cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dz08kprvc
title: Investigating morphological complexes using informational dissonance and bayes factors: A case study in corbiculate bees

description: It is widely recognized that different regions of a genome often have
 different evolutionary histories and that ignoring this variation when
 estimating phylogenies can be misleading. However, the extent to which
 this is also true for morphological data is still largely unknown.
 Discordance among morphological traits might plausibly arise due to either
 variable convergent selection pressures or else phenomena such as
 hemiplasy. Here we investigate patterns of discordance among 282
 morphological characters, which we scored for 50 bee species particularly
 targeting corbiculate bees, a group that includes the well-known eusocial
 honeybees and bumblebees. As a starting point for selecting the most
 meaningful partitions in the data, we grouped characters as morphological
 modules, highly integrated trait complexes that as a result of
 developmental constraints or coordinated selection we expect to share an
 evolutionary history and trajectory. In order to assess conflict and
 coherence across and within these morphological modules, we used recently
 developed approaches for computing Bayesian phylogenetic information
 allied with model comparisons using Bayes factors. We found that despite
 considerable conflict among morphological complexes, accounting for
 among-character and among-partition rate variation with individual gamma
 distributions, rate multipliers, and linked branch lengths can lead to
 coherent phylogenetic inference using morphological data. We suggest that
 evaluating information content and dissonance among partitions is useful
 step in estimating phylogenies from morphological data, just as it is with
 molecular data. Furthermore, we argue that adopting emerging approaches
 for investigating dissonance in genomic datasets may provide new insights
 into the integration and evolution of anatomical complexes.
DOI: 10.5061/dryad.m63xsj3zp
title: Data from: Genomic and plumage variation across the historically controversial Baltimore and Bullock’s oriole hybrid zone

description: Hybrid zones are powerful natural settings for investigating how birds
 diversify into distinct species. Here we present the first genomic-scale
 exploration of the Baltimore (Icterus galbula) and Bullock’s (I.
 bullockii) oriole hybrid zone, which is notable for its long history of
 study and for its prominence in debates about avian species concepts and
 species limits. We used a reduced-representation sequencing approach to
 generate a panel of 3,067 genetic markers for 297 orioles sampled along
 the Platte River, a natural west-to-east transect across the hybrid zone.
 We then explored patterns of hybridization and introgression by comparing
 variation in genomic and plumage traits. We found that hybridization
 remains prevalent in this area, with nearly all orioles within the hybrid
 zone showing some degree of genomic mixing, and 41% assigned as
 recent-generation (F1/F2) hybrids. The center and width of the genomic and
 plumage gradients are concordant and coincident, supporting our finding
 that classically scored plumage traits are an accurate predictor of pure
 versus hybrid genotypes. We find additional support for previous
 suggestions that the center of this hybrid zone has moved westward since
 it was first intensively sampled in the 1950s, but that this westward
 movement had slowed or ceased by the 1970s. Considered in concert, these
 results support previous inferences that some form of ongoing selection is
 counteracting the potential homogenization of these orioles via
 hybridization, thereby supporting their continued taxonomic separation as
 distinct species.
description: Filtered STACKS output for Baltimore and Bullock's Orioles
 sampled for this study. There are two files archived that were generated
 in populations using the following filtering options:
 -r 0.8 -p 1 -t 15 --min_maf 0.05 One file
 ("FinalOrioles_AllSNPS_MAF_Filtered") contains all of the SNPs
 generated in STACKS and the other file
 ("FinalOrioles_SingleSNPS_MAF_Filtered) contains one SNP per locus.
 In both cases, individuals were removed if they had more than 50% missing
 data. We have also included a spreadhseet containing
 plumage scores (see methods for details on plumage scoring).
 Raw data may be made available upon request.
DOI: 10.5061/dryad.fqz612jqb
title: Comparative population genetics of the federally endangered Relict Darter, and its sister taxon the Clarks Darter (Teleostei: Percidae)

