cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3jt6kh3
title: Data from: Contrasting patterns of local richness of seedlings, saplings and trees may have implications for regeneration in rainforest remnants

description: Remnants of lowland rainforest remain following deforestation, but the
 longer-term effects of fragmentation remain poorly understood, partly due
 to the long generation times of trees. We study rainforest trees in three
 size classes: seedlings (&lt;1 cm dbh), saplings (1-5 cm dbh) and
 trees (&gt;5 cm), that broadly reflect pre- and post-fragmentation
 communities, and we examine the impacts of fragmentation on forest
 regeneration in Sabah, Malaysian Borneo. We found that seedling richness
 (measured as the number of genera per plot) in fragments was about 30
 percent lower than in plots in undisturbed forest, and about 20 percent
 lower than in an extensive tract of selectively logged forest, providing
 evidence of recruitment declines in fragments. Seedling richness was
 lowest in small, isolated, and disturbed fragments, potentially signalling
 an extinction debt given that these fragmentation impacts were not
 observed in trees. Unlike seedlings, saplings showed no declines in
 richness in fragments, suggesting that density dependent mortality (where
 rare individuals have a higher survival rate) and/or year-to-year
 variation in which species are recruiting could potentially compensate for
 the reductions in seedling richness we observed. Longer-term studies are
 required to determine whether sporadic or failed recruitment in small
 fragments will eventually translate into reduced richness of mature trees,
 or whether the processes that currently retain high sapling richness will
 continue in fragments.
description: Stem location, identity
 and dbh dataStride_etal_Biotropica.csv
DOI: 10.5061/dryad.1dc65
title: Data from: High cell density upregulates calcium oscillation by increasing calcium store content via basal mitogen-activated protein kinase activity

description: Calcium releases of non-excitable cells are generally a combination of
 oscillatory and non-oscillatory patterns, and factors affecting the
 calcium dynamics are still to be determined. Here we report the influence
 of cell density on calcium increase patterns of clonal cell lines. The
 majority of HeLa cells seeded at 1.5 x 104/cm2 showed calcium oscillations
 in response to histamine and ATP, whereas cells seeded at 0.5 x 104/cm2
 largely showed transient and sustained calcium increases. Cell density
 also affected the response of HEK293 cells to ATP in a similar manner.
 High cell density increased the basal activity of the mitogen-activated
 protein (MAP) kinase and calcium store content, and both calcium
 oscillation and calcium store content were down-regulated by a MAP kinase
 inhibitor, U0126. Thus, MAP kinase-mediated regulation of calcium store
 likely underlie the effect of cell density on calcium oscillation. Calcium
 increase patterns of HeLa cells were conserved at any histamine
 concentrations tested, whereas the overexpression of histamine H1
 receptor, which robustly increased histamine-induced inositol phospholipid
 hydrolysis, converted calcium oscillations to sustained calcium increases
 only at high histamine concentrations. Thus, the consequence of modulating
 inositol phospholipid metabolism was distinct from that of changing cell
 density, suggesting the effect of cell density is not attributed to
 inositol phospholipid metabolism. Collectively, our results propose that
 calcium increase patterns of non-excitable cells reflect calcium store,
 which is regulated by the basal MAP kinase activity under the influence of
 cell density.
description: PLosONE_Morita_2015
DOI: 10.5061/dryad.v4p20
title: Data from: Estimating occupancy using spatially and temporally replicated snow surveys

