cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.g92yts
title: Occurrence Download

description: A dataset containing 914928 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Specimen, Human Observation)",
 "Geometry POLYGON((-123.93579 39.84715,-123.72827 38.34404,-122.69064 36.75366,-121.61843 35.0164,-120.64998 33.87551,-118.6439 33.18355,-116.52227 30.44901,-114.89666 28.49188,-115.8997 27.60667,-113.92821 26.37389,-112.95976 26.68335,-114.2395 29.24909,-115.2752 30.50531,-118.0422 34.38603,-120.04827 35.35085,-121.12048 36.8044,-121.77765 37.76752,-123.93579 39.84715))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Gastropoda"
 ]
}

 The dataset includes 914928 records from 110 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000519-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.94r7j
title: Data from: Intraspecific variation among social insect colonies: persistent regional and colony-level differences in fire ant foraging behavior

description: Individuals vary within a species in many ecologically important ways, but
 the causes and consequences of such variation are often poorly understood.
 Foraging behavior is among the most profitable and risky activities in
 which organisms engage and is expected to be under strong selection. Among
 social insects there is evidence that within-colony variation in traits
 such as foraging behavior can increase colony fitness, but variation
 between colonies and the potential consequences of such variation are
 poorly documented. In this study, we tested natural populations of the red
 imported fire ant, Solenopsis invicta, for the existence of colony and
 regional variation in foraging behavior and tested the persistence of this
 variation over time and across foraging habitats. We also reared
 single-lineage colonies in standardized environments to explore the
 contribution of colony lineage. Fire ants from natural populations
 exhibited significant and persistent colony and regional-level variation
 in foraging behaviors such as extra-nest activity, exploration, and
 discovery of and recruitment to resources. Moreover, colony-level
 variation in extra-nest activity was significantly correlated with colony
 growth, suggesting that this variation has fitness consequences. Lineage
 of the colony had a significant effect on extra-nest activity and
 exploratory activity and explained approximately half of the variation
 observed in foraging behaviors, suggesting a heritable component to
 colony-level variation in behavior.
description: Colony and regional
 variation in fire ant foraging behavior before and after exposure to
 different foraging habitatsRaw data for analysis of
 regional and colony-level variation in fire ant foraging behavior. Data
 includes fire ant foraging behavior before and after five weeks exposure
 to ground-level vs. elevated foraging habitat types. Recruitment to
 ground-level and elevated resources, disovery and trail formation times,
 extra-nest activity, and exploratory activity are included, as well as
 weight of food collected and final colony size.raw_data.xlsx
DOI: 10.5061/dryad.q084s
title: Data from: Detecting hybridization by likelihood calculation of gene tree extra lineages given explicit models

description: Explanations for gene tree discordance with respect to a species tree are
 commonly attributed to deep coalescence (also known as incomplete lineage
 sorting [ILS]), as well as different evolutionary processes such as
 hybridization, horizontal gene transfer and gene duplication. Among these,
 deep coalescence is usually quantified as the number of extra lineages and
 has been studied as the principal source of discordance among gene trees,
 while the other processes that could contribute to gene tree discordance
 have not been fully explored. This is an important issue for hybridization
 because interspecific gene flow is well documented and widespread across
 many plant and animal groups. Here, we propose a new way to detect gene
 flow when ILS is present that evaluates the likelihood of different models
 with various levels of gene flow, by comparing the expected gene tree
 discordance, using the number of extra lineages. This approach consists of
 proposing a model, simulating a set of gene trees to infer a distribution
 of expected extra lineages given the model, and calculating a likelihood
 function by comparing the fit of the real gene trees to the simulated
 distribution. To count extra lineages, the gene tree is first reconciled
 within the species tree, and for a given species tree branch the number of
 gene lineages minus one is counted. We develop a set of R functions to
 parallelize software to allow simulations, and to compare hypotheses via a
 likelihood ratio test to evaluate the presence of gene flow when ILS is
 present, in a fast and simple way. Our results show high accuracy under
 very challenging scenarios of high impact of ILS and low gene flow levels,
 even using a modest dataset of five to ten loci and five to ten
 individuals per species. We present a powerful and fast method to detect
 hybridization in presence of ILS. We discuss its advantage with large
 dataset (such as genomic scale), and also identifies possible issues that
 should be explored with more complex models in future studies.
description: Supporting
 informationTable S1. List of R
 functions developed to automatize and parallelize software. Table S2.
 Lamarc the migration parameter estimates. Figure S1. Density plots for the
 symmetric species tree of the distribution of extra lineages. Figure S2.
 Power of the method applied to the symmetric species tree and theta = 0.01
 scenario. Figure S3. Power of the method applied to the symmetric species
 tree and theta = 0.001 scenario. Figure S4. Comparisons of average time
 consumption by out method and Lamarc based on symmetric tree
 scenario.supplementary.zip
DOI: 10.5061/dryad.ck7pt
title: Data from: Geo-climatic factors drive diatom community distribution in tropical South American freshwaters

