cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q0rv9
title: Data from: Environmental filtering by pH and soil nutrients drives community assembly in fungi at fine spatial scales

description: Whether niche processes, like environmental filtering, or neutral
 processes, like dispersal limitation, are the primary forces driving
 community assembly is a central question in ecology. Here, we use a
 natural experimental system of isolated tree “islands” to test whether
 environment or geography primarily structures fungal community composition
 at fine spatial scales. This system consists of isolated pairs of two
 distantly-related, congeneric pine trees established at varying distances
 from each other and the forest edge, allowing us to disentangle the
 effects of geographic distance versus host and edaphic environment on
 associated fungal communities. We identified fungal community composition
 with Illumina sequencing of ITS amplicons, measured all relevant
 environmental parameters for each tree - including tree age, size, and
 soil chemistry - and calculated geographic distances from each tree to all
 others and to the nearest forest edge. We applied generalized
 dissimilarity modeling to test whether total and ectomycorrhizal fungal
 (EMF) communities were primarily structured by geographic or environmental
 filtering. Our results provide strong evidence that, as in many other
 organisms, niche and neutral processes both contribute significantly to
 turnover in community composition in fungi, but environmental filtering
 plays the dominant role in structuring both free-living and symbiotic
 fungal communities at fine spatial scales. In our study system, we found
 pH and organic matter primarily drive environmental filtering in total
 soil fungal communities and that pH and cation exchange capacity – and,
 surprisingly, not host species - were the largest factors affecting EMF
 community composition. These findings support an emerging paradigm that pH
 may play a central role in the assembly of all soil mediated systems.
description: Tree
 DataThis is the raw data on
 the 40 trees used for their project. Included are the latitude and
 longitude GPS coordinates for each tree, their species identity (Pinus
 contorta or Pinus albicaulis), their age in years, their estimated volume
 in m^3, their distance from the nearest forest edge (m), isolation index
 (number of stems within a 10m radius of the tree), and the soil chemistry
 information (% OM, pH, K, Mg, Na, S, cation exchange capacity, C:N
 ratio).TreeData.xlsxBray Curtis rarefied dissimilarity matrix for EMFThis is the Bray-Curtis rarefied dissimilarity matrix for ectomycorrhizal fungal taxa for the 40 treesbray_curtis_dm_EMFprune2_e647.csvBray Curtis rarefied dissimilarity matrix for total fungiThis is the Bray-Curtis rarefied dissimilarity matrix for the total fungal community for the 40 treesbray_curtis_dm_allfungi_e39721.csv
DOI: 10.5061/dryad.s8f38
title: Data from: Re-growing a tropical dry forest: functional plant trait composition and community assembly during succession

description: A longstanding goal of ecology and conservation biology is to understand
 the environmental and biological controls of forest succession. However,
 the patterns and mechanisms that guide successional trajectories,
 especially within tropical forests, remain unclear. We collected leaf
 functional trait and abiotic data across a 110-year chronosequence within
 a tropical dry forest in Costa Rica. Focusing on six key leaf functional
 traits related to resource acquisition and competition, along with
 measures of forest stand structure, we propose a mechanistic framework to
 link species composition, community trait distributions, and forest
 structure. We quantified the community-weighted trait distributions for
 specific leaf area, leaf dry matter concentration, leaf phosphorus
 concentration, leaf carbon to nitrogen ratio, and leaf stable isotopic
 carbon and nitrogen. We assessed several prominent hypotheses for how
 these functional measures shift in response to changing environmental
 variables (soil water content, bulk density and pH) across the
 chronosequence. Increasingly, older forests differed significantly from
 younger forests in species composition, above ground biomass and shifted
 trait distributions. Early stages of succession were uniformly
 characterized by lower values of community-weighted mean specific leaf
 area, leaf stable nitrogen isotope, and leaf phosphorus concentration.
 Leaf dry matter concentration and leaf carbon to nitrogen ratio were lower
 during earlier stages of succession, and each trait reached an optimum
 during intermediate stages of succession. The leaf carbon isotope ratio
 was the only trait to decrease linearly with increasing stand age
 indicating reduced water use efficiency in older forests. However, in
 contrast to expectations, community-weighted trait variances did not
 generally change through succession, and when compared to null
 expectations were lower than expected. The observed directional shift in
 community-weighted mean trait values is consistent with the ‘productivity
 filtering’ hypothesis where a directional shift in water and light
 availability shifts physiological strategies from ‘slow’ to ‘fast’. In
 contrast to expectations arising from niche based ecology, none of the
 community trait distributions were over-dispersed. Instead, patterns of
 trait dispersion are consistent with the abiotic filtering and/or
 competitive hierarchy hypotheses.
description: FEBuzzardSpTraitsSpecies mean trait data for six traits: SLA (cm2 g-1 ), LDMC, LPC (mg g-1 ), d13C, d15N and CN within each plot across the chronosequence.FEBuzzardCWMCalculations.RR-script for calculating the community weighted mean (CWM) trait values by plot.FEBuzzardCWVCalculation.RR-script for calculating the community weighted variance (CWV) for each plot.
DOI: 10.5061/dryad.7qc3s
title: Data from: A novel growth model evaluating age-size effect on long-term trends in tree growth.

