cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h0cc7
title: Data from: New insights on water buffalo genomic diversity and post-domestication migration routes from medium density SNP chip data

description: The domestic water buffalo is native to the Asian continent but through
 historical migrations and recent importations, nowadays has a worldwide
 distribution. The two types of water buffalo, i.e., river and swamp,
 display distinct morphological and behavioral traits, different karyotypes
 and also have different purposes and geographical distributions. River
 buffaloes from Pakistan, Iran, Turkey, Egypt, Romania, Bulgaria, Italy,
 Mozambique, Brazil and Colombia, and swamp buffaloes from China, Thailand,
 Philippines, Indonesia and Brazil were genotyped with a species-specific
 medium-density 90K SNP panel. We estimated the levels of molecular
 diversity and described population structure, which revealed historical
 relationships between populations and migration events. Three distinct
 gene pools were identified in pure river as well as in pure swamp buffalo
 populations. Genomic admixture was seen in the Philippines and in Brazil,
 resulting from importations of animals for breed improvement. Our results
 were largely consistent with previous archeological, historical and
 molecular-based evidence for two independent domestication events for
 river- and swamp-type buffaloes, which occurred in the Indo-Pakistani
 region and close to the China/Indochina border, respectively. Based on a
 geographical analysis of the distribution of diversity, our evidence also
 indicated that the water buffalo spread out of the domestication centers
 followed two major divergent migration directions: river buffaloes
 migrated west from the Indian sub-continent while swamp buffaloes migrated
 from northern Indochina via an east-south-eastern route. These data
 suggest that the current distribution of water buffalo diversity has been
 shaped by the combined effects of multiple migration events occurred at
 different stages of the post-domestication history of the species.
description: Buffalo SNPchip
 dataSNP data used in buffalo
 diversity study. SNPchip data are in binary PLINK
 format.Colli_buffalo_diversity.zip
DOI: 10.5061/dryad.h5m04
title: Data from: A new species of burnetiid (Therapsida, Burnetiamorpha) from the early Wuchiapingian of South Africa and implications for the evolutionary ecology of the family Burnetiidae.

description: Burnetiidae is a family of basal therapsids that is known from late
 Permian-aged (Lopingian) sequences from southern and eastern Africa and
 European Russia. Recent discoveries of related genera within the broader
 clade Burnetiamorpha have added to our understanding of morphological
 variation in the group but have eroded the list of characters defining the
 family Burnetiidae. We describe a new burnetiid taxon, Leucocephalus
 wewersi gen. et sp. nov., and argue that Burnetiidae can be defined by,
 among other characters, the presence of two bosses on the ventrolateral
 surface of suborbital bar and zygomatic arch, high skull angulation
 between the orbits, and a median frontal crest that becomes wider and
 lower posteriorly. The new specimen was found in the early Wuchiapingian
 Tropidostoma Assemblage Zone of the Main Karoo Basin and, along with
 previous discoveries, indicates that the family reached its greatest
 diversity and abundance in the early Wuchiapingian. Diversity declined
 into the later Wuchiapingian and Changhsingian. Although the clade
 Burnetiamorpha, including the family Burnetiidae, contains at least 11
 genera, each of these is exceptionally rare, with most represented by only
 one specimen. This could be attributed to a genuine ecological
 characteristic or may be the result of biogeographic factors, particularly
 if the Main Karoo Basin was on the periphery of their range.
description: Figure S1 - Synchrotron
 scans of skull SAM-PK-K11112 (annotated)Slices through
 synchrotron image of SAM-PK-K11112 (Leucocephalus amandelboomensis gen. et
 sp. nov.). Scale = 2 cm.Figure
 S1.pdfFigure S2 - Synchrotrons
 scans of skull SAM-PK-K11112 (not annotated)Slices through
 synchrotron image of SAM-PK-K11112 (Leucocephalosaurus amandelboomensis
 gen. et . sp. nov.) without labels. Scale = 2 cm. Slices are identical to
 those in Fig. S1.Figure
 S2.pdfTable S1 - List of
 fossil specimens collected at Amandelboom localityList of fossil specimens
 whose positions are shown on the stratigraphic section in Figure 2 of the
 main article.Table
 S1.xlsxTable S2 - List of
 burnetiamorph specimensBurnetiamorph specimens
 considered in this study.Table
 S2.xlsxAppendix S1 - Character
 matrix for biarmosuchians used in this study.Character matrix for
 biarmosuchians used in this study. TNT input file.Appendix
 S1.tnt
DOI: 10.5061/dryad.9m771
title: Data from: Development and validation of a weather-based warning system to advise fungicide applications to control dollar spot on turfgrass

