cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8gtht76mg
title: Data from: Genetic Variation in Plethodon cinereus and Plethodon hubrichti from in and Around a Contact Zone

description: Climate change poses several challenges to biological communities
 including changes in the frequency of encounters between closely related
 congeners as a result of range shifts. When climate change leads to
 increased hybridization, hybrid dysfunction or genetic swamping may
 increase extinction risk—particularly in range-restricted species with low
 vagility. The Peaks of Otter Salamander, Plethodon hubrichti, is a fully
 terrestrial woodland salamander that is restricted to ~ 18 km of ridgeline
 in the mountains of southwestern Virginia, and its range is surrounded by
 the abundant and widespread Eastern Red-backed Salamander, Plethodon
 cinereus. In order to determine whether these two species are hybridizing
 and how their range limits may be shifting, we assessed variation at eight
 microsatellite loci and a 1008 bp region of Cytochrome B in both species
 at allopatric reference sites and within a contact zone. Our results show
 that hybridization between P. hubrichti and P. cinereus either does not
 occur or is very rare. However, we find that diversity and differentiation
 are substantially higher in the mountaintop endemic P. hubrichti than in
 the widespread P. cinereus, despite similar movement ability for the two
 species as assessed by a homing experiment. Furthermore, estimation of
 divergence times between reference and contact zone populations via
 approximate Bayesian computation is consistent with the idea that P.
 cinereus has expanded into the range of P. hubrichti. Given the apparent
 recent colonization of the contact zone by P. cinereus, future monitoring
 of P. cinereus range limits should be a priority for the management of P.
 hubrichti populations.
description: Microsatellite Data Eight
 microsatellite loci were amplified using PCR and reactions were screened
 for success using agarose gel electrophoresis. Successful reactions were
 subjected to capillary electrophoresis using an ABI 3730 and GENESCAN LIZ
 600 as an internal sizing standard. Standard curve fitting, genotype
 scoring, and binning were performed using the microsatellite plugin for
 GENEIOUS, version R9 (Biomatters). Homing
 Data Please see the associated ReadMe
 file.
description: Microsatellite Data Missing
 genotypes are denoted with '0'. Genotypes are given as binned
 fragment lengths in two column per locus format. Metadata include
 individual identifiers (Animal_ID), species (Pc = <em>Plethodon
 cinereus</em>, Ph = <em>Plethodon hubrichti</em>),
 whether individuals were collected specifically for having unusal
 morphology (yes/no), and the population grouping used in downstream
 analyses (PcCZ = <em>P. cinereus</em> contact zone, THRID =
 Thunder Ridge (<em>P. cinereus</em> reference site), FF =
 Floyd's Field (<em>P. hubrichti</em> reference site),
 PhCZ = P<em>. hubrichti</em> contact zone). 
 Homing Data Please see the
 associated ReadMe file.
DOI: 10.5061/dryad.2z34tmpjk
title: Cardio-metabolic biomarkers measured across a lifestyle gradient

description: The “mismatch” between evolved human physiology and Western lifestyles is
 thought to explain the current epidemic of cardiovascular disease (CVD) in
 industrialized societies. However, this hypothesis has been difficult to
 test because few populations concurrently span ancestral and modern
 lifestyles. To address this gap, we collected interview and biomarker data
 from individuals of Turkana ancestry who practice subsistence-level,
 nomadic pastoralism (the ancestral way of life for this group), as well as
 individuals who no longer practice pastoralism and live in urban areas. We
 found that Turkana who move to cities exhibit poor cardio-metabolic
 health, partially because of a shift toward “Western diets” high in
 refined carbohydrates. We also show that being born in an urban area
 independently predicts adult health, such that life-long city dwellers
 will experience the greatest CVD risk. By focusing on a unique and
 dramatic lifestyle gradient, our work thus informs the timing, magnitude,
 and evolutionary causes of CVD.
description: The data were collected and processed as described in Lea et al.
 2020, Science Advances.
description: Missing values are indicated by NA. The
 columns of the data file are as follows: Individual ID
 - unique identifier for each sampled individual<br> Waist
 circumference - an average of 3 measurements, reported in cm<br>
 Systolic BP - reported in mm Hg<br> Diastolic BP - reported in mm
 Hg<br> Blood glucose - measured from blood, reported in
 mg/dl<br> Body fat - measured using electrical impedence, reported
 as a percentage<br> Total cholesterol - measured from blood,
 reported in mg/dl<br> HDL cholesterol - measured from blood,
 reported in mg/dl<br> Triglycerides - measured from blood, reported
 in mg/dl<br> LDL cholesterol - measured from blood, reported in
 mg/dl<br> Sex - self reported sex<br> Age - self reported
 age<br> BMI - reported in kg/m2<br> Lifestyle category - a
 categorical variable defined as in Lea et al. 2020, Science
 Advances
DOI: 10.5068/d11t2d
title: Data from: Multiple routes to interspecific territoriality in sister species of North American perching birds

