cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gt3gd
title: Data from: Heterogeneous genetic makeup of the Japanese house mouse (Mus musculus) created by multiple independent introductions and spatio-temporally diverse hybridization processes

description: In this study, phylogenetic analysis of relatively long sequences of
 mitochondrial DNA (4225 bp) in the Japanese house mouse Mus musculus
 provides the first evidence that both southern Asian subspecies of Mus
 musculus castaneus (CAS) and northern Asian subspecies of Mus musculus
 musculus (MUS) arrived in Japan through rapid population expansion events,
 from Southern China ~4000 years ago and the Korean Peninsula ~2000 years
 ago, respectively. Nuclear DNA haplotype structure analyses targeting a
 chromosome region with two different tract sizes, 1 and 5 Mb, consisting
 of nine and six tandemly arranged markers, respectively, yielded a
 possible average fragment length of 170 kb of CAS haplotypes in the MUS
 background genome in northern Japan, providing a rough estimate of its
 elapsed time of 815 generations under an assumption of continued
 backcrossing. Less frequent and shortened CAS-like haplotypes specific to
 Japan were detected, suggesting ancient introduction prior to the
 appearance of the South Chinese CAS in Japan. Our analyses also showed
 sporadic appearance of long fragments (2–5 Mb) from the west European
 subspecies Mus musculus domesticus, indicating contemporary stowaway
 introduction. Overall, multiple overseas introductions, and the
 time-lagged inter-subspecies genetic admixture, probably resulted in the
 heterogeneous state of Japanese wild mice.
description: Mitochondrial sequences
 (4,225 bp) from 78 individual mice.Sequence file in Nexus
 format.0_Kuwayama_mtDNA_4225bp_78OTU.nexHaplotype sequences of the nuclear gene Zcchc14.Sequene file in Fasta format.1_Zcchc_fasta.txtHaplotype sequences of the nuclear gene Cdt1.Sequence file in Fasta format.2_Cdt1_fasta.fasHaplotype sequences of the nuclear gene Cbfa2t3.Sequence file in Fasta format.3_Cbfa2t3_fasta.fasHaplotype sequences of the nuclear gene Acsf3.Sequence file in Fasta format.4_Acsf3_fasta.fasHaplotype sequences of the nuclear gene Ankrd11.Sequence file in Fasta format.5_Ankrd11_fasta.fasHaplotype sequences of the nuclear gene Cdk10.Sequence file in Fasta format.6_Cdk10_fasta.txtHaplotype sequences of the nuclear gene Fanca.Sequence file in Fasta format.7_Fanca_fasta.txtHaplotype sequences of the nuclear gene Tcf25.Sequence file in Fasta format.8_Tcf25_fasta.txtHaplotype sequences of the nuclear gene Dbndd1.Sequence file in Fasta format.9_Dbndd1_fasta.txtHaplotype sequences of the nuclear gene Rhou.Sequence file in Fasta format.10_Rhou_fasta.txtHaplotype sequences of the nuclear gene Pgbd5.Sequence file in Fasta format.11_Pgbd5_fasta.fasHaplotype sequences of the nuclear gene Spa1l2.Sequence file in Fasta format.12_Spa1l2_fasta.fasHaplotype sequences of the nuclear gene Irf2bp2.Sequence file in Fasta format.13_Irf2bp2_fasta.fas
DOI: 10.5061/dryad.s652h
title: Data from: Phylogenetic structural equation modelling reveals no need for an 'origin' of the leaf economics spectrum