description: Dollar spot is one of the most common diseases of golf course turfgrass
 and numerous fungicide applications are often required to provide adequate
 control. Weather-based disease warning systems have been developed to more
 accurately time fungicide applications; however, they tend to be
 ineffective and are not currently in widespread use. The primary objective
 of this research was to develop a new weather-based disease warning system
 to more accurately advise fungicide applications to control dollar spot
 activity across a broad geographic and climactic range. The new dollar
 spot warning system was developed from data collected at field sites in
 Madison, WI and Stillwater, OK in 2008 and warning system validation sites
 were established in Madison, WI, Stillwater, OK, Knoxville, TN, State
 College, PA, Starkville, MS, and Storrs, CT between 2011 and 2016. A
 meta-analysis of all site-years was conducted and the most effective
 warning system for dollar spot development consisted of a five-day moving
 average of relative humidity and average daily temperature. Using this
 model the highest effective probability that provided dollar spot control
 similar to that of a calendar-based program across the numerous sites and
 years was 20%. Additional analysis found that the 20% spray threshold
 provided comparable control to the calendar-based program while reducing
 fungicide usage by up to 30%, though further refinement may be needed as
 practitioners implement this warning system in a range of environments not
 tested here. The weather-based dollar spot warning system presented here
 will likely become an important tool for implementing precision disease
 management strategies for future turfgrass managers, especially as
 financial and regulatory pressures increase the need to reduce pesticide
 usage on golf course turfgrass.
description: 2008 to 2010 5 day
 MoveAve datasetsFull Data Sets aligned
 with 5-day Moving Average Weather Data2010 FINAL turf model
 build with Wisc Damon V3 SASSAS code of Logistic
 Regression for building Models2010 FINAL turf model build
 with Wisc Damon V3.sas2010 FINAL turf model
 build with Wisc Damon V3 ROC AnalysisAdditional SAS code for
 model build with ROC curve displayFinal Model Build Brief
 DescriptionA brief text summary of
 the model build approach2016 Data for Primary
 ANOVA SASRaw, multi-site
 validation data for Meta-analysisPrimary ANOVA
 GLIMMIXSAS code to obtain the
 primary ANOVA results for meta-analysis2016 Dollar Spot Model
 Meta-AnalysisSAS code for univariate
 meta-analysis approach to validate model as a fungicide spray
 advisor2016 Meta-Analysis
 ResultsMet-analysis raw data
 and preliminary meta-analysis results
DOI: 10.5061/dryad.n8h25
title: Data from: Strength of selection on Trpc2 gene predicts accessory olfactory bulb form in bat vomeronasal evolution

description: Vestigial characters are common across the tree of life, but the
 underlying evolutionary processes shaping phenotypic loss are poorly
 understood. The mammalian vomeronasal system, which detects social
 chemical cues important to fitness, is an impressive example of a sensory
 system lost multiple times. Three times more losses are inferred among
 bats than in other mammalian orders. We characterized the relationship
 between amino acid substitutions in a gene tightly linked to vomeronasal
 function (Trpc2) and the accessory olfactory bulb, a brain region that
 processes the detection of these vomeronasal chemical cues. By applying a
 phylogenetic logistic regression, we found a strong negative relationship
 between the branch lengths representing rates of codon changes in the
 Trpc2 gene tree and the presence or absence of an accessory olfactory
 bulb. Longer branch lengths predict loss of the accessory olfactory bulb,
 suggesting selection has relaxed on the system as a whole. Based on this
 relationship, we predicted the absence of an accessory olfactory bulb in
 19 bat species with unknown morphology. Several species with predicted
 losses have specialized skull morphology, suggesting a potential tradeoff
 between adaptation in skull shape and maintenance of the vomeronasal
 system. This study offers a new approach to relate genetic mechanisms and
 phenotypes at a macroevolutionary scale.
description: Models_code_alignmentsforDryad.zipMG852085Platyrrhinus brachcephalus Trpc2 sequence
DOI: 10.5061/dryad.r282vk6
title: Data from: Incidence rate of community-acquired pneumonia in adults: a population-based prospective active surveillance study in three cities in South America

