cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q0694
title: Data from: Geography and end use drive the diversification of worldwide winter rye populations

description: To meet the current challenges in human food production, improved
 understanding of the genetic diversity of crop species that maximizes the
 selection efficacy in breeding programs is needed. The present study
 offers new insights into the diversity, genetic structure and demographic
 history of cultivated rye (Secale cereale L.). We genotyped 620
 individuals from 14 global rye populations with a different end use (grain
 or forage) at 32 genome-wide simple sequence repeat markers. We reveal the
 relationships among these populations, their sizes and the timing of
 domestication events using population genetics and model-based inference
 with approximate Bayesian computation. Our main results demonstrate (i) a
 high within-population variation and genetic diversity, (ii) an unexpected
 absence of reduction in diversity with an increasing improvement level and
 (iii) patterns suggestive of multiple domestication events. We suggest
 that the main drivers of diversification of winter rye are the end use of
 rye in two early regions of cultivation: rye forage in the Mediterranean
 area and grain in northeast Europe. The lower diversity and stronger
 differentiation of eastern European populations were most likely due to
 more intensive cultivation and breeding of rye in this region, in contrast
 to the Mediterranean region where it was considered a secondary crop or
 even a weed. We discuss the relevance of our results for the management of
 gene bank resources and the pitfalls of inference methods applied to crop
 domestication due to violation of model assumptions and model complexity.
description: Raw micro-satellite data
 for 14 Rye populationsRaw micro-satellite data
 in arp format with original population names. The populations are grouped
 following the three classes described in the article at the end of the
 data file. Missing information is coded with a "?" and null
 alleles are coded with a "0".dryadRyeData2015.arpPCR Primers and PCR ConditionsA comma separated file containing the primers of the PCR, their source, and the PCR conditions. The legend for the sources and the abbreviations for the PCR conditions can be found in the ReadMe file.PCRPrimersConditions.csv
DOI: 10.5061/dryad.2q242
title: Data from: Density-dependent effects of a widespread invasive herbivore on tree survival and biomass during reforestation

description: Reforestation has been widely adopted as a solution to multiple global
 change issues. However, the role of herbivory by invasive species in the
 restoration of grassland to forest has received little attention. We
 conducted a field experiment to investigate the impacts of a widespread
 invasive mammalian herbivore, the European rabbit (Oryctolagus cuniculus),
 on trees planted in a landscape-scale reforestation program in
 south-eastern Australia. Three native tree species were planted inside and
 outside rabbit-proof exclosures within 10 experimental units, and a random
 half of the units were subjected to intensive and sustained rabbit control
 for the remainder of the experiment. Quarterly survival of trees, and
 total aboveground biomass at the conclusion of the experiment, were
 estimated using hierarchical Bayesian models. Control substantially
 reduced rabbit densities on the five treatment units relative to the five
 non-treatment units. Survival of trees planted outside exclosures was
 highest at lowest rabbit density and declined non-linearly with increasing
 rabbit density for all three tree species, but even very low rabbit
 densities had strong negative effects on the survival of trees outside
 exclosures. There was a three-way interaction between tree height, being
 outside an exclosure, and rabbit density. Smaller trees planted outside
 exclosures always had substantially lower overall survival than trees of
 the same height planted inside exclosures, and the magnitude of the
 difference increased with increasing rabbit density. Increasing rabbit
 densities reduced the overall survival of increasingly taller trees of all
 three species planted outside exclosures. The aboveground biomass of trees
 surviving outside exclosures was significantly greater in treatment units
 compared with non-treatment units for all three species. The combined
 effects of differential survival and accumulation of aboveground biomass
 led to higher biomasses inside exclosures relative to outside exclosures
 just 21 months after planting. The aboveground biomass of trees planted
 outside exclosures declined with increasing rabbit density, and was
 effectively zero when rabbit densities exceeded 100 active warren
 entrances/ha. These results demonstrate that invasive herbivores can
 rapidly arrest the conversion of grassland to forest. Invasive herbivores
 such as the European rabbit may need to be completely excluded in order to
 maximize the benefits of reforestation.
description: Seedling growth and
 survival dataSurvival, growth and
 aboveground biomass data for individually-tagged tree seedlings, with
 species, site, exclosure and treatment codestree_data.csvActive warren entrance counts at experimental sitesCounts of number of active rabbit warren entrances at each of 10 experimental sites, over the course of the tree survival and growth experiment. Included rabbit control treatment and site codes.active_warren_entrances.csv
DOI: 10.5061/dryad.656
title: Data from: Failure of the ILD to determine data combinability for slow loris phylogeny