description: The leaf economics spectrum (LES) is a prominent ecophysiological paradigm
 that describes global variation in leaf physiology across plant ecological
 strategies using a handful of key traits. Nearly a decade ago, Shipley et
 al. (2006) used structural equation modelling to explore the causal
 functional relationships among LES traits that give rise to their strong
 global covariation. They concluded that an unmeasured trait drives LES
 covariation, sparking efforts to identify the latent physiological trait
 underlying the ‘origin’ of the LES. Here, we use newly developed
 phylogenetic structural equation modelling approaches to reassess these
 conclusions using both global LES data as well as data collected across
 scales in the genus Helianthus. For global LES data, accounting for
 phylogenetic non-independence indicates that no additional unmeasured
 traits are required to explain LES covariation. Across datasets in
 Helianthus, trait relationships are highly variable, indicating that
 global-scale models may poorly describe LES covariation at non-global
 scales.
description: Dataset S1. All data
 used for modeling in this study.All datasets used for
 modeling in this study, including: (1) the full GLOPNET dataset with
 missing data, (2) GLOPNET complete cases, (3) GLOPNET complete cases for
 rosids, (3) GLOPNET complete cases for asterids, (4) Population means for
 macroevolutionary analysis across the genus Helianthus [from Mason et al.,
 2015 - Evolution], (5) Family means for microevolutionary analysis among
 populations in Helianthus anomalus [from Brouillette et al., 2014 - New
 Phytologist], (6) Ontogenetic data across stages in Helianthus annuus
 [from Mason et al., 2013 - JXB], (7) Ontogenetic data across stages in
 Helianthus mollis [from Mason et al., 2013 - JXB], (8) Ontogenetic data
 across stages in Helianthus radula [from Mason et al., 2013 -
 JXB].Dataset
 S1.xls
DOI: 10.5061/dryad.s64jp
title: Data from: Molecular variability and genetic structure of Chrysodeixis includens (Lepidoptera: Noctuidae), an important soybean defoliator in Brazil

description: This study provides the first genetic characterization of the soybean
 looper, Chrysodeixis includens (Walker, 1857), an important defoliating
 pest species of soybean crops in Brazil. Population genetic variability
 and the genetic structure of C. includens populations were evaluated by
 using ISSR markers with samples from the major soybean producing regions
 in Brazil in the growing seasons 2011/2012. Seven different primers were
 applied for population characterization of the molecular variability and
 genetic structure of 8 soybean looper populations from 8 states of Brazil.
 The seven ISSR loci generated 247 bands in 246 individuals of C. includens
 sampled. The expected heterozygosity (HE) in the populations varied
 between 0.093 and 0.106, while the overall HE was 0.099, indicating low
 genetic diversity. The analysis of molecular variance indicated that 98%
 of the variability was expressed among individuals within populations (FST
 = 0.021, p = 0.001). The low level of polymorphism over all populations,
 the high levels of gene flow, and the low genetic structure are
 indicatives of the exchange of genetic information between the different
 sampled regions. Population structuring suggests the presence of two major
 groups which do not correlate with their geographic sampling location in
 Brazil. These results may indicate recent recolonization of C. includens
 in Brazil or migration patterns following source-sink dynamics.
 Furthermore, the presence of two groups within C. includens suggests that
 a study on development of resistance or any other genetic-based trait
 needs to be evaluated on both groups, and pest management in soybean
 fields should be aware that differences may come to the control strategies
 they use.
description: Binary matrix
 dataThe binary matrix (1/0)
 was generated using the 139 Bionumerics software (Applied Maths, Belgium).
 The file is in the format GenAlEx 6.5 software. The pop 1 to pop 8 means
 populations of MG, GO, MS, BA, TO, RS, MT, PR, respectively. Number of
 locus: 247; Number of samples: 246; Number of populations: 8; Column 4 to
 11: number of individuals in each population; Number of regions:
 1
DOI: 10.5061/dryad.77bn3
title: Data from: An objective in vivo diagnostic method for inflammatory bowel disease

description: Inflammatory damage to the bowel, as occurs in inflammatory bowel disease
 (IBD), is debilitating to patients. In both patients and animal
 experimental models histological analysis of biopsies and endoscopic
 examinations are used to evaluate the disease state. However such
 measurements often have delays and are invasive, while endoscopy is not
 quantitatively objective. Therefore, a real-time quantitative method to
 assess compromised mucosal barrier function is advantageous. We
 investigated the correlation of in vivo changes in electrical transmural
 impedance with histological measures of inflammation. Four platinum (Pt)
 ball electrodes were placed in the lumen of the rat small intestine, with
 a return electrode under the skin. Electrodes placed within the
 non-inflamed intestine generated stable impedances during the 3 h testing
 period. Following intraluminal injection of 2,4,6-trinitrobenzene
 sulphonic acid (TNBS), an established animal model of IBD, impedances in
 the inflamed region significantly decreased relative to a region not
 exposed to TNBS (P &lt; 0.05). Changes in intestinal transmural
 impedance were correlated (P &lt; 0.05) with histologically assessed
 damage to the mucosa and increases in neutrophil, eosinophil and T-cell
 populations at 3 h compared with tissue from control regions. This
 quantitative, real-time assay may have application in the diagnosis and
 clinical management of IBD.
description: Transmucosal impedance
 change following TNBS infectionData file "Gut
 impedance studies" describes data presented in Figure
 1.Gut
 impedances studies_Shared.pzfxHistological score of
 inflammaed tissueFile contains
 histological score data used in Figure 3E, F.Acute inflammation histology
 scores_shared.pzfxHistological analysis of
 leukocyte infiltrationFiles contains data used
 to generate Figures 4-6.Histological analysis of
 inflammation at 3 hours _shared.pzfx
DOI: 10.5061/dryad.6n660
title: Data from: Trade-offs drive resource specialization and the gradual establishment of ecotypes