description: Behavioral interference between species can influence a wide range of
 ecological and evolutionary processes. Here we test foundational
 hypotheses regarding the origins and maintenance of interspecific
 territoriality, and evaluate the role of interspecific territoriality and
 hybridization in shaping species distributions and transitions from
 parapatry to sympatry in sister species of North American perching birds
 (Passeriformes). We found that interspecific territoriality is pervasive
 among sympatric sister species pairs, and that interspecifically
 territorial species pairs have diverged more recently than sympatric
 non-interspecifically territorial pairs. None of the foundational
 hypotheses alone explain the observed patterns of interspecific
 territoriality, but our results support the idea that some cases of
 interspecific territoriality arise from misdirected intraspecific
 aggression while others are evolved responses to resource competition. The
 combination of interspecific territoriality and hybridization appears to
 be an unstable state associated with parapatry, while species that are
 interspecifically territorial and do not hybridize are able to achieve
 extensive fine- and coarse-scale breeding range overlap. In sum, these
 results suggest that interspecific territoriality has multiple origins and
 that interspecific territoriality and hybridization together can have
 striking impacts on species ranges.
description: These data were collected through literature and database
 searches. Most data were collected for each species, and then the absolute
 value of the difference between species pairs was calculated for certain
 traits (or a correlation or other pairwise similarity measure was used
 when relevant). We report these species differences in traits as well as
 sympatry measures in this dataset.
description: README.csv describes the data in sistertaxa_dataset.csv. The
 analysis.R file contains code to generate the figures and tables in the
 paper. The binomial_covariate.R file is a file with functions used in
 analysis.R.  The data contain a few missing values but
 most rows are complete. Each row represents one species pair.
DOI: 10.5061/dryad.9p8cz8wdf
title: Data from: Asymmetric contributions of seed and pollen to gene dispersal in the marsh orchid Dactylorhiza umbrosa in Asia Minor

description: Orchids differ from other plants in their extremely small and partly
 air-filled seeds that can be transported long distances by wind. Seed
 dispersal in orchids is expected to contribute strongly to overall gene
 flow, and orchids generally express low levels of genetic differentiation
 between populations and low pollen to seed flow ratios. However, studies
 in orchids distributed in northern Europe have often found a poor
 geographic structuring of genetic variation. Here, we studied geographic
 differentiation in the marsh orchid Dactylorhiza umbrosa, which is widely
 distributed in upland regions from Asia Minor to Central Asia. These areas
 were less affected by Pleistocene ice ages than northern Europe and the
 orchid should have been able to survive the last ice age in local refugia.
 In the plastid genome, which is dispersed by seeds, populations at close
 distance were clearly divergent, but the differentiation still increased
 with geographic distance, and a significant phylogeographic structure had
 developed. In the nuclear genome, which is dispersed by both seeds and
 pollen, populations showed an even stronger correlation between genetic
 and geographic distance, but average levels of differentiation were lower
 than in the plastid genome, and no phylogeographic structure was evident.
 Combining plastid and nuclear data, we found that the ratio of pollen to
 seed dispersal (mp/ms) decreases with physical distance. Comparison with
 orchids that grow in parts of Europe that were glaciated during the last
 ice suggests that a balanced structure of genetic diversity develops only
 slowly in many terrestrial orchids, despite of efficient seed dispersal.
description: For details, see: Hedrén, M., Birkedal, S., de Boer,
 H., Ghorbani, A., Gravendeel, B., Hansson, S., Svensson, Å., Zarre,
 S. (202x). Asymmetric contributions of seed and pollen to gene dispersal
 in the marsh orchid <i>Dactylorhiza umbrosa</i> in Asia Minor.
 Molecular Ecology.
description: Base data for " Asymmetric contributions of seed and pollen
 to gene dispersal in the marsh orchid <i>Dactylorhiza
 umbrosa</i> in Asia Minor " by Mikael Hedrén, Sven Birkedal,
 Hugo de Boer, Abdolbaset Ghorbani, Barbara Gravendeel, Sven Hansson, Åke
 Svensson & Shahin Zarre. The data set comprises (a) nuclear
 microsatellite genotype data (four loci, two alleles per locus; allele
 sizes given in base pairs), (b) plastid haplotype data (haplotype number,
 fragment length at five size-variable plastid regions; size in base pairs
 relative to shortest observed fragment). * = missing data.
DOI: 10.6086/d1vt1g
title: Data for differential feeding responses of several bee species to sugar sources containing Iridomyrmecin, an Argentine ant trail pheromone component