description: Tests for incongruence as an indicator of among data partition conflict
 have played an important role in conditional data combination. When such
 tests reveal significant incongruence, this has been interpreted as
 rationale for not combining data in a single phylogenetic analysis. In
 this study of lorisiform phylogeny, we employ the incongruence length
 difference (ILD) test to assess conflict among three independent data
 sets. A large morphological data set and two unlinked molecular data sets,
 the mitochondrial cytochrome b gene and the nuclear interphotoreceptor
 retinoid binding protein (exon 1), are analyzed with various optimality
 criteria and weighting mechanisms in order to determine the phylogenetic
 relationships among slow lorises (Primates, Loridae). When analyzed
 separately, the morphological data show impressive statistical support for
 a monophyletic Loridae. Both molecular data sets resolve the Loridae as
 paraphyletic, though with different branching order depending on
 optimality criterion and/or character weighting employed. When the three
 data partitions are analyzed in various combinations, an inverse
 relationship between congruence and phylogenetic accuracy is observed.
 Nearly all combined analyses that recover monophyly indicate strong data
 partition incongruence (p = 0.00005, in the most extreme case) whereas all
 analyses that recover paraphyly indicate lack of significant incongruence.
 Numerous lines of evidence verify that monophyly is the accurate
 phylogenetic result. Therefore, this study contributes to a growing body
 of information that affirms that measures of incongruence should not be
 employed as indicators of data set combinability.
description: DNA and Morphology Data
 SetDNA.morph.nexuscytB and IRBP Data Setcytb.IRBP.nexuscytB and Morphology Data Setcytb.morph.nexuscytB Data Setcytb.nexusIRBP and Morphology Data SetIRBP.morph.nexusIRBP Data SetIRBP.nexus
DOI: 10.5061/dryad.mm5m1
title: Data from: Do cladistic and morphometric data capture common patterns of morphological disparity?

description: The distinctly non-random diversity of organismal form manifests itself in
 discrete clusters of taxa that share a common body plan. As a result,
 analyses of disparity require a scalable comparative framework. The
 difficulties of applying geometric morphometrics to disparity analyses of
 groups with vastly divergent body plans are overcome partly by the use of
 cladistic characters. Character-based disparity analyses have become
 increasingly popular, but it is not clear how they are affected by
 character coding strategies or revisions of primary homology statements.
 Indeed, whether cladistic and morphometric data capture similar patterns
 of morphological variation remains a moot point. To address this issue, we
 employ both cladistic and geometric morphometric data in an exploratory
 study of disparity focussing on caecilian amphibians. Our results show no
 impact on relative intertaxon distances when different coding strategies
 for cladistic characters were used or when revised concepts of homology
 were considered. In all instances, we found no statistically significant
 difference between pairwise Euclidean and Procrustes distances, although
 the strength of the correlation among distance matrices varied. This
 suggests that cladistic and geometric morphometric data appear to
 summarize morphological variation in comparable ways. Our results support
 the use of cladistic data for characterizing organismal disparity.
description: Hetherington_AJ_et_al_ESMCladistic and geometric morphometric datasets on which this study is based.
DOI: 10.5061/dryad.6dm3c
title: Data from: Hybridization associated with cycles of ecological succession in a passerine bird