description: Occupancy modelling is increasingly used to monitor changes in the spatial
 distribution of rare and threatened species. Occupancy methods have
 traditionally relied on temporally replicated surveys to estimate
 detection probability. Recently, occupancy models with spatial replication
 have been used to estimate detection probabilities over large geographic
 areas that are difficult to survey repeatedly. We developed occupancy
 models that combine spatially and temporally replicated data and applied
 them to snow-tracking surveys of six species including wolverine Gulo gulo
 and Canadian lynx Lynx canadensis. We surveyed thirty-nine 100 km2 cells
 and used one km trail segments within cells as spatial replicates. We
 surveyed 56% of the cells once and 44% of the cells between two and 14
 times resulting in a total of 872 km surveyed. We compared four occupancy
 models that incorporated spatial correlation in detection probability and
 hierarchically estimated occupancy at two spatial scales: cell occupancy
 and segment presence. We detected strong serial correlation in probability
 of detection for all species. Our models with serial correlation had
 higher occupancy estimates with larger confidence intervals than models
 assuming segments were independent and exchangeable. Spatial and temporal
 replicates have identical power to detect decreases in occupancy when
 survey segments are independent but spatial correlation in detection
 probability can reduce the power of spatial replicates. The effects of
 spatial correlation are more pronounced when detection probability is low.
 Application of temporal replicates to spatial replicated surveys increases
 the precision of occupancy estimates but sampling design trade-offs
 between number of sites and spatial versus temporal replicates need to
 balance levels of spatial correlation in detection probability with costs
 to visit sites.
description: Banff_Occupancy_2012Banff_2012.csv
DOI: 10.5061/dryad.gf7b0
title: Data from: Quantitative trait loci for growth and body size in the nine-spined stickleback Pungitius pungitius L.

description: Body size is an ecologically important trait shown to be genetically
 variable both within and among different animal populations as revealed by
 quantitative genetic studies. However, few studies have looked into
 underlying genetic architecture of body size variability in the wild using
 genetic mapping methods. With the aid of quantitative trait loci (QTL)
 analyses based on 226 microsatellite markers, we mapped body size and
 growth rate traits in the nine-spined stickleback (Pungitius pungitius)
 using an F2-intercross (n = 283 offspring) between size divergent
 populations. In total, 15 QTL locations were detected. The proportion of
 phenotypic variation explained by individual body size-related QTL ranged
 from 3% to 9%, and those related to growth parameters and increments from
 3% to 7%. Several of the detected QTL affected either early or late
 growth. These results provide a solid starting point for more in depth
 investigations of structure and function of genomic regions involved in
 determination of body size in this popular model of ecological and
 evolutionary research.
description: Genotype input file for
 GridQTLGenotypes of 226
 microsatellite markers used in GridQTL analyses. Line 1: Number of markers
 Line 2: List of names of the markers Line 3: Names given to each of the
 generations. Line 4: Names given to males and females. Line 5: Symbol or
 symbols for missing genotype data. Line 6 on Data for each individual in
 turn. Contains in order: Individual ID Sire ID Dam ID Sex Line or
 generation Marker genotypesGENOTYPES.txtMap input file for GridQTLThe linkage map, obtained from Crimap, of nine-spined stickleback for GridQTL analyses. Line 1: Number of chromosomes Line 2: Interval for calculation of genotype probabilities and coefficients in cM. Line 3: Name of first chromosome, number of markers on first chromosome and whether map is same for two sexes (=1) or not (=2). Line 4: For first linkage group, marker names in order separated by distances between them in cM.MAP.txtPhenotype input file for GridQTLBody size and growth measurements in nine-spined sticklebacks for QTL mapping analyses in GridQTL. Line 1: Numbers of fixed effects (factors), covariates and traits, respectively Line 2: Name of each fixed effect, covariate and trait. Line 3: Code for missing trait value Line 4 : Individual ID and values for fixed effects, covariates and traits for that individual.PHENOTYPES_size.txt
DOI: 10.5061/dryad.56d7540
title: Data from: The fitness effects of a pale mutant in the aposematic seed bug Lygaeus simulans indicate pleiotropy between warning coloration and life history

