA, preserved as a study skin: adult female, collected by Rafael Barros Valenzuela in Río Blanco, Los Andes province, Valparaíso Region, Chile (latitude 32°54'32.06"S, longitude 70°18'15.30"W, elevation 1,402 m), on 7 April 1924.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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