description: Identifying the diversity of contexts that can lead to hybridization is
 important for understanding its prevalence and dynamics in natural
 populations. Despite the potential of ecological succession to
 dramatically alter species co-occurrence and abundances, it is unknown
 whether it directly promotes hybridization and, if so, has long-lasting
 consequences. Here, we summarize 30 years of survey data across 10
 populations to show that in western and mountain bluebirds, heterospecific
 pairing occurs during repeatable and transient colonization events at the
 early stages of species turnover. Despite mixed pairing occurring only
 during early succession, genetic data showed presence of hybrids at both
 early and late successional stages. Moreover, hybrids showed novel
 patterns of variation in morphology and behavior, emphasizing that even
 ephemeral contexts for hybridization can have important evolutionary
 consequences. Our results suggest that because ecological succession often
 brings together closely related competitors in disparate numbers but lasts
 for only a brief period of time, it may be a widespread but
 underappreciated context for hybridization.
description: Simulations, sampling
 and allele frequenciesDryad_Material.pdf
DOI: 10.5061/dryad.276d6
title: Data from: A bust but no boom: responses of floodplain bird assemblages during and after prolonged drought

description: 1. Climate change alters the frequency and severity of extreme events,
 such as drought. Such events will be increasingly important in shaping
 communities as climate change intensifies. The ability of species to
 withstand extreme events (resistance) and to recover once adverse
 conditions abate (resilience) will determine their persistence. 2. We
 estimated the resistance and resilience of bird species during and after a
 13-year drought (the ‘Big Dry’) in floodplain forests in south-eastern
 Australia. 3. We conducted bird surveys at the beginning and end of the
 Big Dry, and after the abrupt end to the drought (the ‘Big Wet’), to
 evaluate species-specific changes in reporting rates among the three
 periods. We assessed changes in bird-breeding activity before and after
 the Big Wet to estimate demographic resilience based on breeding. 4.
 Between the start and the end of the Big Dry (1998 vs. 2009), 37 of 67
 species declined substantially. Of those, only two had increased reporting
 rates after the Big Wet (2009 vs. 2013) that were equal to or larger than
 their declines, while three partially recovered. All other declining
 species showed low resilience: 25 showed no change in reporting rates and
 seven declined further. The number of breeding species and total breeding
 activity of all species declined after the Big Wet, and there was no
 change in the number of young produced. 5. The Big Dry caused widespread
 declines in the floodplain avifauna. Despite the drought being broken by 2
 years of well-above-average rainfall and subsequent near-average rainfall,
 most species showed low resilience and there was little indication that
 overall breeding had increased. The effects of drought appeared to be
 pervasive for much of the floodplain avifauna, regardless of species
 traits (species body mass, fecundity, mobility or diet). Ecosystems such
 as these are likely to require active management and restoration,
 including reinstatement of natural flooding regimes, to improve ecological
 condition, to enhance resistance and resilience to extreme climate events.
description: Selwood_etal_data_2015_JANEIndividual species reporting rates per site, per year (worksheet= Reprates and Reprates_description for field descriptors) and measures of breeding per site, per year (worksheet = Breeding and Breeding_description for field descriptors).
DOI: 10.5061/dryad.r3q17
title: Data from: Does nasal echolocation influence the modularity of the mammal skull?

description: In vertebrates, changes in cranial modularity can evolve rapidly in
 response to selection. However, mammals have apparently maintained their
 pattern of cranial integration throughout their evolutionary history and
 across tremendous morphological and ecological diversity. Here, we use
 phylogenetic, geometric morphometric and comparative analyses to test the
 hypothesis that the modularity of the mammalian skull has been remodelled
 in rhinolophid bats due to the novel and critical function of the nasal
 cavity in echolocation. We predicted that nasal echolocation has resulted
 in the evolution of a third cranial module, the ‘nasal dome’, in addition
 to the braincase and rostrum modules, which are conserved across mammals.
 We also test for similarities in the evolution of skull shape in relation
 to habitat across rhinolophids. We find that, despite broad variation in
 the shape of the nasal dome, the integration of the rhinolophid skull is
 highly consistent with conserved patterns of modularity found in other
 mammals. Across their broad geographical distribution, cranial shape in
 rhinolophids follows two major divisions that could reflect adaptations to
 dietary and environmental differences in African versus South Asian
 distributions. Our results highlight the potential of a relatively simple
 modular template to generate broad morphological and functional variation
 in mammals.
description: PCA scores for lateral
 shape coordinates of Rhinolophus skullsPCA scores for lateral
 shape coordinates of Rhinolophus skulls, generated from Procrustes
 coordinates from geometric morphometric analyses of museum
 specimensPCA_LateralShapeScores.csvPCA scores for ventral shape coordinates of Rhinolophus skullsPCA scores for ventral shape coordinates of Rhinolophus skulls, generated from Procrustes coordinates from geometric morphometric analyses of museum specimensPCA_VentralShapeScores.csvProcustes coordinates and centroid sizes-Ventral viewProcustes coordinates and centroid sizes from the ventral view of Rhinolophus skullsProcustes coordinates and centroid sizes-Lateral viewProcustes coordinates and centroid sizes from the lateral view of Rhinolophus skulls
DOI: 10.5061/dryad.cm94q95
title: Data from: Soil is the main predictor of secondary rain forest estimated aboveground biomass across a neotropical landscape