description: 1.Patterns that maintain and generate biodiversity of macro-organisms in
 the Neotropics are widely discussed in the scientific literature, yet the
 spatial ecology of microorganisms is largely unknown. The unique character
 of the tropical Andes and adjacent Amazon lowlands generates a wide
 gradient of environmental conditions to advance our understanding of what
 drives community assembly and diversity processes. 2.We analyzed the
 distribution patterns of benthic diatoms (unicellular siliceous algae) as
 a model group of microbial passive dispersers, including predictors that
 describe limnological and geo-climatic gradients for a total of 113
 waterbodies (0–28ºS and 58–80ºW), including lakes and streams.
 Complementary multivariate statistical analyses were performed to
 correlate i) community composition, and ii) diatom species richness with
 environmental and spatial factors to infer niche-based and dispersal-based
 assembly processes, respectively. 3.Results showed that two gradients
 structured both diatom assemblages and waterbodies, namely climate and
 landscape configuration. Variance partitioning revealed that broad-scale
 spatial variables (distance-based Moran's Eigenvectors) outperformed
 the two environmental components (limnological and geo-climatic),
 suggesting dispersal-assembled communities. However, diatom assemblages
 were structured by geo-climatic (regional) factors in certain lakes in the
 northern and central Andes, although their effects were partially
 manifested via local variables after the geographical distances were
 factored out. In a similar way, climatic and topographic structuring
 homogenized lake and stream communities within ecoregions, as indicated by
 the strong overlap between the two community types and the weak
 correlation between biota and limnological variables. Notably, a
 significant increase in diatom species richness was related to increased
 water connectivity, interpreted to indicate that a decrease in the
 remoteness of the system increase species number. 4.Synthesis. We
 emphasize the strength of macroecological gradients (landscape
 configuration and climatic factors) in affecting both diatom diversity and
 community composition in the South American tropics. In this context, our
 results and the commonalities of ecoregion patterning with groups of
 macroorganisms (vegetation), suggest the need to integrate microbial
 ecology into a macroecology framework to unravel mechanisms behind
 diversity gradients.
description: Diatom and waterbodies
 database of tropical South AmericaThis database consists
 of two different datasets: diatom presence/absence data and associated
 environmental variables of the waterbodies of the individual regions of
 studyTropical South America Diatom
 and waterbodies database.xlsx
DOI: 10.5061/dryad.k6q68
title: Data from: African departure rather than migration speed determines variation in spring arrival in pied flycatchers

