cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.p8740
title: Data from: Trait compensation between boldness and the propensity for tail autotomy under different food availabilities in similarly-aged brown anole lizards

description: 1. Trait compensation denotes the situation in which individuals offset
 the costs of one trait with the benefits of another trait. The phenomenon
 of trait compensation is best exemplified by a negative correlation
 between the degree of predator avoidance and the strength of morphological
 defense. 2. In this study, we used the relationship between risk-taking
 tendency (boldness) and the propensity for tail autotomy in the brown
 anole lizards Anolis sagrei to address two important questions regarding
 trait compensation. First, we investigated whether trait compensation
 existed among individuals of similar age. Second, we examined how the
 relationship between boldness and the propensity for tail autotomy
 responds to changes in food availability. 3. Overall, bolder individuals
 autotomized their tails more readily. Although mean values of boldness and
 the propensity for tail autotomy did not differ under high and low food
 availability, the compensatory effect between the two traits was only
 obvious when food was abundant. 4. The existence of trait compensation
 among similarly-aged individuals will serve as the first step to
 understanding the evolution of compensatory effects among traits observed
 at higher level. In addition, food availability affected the dynamics of
 trait compensation by influencing the amount of variation of traits
 involved, rather than altering the mean values of traits per se.
description: Exploratory personality
 and the propensity for tail autotomy in the brown anole
 lizardsDistribution of Anolis
 sagrei individuals along two measurements of boldness during the first (a
 and c) and second personality trials (b and d).personality_date1.csv
DOI: 10.5061/dryad.7h5s5
title: Data from: Resource competition across habitat boundaries asymmetric interactions between benthic and pelagic producers

description: In shallow aquatic systems benthic and pelagic primary producers typically
 compete for light and nutrients along opposing vertical supply axes
 pelagic algae shade the benthic habitat; conversely, benthic algae
 intercept the nutrient flux from the sediment to the pelagic habitat. We
 present a general framework for analyzing such spatially asymmetric
 resource competition across habitat boundaries using a mechanistic,
 dynamical model. We visualize the mechanisms determining the outcome of
 these cross-habitat interactions using zero-net-growth-isoclines, resource
 supply points, and resource consumption vectors. In extensive invasion
 analyses we characterize the abiotic and competitive persistence
 boundaries of pelagic and benthic primary producers, which are set by
 environmental factors determining nutrient and light supply and are
 modified by resource use by the competitor in the respective other
 habitat. We note several qualitative differences between cross-habitat and
 'classical' within-habitat resource competition. First,
 coexistence of cross-habitat competitors is facilitated by, but does not
 require niche differentiation with respect to the utilization of
 resources. Because each species has a competitive edge for the resource
 that is supplied from 'its' side of the system, a competitor
 which is inferior in utilizing both resources can sometimes coexist with -
 or even exclude - a superior competitor. Second, increasing the external
 supply of one resource (the nutrient) may initially favor both competitors
 - until a breakpoint is reached where the benthic producer goes abruptly
 extinct. Finally, whether a given pair of cross-habitat competitors
 coexist or shows alternative states may depend on the environment.
 Specifically, benthic and pelagic algae may coexist at low nutrient and
 light supply but produce alternative states at high nutrient and light
 supply. Alternative states are, in turn, promoted by any algal trait
 combination that increases the spatial asymmetry in resource consumption,
 i.e. leads to a higher nutrient consumption in the benthic habitat and/or
 a higher light consumption in the pelagic habitat. In a first empirical
 application we show that predictions from our model give a good fit to
 published data on benthic and pelagic primary production in temperate and
 arctic lakes spanning a broad range of nutrient environments.
description: Matlab Source
 CodeThis is the Matlab
 source code for the basic model simulations corresponding to Fig. 2 of the
 article.automatic.m
DOI: 10.5061/dryad.26ss3p0
title: Data from: Traits that allow bats of tropical lowland origin to conquer mountains: bat assemblages along elevational gradients in the South American Atlantic Forest