description: These data describe the bioassays associated with published article, doi:
 10.1007/s10905-020-09748-8 (Differential Feeding Responses of Several Bee
 Species to Sugar Sources Containing Iridomyrmecin, an Argentine Ant Trail
 Pheromone Component). We investigated the response of three
 commercially important pollinator species to a
 pheromone deposited by Argentine ants at a food source.
 The Argentine ant Linepithema humile is one of the most invasive and
 problematic ant species; it has been introduced to Mediterranean-type
 habitats around the globe. In invaded areas, the Argentine ant has
 negatively affected a diversity of native plant and animal taxa Using
 three bee species that are commercial pollinators (Megachile rotundata,
 Osmia lignaria, and Apis mellifera), we sought to quantify the effects of
 an invasive Argentine ant pheromone on the resource collection of bees.
 Our study suggests that flowers or other nectar sources that are currently
 visited by Argentine ants are likely to have iridomyrmecin deposited on
 them. 
description: For detailed methods, please refer to the publication which
 reports the collection and analysis of these data
 (https://doi.org/10.1007/s10905-020-09748-8). This reports the feeding
 response of individual bees when given a choice between two sucrose
 solutions, one with and one without pheromone. Each bee is represented by
 a single row. The sugar solutions were dyed yellow or red, such that by
 looking at the color of the bee's fecal material, we could assess
 which sucrose solution they fed upon. Each bee was kept in isolation with
 filter paper lining the bottom of their container. Its feeding response
 was assessed as to whether they fed solely on the control, solely on teh
 pheromone, or on both solutions. Please refer to the usage notes for
 explanation as to how to use these data.
description: The dataset consists of behavioral response data for 3 species of
 choice tests between a control sucrose solution and a sucrose solution
 with an ant pheromone at either 0.1mg/mL or 0.001mg/mL
 iridomyrmecin. Species: Apis mellifera=Apis; Megachile
 rotundata=Megachile; Osmia lignaria=Osmia Pher.Conc.:
 describes the concentration of iridomyrmecin provided in a sucrose
 solution in choice tests to individual bees (0.1=0.1mg/mL;
 0.01=0.01mg/mL) Feed.response: describes the feeding
 behavior of each individual bee. 1= bee fed on control solution only; 2=
 bee fed on both control and pheromone solutions; 3=bee fed on pheromone
 solution only Each bee is only represented once in the
 dataset, such that each line is an individual bee.
DOI: 10.5061/dryad.sxksn0316
title: Microsatellite genotypes

