cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k3b7d
title: Data from: Evaluating the interaction of faecal pellet deposition rates and DNA degradation rates to optimize sampling design for DNA-based mark-recapture analysis of Sonoran pronghorn

description: Knowledge of population demographics is important for species management
 but can be challenging in low-density, wide-ranging species. Population
 monitoring of the endangered Sonoran pronghorn (Antilocapra americana
 sonoriensis) is critical for assessing the success of recovery efforts,
 and noninvasive DNA sampling (NDS) could be more cost-effective and less
 intrusive than traditional methods. We evaluated faecal pellet deposition
 rates and faecal DNA degradation rates to maximize sampling efficiency for
 DNA-based mark–recapture analyses. Deposition data were collected at five
 watering holes using sampling intervals of 1–7 days and averaged one
 pellet pile per pronghorn per day. To evaluate nuclear DNA (nDNA)
 degradation, 20 faecal samples were exposed to local environmental
 conditions and sampled at eight time points from one to 124 days. Average
 amplification success rates for six nDNA microsatellite loci were 81% for
 samples on day one, 63% by day seven, 2% by day 14 and 0% by day 60. We
 evaluated the efficiency of different sampling intervals (1–10 days) by
 estimating the number of successful samples, success rate of individual
 identification and laboratory costs per successful sample. Cost per
 successful sample increased and success and efficiency declined as the
 sampling interval increased. Results indicate NDS of faecal pellets is a
 feasible method for individual identification, population estimation and
 demographic monitoring of Sonoran pronghorn. We recommend collecting
 samples &gt;7 days old and estimate that a sampling interval of 4–7
 days in summer conditions (i.e. extreme heat and exposure to UV light)
 will achieve desired sample sizes for mark–recapture analysis while also
 maximizing efficiency.
description: SW Supp info
 datasetInput file and
 legendFalse allele SAS
 codeSAS code for calculating
 false allelesfa.sasAllelic dropout SAS codeSAS code for calculating Allelic dropoutado.sasPCR sas codeSAS code for PCR successpcr.sas
DOI: 10.15468/dl.ayfvuy
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chamaesaracha rzedowskiana",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 24 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000876-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7mv26
title: Data from: The genetic inheritance of the blue-eyed white phenotype in alpacas (Vicugna pacos)

description: White spotting patterns in mammals can be caused by mutations in the gene
 KIT, whose protein is necessary for the normal migration and survival of
 melanocytes from the neural crest. The alpaca (Vicugna pacos) blue-eyed
 white phenotype (BEW) is characterized by two blue eyes and a solid white
 coat over the whole body. Breeders hypothesize that the BEW phenotype in
 alpacas is caused by the combination of the gene causing grey fleece and a
 white-spotting gene. We performed an association study using KIT flanking
 and intragenic markers with 40 unrelated alpacas, of which 17 were BEW.
 Two microsatellite alleles at KIT-related markers were significantly
 associated (P &lt; 0.0001) with the BEW phenotype (bew1 and bew2). In
 a larger cohort of 171 related individuals we identify an abundance of an
 allele (bew1) in grey animals and the occurrence of bew2 homozygotes that
 are solid white with pigmented eyes. Association tests accounting for
 population structure and familial relatedness are consistent with a
 proposed model where these alleles are in linkage disequilibrium with a
 mutation or mutations that contribute to the BEW phenotype and to
 individual differences in fleece color.
description: Supplementary Table 1
 Microsatellite loci employed for association analysesFlanking and intragenic
 markers employed for the association analysis with KIT, their product size
 in numbers of base pairs, number of alleles detected and their position in
 KIT or in relation to KIT.Jackling_SupMat_table_S1.docSupplementary Table 2 Primer sequencesPrimer sequences used to amplify 60 microsatellites used to adjust for population structure during association analyses.Jackling_SupMat_excel_document_table S2.xlsSupplementary Table 3 Polymorphism levels of markersPolymorphism levels of markers used to test association of markers with the blue-eyed white phenotype. Markers 55270241 and KKDR3 were monomorphic and so not included in this table or further analyses.Jackling_SupMat_table_S3.doc
DOI: 10.5061/dryad.46kb4
title: Data from: The differential contributions of herkogamy and dichogamy as mechanisms of avoiding self-interference in four self-incompatible Epimedium species