description: Aim: This study aims to contribute to the identification of ecological
 determinants of tropical moist forest montane biodiversity, analyzing
 changes in the structure of bat assemblages along an elevational gradient
 and testing the role of species traits shaping those assemblages.
 Location: Mountain ranges in the Brazilian Atlantic Forest. Methods: We
 compiled a dataset with the composition of phyllostomid bat assemblages at
 32 forested sites, ranging from 60m to 1960m a.s.l. We quantified how
 abundance and diversity changed along this elevational gradient, and
 assessed the capacity of each species to be present and abundant at each
 elevation, identifying traits that may influence that capacity. Results:
 Abundance and species diversity declined markedly with increasing
 elevation. Tolerance to low temperatures, low habitat specialization, and
 cave roosting facilitated success at higher elevations. Owing to trait
 filtering, and to changes in resource availability with elevation,
 assemblages were progressively dominated by a smaller number of mostly
 generalist species as elevation increased. Higher elevations harbor only a
 subset of the species that are present in the lowland forest, with no
 mountain specialized species. Main conclusions: High mountains harbor
 phyllostomid assemblages that are impoverished subsets of those at lower
 elevations. Phyllostomids have a tropical origin and may thus have a low
 potential to adapt to montane forest environments, which possibly explains
 the observed climatic trait filtering. Habitat filtering is also
 important, keeping forest specialists mostly at lowest elevations.
 Protected areas in the Atlantic Forest are mostly limited to mountains.
 While these areas are clearly important to protect biodiversity, including
 phyllostomid assemblages, it is now critical to protect and restore the
 few remnants of lower elevation Atlantic Forest where higher productivity
 and resource levels, increased complexity of vertical structure, and fewer
 climatic constraints favor the success of a wider range of phyllostomid
 bat species of tropical origin.
description: Elevation abundance
 index and species traitsThis
 "Elevation_Abundance_Index_and_Species_Traits.csv" file contain
 the data of the Elevation Abundance Index and functional traits for each
 of the 31 bat species used in the analyzes.Elevational_Abundance_Index_and_Species_Traits.csv
DOI: 10.5061/dryad.j0r60
title: Data from: Successful eradication of a suburban Pallas’s squirrel Callosciurus erythraeus (Pallas 1779) (Rodentia, Sciuridae) population in Flanders (northern Belgium)

description: Despite a growing catalogue of eradication projects, documented successful
 vertebrate eradications on the mainland remain scarce. Reporting on
 successful campaigns is crucial to counter pessimism on ambitious
 programmes to tackle invasive species and to allow conservation
 practitioners, wildlife managers and scientist to learn from previous
 experience. Moreover, there is a need for basic information on the
 effectiveness of control methods and management strategies that can be
 used. In this note we report on a successful low-tech eradication campaign
 of a local population of Pallas’s squirrel Callosciurus erythraeus, a
 species of tree squirrel with documented ecological and socio-economic
 impacts in its invasive range. The population was eradicated from a
 suburban park of about 15 ha using baited mesh wire life traps, in five
 consecutive capture campaigns between October 2005 and January 2011. Using
 maximum likelihood estimation from catch-effort data we calculated initial
 densities in the park at 3 squirrels ha−1. Although control started
 quickly and the extent of the invasion was limited, the campaign took over
 5 years and required an estimated investment of over €200,000 including
 1.5 years of post-eradication surveying. We provide basic data on the
 methods used to eradicate this invasive rodent. Critical success factors
 and possible improvements with respect to the specific context of this
 case are discussed. Adding this species to the list of species of EU
 concern currently under development could provide incentive to minimise
 impact of this tree squirrel at the continental scale.
description: Pallassquirrel_capture_dataThis data file (.csv with UTF-8 encoding) is associated to [Adriaens T., Baert K., Breyne P., Casaer J., Devisscher S., Onkelinx T., Pieters S., Stuyck J. (2015). Successful eradication of a suburban Pallas’s squirrel *Callosciurus erythraeus* (Pallas 1779)(Rodentia, Sciuridae) population in Flanders (northern Belgium). Biological Invasions. Doi:10.1007/s10530-015-0898-z] which reports on an eradication campaign of an invasive squirrel in Dadizele (western Flanders, Belgium) (Lat=50.851389, Lon=3.094444). This population was eradicated from a suburban park of about 15 ha using baited mesh wire life traps, in five consecutive capture campaigns between October 2005 and January 2011. For the period February 2006–April 2007 (dashed line) capture data are lacking. The data represent the capture day (in ISO 8601 format) and the number of squirrels captured on that day and were used to draft figure 2 in the associated manuscript.
DOI: 10.5061/dryad.nd93j
title: Data from: Remote sensing data predict indicators of soil functioning in semi-arid steppes, central Spain