description: 1.One of the major problems in understanding growth trends in long-lived
 trees is the difficulty of separately quantifying the effects of tree size
 and age. Careful statistical control of the axiomatic age×size covariation
 is therefore required to identify long-term trends in tree growth and
 their drivers, and to predict forests’ responses to environmental changes
 reliably. 2.To address this issue, we present a novel tree growth model: a
 ‘two-dimensional lognormal growth model’. This is an extension of the
 one-dimensional lognormal growth model, in which tree growth is modelled
 primarily as a function of size. Our model assesses the trend in tree
 growth over time by explicitly partitioning the effects of age and size,
 controlling the covariation. The model is then extended to incorporate the
 effects of neighbourhood crowding and individual tree variation. 3.To
 demonstrate our model, we apply it to long-term monitoring data from a
 mature (104-year- old) plantation of Japanese cedar. Thinning operations
 of various intensities have been applied to this plantation, and the
 diameter of each individual tree has been measured repeatedly. 4.We
 observed a pronounced age-related decline in diameter growth. However, at
 each age, greater tree size was associated with a higher growth rate. The
 growth-size curve predicted from the model became flatter with tree age,
 and the curve's peak shifted rightwards as tree age increased. The
 model reveals that the sensitivity of a target tree to neighbourhood
 crowding depends strongly on neighbours’ size, and also provides an
 estimate of among-tree variation in growth performance. 5.Although the
 relationships between growth, size and age in long-lived trees are very
 complex, our growth model supports the conclusion that it is possible to
 predict long-term trends in tree growth reliably with respect to both age
 and size. In addition, the model's flexibility will facilitate more
 robust testing of species-specific responses to long-term environmental
 changes.
description: Tree diameter growth
 data of Japanse cedarThe individual tree
 growth was monitored for a long-term in a mature plantation of Japanese
 cedar.tree.data_Japanese.cedar.xlsx
DOI: 10.5061/dryad.bn7h0
title: Data from: Genetic wealth, population health: major histocompatibility complex variation in captive and wild ring-tailed lemurs (Lemur catta)