description: Self-interference is one of the most important selective forces in shaping
 floral evolution. Herkogamy and dichogamy both can achieve reductions in
 the extent of self-interference, but they may have different roles in
 minimizing self-interference in a single species. We used four
 self-incompatible Epimedium species to explore the roles of herkogamy and
 dichogamy in avoiding self-interference and to test the hypothesis that
 herkogamy and dichogamy may be separated and become selected
 preferentially in the taxa. Two species (E. franchetii and E. mikinorii)
 expressed strong herkogamy and weak protogyny (adichogamy), whereas
 another two species (E. sutchuenense and E. leptorrhizum) expressed slight
 herkogamy and partial protandry. Field investigations indicated that there
 was no physical self-interference between male function and female
 function regarding pollen removal and pollen deposition in all species.
 Self-pollination (autonomous or facilitated) was greater in species with
 slight herkogamy than in those with strong herkogamy. Artificial
 pollination treatments revealed that self-pollination could reduce
 outcrossed female fertility in all species, and we found evidence that
 self-interference reduced seed set in E. sutchuenense and E. leptorrhizum
 in the field, but not in E. franchetii and E. mikinorii. These results
 indicate that well-developed herkogamy is more effective compared with
 dichogamy in avoiding self-interference in the four species. In genus
 Epimedium, herkogamy instead of dichogamy should be selected
 preferentially and evolved as an effective mechanism for avoiding
 self-interference and might not need to evolve linked with dichogamy.
description: Li et al. data of in
 four Epimedium speciesFive data files as
 presented in main experiment of the article.Li et al.
 data.xls
DOI: 10.5061/dryad.8579
title: Data from: Range size heritability in Carnivora is driven by geographic constraints

description: Range size heritability refers to an intriguing pattern where closely
 related species occupy geographic ranges of similar extent. Its existence
 may indicate selection on traits only emergent at the species level, with
 interesting consequences for evolutionary processes. We explore whether
 range size heritability may be attributable to the fact that range size is
 largely driven by the size of geographic domains (i.e. continents, biomes,
 areas given by species' climatic tolerance) which tend to be similar
 in phylogenetically related species. Using a well resolved phylogeny of
 carnivorans, we show that range sizes are indeed constrained by geographic
 domains and that the phylogenetic signal in range sizes diminishes if the
 domain sizes are accounted for. Moreover, detailed delimitation of
 species' geographic domain leads to a weaker signal in range size
 heritability, indicating the importance of definition of the null model
 against which the pattern is tested. Our findings do not reject the
 hypothesis of range size heritability, but rather unravel its underlying
 mechanisms. Additional analyses imply that evolutionary conservatism in
 niche breadth delimits the species' geographic domain, which in turn
 shapes the species' range size. Range size heritability patterns thus
 emerge as a consequence of this interplay between evolutionary and
 geographic constraints.
description: Machac et al.
 DatasetBrief description of the
 data is provided within the file itself. For details, please, see our
 study "Range size heritability in Carnivora is driven by geographic
 constraints".Machac et al
 PhylogenyNexus format of the
 phylogeny used in our study "Range size heritability in Carnivora is
 driven by geographic constraints".
DOI: 10.5061/dryad.51t5s6b
title: Data from: Estimating infection prevalence: best practices and their theoretical underpinnings

description: Accurately estimating infection prevalence is fundamental to the study of
 population health, disease dynamics, and infection risk factors.
 Prevalence is estimated as the proportion of infected individuals
 (“individual-based estimation”), but is also estimated as the proportion
 of samples from which the disease-causing organisms are recovered
 (“anonymous estimation”). The latter method is often used when researchers
 lack information on individual host identity, which can occur during
 noninvasive sampling of wild populations or when the individual that
 produced a fecal sample is unknown. The goal of this study was to
 investigate biases in individual-based versus anonymous prevalence
 estimation theoretically and to test whether mathematically derived
 predictions are evident in a comparative dataset of gastrointestinal
 helminth infections in nonhuman primates. Using a mathematical model, we
 predict that anonymous estimates of prevalence will be lower than
 individual-based estimates when (a) samples from infected individuals do
 not always contain evidence of infection and/or (b) when false negatives
 occur. The mathematical model further predicts that no difference in bias
 should exist between anonymous estimation and individual-based estimation
 when one sample is collected from each individual. Using data on helminth
 parasites of primates, we find that anonymous estimates of prevalence are
 significantly and substantially (12.17%) lower than individual-based
 estimates of prevalence. We also observed that individual-based estimates
 of prevalence from studies employing single sampling are on average 6.4%
 higher than anonymous estimates, suggesting a bias toward sampling
 infected individuals. We recommend that researchers use individual-based
 study designs with repeated sampling of individuals to obtain the most
 accurate estimate of infection prevalence. Moreover, to ensure accurate
 interpretation of their results and to allow for prevalence estimates to
 be compared among studies, it is essential that authors explicitly
 describe their sampling designs and prevalence calculations in
 publications.
description: Miller et al. 2018
 dataThe data are prevalence
 estimates of helminth infections in non-human primates compiled from
 multiple sources.
DOI: 10.5061/dryad.5k6gb
title: Data from: Magnetic field inhomogeneities due to CO 2 incubator shelves: a source of experimental confounding and variability?