description: We studied the relative effects of landscape configuration, environmental
 variables, forest age and spatial variables on estimated aboveground
 biomass (AGB) in Costa Rican secondary rain forests patches. We measured
 trees &gt; 5 cm dbh in 24, 0.25 ha plots and estimated AGB for trees
 5-24.9 cm dbh and for trees &gt; 25 cm dbh using two allometric
 equations based on multispecies models using tree dbh and wood specific
 gravity. AGB averaged 87.3 Mg/ha for the 24 plots (not including remnant
 trees) and 123.4 Mg/ha including remnant trees (20 plots). There was no
 effect of forest age on AGB. Variation partitioning analysis showed that
 soils, climate, landscape configuration and space together explained 61%
 of tree AGB variance. When controlling for the effects of the other three
 variables, only soils remained significant. Soil properties, specifically
 K and Cu, had the strongest independent effect on AGB (variation
 partitioning, R2=0.17, p=0.0310), indicating that in this landscape, AGB
 variation in secondary forest patches is influenced by soil chemical
 properties. Elucidating the relative influence of soils in AGB variation
 is critical for understanding changes associated to land cover
 modification across neotropical landscapes, as it could have important
 consequences for land use planning since secondary forests are considered
 carbon sinks.
description: DBH of trees per
 plotThis is the raw dbh data
 collected n the field per plotPlotTreesDBH-SantiagoGarciaFineganBosquePerz.xlsxRemnant Trees DataThs is the AGB calculations for the remnant trees per plot.Remnant Trees-SantiagoGarciaFineganBosquePerez.xlsx
DOI: 10.5061/dryad.11243
title: Data from: Adaptive evolution and divergent expression of heat stress transcription factors in grasses

description: Background: Heat stress transcription factors (Hsfs) regulate gene
 expression in response to heat and many other environmental stresses in
 plants. Understanding the adaptive evolution of Hsf genes in the grass
 family will provide potentially useful information for the genetic
 improvement of modern crops to handle increasing global temperatures.
 Results: In this work, we performed a genome-wide survey of Hsf genes in 5
 grass species, including rice, maize, sorghum, Setaria, and Brachypodium,
 by describing their phylogenetic relationships, adaptive evolution, and
 expression patterns under abiotic stresses. The Hsf genes in grasses were
 divided into 24 orthologous gene clusters (OGCs) based on phylogeneitc
 relationship and synteny, suggesting that 24 Hsf genes were present in the
 ancestral grass genome. However, 9 duplication and 4 gene-loss events were
 identified in the tested genomes. A maximum-likelihood analysis revealed
 the effects of positive selection in the evolution of 11 OGCs and
 suggested that OGCs with duplicated or lost genes were more readily
 influenced by positive selection than other OGCs. Further investigation
 revealed that positive selection acted on only one of the duplicated genes
 in 8 of 9 paralogous pairs, suggesting that neofunctionalization
 contributed to the evolution of these duplicated pairs. We also
 investigated the expression patterns of rice and maize Hsf genes under
 heat, salt, drought, and cold stresses. The results revealed divergent
 expression patterns between the duplicated genes. Conclusions: This study
 demonstrates that neofunctionalization by changes in expression pattern
 and function following gene duplication has been an important factor in
 the maintenance and divergence of grass Hsf genes.
description: Phylogenetic
 treeThe NJ tree for the Hsf
 proteins in grassesNJ_JTT1.nwkAlignmentThe alignment of the Hsf proteins in grassesprotein.fasSummary of 125 Hsf genes identified in 5 grass genomesSummary of 125 Hsf genes identified in 5 grass genomesA_file_1.xlsx
DOI: 10.5061/dryad.vv28j
title: Data from: Genome-wide prediction models that incorporate de novo GWAS are a powerful new tool for tropical rice improvement