description: A substantial part of current research efforts on desertification are
 devoted to establish monitoring systems to evaluate the status of natural
 resources and the onset of desertification processes. Methodologies based
 on ground-collected soil and plant indicators are being increasingly used
 for this aim because they are affordable yet do not compromise accuracy.
 Despite their inherent value, these methods have limitations regarding the
 extent of the area that can be monitored using them. Such limitations can
 be overcome combining field-based approaches with remote sensing data,
 which allow the establishment of monitoring programs over large areas. In
 this article we tested the relationship between a field methodology based
 on indicators of ecosystem functioning, the landscape function analysis
 (LFA), and a vegetation index (NDVI) obtained from satellite images of the
 ASTER sensor using data gathered in Stipa tenacissima steppes from central
 Spain. LFA uses soil surface indicators to assess the condition of a given
 ecosystem by producing three numerical indices (stability, infiltration
 and nutrient cycling) reflecting the status of basic soil functions. We
 found a significant positive linear relationship between the NDVI, the
 three LFA indices and some key structural attributes of vegetation related
 to the cover of perennial plants. Our results indicate that NDVI can be
 used as a surrogate of ecosystem functioning in semi-arid Mediterranean
 steppes, and thus can be a helpful index to monitor the functional status
 of large areas in these ecosystems, and the possible onset of
 desertification processes.
description: Data on indicators of
 soil functioning, vegetation attributes and a vegetation index (NDVI)
 obtained from satellite images of the ASTER sensor using data gathered in
 Stipa tenacissima steppes from Central SpainGarcia_Gomez_ECIND2011.txt
DOI: 10.5061/dryad.qd6gr5v
title: Data from: Autumn freeze-thaw events carry over to depress late-winter reproductive performance in Canada Jays

description: Evidence suggests that range-edge populations are highly vulnerable to the
 impacts of climate change but few studies have examined the specific
 mechanisms that are driving observed declines. Species that store
 perishable food for extended periods of time may be particularly
 susceptible to environmental change because shifts in climatic conditions
 could accelerate the natural degradation of their cached food. Here, we
 use 40 years of breeding data from a marked population of Canada jays
 (Perisoreus canadensis) located at the southern edge of their range in
 Algonquin Provincial Park, Ontario, to examine whether climatic conditions
 prior to breeding carry over to influence reproductive performance. We
 found that the number of fall freeze-thaw events was negatively correlated
 with reproductive performance (brood size, nest success, and nestling
 condition) in the subsequent late-winter breeding season of the Canada
 jay. Our results suggest that freeze-thaw events have a significant
 negative impact on the quality and/or quantity of cached food available to
 Canada jays. Future increases in such events, caused by climate change,
 could pose a serious threat to Canada jays and other food caching species
 that store perishable foods for long periods of time.
description: Climatic effects on
 reproductive performance of Canada jaysData was collected from
 the field at our study site located in Algonquin Provincial Park, ON, CA.
 Three metrics of reproductive performance (Brood size: the number of young
 in a nest at time of banding, Nest success: whether a nest was active at
 time of banding approximately 11 days after hatch and Nestling condition:
 the residual of a mass vs. size comparison) are summarized in our data
 sheet. Additionally, all climate variables used in our analysis (fall mean
 temperature, pre-breeding mean temperature, the number of fall freeze-thaw
 events and the number of pre-breeding freeze-thaw events) are also
 summarized by year.Freeze-thaw Data
 RSOS.csv
DOI: 10.5061/dryad.q32c14q5
title: Data from: Natural variation in GL1 and its effects on trichome density in Arabidopsis thaliana