description: Phylogeographic divergence and population genetic diversity within species
 reflect the impacts of habitat connectivity, demographics, and landscape
 level processes in both the recent and distant past. Characterizing
 patterns of differentiation across the geographic range of a species
 provides insight on the roles of organismal and environmental traits, on
 evolutionary divergence, and future population persistence. This is
 particularly true of habitat specialists where habitat availability and
 resource dependence may result in pronounced genetic structure as well as
 increased population vulnerability. We use DNA sequence data as well as
 microsatellite genotypes to estimate range-wide phylogeographic
 divergence, historical population connectivity, and historical
 demographics in an endemic habitat specialist, the dunes sagebrush lizard
 (Sceloporus arenicolus). This species is found exclusively in dune
 blowouts and patches of open sand within the shinnery oak-sand dune
 ecosystem of southeastern New Mexico and adjacent Texas. We find evidence
 of phylogeographic structure consistent with breaks and constrictions in
 suitable habitat at the range-wide scale. In addition, we find support for
 a dynamic and variable evolutionary history across the range of S.
 arenicolus. Populations in the Monahans Sandhills have deeply divergent
 lineages consistent with long-term demographic stability. In contrast,
 populations in the Mescalero Sands are not highly differentiated, though
 we do find evidence of demographic expansion in some regions and relative
 demographic stability in others. Phylogeographic history and population
 genetic differentiation in this species has been shaped by the
 configuration of habitat patches within a geologically complex and
 historically dynamic landscape. Our findings identify regions as
 genetically distinctive conservation units as well as underscore the
 genetic and demographic history of different lineages of S. arenicolus.
description: Multilocus genotypes at 27 microsatellite loci were collected via
 multiplex PCR and capillary gel electrophoresis. All allele calls were
 scored in GeneMapper.
 <em>collapse_cleanup.py</em> script is a Python
 script that extends the functions of the BioPython script
 sequence_cleaner.py to produce nexus and fasta alignments for subsequent
 analyses.
description: Genepop formatted file with original allele sizes. Divided into
 populations delineating the 10 regions indicated in the paper.
DOI: 10.5061/dryad.2547d7wnv
title: Learning can be detrimental for a parasitic wasp: R scripts and Telenomus podisi data

description: Animals have evolved the capacity to learn, and the conventional view is
 that learning allows individuals to improve foraging decisions. We
 describe a first case of maladaptive learning where a parasitoid learns to
 associate chemical cues from an unsuitable host, thereby re-enforcing a
 reproductive cul-de-sac (evolutionary trap). Telenomus podisi parasitizes
 eggs of the exotic stink bug Halyomorpha halys at the same rate as eggs of
 its coevolved host, Podisus maculiventris, but the parasitoid cannot
 complete its development in the exotic species. We hypothesized that T.
 podisi learns to exploit cues from this non-coevolved species, thereby
 increasing unsuccessful parasitism rates. We conducted bioassays to
 compare the responses of naïve vs. experienced parasitoids on chemical
 footprints left by one of the two host species. Both naïve and experienced
 females showed a higher response to footprints of P. maculiventris than of
 H. halys. Furthermore, parasitoids that gained an experience on H. halys
 significantly increased their residence time within the arena and the
 frequency of re-encounter with the area contaminated by chemical cues.
 Maladaptive learning in the T. podisi - H. halys association is expected
 to further decrease parasitoid reproductive success and have consequences
 for population dynamics of sympatric native and exotic host species.
description: Generalized linear models
 (GLMs with Gaussian distribution for time data or Poisson distribution for
 count data) were fitted to test the effects of host herbivore species
 (<i>H. halys</i> or <i>P. maculiventris</i>) and
 parasitoid previous experience (experienced or naïve) on total parasitoid
 residence time and number of re-encounters with the contaminated area.
 Residence time data were subjected to Box-Cox transformation for
 normalization before the analyses. Significance of the model terms was
 evaluated by means of F test or Likelihood Ratio Test. Significance of the
 different variable levels was assessed using the Tukey HSD multiple
 comparisons procedure, adopting a significance level α = 0.05. Analyses
 were conducted under R statistical environment (R Core Team,
 2020).
DOI: 10.5061/dryad.xsj3tx9ch
title: Knowledge, attitude and practice (KAP) survey of canine rabies in Khyber Pakhtunkhwa and Punjab Province of Pakistan

