cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.85078
title: Data from: The genomic consequences of adaptive divergence and reproductive isolation between species of manakins

description: The processes of adaptation and speciation are expected to shape genomic
 variation within and between diverging species. Here we analyze genomic
 heterogeneity of genetic differentiation and introgression in a hybrid
 zone between two bird species (Manacus candei and M. vitellinus) using 59
 100 SNPs, a whole genome assembly, and Bayesian models. Measures of
 genetic differentiation (inline image) and introgression (genomic cline
 center [α] and rate [β]) were highly heterogeneous among loci. We
 identified thousands of loci with elevated parameter estimates, some of
 which are likely to be associated with variation in fitness in Manacus
 populations. To analyze the genomic organization of differentiation and
 introgression, we mapped SNPs onto a draft assembly of the M. vitellinus
 genome. Estimates of inline image, α, and β were autocorrelated at very
 short physical distances (&lt; 100 bp), but much less so beyond this.
 In addition, average statistical associations (linkage disequilibrium)
 between SNPs were generally low and were not higher in admixed populations
 than in populations of the parental species. Although they did not occur
 with a constant probability across the genome, loci with elevated inline
 image, α, and β were not strongly co-localized in the genome. Contrary to
 verbal models that predict clustering of loci involved in adaptation and
 isolation in discrete genomic regions, these results are consistent with
 the hypothesis that genetic regions involved in adaptive divergence and
 reproductive isolation are scattered throughout the genome. We also found
 that many loci were characterized by both exceptional genetic
 differentiation and introgression, consistent with the hypothesis that
 loci involved in isolation are also often characterized by a history of
 divergent selection. However, the concordance between isolation and
 differentiation was only partial, indicating a complex architecture and
 history of loci involved in isolation.
description: manacus_snpcntThis file contains information on the number of reads representing each of two SNP states in each individual manakin across 59,100 loci. The file is organized by locus. For further details on how this file was generated, see the manuscript.manacus_assembly.bamThis file contains the entire assembly for the reference based assembly described in the manuscript.manacus_parchman.bamMvitellinus_draft_genomeThis file contains the first draft assembly of the M. vitellinus genome. This file will be embargoed until a paper containing a full description of this and 49 other avian genomes is published, most likely in early 2013.manacus_parchman.bam.bai
DOI: 10.5061/dryad.jr67t
title: Data from: Genomics of speciation and introgression in Princess cichlid fishes from Lake Tanganyika

description: How variation in the genome translates into biological diversity and new
 species originate has endured as the mystery of mysteries in evolutionary
 biology. African cichlid fishes are prime model systems to address
 speciation-related questions for their remarkable taxonomic and phenotypic
 diversity, and the possible role of gene flow in this process. Here, we
 capitalize on genome sequencing and phylogenomic analyses to address the
 relative impacts of incomplete lineage sorting, introgression and hybrid
 speciation in the Neolamprologus savoryi-complex (the ‘Princess cichlids’)
 from Lake Tanganyika. We present a time-calibrated species tree based on
 whole-genome sequences and provide strong evidence for incomplete lineage
 sorting in the early phases of diversification and multiple introgression
 events affecting different stages. Importantly, we find that the
 Neolamprologus chromosomes show centre-to-periphery biases in nucleotide
 diversity, sequence divergence, GC content, incomplete lineage sorting and
 rates of introgression, which are likely modulated by recombination
 density and linked selection. The detection of heterogeneous genomic
 landscapes has strong implications on the genomic mechanisms involved in
 speciation. Collinear chromosomal regions can be protected from gene flow
 and harbour incompatibility genes if they reside in lowly recombining
 regions, and coupling can evolve between nonphysically linked genomic
 regions (chromosome centres in particular). Simultaneously, higher
 recombination towards chromosome peripheries makes these more dynamic,
 evolvable regions where adaptation polymorphisms have a fertile ground.
 Hence, differences in genome architecture could explain the levels of
 taxonomic and phenotypic diversity seen in taxa with collinear genomes and
 might have contributed to the spectacular cichlid diversity observed
 today.
description: RAxML
 treesTrees in nexus
 formatraxml.treesMultiple_alignments_LGsMultiple sequence alignments, all linkage groups, FASTAMultiple species alignments 500kb "most reliable segments"Alignment blocks of 500,000 bp sampled from all “most reliable segments”, totaling 426 blocks, FASTAalignments.zipMultiple_sequence_alignments_most_reliable_segments224 multiple sequence alignments "most reliable segments", FASTAmost_reliable_alignments.zip
DOI: 10.5061/dryad.4bq4q
title: Data from: The regulation of behavioral plasticity by performance-based feedback and an experimental test with avian egg production