description: Across species, diversity at the major histocompatibility complex (MHC) is
 critical to individual disease resistance and, hence, to population
 health; however, MHC diversity can be reduced in small, fragmented, or
 isolated populations. Given the need for comparative studies of functional
 genetic diversity, we investigated whether MHC diversity differs between
 populations which are open, that is experiencing gene flow, versus
 populations which are closed, that is isolated from other populations.
 Using the endangered ring-tailed lemur (Lemur catta) as a model, we
 compared two populations under long-term study: a relatively “open,” wild
 population (n = 180) derived from Bezà Mahafaly Special Reserve,
 Madagascar (2003–2013) and a “closed,” captive population (n = 121)
 derived from the Duke Lemur Center (DLC, 1980–2013) and from the
 Indianapolis and Cincinnati Zoos (2012). For all animals, we assessed
 MHC-DRB diversity and, across populations, we compared the number of
 unique MHC-DRB alleles and their distributions. Wild individuals possessed
 more MHC-DRB alleles than did captive individuals, and overall, the wild
 population had more unique MHC-DRB alleles that were more evenly
 distributed than did the captive population. Despite management efforts to
 maintain or increase genetic diversity in the DLC population, MHC
 diversity remained static from 1980 to 2010. Since 2010, however,
 captive-breeding efforts resulted in the MHC diversity of offspring
 increasing to a level commensurate with that found in wild individuals.
 Therefore, loss of genetic diversity in lemurs, owing to small founder
 populations or reduced gene flow, can be mitigated by managed breeding
 efforts. Quantifying MHC diversity within individuals and between
 populations is the necessary first step to identifying potential
 improvements to captive management and conservation plans.
description: List of Lemur catta
 individual genotypesThis CSV file contains
 the MHC-DRB genotypes for all ring-tailed lemurs included in this study.
 The first column describes the population from which each individual
 originated, either the wild population located at Beza Mahafaly Special
 Reserve, Madagascar, or the captive population, including animals from the
 Cincinnati Zoo, the Indianapolis Zoo, and the Duke Lemur Center. The
 second column gives the name of each individual lemur. The third column
 lists each allele possessed by the individual listed in the second column,
 such that an individual with 4 MHC-DRB alleles will be listed in 4 rows,
 each row containing a different allele in the third column. Lastly, the
 fourth column contains the total number of MHC-DRB alleles possessed by
 that individual.
DOI: 10.5061/dryad.f0090
title: Data from: Social learning in a high-risk environment: incomplete disregard for the ‘minnow that cried pike’ results in culturally transmitted neophobia

description: Many prey species rely on conspecifics to gather information about unknown
 predation threats, but little is known about the role of varying
 environmental conditions on the efficacy of social learning. We examined
 predator-naive minnows that had the opportunity to learn about predators
 from experienced models that were raised in either a low- or high-risk
 environment. There were striking differences in behaviour among models;
 high-risk models showed a weaker response to the predator cue and became
 neophobic in response to the control cue (a novel odour, NO). Observers
 that were previously paired with low-risk models acquired a strong
 antipredator response only to the predator cue. However, observers that
 interacted with high-risk models, displayed a much weaker response to the
 predator odour and a weak neophobic response to the NO. This is the first
 study reporting such different outcomes of social learning under different
 environmental conditions, and suggests high-risk environments promote the
 cultural transmission of neophobia more so than social learning. If such a
 transfer can be considered similar to secondary traumatization in humans,
 culturally transmitted neophobia in minnows may provide a good model
 system for understanding more about the social ecology of fear disorders.
description: data for
 culturally-transmitted neophobiaTabs are data for
 conditioning and testing trials.data
 ProcB.xlsx
DOI: 10.5061/dryad.ff52k
title: Data from: Lifetime fitness and age-related female ornament signalling: evidence for survival and fecundity selection in the pied flycatcher

description: Ornaments displayed by females have often been denied evolutionary
 interest due to their frequently reduced expression relative to males,
 habitually attributed to a genetic correlation between the sexes. We
 estimated annual and lifetime reproductive success of female pied
 flycatchers (Ficedula hypoleuca) and applied capture–mark–recapture models
 to analyse annual survival rates in relation to the patterns of expression
 (absence/presence) of an ornament displayed by all males and a fraction of
 females. Overall, the likelihood of expressing the ornament increased
 nonlinearly with female age and was due to within-individual variation,
 not to the selective appearance or disappearance of ornament-related
 expression of phenotypes in the population. Accordingly, expressing the
 forehead patch in a given year did not influence survival probability.
 However, those females expressing the ornament at early ages (1–2 years
 old) enjoyed survival advantages throughout lifetime. Although ornamented
 females had higher lifetime fecundity and fledging success, their yearly
 reproductive performance, in terms of fledging productivity, decreased as
 they aged so that, late in life, ornamented females reared fewer offspring
 than nonexpressing females of the same age. In addition, both strategies
 (expressing vs. not expressing the trait) returned similar fitness payoffs
 in terms of recruited offspring. Our results support the hypothesis that
 fecundity and survival selection are involved in the displaying of this
 ‘male’ ornament by females.
description: longitudinallongitudinal data on female yearly reproductive success and ornament expressionlifetimeincludes variables used for female lifetime reproductive success and ornament expression
DOI: 10.5061/dryad.g2b4h
title: Data from: Evolutionary dynamics of a rapidly receding southern range boundary in the threatened California Red-Legged Frog (Rana draytonii)