description: Conspicuous warning colours that signal chemical or other defences are
 common in the natural world. For instance, such aposematic warning
 patterns of red-and-black or yellow-and-black are common among insect
 taxa, particularly in the order Hemiptera, often forming the basis of
 Batesian and/or Müllerian mimicry rings. In addition, it has been
 repeatedly noted that colour polymorphisms or mutants that influence
 pigmentation can show pleiotropy with other behavioural, physiological or
 life-history traits. Here we describe a pale mutant of the seed bug
 Lygaeus simulans that appeared in our lab population in 2012, which
 differs in colour to the wild-type bugs. Through multigenerational
 experimental crosses between wild-type and pale mutant L. simulans, we
 first show that the pale phenotype segregates as a single Mendelian locus,
 with the pale allele being recessive to the wild-type. Next, we show (1)
 that there is a large heterozygous advantage in terms of fecundity, (2)
 that pale females suffer reduced longevity, and (3) that pale males have
 increased body length compared to wild-type homozygotes. Our data
 therefore suggest that the colour locus is pleiotropic with a number of
 life-history traits, opening the door for a more complete genetic analysis
 of aposematic colouration in this species. In addition, this phenotype
 will be useful as a visible genetic marker, providing a tool for
 investigating sperm competition and other post-copulatory drivers of
 sexual selection in this species.
description: Pale L. simulans
 Experiments 1 and 2 Data and AnalysisThis zip folder contains
 all the raw and processed data from Experiments 1 and 2 (in .xls format)
 and the associated .csv files created from these which were used for
 analysis in R statiscical software along with the .R files containing the
 code for the analysis of each of these files. Two README files are
 included, one for each experiment. These contain information about what
 each file contains and explanations for what data each of the tabs and
 columns contain.Balfour-2018-Pale-L.simulans-Data-and-Analysis.zip
DOI: 10.5061/dryad.r6d8h
title: Data from: The escalatory Red Queen: population extinction and replacement following arms-race dynamics in poplar rust

description: Host-parasite systems provide convincing examples of Red Queen
 co-evolutionary dynamics. Yet, a key process underscored in Van
 Valen's theory – that arms-race dynamics can result in extinction –
 has never been documented. One reason for this may be that most sampling
 designs lack the breadth needed to illuminate the rapid pace of adaptation
 by pathogen populations. In this study we used a 25-years temporal
 sampling to decipher the demographic history of a plant pathogen: the
 poplar rust fungus, Melampsora larici-populina. A major adaptive event
 occurred in 1994 with the breakdown of R7 resistance carried by several
 poplar cultivars widely planted in Western Europe since 1982. The
 corresponding virulence rapidly spread in M. larici-populina populations,
 and nearly reached fixation in northern France, even on susceptible hosts.
 Using both temporal records of virulence profiles and temporal population
 genetic data, our analyses revealed that (i) R7 resistance breakdown
 resulted in the emergence of a unique and homogeneous genetic group, the
 so-called cultivated population, which predominated in northern France for
 about 20 years, (ii) selection for Vir7 individuals brought with it
 multiple other virulence types via hitchhiking, resulting in an overall
 increase in the population-wide number of virulence types and (iii) –
 above all – the emergence of the cultivated population superseded the
 initial population which predominated at the same place before R7
 resistance breakdown. Our temporal analysis illustrates how antagonistic
 co-evolution can lead to population extinction and replacement, hence
 providing direct evidence for the escalation process which is at the core
 of Red Queen dynamics.
description: Microsatellite profiles
 for the Melampsora larici-populina individuals analyzed in Persoons et al.
 MEC16-1416Genotypes at 25
 microsatellite markers for 594 individuals of Melampsora larici-populina
 sampled in France and Belgium from 1982 to 2011. Columns labels are
 detailed in the Read Me fileDataSSR-Persoons-etal-MEC16-1416.csvVirulence profiles of Melampsora larici-populina in France from 1992 to 2011Virulence types of Melampsora larici-populina sampled in France from 1992 to 2011. Isolates were inoculated on a differential set of eight poplar cultivars, each bearing a single qualitative resistance, to determine which virulence type(s) they possessed. In total 6494 isolates from 44 samples have been phenotyped. Columns labels are detailed in the Read Me fileDataVir-Persoons-etal-MEC16-1416.csv
DOI: 10.5061/dryad.65tn4
title: Data from: Robustness to divergence time underestimation when inferring species trees from estimated gene trees