description: Properly timed spring migration enhances reproduction and survival.
 Climate change requires organisms to respond to changes such as advanced
 spring phenology. Pied flycatchers Ficedula hypoleuca have become a model
 species to study such phenological adaptations of long-distance migratory
 songbirds to climate change, but data on individuals’ time schedules
 outside the breeding season are still lacking. Using light-level
 geolocators, we studied variation in migration schedules across the year
 in a pied flycatcher population in the Netherlands, which sheds light on
 the ability for individual adjustments in spring arrival timing to track
 environmental changes at their breeding grounds. We show that variation in
 arrival dates to breeding sites in 2014 was caused by variation in
 departure date from sub-Saharan Africa and not by environmental conditions
 encountered en route. Spring migration duration was short for all
 individuals, on average 2 weeks. Males migrated ahead of females in
 spring, while migration schedules in autumn were flexibly adjusted
 according to breeding duties. Individuals were therefore not consistently
 early or late throughout the year. In fast migrants like our Dutch pied
 flycatchers, advancement of arrival to climate change likely requires
 changes in spring departure dates. Adaptation for earlier arrival may be
 slowed down by harsh circumstances in winter, or years with high costs
 associated with early migration.
description: return_in_2014Observed local return in 2014 of pied flycatchers with and without geolocator devices in 2013, based on field observations and catches. This file is used to study potential effects of geolocator deployment and harness types on the survival of pied flycatchers, compared to birds without these devices.timing_in 2013-2014Timing of breeding arrival dates (in males and females) and first egg laying dates (females) in 2013 and 2014 in Drenthe (The Netherlands), as shown for pied flycatchers deployed with geolocator devices in 2013 or without such devices. Arrival and egg laying are based on field observations. This file is used to study potential effects of geolocator deployment and harness types on the timing of arrival and egg laying of pied flycatchers, compared to birds without these devices. Timing is expressed as days relative to the sex-specific annual mean of the population.transitionsContains raw data on sunset and sunrise times (so called 'transitions') used to estimate longitude, movement and stationary periods. The file shows data of 27 solar geolocator-loggers deployed on pied flycatchers, Ficedula hypoleuca, in Drenthe The Netherlands (Longitude: 6.378, Latitude: 52.820) in 2013, using Intigeo-W50 made by Migrate Technology Ltd logger. Data was processed using the program BASTrack.
DOI: 10.5061/dryad.1vf74
title: Data from: Molecular prey identification in Central European piscivores

description: Diet analysis is an important aspect when investigating the ecology of
 fish-eating animals and essential for assessing their functional role in
 food webs across aquatic and terrestrial ecosystems. The identification of
 fish remains in dietary samples, however, can be time-consuming and
 unsatisfying using conventional morphological analysis of prey remains.
 Here, we present a two-step multiplex PCR system, comprised of six assays,
 allowing for rapid, sensitive and specific detection of fish DNA in
 dietary samples. This approach encompasses 78 fish and lamprey species
 native to Central European freshwaters and enables the identification of
 31 species, six genera, two families, two orders and two fish family
 clusters. All targeted taxa were successfully amplified from 25 template
 molecules, and each assay was specific when tested against a wide range of
 invertebrates and vertebrates inhabiting aquatic environments. The
 applicability of the multiplex PCR system was evaluated in a feeding
 trial, wherein it outperformed morphological prey analysis regarding
 species-specific prey identification in faeces of Eurasian otters.
 Additionally, a wide spectrum of fish species was detected in
 field-collected faecal samples and regurgitated pellets of Common
 Kingfishers and Great Cormorants, demonstrating the broad applicability of
 the approach. In conclusion, this multiplex PCR system provides an
 efficient, easy to use and cost-effective tool for assessing the trophic
 ecology of piscivores in Central Europe. Furthermore, the multiplex PCRs
 and the primers described therein will be applicable wherever DNA of the
 targeted fish species needs to be detected at high sensitivity and
 specificity.
description: Eurasian otter feeding
 trialThis are data from a
 fish feeding trial on Eurasian Otters. The animals were fed a different
 fish species every day; 5 otter spraints were collected per evening; these
 were analyzed molecularely for fish DNA and morphologically for
 fishbones.kingfisher and cormorant
 molecular screeningThe data show the
 results of a molecular screening (multiplex PCR) of field collected feces
 of the Common Kingfisher and the Great Cormorant, as well as regurgitated
 pellets of the latter. readme is included in the file16S alignment of
 sequences for genbankThis BioEdit file
 provides an alignment of the 16S sequences uploaded to genbank for this
 publication. Please note, that for GenBank publication sequences were
 cropped to achieve clear and identical sequences from forward and reverse
 direction reads.COI alignment of
 sequences for genbankThis BioEdit file
 provides an alignment of the COI sequences uploaded to genbank for this
 publication. Please note, that for GenBank publication sequences were
 cropped to achieve clear and identical sequences from forward and reverse
 direction reads.
DOI: 10.5061/dryad.d2f79
title: Data from: Dragons in our midst: phyloforensics of illegally traded Southeast Asian monitor lizards