description: OBJECTIVE: To determine the incidence rate and mortality of
 community-acquired pneumonia (CAP) in adults in three cities in Latin
 America during a three-year period. DESIGN: Prospective population based
 study. SETTING: Healthcare facilities (outpatient centers and hospitals)
 in the cities of General Roca (Argentina), Rivera (Uruguay) and Concepcion
 (Paraguay). PARTICIPANTS: 2302 adults aged 18 years and older with CAP
 were prospectively enrolled between January 2012 and March 2015. MAIN
 OUTCOME MEASURES: Incidence rate of CAP in adults, predisposing conditions
 for disease, mortality at 14 days and at one year were estimated.
 Incidence rate of CAP, within each age group, was calculated by dividing
 the number of cases by the person-years of disease-free exposure time
 based on the last census; incidence rates were expressed per 1000
 person-years. RESULTS: Median age of participants was 66 years, 46.44 %
 were men, 68% were hospitalized. Annual incidence rate was 7.03 (CI95%
 6.64-7.44) per 1000 person-years in General Roca, 6.33 (CI95% 5.92-6.78)
 per 1000 person-years in Rivera and 1.76 (CI95% 1.55-2.00) per 1000
 person-years in Concepcion. Incidence rates were highest in participants
 aged over 65 years. 82.4% had at least one predisposing condition and 48%
 had 2 or more (multi-morbidity). Chronic heart disease (43.6%) and smoking
 (37.3%) were the most common risk factors. 14-day mortality rate was 12.1%
 and one-year mortality was 24.9%. Multi-morbidity was associated with an
 increased risk of death at 14 days (OR 2.91; 2.23 to 3.80) and at 1 year
 (OR 3.00; 2.44 to 3.70). CONCLUSIONS: We found a high incidence rate of
 CAP in adults, ranging from 1.76 to 7.03 per 1000 person-years, in three
 cities in South America, disclosing the high burden of disease in the
 region. Efforts to improve prevention strategies are needed.
description: Database NACREG 1
 v21feb2018
DOI: 10.5061/dryad.b273q6p
title: Data from: Genomic predictions and genome-wide association study of resistance against Piscirickettsia salmonis in coho salmon (Oncorhynchus kisutch) using ddRAD sequencing

description: Piscirickettsia salmonis is one of the main infectious diseases affecting
 coho salmon (Oncorhynchus kisutch) farming, and current treatments have
 been ineffective for the control of this disease. Genetic improvement for
 P. salmonis resistance has been proposed as a feasible alternative for the
 control of this infectious disease in farmed fish. Genotyping by
 sequencing (GBS) strategies allow genotyping of hundreds of individuals
 with thousands of single nucleotide polymorphisms (SNPs), which can be
 used to perform genome wide association studies (GWAS) and predict genetic
 values using genome-wide information. We used double-digest
 restriction-site associated DNA (ddRAD) sequencing to dissect the genetic
 architecture of resistance against P. salmonis in a farmed coho salmon
 population and to identify molecular markers associated with the trait. We
 also evaluated genomic selection (GS) models in order to determine the
 potential to accelerate the genetic improvement of this trait by means of
 using genome-wide molecular information. A total of 764 individuals from
 33 full-sib families (17 highly resistant and 16 highly susceptible) were
 experimentally challenged against P. salmonis and their genotypes were
 assayed using ddRAD sequencing. A total of 9,389 SNPs markers were
 identified in the population. These markers were used to test genomic
 selection models and compare different GWAS methodologies for resistance
 measured as day of death (DD) and binary survival (BIN). Genomic selection
 models showed higher accuracies than the traditional pedigree-based best
 linear unbiased prediction (PBLUP) method, for both DD and BIN. The models
 showed an improvement of up to 95% and 155% respectively over PBLUP. One
 SNP related with B-cell development was identified as a potential
 functional candidate associated with resistance to P. salmonis defined as
 DD.
description: Genotype data from 580
 coho salmon individualsTable
 S1.csv
DOI: 10.5061/dryad.3p008p4
title: Data from: Human birth seasonality: latitudinal gradient and interplay with childhood disease dynamics