description: The southeastern United States harbors one of the most diverse temperate
 freshwater fish faunas of the world. Unfortunately, due to improper land
 use practices and habitat degradation, many of the species in this region
 are imperiled and may become extinct without appropriate conservation
 efforts. This study examined the population dynamics of an endangered
 endemic darter of southwest Kentucky, the Relict Darter (Etheostoma
 chienense) and its sister taxon, the undescribed Clarks Darter (Etheostoma
 cf. oophylax). Mitochondrial sequence data coupled with SNP data were used
 to infer population structure, gene flow, genetic variation, and effective
 population sizes of both species. The results from this study, based on
 160 individuals from nine localities, indicate that the endangered Relict
 Darter possesses limited genetic variation based on mitochondrial DNA
 haplotypes (N=4).  In addition, SNP data (6.8k markers) further
 indicates limited genetic structure (K=1), as well as a low effective
 population size (143-918), suggesting that the Relict Darter can be
 managed as a single, panmictic conservation unit. It is suggested that
 conservation efforts be taken to protect remaining habitats, augment the
 system with artificial spawning substrates, and, as a last resort (if
 needed), supplement the natural population with captive reared
 individuals. Ethesotoma cf. oophylax showed some genetic variation among
 distant sites, but more samples are needed throughout the range in order
 to fully understand the population dynamics of this species.
description: This dataset was collected at Southeastern Louisiana Univeristy
 in the Piller lab using ddRADseq. Fin clips were taken from the caudal fin
 of the fish and placed in 90% ethanol for short term stoarage. DNA was
 extracted using Promega and Qiagen DNA extraction kits. Double Digest 
 RADseq (Peterson et al. 2012) was implemented for single end Illumina
 library prep at Southeastern Louisiana Univeristy in the Piller lab.
 Illumina sequencing on an Illumina Hiseq 4000 was done at University of
 Oregon. The raw data was processed using ipyrad v0.7.30 and then vcftools.
 Several standard population genetic analyses were run on these datasets
 (STRUCTURE, DAPC, pwFst, Effective population size, etc.)
description: For raw fastq data files go to NCBI SRA project number
 PRJNA635125. Here we have provided ipyrad params files,
 and final alignment files. See paper for details on analyses.
DOI: 10.5061/dryad.bzkh18962
title: Data from: Declining human pressure and opportunities for rewilding in the steppes of Eurasia

description: Large and ecologically functioning steppe complexes have been lost
 historically across the globe, but recent land-use changes may allow the
 reversal of this trend in some regions. We aimed to develop and map
 indicators of changing human influence using satellite imagery and
 historical maps, and to use these indicators to identify areas for
 broad-scale steppe rewilding. Location Eurasian Steppes of Kazakhstan.
 Methods We mapped decreasing human influence indicated by cropland
 abandonment, declining grazing pressure, and rural outmigration in the
 steppes of northern Kazakhstan. We did this by processing ~5,500 Landsat
 scenes to map changes in cropland between 1990 and 2015, and by digitizing
 Soviet topographic maps and examining recent high-resolution satellite
 imagery to assess the degree of abandonment of &gt;2,000 settlements
 and &gt;1,300 livestock stations. We combined this information into a
 human influence index (HI), mapped changes in HI to highlight where
 rewilding might take place, and assessed how this affected the
 connectivity of steppe habitat. Results Across our study area, about 6.2
 million ha of cropland were abandoned (30.5%), 14% of all settlements were
 fully and 81% partly abandoned, and 76% of livestock stations were
 completely dismantled between 1990-2015, suggesting substantially
 decreasing human pressure across vast areas. This resulted in increased
 connectivity of steppe habitat. Main conclusions The steppes of Eurasia
 are experiencing massively declining human influence, suggesting
 large-scale passive rewilding is taking place. Many of these areas are now
 important for the connectivity of the wider steppe landscape and can
 provide habitat for endangered megafauna such as the critically endangered
 saiga antelope. Yet this window of opportunity may soon close, as
 recultivation of abandoned cropland is gaining momentum. Our aggregate
 human influence index captures key components of rewilding, and can help
 to devise strategies for fostering large, connected networks of protected
 areas in the steppe.
DOI: 10.5061/dryad.37pvmcvgp
title: Heterogeneity in the rate of molecular sequence evolution substantially impacts the accuracy of detecting shifts in diversification rates