description: Populations forming the edge of a species range are often imperiled by
 isolation and low genetic diversity, with proximity to human population
 centers being a major determinant of edge stability in modern landscapes.
 Since the 1960s, the California red-legged frog (Rana draytonii) has
 undergone extensive declines in heavily urbanized southern California,
 where the range edge has rapidly contracted northward while shifting its
 cardinal orientation to an east-west trending axis. We studied the genetic
 structure and diversity of these frontline populations, tested for
 signatures of contemporary disturbance, specifically fire, and attempted
 to disentangle these signals from demographic events extending deeper into
 the past. Consistent with the genetic expectations of the
 ‘abundant-center’ model, we found that diversity, admixture, and
 opportunity for random mating increases in populations sampled
 successively further away from the range boundary. Demographic simulations
 indicate that bottlenecks in peripheral isolates are associated with
 processes extending tens to a few hundred generations in the past, despite
 the demographic collapse of some due to recent fire-flood events. While
 the effects of recent disturbance have left little genetic imprint on
 these populations, they likely contribute to an extinction debt that will
 lead to continued range contraction unless management intervenes to stall
 or reverse the process.
description: EVA-2012-178-OA_msat_DATARaw allele scores for 15 microsatellite loci developed from a species-specific library for Rana draytonii. The data file is formatted for Convert v.1.31 (Glaubitz, JC. 2004. Molecular Ecology Notes 4:309-310). Locus names match those in Table S1 of the electronic supplementary materials (linked to the article on the Evolutionary Applications website). Population identifiers match sampling localities detailed in Figure 1 in the paper. Asterisks denote missing data.
DOI: 10.5061/dryad.kb00n
title: Data from: Effects of warming on predator–prey interactions – a resource-based approach and a theoretical synthesis

description: We theoretically explore consequences of warming for predator-prey
 dynamics, broadening previous approaches in three ways: we include
 beyond-optimal temperatures, predators may have a type III functional
 response, and prey carrying capacity depends on explicitly modeled
 resources. Several robust patterns arise. The relationship between prey
 carrying capacity and temperature can range from near-independence to
 monotonically declining/increasing to hump-shaped. Predators persist in a
 U-shaped region in resource supply (=enrichment)-temperature space. Type
 II responses yield stable persistence in a U-shaped band inside this
 region, giving way to limit cycles with enrichment at all temperatures. In
 contrast, type III responses convey stability at intermediate temperatures
 and confine cycles to low and high temperatures. Warming-induced state
 shifts can be predicted from system trajectories crossing stability and
 persistence boundaries in enrichment-temperature space. Results of earlier
 studies with more restricted assumptions map onto this graph as special
 cases. Our approach thus provides a unifying framework for understanding
 warming effects on trophic dynamics.
description: Functional response
 experiments datadata Uszko et al. 2017
 ELE.xlsx
DOI: 10.5061/dryad.91jq5
title: Data from: Genetic analysis of inflorescence and plant height components in sorghum (Panicoidae) and comparative genetics with rice (Oryzoidae)