description: We provide a phylogenetic and population genetic evaluation of the illegal
 pet and bush meat trade of monitor lizards in the Philippines. We use a
 molecular dataset assembled from vouchered samples with known localities
 throughout the country, as a reference for statistical phylogenetic,
 population genetic, and DNA barcoding analyses of genetic material
 obtained during a three year survey of the Manila pet trade. Our results
 provide the first genetic evaluation of a major Southeast Asian city’s
 illegal trade in monitors and allow us to establish several important
 conclusions regarding actual, versus reported, origins of Manila’s black
 market Varanus. Monitor lizards are clearly transported throughout the
 archipelago for trade; we identified genotypes from areas surrounding
 Manila, the distinct Bicol faunal subregion of Luzon, Mindanao Island, the
 Visayan islands, islands of the Romblon Province, the Babuyan islands, and
 Mindoro Island. Numerous species are involved, including multiple endemic
 Philippine taxa, the threatened Gray’s monitor (Varanus olivaceus), and
 the presumably non-Philippine rough-neck monitor (Varanus rudicollis). Our
 results suggest that traders frequently and deliberately misrepresent the
 provenance of traded animals, in an apparent effort to increase their
 perceived market value.
description: Varanus_CombinedNexus file with character block. Alignment used in phylogenetic analyses for the study.MLBootstrapMaximum Likelihood bootstrap topology reported in study.
DOI: 10.15468/dl.bkc6hg
title: Occurrence Download

description: A dataset containing 653 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Funaria hygrometrica"
 ]
}

 The dataset includes 653 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000539-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.dq335ff
title: Data from: The Metapopulation Microcosm Plate: a modified 96-well plate for use in microbial metapopulation experiments

description: 1. Researchers in many sub-fields of ecology and evolutionary biology test
 hypotheses relating to metapopulation dynamics and landscape spatial
 structure. Key aspects of these hypotheses are often (a) large numbers of
 subpopulations and dispersal corridors and (b) their positions relative to
 each other. Testing such spatial hypotheses using traditional lab
 equipment and methods can be impractical, unwieldy, expensive, or
 impossible. 2. The Metapopulation Microcosm Plate (MMP) overcomes these
 difficulties. This device resembles a 96-well microtiter plate, but
 contains dispersal corridors between wells that can be modified in their
 spatial position to create various artificial landscapes, each with up to
 96 habitat patches and hundreds of non-intersecting dispersal corridors of
 varying lengths. The device can be filled with nutrient broth and used to
 culture microbial metapopulations. 3. Here I describe how MMPs are
 designed, assembled, sterilized, and filled and demonstrate that MMPs can
 remain water tight and sterile with minimal evaporation for 5-7 days. 4.
 MMPs can be used to test many spatial hypotheses that have previously been
 prohibitively difficult to test. Further, by incorporating individual
 behavioral responses to within-patch conditions, MMPs can incorporate
 greater realism than do directed pipetting or other artificial dispersal
 methods.
description: Kurkjian_2018_MMP_MethodsZipped folder containing all raw data, processed data files, and code for analyses and figures for Kurkjian, H. M. 2018. The Metapopulation Microcosm Plate: A modified 96-well plate for use in microbial metapopulation experiments. Methods in Ecology and Evolution.
DOI: 10.5061/dryad.t57k5
title: Data from: Consequences for conservation: population density and genetic effects on reproduction of an endangered lagomorph