description: A thorough assessment of the static magnetic field (SMF) inside a CO2
 incubator allowed us to identify non-negligible inhomogeneities close to
 the floor, ceiling, walls and the door. Given that incubator's
 shelves are made of a non-magnetic stainless steel alloy, we did not
 expect any important effect of them on the SMF. Surprisingly, we did find
 relatively strong distortion of the SMF due to shelves. Indeed, our
 high-resolution maps of the SMF revealed that distortion is such that
 field intensities differing by a factor of up to 36 were measured on the
 surface of the shelf at locations only few millimetres apart from each
 other. Furthermore, the most intense of these fields was around five times
 greater than the ones found inside the incubator (without the metallic
 shelves in), while the lowest one was around 10 times lower, reaching the
 so-called hypomagnetic field range. Our findings, together with a survey
 of the literature on biological effects of hypomagnetic fields, soundly
 support the idea that SMF inhomogeneities inside incubators, especially
 due to shelves' holes, are a potential source of confounding and
 variability in experiments with cell cultures kept in an incubator.
description: Magnetic Maps Raw
 DataThe file contains a
 folder with all the raw data from magnetic maps of figures 2, 3 and 4 of
 our article: L. Makinistian, I. Belyaev. 2018. Magnetic field
 inhomogeneities due to CO2 incubators shelves: A source of experimental
 confounding and variability? Royal Society Open
 Science.MagneticMapsDataFromMakinistian-BelyaevMagnetic field inhomogeneities due to CO2 incubators shelves_RoySocOpenSci.zip
DOI: 10.5061/dryad.s8k68
title: Data from: Cannibalism and activity rate in larval damselflies increase along a latitudinal gradient as a consequence of time constraints

description: Background: Predation is ubiquitous in nature. One form of predation is
 cannibalism, which is affected by many factors such as size structure and
 resource density. However, cannibalism may also be influenced by abiotic
 factors such as seasonal time constraints. Since time constraints are
 greater at high latitudes, cannibalism could be stronger at such
 latitudes, but we know next to nothing about latitudinal variation in
 cannibalism. In this study, we examined cannibalism and activity in larvae
 of the damselfly Lestes sponsa along a latitudinal gradient across Europe.
 We did this by raising larvae from the egg stage at different temperatures
 and photoperiods corresponding to different latitudes. Results: We found
 that the more seasonally time-constrained populations in northern
 latitudes and individuals subjected to greater seasonal time constraints
 exhibited a higher level of cannibalism. We also found that activity was
 higher at north latitude conditions, and thus correlated with cannibalism,
 suggesting that this behaviour mediates higher levels of cannibalism in
 time-constrained animals. Conclusions: Our results go counter to the
 classical latitude-predation pattern which predicts higher predation at
 lower latitudes, since we found that predation was stronger at higher
 latitudes. The differences in cannibalism might have implications for
 population dynamics along the latitudinal gradients, but further
 experiments are needed to explore this.
description: Sniegula et
 al._REPOSITORYData saved in Excel
 file. Data file has the following columns: region - region of origin;
 latitude - latitude of origin; pop - population; measure - number of
 larvae survived unitl day 12 (m1) and day 28 (m2); surviv - either
 survived (1) or was cannibilized (2); larvae - number of days until one
 larva left in a container; walk.dist - total distance moved; walk.mean -
 mean distance per move; moves - number of moves; eaten - number of larvae
 cannibalized;
DOI: 10.5061/dryad.d2pd6
title: Data from: Linking phenology to mating system: exploring the reproductive biology of the threatened palm species Butia eriospatha