description: Optimizing plasticity in behavioral performances requires the abilities to
 regulate physiological effort and to estimate the effects of the
 environment. To describe how performance-based feedback could play a role
 in regulating recursive or continuous behavioral performances, I developed
 two models, one (environmental feedback) that assumes an initial ability
 to regulate effort but not to predict the effects of the environment and
 the other (effort feedback) that assumes an initial ability to predict the
 effects of the environment but not to regulate effort. I tested them by
 manipulating feedback on egg production, using an egg-substitution
 experiment in wild, free-ranging Lincoln’s sparrows (Melospiza lincolnii).
 I discovered that females adjusted the size of their clutches’ third laid
 eggs in response to the size of an experimentally substituted first laid
 egg, such that the size of the third laid egg increased with the size of
 the substitute. Results were largely consistent with the environmental
 feedback model, though small portions of the response surface were
 consistent with the effort feedback model or with neither. Regardless,
 such feedback-based regulation predicted by either model may help females
 maximize net benefits of egg production and may be a basis for mechanisms
 regulating a wide range of other behavioral performances, as well.
description: Egg Volumes for
 Experimental Lincoln's Sparrow NestsThese are the data used
 in statistical analyses presented in this manuscript.Data_for_Dryad.csv
DOI: 10.5061/dryad.8fg95
title: Data from: Strategic reduction of help before dispersal in a cooperative breeder

description: In cooperative breeders, sexually mature subordinates can either queue for
 chances to inherit the breeding position in their natal group, or disperse
 to reproduce independently. The choice of one or the other option may be
 flexible, as when individuals respond to attractive dispersal options, or
 they may reflect fixed life-history trajectories. Here, we show in a
 permanently marked, natural population of the cooperatively breeding
 cichlid fish Neolamprologus pulcher that subordinate helpers reduce
 investment in territory defence shortly before dispersing. Such reduction
 of effort is not shown by subordinates who stay and inherit the breeding
 position. This difference suggests that subordinates ready to leave reduce
 their investment in the natal territory strategically in favour of future
 life-history perspectives. It seems to be part of a conditional choice of
 the dispersal tactic, as this reduction in effort appears only shortly
 before dispersal, whereas philopatric and dispersing helpers do not differ
 in defence effort earlier in life. Hence, cooperative territory defence is
 state-dependent and plastic rather than a consistent part of a fixed
 life-history trajectory.
description: Long term data from
 2009ID= individual,
 Disperser: 0=heir 1=disperser, agg_gm= frequency of agression against
 group members, agg_ngm= frequency of agression against non-group members,
 sub_gm= frequency of submission, pred_def= frequency of defence against
 predators, dig_tot= frequency of territory maintenance; each line
 represents a case2009data_forpub_final.txt2010 data.Short term behavioural changes. ID= Individaul identifier, observer_cap= person who captured individual, before= timing of the observation (before or after takeover), disperser: 0=heir, 1=disperser, pred_def_foc= Frequency of territory defence, sub_grp_mem= Frequency of sumbission, tot_dig=frequency of territory maintenence, log_tot_dig= natural log of "tot_dig", agg_strangers= frequency of territory defence against non group members2010data_forpub_final.txt
DOI: 10.5061/dryad.93k26
title: Data from: Coexistence of three sympatric cormorants (Phalacrocorax spp.); partitioning of time as an ecological resource