description: Understanding reproduction and mating systems is important for managers
 tasked with conserving vulnerable species. Genetic tools allow biologists
 to investigate reproduction and mating systems with high resolution and
 are particularly useful for species that are otherwise difficult to study
 in their natural environments. We conducted parentage analyses using 19
 nuclear DNA microsatellite loci to assess the influence of population
 density, genetic diversity, and ancestry on reproduction, and to examine
 the mating system of pygmy rabbits (Brachylagus idahoensis) bred in large
 naturalized enclosures for the reintroduction and recovery of the
 endangered distinct population in central Washington, USA. Reproductive
 output for females and males decreased as population density and
 individual homozygosity increased. We identified an interaction indicating
 that male reproductive output decreased as genetic diversity declined at
 high population densities, but there was no effect at low densities. Males
 with high amounts (&gt;50%) of Washington ancestry had higher
 reproductive output than the other ancestry groups, while reproductive
 output was decreased for males with high northern Utah/Wyoming ancestry
 and females with high Oregon/Nevada ancestry. Females and males bred with
 an average of 3.8 and 3.6 mates per year, respectively, and we found no
 evidence of positive or negative assortative mating with regards to
 ancestry. Multiple paternity was confirmed in 81% of litters, and we
 report the first documented cases of juvenile breeding by pygmy rabbits.
 This study demonstrates how variation in population density, genetic
 diversity, and ancestry impact fitness for an endangered species being
 bred for conservation. Our results advance understanding of basic life
 history characteristics for a cryptic species that is difficult to study
 in the wild, and provide lessons for managing populations of vulnerable
 species in captive and free-ranging populations.
description: Pygmy rabbit
 reproduction dataDemographic and genetic
 data used to evaluate pygmy rabbit reproduction in field breeding
 enclosures in central Washington, USA during 2012-2014 as part of the
 recovery for the endangered Columbia Basin pygmy
 rabbit.PYRA
 Reproduction Data Dryad.xlsx
DOI: 10.5061/dryad.f1q20jr4
title: Data from: A hierarchical Bayesian model for calibrating estimates of species divergence times

description: In Bayesian divergence time estimation methods, incorporating calibrating
 information from the fossil record is commonly done by assigning prior
 densities to ancestral nodes in the tree. Calibration prior densities are
 typically parametric distributions offset by minimum age estimates
 provided by the fossil record. Specification of the parameters of
 calibration densities requires the user to quantify his or her prior
 knowledge of the age of the ancestral node relative to the age of its
 calibrating fossil. The values of these parameters can, potentially,
 result in biased estimates of node ages if they lead to overly informative
 or excessively vague prior distributions. Accordingly, determining
 parameter values that lead to adequate prior densities is not
 straightforward. In this study, I present a hierarchical Bayesian model
 for calibrating divergence time analyses with multiple fossil age
 constraints. This approach applies a Dirichlet process prior as a
 hyperprior on the parameters of calibration prior densities. Specifically,
 this model assumes that the rate-parameters of exponential prior
 distributions on calibrated nodes are distributed according to a Dirichlet
 process, whereby the rate-parameters are clustered into distinct parameter
 categories. Both simulated and biological data are analyzed to evaluate
 the performance of the Dirichlet process hyperprior. Compared to fixed
 exponential prior densities, the hierarchical Bayesian approach results in
 more accurate and precise estimates of internal node ages. When this
 hyperprior is applied using Markov chain Monte Carlo methods, the ages of
 calibrated nodes are sampled from mixtures of exponential distributions
 and uncertainty in the values of calibration density parameters is taken
 into account.
description: dppdiv_1.0b.tarturtlessimulated_data_files.tar