description: More than a century of ecological studies have demonstrated the importance
 of demography in shaping spatial and temporal variation in population
 dynamics. Surprisingly, the impact of seasonal recruitment on infectious
 disease systems has received much less attention. Here, we present data
 encompassing 78 years of monthly natality in the USA, and reveal
 pronounced seasonality in birth rates, with geographical and temporal
 variation in both the peak birth timing and amplitude. The timing of
 annual birth pulses followed a latitudinal gradient, with northern states
 exhibiting spring/summer peaks and southern states exhibiting autumn
 peaks, a pattern we also observed throughout the Northern Hemisphere.
 Additionally, the amplitude of United States birth seasonality was more
 than twofold greater in southern states versus those in the north. Next,
 we examined the dynamical impact of birth seasonality on childhood disease
 incidence, using a mechanistic model of measles. Birth seasonality was
 found to have the potential to alter the magnitude and periodicity of
 epidemics, with the effect dependent on both birth peak timing and
 amplitude. In a simulation study, we fitted an
 susceptible-exposed-infected-recovered model to simulated data, and
 demonstrated that ignoring birth seasonality can bias the estimation of
 critical epidemiological parameters. Finally, we carried out statistical
 inference using historical measles incidence data from New York City. Our
 analyses did not identify the predicted systematic biases in parameter
 estimates. This may be owing to the well-known frequency-locking between
 measles epidemics and seasonal transmission rates, or may arise from
 substantial uncertainty in multiple model parameters and estimation
 stochasticity.
description: USA_Monthly_Births_1915_2008Monthly Births in the United States for individual states. All state data are available following 1933, only certain states reported between 1915-1932.US_BIRTH_1915_2008.csvWorld_Monthly_Birth_Rates_1960_2014Monthly birth rates at the country level from 1960-2014.World_BR_1960_2014.csv
DOI: 10.5061/dryad.72r4b86
title: Data from: Leapfrogging the Mexican highlands: influence of biogeographical and ecological factors on the diversification of highland species

description: In order to understand the processes that generate and maintain diversity,
 it is important to disentangle the roles of ecology and geography in
 speciation. We investigated the biogeographical and ecological factors
 that influenced the diversification of tree frogs (genus Sarcohyla) in the
 Mexican highlands, a region with high levels of endemism. Using single
 nucleotide polymorphism data for 58 samples, we found support for seven
 distinct genetic clusters within the Sarcohyla bistincta species complex,
 corresponding to Sarcohyla calthula, Sarcohyla pentheter and five
 populations within S. bistincta. A species tree analysis using the
 multispecies coalescent model did not support the monophyly of the five S.
 bistincta populations. We used niche modelling to calculate the ecological
 overlap among lineages; we found a degree of overlapping for most of the
 lineages, suggesting that ecological differentiation did not play a key
 role in their genetic divergence. Speciation and population structure in
 the complex have been shaped primarily by geological events, landscape
 modifications and climate changes during the Pleistocene. We discuss the
 relevance of genetic diversity for inferring the degree of species threats
 and recovery for conservation assessments.
description: ddRAD Sarcohyla
 bistincta complexddRAD sequences for the
 Sarcohyla bistincta species complex: Sarcohyla bistincta, Sarcohyla
 calthula and Sarcohyla pentheter. The file includes alignments for 10, 25
 and 50% missing data.ddRAD_Sarcohyla.snps
DOI: 10.5061/dryad.3jj92rq
title: Data from: A global database and ‘state of the field’ review of research into ecosystem engineering by land animals.