description: Background: Speciation is driven by many different factors. Among those
 are trade-offs between different ways an organism utilizes resources, and
 these trade-offs can constrain the manner in which selection can optimize
 traits. Limited migration among allopatric populations and species
 interactions can also drive speciation, but here we ask if trade-offs
 alone are sufficient to drive speciation in the absence of other factors.
 Results: We present a model to study the effects of trade-offs on
 specialization and adaptive radiation in asexual organisms based solely on
 competition for limiting resources, where trade-offs are stronger the
 greater an organism’s ability to utilize resources. In this model
 resources are perfectly substitutable, and fitness is derived from the
 consumption of these resources. The model contains no spatial parameters,
 and is therefore strictly sympatric. We quantify the degree of
 specialization by the number of ecotypes evolved and the niche breadth of
 the population, and observe that these are sensitive to resource influx
 and trade-offs. Resource influx has a strong effect on the degree of
 specialization, with a clear transition between minimal diversification at
 high influx and multiple species evolving at low resource influx. At low
 resource influx the degree of specialization further depends on the
 strength of the trade-offs, with more ecotypes evolving the stronger
 trade-offs are. The specialized organisms persist through negative
 frequency-dependent selection. In addition, by analyzing one of the
 evolutionary radiations in greater detail we demonstrate that a single
 mutation alone is not enough to establish a new ecotype, even though
 phylogenetic reconstruction identifies that mutation as the branching
 point. Instead, it takes a series of additional mutations to ensure the
 stable coexistence of the new ecotype in the background of the existing
 ones. Conclusions: Trade-offs are sufficient to drive the evolution of
 specialization in sympatric asexual populations. Without trade-offs to
 restrain traits, generalists evolve and diversity decreases. The
 observation that several mutations are required to complete speciation,
 even when a single mutation creates the new species, highlights the
 gradual nature of speciation and the importance of phyletic evolution.
description: Trade-offs BMC Evol Biol
 Matlab scripts + dataMatlab scripts to
 collect data. Data used for analysis.Trade-offs_data_Dryad.zip
DOI: 10.15468/dl.pgkj7d
title: Occurrence Download

description: A dataset containing 78973 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Specimen)",
 "Geometry POLYGON((-127.08 59.12,-84.39 59.12,-84.39 70.13,-127.08 70.13,-127.08 59.12))",
 "HasCoordinate is true",
 "License is one of (CC-BY-NC 4.0, CC-BY 4.0, CC0 1.0)",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 78973 records from 218 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000556-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.kb418
title: Data from: Polygamy and an absence of fine-scale structure in Dendroctonus ponderosae (Hopk.) (Coleoptera: Curcilionidae) confirmed using molecular markers