description: To infer species trees from gene trees estimated from phylogenomic data
 sets, tractable methods are needed that can handle dozens to hundreds of
 loci. We examine several computationally efficient approaches—MP-EST,
 STAR, STEAC, STELLS, and STEM—for inferring species trees from gene trees
 estimated using maximum likelihood (ML) and Bayesian approaches. Among the
 methods examined, we found that topology-based methods often performed
 better using ML gene trees and methods employing coalescent times
 typically performed better using Bayesian gene trees, with MP-EST, STAR,
 STEAC, and STELLS outperforming STEM under most conditions. We examine why
 the STEM tree (also called GLASS or Maximum Tree) is less accurate on
 estimated gene trees by comparing estimated and true coalescence times,
 performing species tree inference using simulations, and analyzing a great
 ape data set keeping track of false positive and false negative rates for
 inferred clades. We find that although true coalescence times are more
 ancient than speciation times under the multispecies coalescent model,
 estimated coalescence times are often more recent than speciation times.
 This underestimation can lead to increased bias and lack of resolution
 with increased sampling (either alleles or loci) when gene trees are
 estimated with ML. The problem appears to be less severe using Bayesian
 gene-tree estimates.
description: Robustness
 SupplementThe zip file contains
 all supplemental files, including supplemental figures, a C program (with
 README.txt file) for computing false positive, false negative, etc. clades
 for an estimated tree and reference tree, and list of alignment lengths
 for loci in the 8881-locus great ape dataset.DeGiorgioDegnanRobustness.zip
DOI: 10.5061/dryad.bk58j54t
title: Data from: Hybridization between two gartersnake species (Thamnophis) of conservation concern: A threat or an important natural interaction?

description: Distinguishing between hybrid zones formed by secondary contact versus
 parapatric divergence-with-gene-flow is an important challenge for
 understanding the interplay of geographic isolation and local adaptation
 in the origin of species. Similarly, distinguishing between natural hybrid
 zones and those that formed as a consequence of recent human activities
 has important conservation implications. Recent work has demonstrated the
 existence of a narrow hybrid zone between the plains gartersnake
 (Thamnophis radix) and Butler’s gartersnake (T. butleri) in the Great
 Lakes region of North America, raising questions about the history and
 conservation value of genetically admixed populations. Both taxa are of
 conservation concern, and it is not clear whether to regard hybridization
 as a threat or a natural interaction. Here we use phylogeographic and
 population genetic methods to assess the timescales of divergence and
 hybridization, and test for evidence that the hybrid zone is of recent
 origin. We assayed AFLP markers and ND2 mitochondrial DNA (mtDNA)
 sequences from T. radix, T. butleri, and the closely related short-headed
 gartersnake (T. brachystoma) throughout their North American ranges. We
 find shallow mtDNA divergence overall and high levels of variation within
 the contact zone. These patterns are inconsistent with recent contact of
 long-diverged taxa. It is not possible to distinguish true
 divergence-with-gene-flow from a long-term secondary contact zone, but we
 infer that the hybrid zone is a long-standing, natural interaction.
description: AFLP data structure
 #1AFLP_data_1x.txtAFLP data structure #2AFLP_data_1x.txtR syntax for gene diversity for AFLPsGene diversity for AFLP.txt
DOI: 10.15468/dl.z6r84t
title: Occurrence Download

description: A dataset containing 14711 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Adinetidae, Brachionidae, Gastropodidae, Dicranophoridae, Asplanchnidae, Euchlanidae, Proalidae, Notommatidae, Philodinidae, Collothecidae, Lepadellidae, Conochilidae, Trichocercidae, Epiphanidae, Trochosphaeridae, Flosculariidae, Habrotrochidae, Hexarthridae, Ituridae, Lecanidae, Lindiidae, Mytilinidae, Trichotriidae, Microcodidae, Philodinavidae, Synchaetidae, Testudinellidae, Scaridiidae, Tetrasiphonidae, Centropagidae, Diaptomidae, Cyclopidae, Halicyclopidae, Lernaeidae, Canthocamptidae, Ameiridae, Laophontidae, Phyllognathopodidae, Miraciidae, Ergasilidae, Daphniidae, Moinidae, Bosminidae, Chydoridae, Macrothricidae, Ilyocryptidae, Neothricidae)",
 "Geometry POLYGON ((-181.131592 -37.12775, -187.78141 -33.078885, -189.068184 -33.987495, -186.411552 -37.925243, -192.774353 -44.251839, -195.387383 -46.345032, -192.379532 -48.31083, -188.062592 -45.989329, -183.377609 -41.69727, -180.416107 -38.542795, -181.131592 -37.12775))"
 ]
}