description: To address the multiple challenges to food security posed by global
 climate change, population growth and rising incomes, plant breeders are
 developing new crop varieties that can enhance both agricultural
 productivity and environmental sustainability. Current breeding practices,
 however, are unable to keep pace with demand. Genomic selection (GS) is a
 new technique that helps accelerate the rate of genetic gain in breeding
 by using whole-genome data to predict the breeding value of offspring.
 Here, we describe a new GS model that combines RR-BLUP with markers fit as
 fixed effects selected from the results of a genome-wide-association study
 (GWAS) on the RR-BLUP training data. We term this model GS + de novo GWAS.
 In a breeding population of tropical rice, GS + de novo GWAS outperformed
 six other models for a variety of traits and in multiple environments. On
 the basis of these results, we propose an extended, two-part breeding
 design that can be used to efficiently integrate novel variation into
 elite breeding populations, thus expanding genetic diversity and enhancing
 the potential for sustainable productivity gains.
description: IRRI MET 2011 2012
 phenotype data all filesThis archive contains
 the raw multi-environment (MET) phenotype data used for the MET GS
 experiments reported in this publication. Each .csv file in the archive
 contains the data for a particular year, season, and site. See ReadMe file
 for description of columns.MET_2011_2012_pheno_data_all.zip
DOI: 10.5061/dryad.ct849
title: Data from: Genetic variation, multiple paternity and measures of reproductive success in the critically endangered hawksbill turtle (Eretmochelys imbricata)

description: The Yucatán Peninsula in Mexico contains some of the largest breeding
 groups of the globally distributed and critically endangered hawksbill
 turtle (Eretmochelys imbricata). An improved understanding of the breeding
 system of this species and how its genetic variation is structured among
 nesting areas is required before the threats to its survival can be
 properly evaluated. Here, we genotype 1195 hatchlings and 41 nesting
 females at 12 microsatellite loci to assess levels of multiple paternity,
 genetic variation and whether individual levels of homozygosity are
 associated with reproductive success. Of the 50 clutches analyzed, only 6%
 have multiple paternity. The distribution of pairwise relatedness among
 nesting localities (rookeries) was not random with elevated within-rookery
 relatedness, and declining relatedness with geographic distance indicating
 some natal philopatry. Although there was no strong evidence that
 particular rookeries had lost allelic variation via drift, younger turtles
 had significantly lower levels of genetic variation than older turtles,
 suggesting some loss of genetic variation. At present there is no
 indication that levels of genetic variation are associated with measures
 of reproductive success such as clutch size, hatching success, and
 frequency of infertile eggs.
description: Ei-genotypesThe database contains the genotypes of 41 nesting hawksbills and 1,188 hatchling that were successfully genotyped at 12 polymorphic microsatellite loci. Paternal reconstructed genotypes are also includes. The name of the rookery is abreviated where: XV=Xicalango-Victoria, CK=Chenkan, CE=Celestun, CL=Las Coloradas, CY=El Cuyo, H=Holbox. Id letters identifies each nesting females, her offspring and the male that sired that clutch. In those cases where offspring contain and Id letter that is not on the females or fathers id indicates that it is a successive clutches of the same previously reported females (i.e. if there are offspring with and Id=B, but there are no females with these Id, then is a successive clutch from female A). In the cases where males Id have letter and number indicate that those multiple males sired a same clutch indicating multiple paternityReproductive successInformation of nesting females and reproductive success data of their clutches. Females that were marked were considered as neophytes or first time nesters, while recaptures were considered as experienced or older females. CCL= curve carapace length