description: The ultimate understanding of how biological diversity arises, is
 maintained, and lost depends on identifying the genes responsible.
 Although a good deal has been discovered about gene function over the past
 few decades, far less is understood about gene effects; i.e., how natural
 variation in a gene contributes to natural variation in phenotypes.
 Trichome density in Arabidopsis thaliana is an ideal trait for studies of
 natural molecular and phenotypic variation, as trichome initiation is
 genetically well-characterised and trichome density is highly variable in
 and among natural populations. Here, we show that variation at GLABRA1
 (GL1), an R2R3 MYB transcription factor gene, which has a role in trichome
 initiation, has qualitative and likely quantitative effects on trichome
 density in natural accessions of A. thaliana. Specifically, we
 characterize four independent loss-of-function alleles for GL1, each of
 which yields a glabrous phenotype. Further, we find that a pattern of
 common polymorphisms confined to the GL1 locus is associated with
 quantitative variation for trichome density. While mutations resulting in
 a glabrous phenotype are primarily coding changes, the pattern resulting
 in quantitative variation spans both coding and regulatory regions. These
 data show that GL1 is an important source of trichome density variation
 within A. thaliana and, along with recent reports, suggest that the TTG1
 epidermal cell fate pathway generally may be the key molecular genetic
 source of natural trichome density variation and an important model for
 the study of molecular evolution.
description: GL1 density scores and
 GenBank accessionsGL1 density scores and genbank
 accessions CSV2.csv
DOI: 10.5061/dryad.87pk2
title: Data from: Strategic adjustments in sperm production within and between two island populations of house mice

description: Sperm production is physiologically costly. Consequently, males are
 expected to be prudent in their sperm production, and tailor their
 expenditure according to prevailing social conditions. Differences in
 sperm production have been found across island populations of house mice
 that differ in the level of selection from sperm competition. Here, we
 determined the extent to which these differences represent phenotypic
 plasticity and/or population divergence in sperm production. We sourced
 individuals from two populations at the extreme levels of sperm
 competition, and raised them under common-garden conditions while
 manipulating the social experience of developing males. Males from the
 high-sperm competition population produced more sperm and better quality
 sperm than did males from the low-sperm competition population. In
 addition, males reared under a perceived “risk” of sperm competition
 produced greater numbers of sperm than males reared with “no risk.”
 However, our analyses revealed that phenotypic plasticity in sperm
 production was greater for individuals from the high-sperm competition
 population. Our results are thus consistent with both population
 divergence and phenotypic plasticity in sperm production, and suggest that
 population level of sperm competition might affect the degree of adaptive
 plasticity in sperm production in response to sperm competition risk.
description: Male anatomical and
 sperm data13-0099.R1.csv
DOI: 10.5061/dryad.vj310
title: Data from: A new phylogenetic method for identifying exceptional phenotypic diversification