description: Resource partitioning is well known along food and habitat for reducing
 competition among sympatric species, yet a study on temporal partitioning
 as a viable basis for reducing resource competition is not empirically
 investigated. Here, I attempt to identify the mechanism of temporal
 partitioning by intra- and interspecific diving analyses of three
 sympatric cormorant species at different freshwater wetlands around the
 Delhi region. Diving results indicated that cormorants opted for a shallow
 diving; consequently, they did not face any physiological stress.
 Moreover, diving durations were linked with seasons, foraging time and
 foraging habitats. Intraspecific comparison suggested that cormorants
 spent a longer time underwater in early hours of the day. Therefore, time
 spent for dive was higher in the forenoon than late afternoon, and the
 interspecific analysis also yielded a similar result. When Phalacrocorax
 niger and Phalacrocorax fuscicollis shared the same foraging habitat, they
 tended to differ in their foraging time (forenoon/afternoon). However,
 when P. niger and Phalacrocorax carbo shared the same foraging time, they
 tended to use different foraging habitats (lentic/lotic) leading to a
 mechanism of resource partitioning. Thus, sympatric cormorants effectively
 use time as a resource to exploit the food resources and successful
 coexistence.
description: Summary stat of DT DP
 resiinformation on the
 Diving and Surface time of three species of cormorants studied at Delhi
 region, India.
DOI: 10.5061/dryad.v2q66
title: Data from: A new species of Coryphophylax fitzinger in: Steindachner, 1867 (Sauria: Iguania: Agamidae) from the Andaman Islands, India

description: The systematic position of the agamid genus Coryphophylax (Squamata:
 Agamidae) is given as monotypic and endemic to the Andaman and Nicobar
 Islands in the Bay of Bengal, India. After having surveyed intensively in
 thirteen different Islands and examined several individuals in the
 Andamans group of islands, we describe a second species of Coryphophylax
 from the lowland rainforests of the South Andaman Island. Coryphophylax
 brevicaudus sp. nov. is differentiated from its congener, C. subcristatus
 (Blyth, “1860” 1861) by its smaller size, relatively shorter tail,
 presence of nuchal and dorsal crests in both sexes, midbody scale row
 counts and colour pattern. The new species lives in sympatry with C.
 subcristatus. The taxonomic history and systematic status of the genus
 Coryphophylax are discussed, and the need for continued surveys in the
 Islands is emphasized.
description: Morphometric data on two
 species of Coryphophylax from the Andaman IslandsThe data file
 Coryphophylax morphometry.csv contains morphometric data on two species of
 Coryphophylax, C. subcristatus and C. brevicaudus. These data were used in
 morphometric analyses which were part of the description of the new
 species (C. brevicaudus) (Harikrishnan et al, 2012).Coryphophylax.zip
DOI: 10.5061/dryad.51b25
title: Data from: Reproductive success is driven by local site fidelity despite stronger specialisation by individuals for large scale habitat preference

description: 1. There is widespread evidence that within populations, specialists and
 generalists can coexist and this is particularly prevalent in marine
 ecosystems, where foraging specialisations are evident. 2. While
 individuals may limit niche overlap by consistently foraging in specific
 areas, site fidelity may also emerge as an artefact of habitat choice but
 both drivers and fitness consequences of site fidelity are poorly
 understood. 3. Here we examine an individual metric of site and habitat
 fidelity, using tracking data collected over 11 years for black-browed
 albatrosses (Thalassarche melanophris). Fidelity was calculated as the
 similarity between pairs of foraging zones, quantifying measures for
 within and between years. Foraging areas were identified using area
 restricted search, defined as periods during which birds decrease speed
 and increase turning. 4. Our results demonstrate that birds were
 considerably more specialised in the habitat in which they forage than the
 exact location they use within years, and there was a similar pattern
 between years. However, despite this, it was site fidelity that explained
 reproductive success. Within a single year, females which were more
 faithful to a specific location had higher reproductive success than
 non-specialists and between years there was tendency for both sexes. 5.
 Our results suggest that black-browed albatrosses are highly faithful in
 their foraging habitat but it is rather site fidelity that is more clearly
 associated with reproductive success.
description: Dryad - Between year
 estimates SPatrick JAE 2016Data for all analyses of
 between year differences in fidelityDryad - Within year
 estimates SPatrick JAE 2016Data for all the within
 year estimates of fidelity used for all analyses
DOI: 10.5061/dryad.6q5vf
title: Data from: Quantifying the link between art and property prices in urban neighbourhoods