description: 1. Ecosystem engineers have been widely studied for terrestrial systems,
 but global trends in research encompassing the range of taxa and functions
 have not previously been synthesised. 2. We synthesised contemporary
 understanding of engineer fauna in terrestrial habitats and assessed the
 methods used to document patterns and processes, asking: 1.Which species
 act as ecosystem engineers and with whom do they interact? 2. What are the
 impacts of ecosystem engineers in terrestrial habitats and how are they
 distributed? 3. What are the primary methods used to examine engineer
 effects and how have these developed over time? We considered the
 strengths, weaknesses and gaps in knowledge related to each of these
 questions, and suggested a conceptual framework to delineate ‘significant
 impacts’ of engineering interactions for all terrestrial animals. 3. We
 collected peer-reviewed publications examining ecosystem engineer impacts
 and created a database of engineer species to assess experimental
 approaches and any additional covariates that influenced the magnitude of
 engineer impacts. 4. One hundred and twenty-two species from twenty-eight
 orders were identified as ecosystem engineers, performing five ecological
 functions. Burrowing mammals were the most researched group (27%). Half of
 all studies occurred in dry/arid habitats. Mensurative studies comparing
 sites with and without engineers (80%) were more common than manipulative
 studies (20%). These provided a broad framework for predicting engineer
 impacts upon abundance and species diversity. However, the roles of
 confounding factors, processes driving these patterns, and the
 consequences of experimentally adjusting variables, such as engineer
 density, have been neglected. True spatial and temporal replication have
 also been limited, particularly for emerging studies of engineer
 reintroductions. 5. Climate change and habitat modification will challenge
 the roles that engineers play in regulating ecosystems, and these will
 become important avenues for future research. We recommend future studies
 include simulation of engineer effects and experimental manipulation of
 engineer densities to determine the potential for ecological cascades
 through trophic and engineering pathways due to functional decline. We
 also recommend improving knowledge of long-term engineering effects and
 replication of engineer reintroductions across landscapes to better
 understand how large-scale ecological gradients alter the magnitude of
 engineering impacts.
description: jae-f-databaseA global database and ‘state of the field’ review of research into ecosystem engineering by land animals.
DOI: 10.5061/dryad.3q67545
title: Data from: Climate change and temporal trends in body size: the case of rodents

description: A reduction in body size has been proposed as the third universal
 ecological response to global warming, after species distributional shifts
 and phenological changes. However, some recent studies raise doubts about
 the validity of this pattern, in particular for endotherms. Within this
 context, here we analyzed data on body mass (mb) for 17 rodent species,
 covering (at least) the last six decades, together with data on
 temperature change and basal metabolic rate (BMR) for each species. We
 found that: 1) ten species (58.8%) showed no significant changes in mb,
 while the remaining seven species (41.2%) decreased their size during the
 20th century; 2) phylogenetic generalized linear mixed models indicate
 that there is a significant and negative effect of the year of collection
 on mb; 3) the correlation coefficient between mb and the year of
 collection (ryear) was not correlated with species mean mb, species
 distributional range, the length of the time series, or the change in
 ambient temperature; and 4) the correlation between ryear and (residual)
 BMR was significant (and negative) only for species that do not use
 torpor. In summary, our results suggest that reductions in mb are common
 among rodents, but we were unable to identify a clear cause behind these
 changes (e.g. some results support the energetic argument behind the
 Bergmann rule but other do not). We concluded that with less than 0.5% of
 the extant (known) rodent species analyzed to date, we still are far from
 reaching a clear understanding of current patterns of variation in body
 size that are associated with global environmental change for this group.
description: Villar&Naya_DatasetS1Body mass, year of collection and geoprhafic coordinates for 17 rodents speces (taken from Arctos database).