description: As species richness varies along the tree of life, there is a great
 interest in identifying factors that affect the rates by which lineages
 speciate or go extinct. To this end, theoretical biologists have developed
 a suit of phylogenetic comparative methods that aim to identify where
 shifts in diversification rates had occurred along a phylogeny and whether
 they are associated with some traits. Using these methods, numerous
 studies have predicted that speciation and extinction rates vary across
 the tree of life. In this study we show that asymmetric rates of sequence
 evolution rates lead to systematic biases in the inferred phylogeny, which
 in turn lead to erroneous inferences regarding lineage diversification
 patterns. The results demonstrate that as the asymmetry in sequence
 evolution rates increases, so does the tendency to select more complicated
 models that include the possibility of diversification rate shifts. These
 results thus suggest that any inference regarding shifts in
 diversification pattern should be treated with great caution, at least
 until any biases regarding the molecular substitution rate have been ruled
 out.
description: All data were created using simulations. All
 the trees were simulated using the Diversitree package (https://www.zoology.ubc.ca/prog/diversitree/). The multiple sequence alignments were simulated using INDELible (http://abacus.gene.ucl.ac.uk/software/indelible/). The maximum likelihood trees were inferred using PhyML (http://www.atgc-montpellier.fr/phyml/). The time-calibrated trees were achieved using MrBayes (http://nbisweden.github.io/MrBayes/), PATHd8 (https://www2.math.su.se/PATHd8/) and the penalized likelihood method implemented in r8s (https://sourceforge.net/projects/r8s/). Trait-dependent diversification was tested using BiSSE (https://www.zoology.ubc.ca/prog/diversitree/) and HiSSE (https://CRAN.R-project.org/package=hisse). Trait-independent shifts in diversification were inferred using BAMM (http://bamm-project.org/) and MEDUSA (https://github.com/josephwb/turboMEDUSA).
description: The compressed data is stored in the following files:
 SimulationSet1_4.tar.gz
 SimulationSet2.tar.gz
 SimulationSet3.tar.gz
 SimulationSet5a.tar.gz
 SimulationSet5b.tar.gz
 SimulationSetSeqLen_250.tar.gz
 SimulationSetSeqLen_2000.tar.gz 
 The scripts can be found in the scripts.zip compressed folder.
 Readme.txt and DataInfo.txt files are attached for further explanation
 about the scripts and the data.
DOI: 10.5068/d1z964
title: Data from: A search for technosignatures from TRAPPIST-1, LHS 1140, and 10 planetary systems in the Kepler field with the Green Bank Telescope at 1.15–1.73 GHz

description: This dataset includes candidate signal detections obtained at the Green
 Bank Telescope in 2017 and reprocessed with the 2020 UCLA SETI Group data
 processing pipeline. As part of our ongoing search for technosignatures,
 we collected over three terabytes of data in May 2017 with the L-band
 receiver (1.15–1.73 GHz) of the 100 m diameter Green Bank Telescope. These
 observations focused primarily on planetary systems in the Kepler field,
 but also included scans of the recently discovered TRAPPIST-1 and LHS 1140
 systems. We present the results of our search for narrowband signals in
 this data set with techniques that are generally similar to those
 described by Margot et al. 2018. Our improved data processing pipeline
 classified over 98% of the ~6 million detected signals as anthropogenic
 Radio Frequency Interference (RFI). Of the remaining candidates, 30 were
 detected outside of densely populated frequency regions attributable to
 RFI. These candidates were carefully examined and determined to be of
 terrestrial origin.
description: Please see journal article for methods.  
description: The field descriptions are as follows: 
 ID: a unique integer identifier for the signal
 NAME: the name of the source SCAN: the scan
 index number (1, 2) for the source MJD: the Modified
 Julian Date at the start of the scan FREQ: the
 frequency (Hz) at the start of the scan DFDT: the
 rate of change in frequency (Hz/s) Z: the signal
 power integrated over the scan duration aka Z score (standard deviations
 of the noise) BW: an estimate of the bandwidth (FWHM)
 of the signal (Hz) FSNR: a flag set to Y if signal
 power exceeds detection threshold FDOP: a flag set to
 Y if DFDT is <strong>not</strong> zero
 FBTH: a flag set to Y if signal is detected in both scans of
 this source FOTH: a flag set to Y if signal
 is <strong>not</strong> detected in scans of other
 sources FAND: a flag set to Y if
 FSNR=FDOP=FBTH=FOTH=Y PARTNER: the ID of the signal
 in a subsequent scan of this source, if known
 RFICODE: an identifier for the probable source of RFI
 NOTES: additional notes <pre> The
 field names and types are as follows: +---------+--------------+ | Field |
 Type | +---------+--------------+ | ID | int(11) | | NAME | varchar(50) |
 | SCAN | int(4) | | MJD | double(16,8) | | FREQ | double(20,6) | | DFDT |
 double(14,8) | | Z | double(15,3) | | BW | double(8,1) | | FSNR | char(1)
 | | FDOP | char(1) | | FBTH | char(1) | | FOTH | char(1) | | FAND |
 char(1) | | PARTNER | int(11) | | RFICODE | char(5) | | NOTES | text |
 +---------+--------------+</pre>
DOI: 10.5061/dryad.g1jwstqnr
title: Data from: Prey availability and ambient temperature influence carrion persistence in the boreal forest