description: The reproductive biology of the vulnerable palm species Butia eriospatha
 was studied to provide important information that contributes to our
 understanding and conservation of the species. In order to determine when
 and how B. erisopatha reproduces, we combined data from seven nuclear
 microsatellite loci with ecological data on flowering and fruiting
 phenology collected between 2009 and 2011 from a population (N=515) in the
 Atlantic Rainforest, Southern Brazil. Periods of flowering and fruit
 production were seasonal and variable across reproductive events. Mating
 system analyses indicate that B. eriospatha is a predominantly outcrossing
 species, (t ̂m=0.961), since a certain degree of biparental inbreeding
 does occur. The species is self-compatible and reproduction may also occur
 by geitonogamy, indicating the ability of isolated populations to survive
 and persist. Open-pollinated seeds varied in relatedness, including mainly
 half-sibs and full-sibs. The effective population size was lower than that
 expected for panmictic populations. Hence, seeds for conservation programs
 must be collected from a large number of seed-trees to ensure an adequate
 effective population in the sample. The collection of germplasm is a high
 priority strategy that should be employed to maintain the genetic
 variability that remains.
description: Mendelian segregation
 analysisG statistic for the
 hypothesis of Mendelian segregation of microsatellite markers for Butia
 eriospatha (Martius ex Drude) Beccari from the Atlantic Rainforest, Santa
 Catarina State, Southern Brazil.Nazareno_SupMat_Table1.docx
DOI: 10.5061/dryad.pf0s5
title: Data from: Genetic and epigenetic variation in Spartina alterniflora following the Deepwater Horizon oil spill

description: Catastrophic events offer unique opportunities to study rapid population
 response to stress in natural settings. In concert with genetic variation,
 epigenetic mechanisms like DNA methylation may offer a mechanism of rapid
 response to organisms facing severe environmental challenges, and
 contribute to the high resilience of species like Spartina alterniflora, a
 foundation salt marsh grass which shows resilience to strong environmental
 disturbance. In 2010, the Deepwater Horizon oil spill devastated large
 portions of the coastline along the Gulf of Mexico. Following the spill,
 we simultaneously examined the genetic and epigenetic structure of
 recovering populations of S. alterniflora to oil exposure. We quantified
 genetic and DNA methylation variation using AFLP and MS-AFLP to test the
 hypothesis that response to oil exposure in S. alterniflora resulted in
 genetically and epigenetically based population differentiation. We found
 high genetic and epigenetic variation within and among sites, and found
 significant genetic differentiation between contaminated and
 uncontaminated sites, which may reflect non-random mortality in response
 to oil exposure. Additionally, despite a lack of genome wide patterns in
 DNA methylation between contaminated and uncontaminated sites, we found
 five MS-AFLP loci (12% of polymorphic MS-AFLP loci) that were correlated
 with oil exposure. Overall, our findings support genetically based
 differentiation correlated to exposure to the oil spill in this system,
 but also suggest a potential role for epigenetic mechanisms in population
 differentiation.
description: AFLPAFLP
 lociMSAFLPMSAFLP
 loci
DOI: 10.5061/dryad.sv680
title: Data from: Contemporary variations of immune responsiveness during range expansion of two invasive rodents in Senegal

description: Biological invasions provide unique opportunities for studying life
 history trait changes over contemporary time scales. As spatial spread may
 be related to changes in parasite communities, several hypotheses (such as
 the evolution of increased competitive ability (EICA) or EICA-refined
 hypotheses) suggest immune changes in invasive species along invasion
 gradients. Although native hosts may be subject to similar changes in
 parasite selection pressures, their immune responses have been rarely
 investigated in invasion contexts. In this study, we evaluated immune
 variations for invasive house mice Mus musculus domesticus, invasive black
 rats Rattus rattus and native rodents Mastomys erythroleucus and Mastomys
 natalensis along well-characterised invasion gradients in Senegal. We
 focused on antibody-mediated (natural antibodies and complement) and
 inflammatory (haptoglobin) responses. One invasion route was considered
 for each invasive species, and environmental conditions were recorded.
 Natural-antibody mediated responses increased between sites of
 long-established invasion and recently invaded sites only in house mice.
 Both invasive species exhibited higher inflammatory responses at the
 invasion front than in sites of long-established invasion. The immune
 responses of native species did not change with the presence of invasive
 species. These patterns of immune variations do not support the EICA and
 EICA refined hypotheses, and they rather suggest a higher risk of exposure
 to parasites on the invasion front. Altogether, these results provide a
 first basis to further assess the role of immune changes in invasion
 success.
description: Individual and immune
 variables of rodents from the black rat invasion route.This file contains all
 the individual (sex, body mass, age class), methodological (plate factor,
 initial hemolysis of the serum) and immune (HA, HL, Hp) variables
 considered in the statistical analyses carried out on rodents from the
 black rat invasion route.OIK03470 - Rat_invasion_route -
 HAHL_Hp.csvIndividual and immune
 variables of rodents from the house mouse invasion
 route.This file contains all
 the individual (sex, body mass, age class), methodological (plate factor,
 initial hemolysis of the serum) and immune (HA, HL, Hp) variables
 considered in the statistical analyses carried out on rodents from the
 house mouse invasion route.OIK03470 - Mouse_invasion_route
 - HAHL_Hp.csv