 The dataset includes 14711 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000555-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.nt7kg5g
title: Data from: Evaluating the ability of community‐protected forests in Cambodia to prevent deforestation and degradation using temporal remote sensing data

description: Community forests are known to play an important role in preserving
 forests in Cambodia, a country that has seen rapid deforestation in recent
 decades. The detailed evaluation of the ability of community‐protected
 forests to retain forest cover and prevent degradation in Cambodia will
 help to guide future conservation management. In this study, a combination
 of remotely sensing data was used to compare the temporal variation in
 forest structure for six different community forests located in the Phnom
 Kulen National Park (PKNP) in Cambodia and to assess how these dynamics
 vary between community‐protected forests and a wider study area.
 Medium‐resolution Landsat, ALOS PALSAR data, and high‐resolution LiDAR
 data were used to study the spatial distribution of forest degradation
 patterns and their impacts on above‐ground biomass (AGB) changes. Analysis
 of the remotely sensing data acquired at different spatial resolutions
 revealed that between 2012 and 2015, the community forests had higher
 forest cover persistence and lower rates of forest cover loss compared to
 the entire study area. Furthermore, they faced lower encroachment from
 cashew plantations compared to the wider landscape. Four of the six
 community forests showed a recovery in canopy gap fractions and
 subsequently, an increase in the AGB stock. The levels of degradation
 decreased in forests that had an increase in AGB values. However, all
 community forests experienced an increase in understory damage as a result
 of selective tree removal, and the community forests with the sharpest
 increase in understory damage experienced AGB losses. This is the first
 time multitemporal high‐resolution LiDAR data have been used to analyze
 the impact of human‐induced forest degradation on forest structure and
 AGB. The findings of this work indicate that while community‐protected
 forests can improve conservation outcomes to some extent, more
 interventions are needed to curb the illegal selective logging of valuable
 timber trees.
description: RFDI
 DataRFDI
 dataRFDI.zipNDVI DataNDVI.zip
DOI: 10.5061/dryad.1sm6c
title: Data from: Colonization of the Mediterranean Basin by the vector biting midge species Culicoides imicola: an old story

description: Understanding the demographic history and genetic make-up of colonizing
 species is critical for inferring population sources and colonization
 routes. This is of main interest for designing accurate control measures
 in areas newly colonized by vector species of economically important
 pathogens. The biting midge Culicoides imicola is a major vector of
 orbiviruses to livestock. Historically, the distribution of this species
 was limited to the Afrotropical region. Entomological surveys first
 revealed the presence of C. imicola in the south of the Mediterranean
 basin by the 1970s. Following recurrent reports of massive bluetongue
 outbreaks since the 1990s, the presence of the species was confirmed in
 northern areas. In this study, we addressed the chronology and processes
 of C. imicola colonization in the Mediterranean basin. We characterized
 the genetic structure of its populations across Mediterranean and African
 regions using both mitochondrial and nuclear markers, and combined
 phylogeographical analyses with population genetics and approximate
 Bayesian computation. We found a west/east genetic differentiation between
 populations, occurring both within Africa and within the Mediterranean
 basin. We demonstrated that three of these groups had experienced
 demographic expansions in the Pleistocene, probably because of climate
 changes during this period. Finally, we showed that C. imicola could have
 colonized the Mediterranean basin in the Late Pleistocene or Early
 Holocene through a single event of introduction; however, we cannot
 exclude the hypothesis involving two routes of colonization. Thus, the
 recent bluetongue outbreaks are not linked to C. imicola colonization
 event, but rather to biological changes in the vector or the virus.
description: Jacquet_C.imicola_Efa_alignment.nexSequences of the nuclear gene Elongation factor alpha (Efa) of Culicoides imicola. Sequences were phased using the option phase implemented in DNASP v5.10 software. The two first letters of each sequence name, correspond to the location code described in Table 1.Jacquet_C.imicola_Efa_alignement.nexJacquet_C.imicola_microsatellite_dataJacquet_C.imicola_COI_alignment.nexJacquet_C.imicola_COI_alignment.fastaJacquet_C.imicola_Cytb_alignmentJacquet_C.imicola_Cytb_alignement.fastaJacquet_C.imicola_SamplesID