description: Is there an association between art and changes in the economic conditions
 of urban neighbourhoods? While the popular media and policymakers commonly
 believe this to be the case, quantitative evidence remains lacking. Here,
 we use metadata of geotagged photographs uploaded to the popular
 image-sharing platform Flickr to quantify the presence of art in London
 neighbourhoods. We estimate the presence of art in neighbourhoods by
 determining the proportion of Flickr photographs which have the word ‘art’
 attached. We compare this with the relative gain in residential property
 prices for each Inner London neighbourhood. We find that neighbourhoods
 which have a higher proportion of ‘art’ photographs also have greater
 relative gains in property prices. Our findings demonstrate how online
 data can be used to quantify aspects of the visual environment at scale
 and reveal new connections between the visual environment and crucial
 socio-economic measurements.
description: Data for Quantifying the
 Link Between Art and Property Prices in Urban
 NeighbourhoodsThe variable
 "Rank.Mean.Change" is calculated using data from residential
 property sales registered at the Land Registry from 2004 to 2013
 (https://www.gov.uk/government/collections/price-paid-data). We calculate
 the mean residential property price per London postcode district. We rank
 the postcodes according to mean residential property price, where a rank
 of 1 indicates the highest mean residential property price. We calculate
 the variable "Rank.Mean.Change", the relative changes in
 property price, by determining the difference between the 2013 rank and
 the 2004 rank for each London postcode district.
 "Proportion.Art.Photos" is calculated using data from the
 popular image sharing website Flickr. For photographs in each London
 postcode district, we deem a photo as "art" related if there is
 a mention of "art" in its associated textual metadata. We search
 all the textual elements of each image, including the title, description
 and tags, using the following regular expression " \
 ". We divide the number of "art" images by the total number
 of images for each postcode for the whole time period (2004 to 2013), in
 order to create a normalised indicator of "art" per area:
 "Proportion.Art.Photos".London_Prices_Flickr_Art_Agg.csv
DOI: 10.5061/dryad.j83258j
title: Data from: The perils of paradise: an endangered species conserved on an island loses antipredator behaviours within 13 generations

description: When imperilled by a threatening process, the choice is often made to
 conserve threatened species on offshore islands that typically lack the
 full suite of mainland predators. Whilst keeping the species extant, this
 releases the conserved population from predator-driven natural selection.
 Antipredator traits are no longer maintained by natural selection and may
 be lost. It is implicitly assumed that such trait loss will happen slowly,
 but there are few empirical tests. In Australia, northern quolls (Dasyurus
 hallucatus) were moved onto a predator-free offshore island in 2003 to
 protect the species from the arrival of invasive cane toads on the
 mainland. We compared the antipredator behaviours of wild-caught quolls
 from the predator-rich mainland to those from this predator-free island.
 We compared the responses of both wild-caught animals and their
 captive-born offspring, to olfactory cues of two of their major predators
 (feral cats and dingoes). Wild-caught, mainland quolls recognised and
 avoided predator scents, as did their captive-born offspring. Island
 quolls, isolated from these predators for only 13 generations, showed no
 recognition or aversion to these predators. This study suggests that
 predator aversion behaviours can be lost very rapidly, and that this may
 make a population unsuitable for reintroduction to a predator-rich
 mainland.
description: Jolly_BiologyLettersMS_Data
DOI: 10.5061/dryad.m61p4h3
title: Data from: Corydalis huangshanensis (Fumariaceae), a new species from Anhui, China

description: Corydalis huangshanensis L.Q.Huang & H.S.Peng, a new species from
 Anhui, China, is described and illustrated. It is similar to C. decumbens
 but can be easily distinguished by its more robust erect habit, rounded
 ultimate leaflets and horned tubers. Phylogenetic analysis of combined
 sequences confirm that the new species is distinct from morphologically
 similar species.
description: GenBank
DOI: 10.5061/dryad.h67kv
title: Data from: On the relative importance of CSR ecological strategies and integrative traits to explain species dominance at local scales