description: Background This study aimed to assess the extent of knowledge and
 understanding of rabies disease in rural and urban communities of
 Pakistan. It also identified malpractices after suspected dog bite that
 might pose a risk for humans contracting rabies. Methods A cross-sectional
 study was conducted (n = 1466) on people having different age
 groups and educational levels in four different geographic regions of
 Punjab and Khyber Pakhtunkhwa provinces in Pakistan. Knowledge, attitude,
 and practices of people were assessed using a structured questionnaire. We
 used a bivariate and multivariate analysis to study the association
 between rabies related mortalities in near or extended family members and
 different risk behaviors. Results Our results demonstrate that the
 majority of the juvenile population (less than 18 years of age) were not
 aware of the clinical signs of rabies in animals. 75% of the total
 respondents were not vaccinated against rabies, 60% did not seek a
 doctor’s advice after a suspected animal bite, and 55% had inadequate
 health care facilities for rabies patients in local hospitals. Respondents
 that had pets at home had not vaccinated (38%; p &lt; 0.05; odds ratio
 1.58) themselves against rabies due to lack of knowledge and awareness of
 pre-exposure prophylaxis for rabies (51%; p &lt; 0.05; odds ratio
 1.25). They also tend to not visit doctor after suspected bite (52%;
 p &lt; 0.05; odds ratio 1.97), which may had resulted in more
 deaths (65%; p &lt; 0.05; odds ratio 1.73) of someone in
 their near or extended family due to rabies. Conclusions Lack of knowledge
 about the nature of rabies disease and prophylaxis has contributed to
 increase of rabies related deaths. Inadequate health care facilities and
 poor attitude of not seeking medical attention after suspected dog bite
 are the major reasons of rabies related deaths. These findings could help
 in devising a targeted management strategy and awareness program to
 control and reduce the incidence of human rabies related deaths in
 Pakistan.
description: Data was collected on a pre-designed, structured questionnaire
 from different sites in the 4 aforementioned geographic regions of Punjab
 and KPK province by trained enumerators. Convenient sampling technique was
 used to collect data regarding knowledge, attitude, and practices of
 rabies. For the sake of convenience, to maximize accuracy along with
 response rate, and to avoid any sort of confusion by the respondents, the
 questionnaire was translated into the local language in that region. Data
 was collected after obtaining informed verbal consent using debriefing
 form. Each respondent including guardian or parent of respondent below
 16 year of age was informed using same debriefing form. Verbal consent is
 preferred because it is socially and culturally acceptable in comparison
 to written consent which creates lot of suspicion.
DOI: 10.5061/dryad.12jm63xvn
title: Data from: Mapping molar shapes on signaling pathways

description: A major challenge in evolutionary developmental biology is to understand
 how genetic mutations underlie phenotypic changes. In principle, selective
 pressures on the phenotype screen the gene pool of the population. Teeth
 are an excellent model for understanding evolutionary changes in the
 genotype-phenotype relationship since they exist throughout vertebrates.
 Genetically modified mice (mutants) with abnormalities in teeth have been
 used to explore tooth development. The relationship between signaling
 pathways and molar shape, however, remains elusive due to the high
 intrinsic complexity of tooth crowns. This hampers our understanding of
 the extent to which developmental factors explored in mutants explain
 developmental and phenotypic variation in natural species that represent
 the consequence of natural selection. Here we combine a novel morphometric
 method with two kinds of data mining techniques to extract data sets from
 the three-dimensional surface models of lower first molars: i) machine
 learning to maximize classification accuracy of 22 mutants, and ii)
 phylogenetic signal for 31 Murinae species. Major shape variation among
 mutants is explained by the number of cusps and cusp distribution on a
 tooth crown. The distribution of mutant mice in morphospace suggests a
 nonlinear relationship between the signaling pathways and molar shape
 variation. Comparative analysis of mutants and wild murines reveals that
 mutant variation overlaps naturally occurring diversity, including more
 ancestral and derived morphologies. However, taxa with transverse lophs
 are not fully covered by mutant variation, suggesting experimentally
 unexplored developmental factors in the evolutionary radiation of Murines.
description: <strong>Mutant mice molar shape
 dataset</strong><br> .csv file including PCA results for only
 mutant mice molar shape obtained from vertex normal with low-pass
 filtering (size = 6).<br> <strong>Mutants and wild murines
 molar shape dataset</strong><br> .csv file including PCA
 results for mutant mice and wild murine molar shape obtained from vertex
 normal and radius with low-pass filtering (size = 2).