description: An understanding of mating systems and fine-scale spatial genetic
 structure is required to effectively manage forest pest species such as
 Dendroctonus ponderosae (mountain pine beetle). Here we used genome-wide
 single-nucleotide polymorphisms to assess the fine-scale genetic structure
 and mating system of D. ponderosae collected from a single stand in
 Alberta, Canada. Fine-scale spatial genetic structure was absent within
 the stand and the majority of genetic variation was best explained at the
 individual level. Relatedness estimates support previous reports of
 pre-emergence mating. Parentage assignment tests indicate that a
 polygamous mating system better explains the relationships among
 individuals within a gallery than the previously reported female
 monogamous/male polygynous system. Furthermore, there is some evidence to
 suggest that females may exploit the galleries of other females, at least
 under epidemic conditions. Our results suggest that current management
 models are likely to be effective across large geographic areas based on
 the absence of fine-scale genetic structure.
description: Janes et. al. (2015).
 Heredity - Polygamy and fine-scale structure of mountain pine
 beetleThis file contains
 individual, population, geographic, sex and life stage information for
 samples. The alleles for each SNP and a corresponding 200 base sequence
 for each are provided also. Accession numbers for SNPs previously used in
 Janes et al. (2014). How the mountain pine beetle (Dendroctonus
 ponderosae) breached the Canadian Rocky Mountains. Molecular Biology and
 Evolution. 31(7):1803-1815 are supplied in the dbSNP
 format.Fairview_Heredity_Dryad_submission_2015.xlsx
DOI: 10.5281/zenodo.18381764
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Sven Berggren, http://www.wikidata.org/entity/Q2600462. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q2600462
DOI: 10.5281/zenodo.8038936
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Sven Berggren, http://www.wikidata.org/entity/Q2600462. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q2600462
DOI: 10.5061/dryad.271cs
title: Data from: Leaf size in three generations of a dioecious tropical tree, Ocotea tenera (Lauraceae): sexual dimorphism and changes with age

description: PREMISE OF THE STUDY: In dioecious species, selection should favor
 different leaf sizes in males and females whenever the sexes experience
 distinct environments or constraints, such as different costs of
 reproduction. We took advantage of a long-term experimental study of
 Ocotea tenera (Lauraceae), a dioecious understory tree in Monteverde,
 Costa Rica, to explore leaf size differences between genders and age
 classes across generations. METHODS: We measured leaf size in adult trees
 in a natural population, in their adult F1 offspring in two experimental
 populations, and in their F2 offspring at the seedling stage. Individual
 trees were measured at various times over a 20-year period. RESULTS:
 Leaves of female trees averaged 8% longer and 12% greater in area than
 those of males. Leaves were sexually dimorphic at reproductive maturity.
 Leaf size declined over the course of most trees’ lifetimes. Heritability
 estimates for leaf length were positive although not statistically
 significant (h2 = 0.63, SE = 0.48, P= 0.095). CONCLUSIONS: We ruled out
 the “ecological causation” hypothesis for sexual dimorphism in leaf size
 because male and female trees co-occurred in the same habitats. Sexual
 dimorphism appeared not to result from genetic or phenotypic correlations
 with other traits such as height or flower size. Rather, females appear to
 compensate for higher costs of reproduction and diminished photosynthetic
 capacity by producing larger leaves. Additive genetic variance in leaf
 size, a prerequisite for an evolutionary response to selection for sexual
 dimorphism, was suggested by positive (although only marginally
 significant) heritability estimates.
description: Leaf size and shape in
 Ocotea tenera (Lauraceae)measurements of almost
 3000 leaves over a 26-year periodWheelwrightOcoteaData.txt
DOI: 10.5061/dryad.9519kj3
title: Data from: Factors influencing organic carbon accumulation in mangrove ecosystems

description: There is growing interest in the capacity of mangrove ecosystems to
 sequester and store “blue carbon”. Here we provide a synthesis of
 sixty-six dated sediment cores with previously calculated carbon
 accumulation rates in mangrove ecosystems to assess the effects of
 environmental and anthropogenic pressures. Conserved sedimentary
 environments were found to be within the range of the current global
 average for sediment accretion (~2.5 mm yr-1) and carbon accumulation
 (~160 g m-2yr-1). Moreover, similar sediment accretion and carbon
 accumulation rates were found between mixed and monotypic mangrove
 forests, however higher mean and median values were noted from within the
 forest as compared to adjacent areas such as mudflats. The carbon
 accumulation within conserved environments were up to fourfold higher than
 in degraded or deforested environments but threefold lower than those
 impacted by domestic or aquaculture effluents (&gt; 900 g m-2 yr-1)
 and, twofold lower than those impacted by storms and flooding (&gt;
 500 g m-2yr-1). These results suggest that depending on the type of
 impact, the blue carbon accumulation capacity of mangrove ecosystems may
 become substantially modified.
description: Electronic supplementary
 Material (Pérez et al.)This file content the
 data, own tables and own figures from: Factors influencing organic carbon
 accumulation in mangrove ecosystems, Pérez Segovia, Alexander, G.
 Libardoni, Bruno, Sanders, ChristianESM (Pérez et
 al.).docx
DOI: 10.5061/dryad.42qq0
title: Data from: Constructing an invasion machine: the rapid evolution of a dispersal-enhancing phenotype during the cane toad invasion of Australia