description: Currently available phylogenetic methods for studying the rate of
 evolution in a continuously valued character assume that the rate is
 constant throughout the tree or that it changes along specific branches
 according to an a priori hypothesis of rate variation provided by the
 user. Herein, we describe a new method for studying evolutionary rate
 variation in continuously valued characters given an estimate of the
 phylogenetic history of the species in our study. According to this
 method, we propose no specific prior hypothesis for how the variation in
 evolutionary rate is structured throughout the history of the species in
 our study. Instead, we use a Bayesian Markov Chain Monte Carlo approach to
 estimate evolutionary rates and the shift-point between rates on the tree.
 We do this by simultaneously sampling rates and shift-points in proportion
 to their posterior probability, and then collapsing the posterior sample
 into an estimate of the parameters of interest. We use simulation to show
 that the method is quite successful at identifying the phylogenetic
 position of a shift in the rate of evolution, and that estimated rates are
 asymptotically unbiased. We also provide an empirical example of the
 method using data for Anolis lizards.
description: Anolis.subtreeAnolis phylogeny used in the empirical example. Subtree from maximum clade credibility tree of Mahler et al. (2010; DOI:10.1111/j.1558-5646.2010.01026.x).Anolis.rawdata.subtreeMorphological data for Anolis subtree used in empirical example. Data originally from Mahler et al. (2010; DOI:10.1111/j.1558-5646.2010.01026.x).Anolis.analysis.scriptR script used to run empirical example.
DOI: 10.5061/dryad.f4114
title: Data from: Extensive introgression in a malaria vector species complex revealed by phylogenomics

description: Introgressive hybridization is now recognized as a widespread phenomenon,
 but its role in evolution remains contested. Here we use newly available
 reference genome assemblies to investigate phylogenetic relationships and
 introgression in a medically important group of Afrotropical mosquito
 sibling species. We have identified the correct species branching order to
 resolve a contentious phylogeny, and show that lineages leading to the
 principal vectors of human malaria were among the first to split.
 Pervasive autosomal introgression between these malaria vectors means that
 only a small fraction of the genome, mainly on the X chromosome, has not
 crossed species boundaries. Our results suggest that traits enhancing
 vectorial capacity may be gained through interspecific gene flow,
 including between non-sister species.
description: Mitochondrial genome
 alignment of the field individuals in the An. gambiae
 complexFasta alignment of the
 mitochondrial genome (14,843 bps) assembled from 75 individual mosquitoes
 from the Anopheles gambiae species complex (Cf SOM, section S2.2.4). It
 includes 73 individuals from each of the six ingroup species and the two
 outgroups, An. christyi and An. epiroticus, and the reference mtDNA genome
 (GeneBank Accession NC_002084).mtDNA_all_copy_N75_CUT14845_ID4GBK.fasVCF files of field individual samples from the AGC complexThis is a tar archive including the VCF files (one per chromosome arm) for the 69 individual mosquito samples sequenced at low-depth that passed QC filters, plus 2 outgroups (see SOM, section 2.2).VCFfile4DRYAD.tar.gzMAF TBA genome alignment of reference assemblies from the An gambiae complexWhole genome alignment of the of the reference assemblies from the members of the Anopheles gambiae species complex (AGC). The reference assemblies are mostly derived from colonized anopheline mosquitoes. This multiple genome alignment, in MAF format, include the new reference assemblies from six genomes of the AGC, plus the assemblies of An. gambiae PEST, An. gambiae Pimperena S, An. coluzzii, and two outgroup Pyretophorus species (An. christyi and An epiroticus). MAF for each chromosome arm are provided. See the SOM, section S1 for a full description of the methodology.AgamP3-C9-7chr.tba.unmasked.mafs.tar.gzMAF genome alignment from HD field samples of An gambiae complexMultiple whole genome alignments of the field individual samples from the members of the Anopheles gambiae species complex (AGC) sequenced at high depth. This multiple genome alignment, in MAF format, include the haploid genome of one individual sequenced at high depth in each six genomes of the AGC. The An gambiae PEST reference assembly and two outgroup Pyretophorus species (An christyi and An epiroticus) are also included. MAF for each chromosome arm are provided. See the SOM, section S2.1 and S3.1 for a full description of the methodology.MAF_HD_V4_TBA.C9.DRYAD.tar.gz