description: 1. Scavenging by vertebrates can have important impacts on food web
 stability and persistence, and can alter the distribution of nutrients
 throughout the landscape. However, scavenging communities have been
 understudied in most regions around the globe, and we lack understanding
 of the biotic drivers of vertebrate scavenging dynamics. 2. In this paper,
 we examined how changes in prey density and carrion biomass caused by
 population cycles of a primary prey species, the snowshoe hare (Lepus
 americanus), influence scavenging communities in the northern boreal
 forest. We further examined the impact of habitat and temperature on
 scavenging dynamics. 3. We monitored the persistence time, time until
 first scavenger, and number of species scavenging experimentally-placed
 hare carcasses over four consecutive years in the southwestern Yukon. We
 simultaneously monitored hare density and carrion biomass to examine their
 influence relative to temperature, habitat, and seasonal effects. For the
 primary scavengers, we developed species-specific scavenging models to
 determine variation on the effects of these factors across species, and
 determine which species may be driving temporal patterns in the entire
 community. 4. We found that the efficiency of the scavenging community was
 affected by hare density, with carcass persistence decreasing when
 snowshoe hare densities declined, mainly due to increased scavenging rates
 by Canada lynx (Lynx canadensis). However, prey density did not influence
 the number of species scavenging a given carcass, suggesting prey
 abundance affects carrion recycling but not necessarily the number of
 connections in the food web. In addition, scavenging rates increased in
 warmer temperatures, and there were strong seasonal effects on the
 richness of the vertebrate scavenging community. 5. Our results
 demonstrate that vertebrate scavenging communities are sensitive to
 changes in species’ demography and environmental change, and that future
 assessments of food web dynamics should consider links established through
 scavenging.
DOI: 10.5061/dryad.12jm63xv6
title: The frugivory network between birds and plants in a Neotropical periurban park

description: Frugivory networks exhibit a set of properties characterized by a number
 of network-theory derived metrics. Their structure often form
 deterministic patterns that can be explained by the functional roles of
 interacting species. Although we know lots about how these networks are
 organized when ecosystems are in a complete, functional condition, we know
 much less about how incomplete and simplified networks (such as those
 found in urban and periurban parks) are organized, which features are
 maintained, which ones are not, and why. In this paper, we examine the
 properties of a network between frugivorous birds and plants in a small
 Neotropical periurban park. We found a frugivory network composed of 29
 species of birds and 23 of plants. The main roles in this network are
 played by four species of generalist birds (three resident, one migratory:
 Myiozetetes similis, Turdus grayi, Chlorospingus flavopectus, and
 Dumetella carolinensis) and three species of plants (one exotic, two early
 successional: Phoenix canariensis, Phoradendron sp., and Witheringia
 stramoniifolia). When compared to reference data from other locations in
 the Neotropics, species richness is low, one important network-level
 metric is maintained (modularity) whereas another one is not (nestedness).
 Nestedness, a metric associated with network specialists, is a feature
 this network lacks. Species-level metrics such as degree, species
 strength, and module roles, are not maintained. Our work supports
 modularity as the most pervasive network-level metric of altered habitats.
 From a successional point of view, our results suggest that properties
 revealed by species-level indices may be developed at a later time,
 lagging the acquisition of structural elements.
description: See Methods section of Salazar-Rivera et al. (2020) and the
 metadata of this dataset.
DOI: 10.5061/dryad.9s4mw6mcv
title: Data from: Social transmission in the wild reduces predation pressure on novel prey signals