description: Biological invasions can induce rapid evolutionary change. As cane toads
 (Rhinella marina) have spread across tropical Australia over an 80-year
 period, their rate of invasion has increased from around 15 to 60 km per
 annum. Toads at the invasion front disperse much faster and further than
 conspecifics from range-core areas, and their offspring inherit that rapid
 dispersal rate. We investigated morphological changes that have
 accompanied this dramatic acceleration, by conducting three-dimensional
 morphometric analyses of toads from both range-core and invasion-front
 populations. Morphology of heads, limbs, pectoral girdles and pelvic
 girdles differed significantly between toads from the two areas, ranging
 from 0.5% to 16.5% difference in mean bone dimensions between populations,
 with invasion-front toads exhibiting wider forelimbs, narrower hindlimbs
 and more compact skulls. Those changes plausibly reflect an increased
 reliance on bounding (multiple short hops in quick succession) rather than
 separate large leaps. Within an 80-year period, invasive cane toads have
 converted the basic anuran body plan – which evolved for occasional large
 leaps to evade predators – into a morphotype better-suited to sustained
 long-distance travel.
description: Landmark points for cane
 toad bonesA collection of
 landmarked .pts files for all cane toad bones used in this
 study.Landmark
 points.zipMorphologika output
 filesOutput from generalized
 Procrustes analysis in Morphologika (version 2.5) on landmark
 data
DOI: 10.5061/dryad.24v57
title: Data from: Epistatic interaction of the melanocortin 1 receptor and agouti signaling protein genes modulates wool color in the Brazilian Creole sheep

description: Different pigmentation genes have been associated with color diversity in
 domestic animal species. The melanocortin 1 receptor (MC1R), agouti
 signaling protein (ASIP), tyrosinase related protein-1 (TYRP1) and v-kit
 Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog (KIT) genes are
 candidate genes responsible for variation in wool color among breeds of
 sheep. Although the influence of these genes has been described in some
 breeds, in many others the effect of interactions among genes underlying
 wool color has not been investigated. The Brazilian Creole sheep is a
 local breed with a wide variety of wool color, ranging from black to white
 with several intermediate hues. We analyzed in this study the influence of
 the genes MC1R, ASIP, TYRP1 and KIT on the control of wool color in this
 breed. A total of 410 samples were analyzed, including 148 white and 262
 colored individuals. The MC1R and ASIP polymorphisms were significantly
 associated with the segregation of either white or colored wool. The
 dominant MC1R allele (ED p.M73K and p.D121N) was present only in colored
 animals. All white individuals were homozygous for the MC1R recessive
 allele (E+) and carriers of the duplicated copy of ASIP. A gene expression
 essay showed that only the carrier of the duplicated copy of ASIP produces
 increased levels in skin, not detectable in the single homozygous copy.
 These results demonstrate that the epistatic interaction of the genotypes
 in the MC1R and ASIP gene is responsible for the striking color variation
 in the Creole breed.
description: Table 1 MC1R and ASIP
 genotype in total populationGenotype of the MC1R and
 ASIP gene in 328 samples from Creole sheep breed classified in color
 groups.Table 2 MC1R and ASIP
 genotype in Quantification experimentGenotype of MC1R and
 ASIP gene, color group classification and Real Time PCR Ct in 82 samples
 from expression quantification experiment.Table 3 Colorimetric
 parameters in total populationColorimetric parameters
 data in CIELAB color space in 115 wool samples from Creole sheep
 breed.Table
 3 Color parameters in total
 population.csvTable 4 Colorimetric
 parameters in quantification experimentColorimetric parameters
 in CIELAB color space in 82 wool samples from expression quantification
 experimentAligment MC1R gene total
 samplesSequence alignment from
 MC1R gene in 328 samples from Creole sheep breed.Alignment gene
 TYRP1Sequence alignment from
 TYRP1 gene exons 1 to 8 in Creole sheep breed.Alignment KIT
 geneSequence alignment from
 KIT gene exons 2 to 21 in Creole sheep breed.