description: PLEASE NOTE, PART OF THESE DATA ARE ALSO REFERRED TO ANOTHER ARTICLE.
 PLEASE SEE http://dx.doi.org/10.1111/j.1654-1103.2009.01119.x FOR MORE
 INFORMATION. 1. Identifying ecological strategies based on functional
 traits has been one of the main focuses of studies on plant community
 assembly. Recently, an important and timely tool, “StrateFy”, has been
 proposed for detecting plant strategies across the globe according to the
 CSR scheme. The CSR scheme is undeniably efficient across scales, and
 distinct CSR strategies among species have been proposed to explain
 differing degrees of dominance among species. However, in a previous study
 we showed that dominance ranking of woody species in a resource-poor
 habitat (coastal sandy plain) was not explained by morphological traits
 commonly measured in functional approaches (such as those used to estimate
 CSR strategies), but by integrative traits (i.e. traits that are the
 result of different combinations of functional traits) more related to
 plant performance. 2. Here, we used CSR analysis and StrateFy on a dataset
 collected on a coastal sandy plain to test the hypothesis that the
 dominance ranking would be compatible with the CSR strategies; i.e., that
 dominant species would show a greater proportion of the stress-tolerance
 (S%) strategy than subordinate species. 3. Contrary to our hypothesis, all
 species exhibited an S/CS strategy, and the most-dominant species had
 neither similar values nor the highest S%. The inability of CSR analysis
 (as applied using StrateFy) to predict dominance ranking suggests that it
 can explain relative dominance when different strategies co-occur, but not
 in cases where dominant and subordinate plants share the same strategy. 4.
 We argue that the relative importance of CSR and integrative traits for
 describing dominance ranking may depend on how CSR strategies are filtered
 in each environment. In environments where only a narrow range of strategy
 classes are viable, integrative traits may be more important for
 explaining variation in degrees of dominance. Thus, the ability of a given
 species to achieve dominance may depend on integrative traits resulting
 from multiple trait arrays, not necessarily captured by the SLA, LDMC and
 LA measurements that are used to calculate the relative proportions of
 strategies in StrateFy.
description: Rosado and de Mattos
 datasetFunctional traits
 (morphological, physiological and phenological) measured in ten woody
 species occuring in a coastal sandy plain (restinga) in
 Brazil
DOI: 10.5061/dryad.2r76f
title: Data from: A population study of killer viruses reveals different evolutionary histories of two closely related Saccharomyces sensu stricto yeasts

description: Microbes have evolved ways of interference competition to gain advantage
 over their ecological competitors. The use of secreted killer toxins by
 yeast cells through acquiring double-stranded RNA viruses is one such
 prominent example. Although the killer behaviour has been well studied in
 laboratory yeast strains, our knowledge regarding how killer viruses are
 spread and maintained in nature and how yeast cells co-evolve with viruses
 remains limited. We investigated these issues using a panel of 81 yeast
 populations belonging to three Saccharomyces sensu stricto species
 isolated from diverse ecological niches and geographic locations. We found
 that killer strains are rare among all three species. In contrast, killer
 toxin resistance is widespread in Saccharomyces paradoxus populations, but
 not in Saccharomyces cerevisiae or Saccharomyces eubayanus populations.
 Genetic analyses revealed that toxin resistance in S. paradoxus is often
 caused by dominant alleles that have independently evolved in different
 populations. Molecular typing identified one M28 and two types of M1
 killer viruses in those killer strains. We further showed that killer
 viruses of the same type could lead to distinct killer phenotypes under
 different host backgrounds, suggesting co-evolution between the viruses
 and hosts in different populations. Taken together, our data suggest that
 killer viruses vary in their evolutionary histories even within closely
 related yeast species.
description: killer toxin mRNA,
 complete cds1. Saccharomyces
 cerevisiae M1 killer toxin mRNA, complete cds. 2.Saccharomyces paradoxus
 M1 killer toxin mRNA, complete cds 3. Saccharomyces paradoxus M28 killer
 toxin mRNA, complete cdskiller
 toxin.txt
DOI: 10.5281/zenodo.18385700
title: Dataset of LiB8 monolayer

description: Structural information of 2D LiB8 identified in the PES search.
DOI: 10.5281/zenodo.18385701
title: Dataset of LiB8 monolayer

description: Structural information of 2D LiB8 identified in the PES search.