description: Social transmission of information is taxonomically widespread and could
 have profound effects on the ecological and evolutionary dynamics of
 animal communities. Demonstrating this in the wild, however, has been
 challenging. Here we show by field experiment that social transmission
 among predators can shape how selection acts on prey defences. Using
 artificial prey and a novel approach in statistical analyses of social
 networks, we find that blue tit (Cyanistes caeruleus) and great tit (Parus
 major) predators learn about prey defences by watching others. This shifts
 population preferences rapidly to match changes in prey profitability, and
 reduces predation pressure from naïve predators. Our results may help
 resolve how costly prey defences are maintained despite influxes of naïve
 juvenile predators, and suggest that accounting for social
 transmission is essential if we are to understand coevolutionary
 processes.
description: This data was collected at Madingley Wood (Cambridgeshire, UK)
 during summer 2018. We introduced novel palatable and unpalatable foods
 into a wild blue tit and great tit population and recorded individuals’
 food choices using RFID technology at feeding stations. We have five
 different datasets that include records of birds' visits to feeders
 with 1) plain almonds ("PooledForSocNet"), 2) palatable green
 and unpalatable red almonds ("GreenRedRawData2"), 3) palatable
 purple and unpalatable blue almonds ("PurpleBlueRawData2"), 4)
 palatable purple and palatable blue almonds
 ("PurpleBlueReversalRawData2"), and 5) palatable orange and
 unpalatable yellow almonds ("OrangeYellowRawData2"). In
 addition, we have a datasheet that includes individual
 attributes ("IndividualsData"). 
description: In addition to raw data, we have provided example R scripts for
 1) an analysis to test whether birds use social information during
 avoidance learning and whether these effects follow social network
 ("Example analysis scripts and data"), 2) simulations to
 validate our model approach ("Example validation scripts and
 data"), and 3) a network-based diffusion analysis to investigate
 social information use during avoidance learning ("NBDA scripts and
 data"). Avoidance learning scripts use data from the yellow/orange
 experiment, but the same approach applies to each colour pair.
DOI: 10.5061/dryad.b8gtht799
title: Data from: Estimating transmission dynamics and serial interval of the first wave of COVID-19 infections under different control measures: A statistical analysis in Tunisia from February 29 to May 5, 2020

description: Background: Describing transmission dynamics of the outbreak and impact of
 intervention measures are critical to planning responses to future
 outbreaks and providing timely information to guide policy makers
 decision. We estimate serial interval (SI) and temporal reproduction
 number (Rt) of SARS-CoV-2 in Tunisia. Methods: We collected data of
 investigations and contact tracing between March 1, 2020 and May 5, 2020
 as well as illness onset data during the period February 29-May 5, 2020
 from National Observatory of New and Emerging Diseases of Tunisia. Maximum
 likelihood (ML) approach is used to estimate dynamics of Rt. Results: 491
 of infector-infectee pairs were involved, with 14.46% reported
 pre-symptomatic transmission. SI follows Gamma distribution with mean 5.30
 days [95% CI 4.66-5.95] and standard deviation 0.26 [95% CI 0.23-0.30].
 Also, we estimated large changes in Rt in response to the combined
 lockdown interventions. The Rt moves from 3.18 [95% CI 2.73-3.69] to 1.77
 [95% CI 1.49-2.08] with curfew prevention measure, and under the epidemic
 threshold (0.89 [95% CI 0.84-0.94]) by national lockdown measure.
 Conclusions: Overall, our findings highlight contribution of interventions
 to interrupt transmission of SARS-CoV-2 in Tunisia.
description: Data is obtained from contact tracing between March 1 and May 5,
 2020 from the National Observatory of New and Emerging Diseases of Tunis,
 Tunisia. It was screened to clearly identified transmission events, which
 are a known pairs of index and secondary cases and the dates of symptom
 onset for both cases.
description: This metadata includes two datasets: the first one consists of
 contact tracing including information for pairs, dates of symptoms onset
 for both infector and infectee as well as the ID for them, the second one
 consists of a daily time series including information for dates and number
 of incident cases.