description: Background: Domestication has played an important role in shaping
 characteristics of the inflorescence and plant height in cultivated
 cereals. Taking advantage of meta-analysis of QTLs, phylogenetic analyses
 in 502 diverse sorghum accessions, GWAS in a sorghum association panel
 (n = 354) and comparative data, we provide insight into the genetic basis
 of the domestication traits in sorghum and rice. Results: We performed
 genome-wide association studies (GWAS) on 6 traits related to
 inflorescence morphology and 6 traits related to plant height in sorghum,
 comparing the genomic regions implicated in these traits by GWAS and QTL
 mapping, respectively. In a search for signatures of selection, we
 identify genomic regions that may contribute to sorghum domestication
 regarding plant height, flowering time and pericarp color. Comparative
 studies across taxa show functionally conserved ‘hotspots’ in sorghum and
 rice for awn presence and pericarp color that do not appear to reflect
 corresponding single genes but may indicate co-regulated clusters of
 genes. We also reveal homoeologous regions retaining similar functions for
 plant height and flowering time since genome duplication an estimated 70
 million years ago or more in a common ancestor of cereals. In most such
 homoeologous QTL pairs, only one QTL interval exhibits strong selection
 signals in modern sorghum. Conclusions: Intersections among QTL, GWAS and
 comparative data advance knowledge of genetic determinants of
 inflorescence and plant height components in sorghum, and add new
 dimensions to comparisons between sorghum and rice.
description: Figure_1b_treeNewick file for figure 1b. Neighbor-joining tree of 502 sorghum accessions for 265,487 SNPsFigure_S4b_treeNewick file for figure S4b. Neighbor-joining tree of 502 sorghum accessions for 194,852 SNPs with MAF&gt;=0.02 and missing rate&lt;=50%
DOI: 10.5061/dryad.8h9f5
title: Data from: Taxonomic revision of imitating carpenter ants, Camponotus subgenus Myrmopytia (Hymenoptera, Formicidae) of Madagascar, using morphometry and qualitative traits

description: The ant genus Camponotus (Mayr, 1861) is one of the most abundant and
 species rich ant genera in the Malagasy zoogeographical region. Although
 this group is commonly encountered, its taxonomy is far from complete.
 Here, we clarify the taxonomy of the Malagasy-endemic Camponotus subgenus
 Myrmopytia (Emery, 1920). Species delimitation was based on traditional
 morphological characters and multivariate morphometric analyses, including
 exploratory Nest Centroid clustering and confirmatory cross-validated
 Linear Discriminant Analysis. Four species are recognized: Camponotus
 imitator (Forel, 1891), Camponotus jodina sp. n., Camponotus karaha sp.
 n., and Camponotus longicollis sp. n. All four species appear to mimic
 co-occurring Aphaenogaster species. A diagnosis of the subgenus
 Myrmopytia, species descriptions, an identification key based on minor and
 major subcastes of workers, and the known geographical distribution of
 each species are provided.
description: Morphometric_data_mmMorphometric data recorded from 96 minor workers and 34 major workers of Camponotus subgenus Myrmopytia, with 19 morphometric traits.
DOI: 10.5061/dryad.n710v
title: Data from: Occurrence, costs and heritability of delayed selfing in a free-living flatworm

description: Evolutionary theory predicts that in the absence of outcrossing
 opportunities, simultaneously hermaphroditic organisms should eventually
 switch to self-fertilization as a form of reproductive assurance. Here we
 report the existence of facultative self-fertilization in the free-living
 flatworm Macrostomum hystrix, a species in which outcrossing occurs via
 hypodermic insemination of sperm into the parenchyma of the mating
 partner. First, we show that isolated individuals significantly delay the
 onset of reproduction compared to individuals with outcrossing
 opportunities (“delayed selfing”) as predicted by theory. Second,
 consistent with the idea of M. hystrix being a preferential outcrosser
 under natural conditions, we report likely costs of selfing manifested via
 reduced hatchling production and offspring survival. Third, we demonstrate
 that selfing propensity has a genetic basis in this species, with a
 heritability estimated at 0.43 ± 0.11. Variation in selfing propensity
 could arise due to differing costs of inbreeding among families, though
 despite marked inter-family variation in apparent costs of inbreeding we
 found no evidence for such a link. Alternatively, selfing propensity might
 differ across families because of heritable variation in reproductive
 traits that determine the likelihood of selfing. We speculate that
 adaptations to hypodermic insemination under outcrossing, most notably a
 highly modified copulatory stylet (male copulatory organ) and reduced
 sperm complexity, could also facilitate facultative selfing in this
 species.
description: Source data for
 paperRamm_et_al_JEB_Dryad.xls