cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.s4h2j
title: Data from: Delimiting species in the genus Otospermophilus (Rodentia: Sciuridae) using genetics, ecology, and morphology

description: We apply an integrative taxonomy approach to delimit species of ground
 squirrels in the genus Otospermophilus because the diverse evolutionary
 histories of organisms shape the existence of taxonomic characters.
 Previous studies of mitochondrial DNA from this group recovered three
 divergent lineages within Otospermophilus beecheyi separated into
 northern, central, and southern geographical populations, with
 Otospermophilus atricapillus nested within the southern lineage of
 O. beecheyi. To further evaluate species boundaries within this complex,
 we collected additional genetic data (one mitochondrial locus, 11
 microsatellite markers, and 11 nuclear loci), environmental data (eight
 bioclimatic variables), and morphological data (23 skull measurements). We
 used the maximum number of possible taxa (O. atricapillus, Northern
 O. beecheyi, Central O. beecheyi, and Southern O. beecheyi) as our
 operational taxonomic units (OTUs) and examined patterns of divergence
 between these OTUs. Phenotypic measures (both environmental and
 morphological) showed little differentiation among OTUs. By contrast, all
 genetic datasets supported the evolutionary independence of Northern
 O. beecheyi, although they were less consistent in their support for other
 OTUs as distinct species. Based on these data, we support the conclusions
 from a previous study that synonymized O. atricapillus with O. beecheyi,
 and we elevate the northern lineage of O. beecheyi to a separate species.
description: Phuongetal_BJLS_Squirrel_species_delimitationThe following file contains: (1) microsatellite genotyping calls (2) mitochondrial and nuclear sequence data alignments (3) morphological data and (4) environmental data
DOI: 10.5061/dryad.n9v91
title: Data from: On-shelf larval retention limits population connectivity in a coastal broadcast spawner

description: Broadcast-spawning marine organisms with long pelagic larval duration are
 often expected to be genetically homogeneous throughout their ranges. When
 genetic structure is found in such taxa, it may be in the form of chaotic
 genetic patchiness: i.e. patterns that might seem independent of any
 underlying environmental variation. The joint analysis of population
 genetic data and marine environmental data can elucidate factors driving
 such spatial genetic diversity patterns. Using meso-scale sampling (at a
 scale of 10s to 100s of km), microsatellite data and advection
 connectivity simulations, we studied the effect of temperate southern
 Australian ocean circulation on the genetic structure of the snail Nerita
 atramentosa. This species has a long pelagic larval duration and is
 represented as a single metapopulation throughout its ~3000 km range, but
 even so, we found that its dispersal potential is lower than expected.
 Connectivity simulations indicate that this is a result of the larvae that
 remain on the continental shelf (where currents are erratic and often
 shoreward) returning to the coast in much larger numbers than larvae that
 become entrained in the region’s shelf-edge boundary currents. Our study
 contributes to the growing evidence that departures from the expectations
 of panmixia along continuous and environmentally homogeneous coastlines
 are not limited to low-dispersal species, and it identifies on-shelf
 larval retention as an important factor limiting dispersal.
description: NeritaMicrosatsMicrosatellite data of Nerita atramentosa in GenAlEx file format.
DOI: 10.5061/dryad.8n2f2
title: Data from: Structure and dynamics of hybrid zones at multiple stages of speciation in the common vole (Microtus arvalis)

description: The genetic structure and dynamics of hybrid zones provides crucial
 information for the understanding of the processes and mechanisms of
 evolutionary divergence and speciation. In general, higher levels of
 evolutionary divergence between taxa are more likely to be associated with
 reproductive isolation and may result in suppressed or strongly restricted
 hybridization. In this study, we examined the structure and processes in
 two secondary contact zones between three deep evolutionary lineages in
 the common vole (Microtus arvalis). Differences in divergence times
 between the lineages have the potential to shed light on different stages
 of reproductive isolation and thus provide information on the ongoing
 speciation process in M. arvalis. We examined more than 800 individuals
 for mitochondrial (mtDNA), Y-chromosome and autosomal markers, and used
 assignment and cline analysis methods to characterize the extent and
 direction of gene flow in the contact zones. Introgression of both
 autosomal and mtDNA markers in a relatively broad area of admixture
 indicates selectively neutral hybridization between the least-divergent
 lineages (Central and Eastern) without evidence for partial reproductive
 isolation. In contrast, a very narrow area of hybridization, shifts in
 marker clines and the quasi-absence of Y-chromosome introgression support
 a moving hybrid zone and unidirectional selection against male hybrids
 between the lineages with older divergence (Central and Western). Data
 from a replicate sampling transect provided further support for
 non-neutral processes in this hybrid zone and suggests additionally a role
 for the landscape history in the extent of the movement and shaping of
 gene flow profiles.
description: Jura1Genotypes of the
 individuals of the Jura 1 transect. Missing data are scored by a
 -9Jura2Genotypes of the
 individuals of the Jura 2 transect. Missing data are scored by a
 -9BavariaGenotypes of the individuals of the Bavaria transect. Missing data are scored by a -9MtDNA & YchromsomesMtDNA and Y chromosome origin for each individuals.MtDNA_Ychr.xlsx
DOI: 10.5061/dryad.1s1h1530
title: Data from: Niche specialization influences adaptive phenotypic plasticity in threespine stickleback

description: Phenotypic plasticity may be favored in generalist populations if it
 increases niche width, even in temporally constant environments.
 Phenotypic plasticity can increase the frequency of extreme phenotypes in
 a population and thus allow it to make use of a wide resource spectrum.
 Here we test the prediction that generalist populations should be more
 plastic than specialists. In a common-garden experiment, we show that
 solitary, generalist populations of threespine sticklebacks inhabiting
 small coastal lakes of British Columbia have a higher degree of
 morphological plasticity than the more specialized sympatric limnetic and
 benthic species. The ancestral marine stickleback showed low levels of
 plasticity similar to those of sympatric sticklebacks, implying that the
 greater plasticity of the generalist population has evolved recently.
 Measurements of wild populations show that those with mean trait values
 intermediate between the benthic and limnetic values indeed have higher
 morphological variation. Our data indicate that plasticity can evolve
 rapidly after colonization of a new environment in response to changing
 niche use.
description: fieldMorphological
 measurements for all the field caught individualsexperimentMorphological measurements for all the experimental individuals
DOI: 10.5061/dryad.bc1k2b3
title: Data from: Estimating transient populations of unmarked individuals at a migratory stopover site using generalized N-mixture models

description: 1. Migration counts are popular indices used to monitor population trends
 over time. Advanced analytical methods for estimating abundance of
 unmarked, open populations now incorporate population growth models and
 simultaneously test for covariate effects on abundance and detection
 probability. However, estimating population abundance at a staging site is
 complicated by daily immigration and emigration of unmarked individuals.
 2. We applied a set of generalized N-mixture models to simulated count
 data to test their applicability for transient populations. Using
 simulated datasets, parameters were unbiased when the apparent survival
 rate varied within a season or was mis-specified in a model, but not when
 the immigration or detection probability was mis-specified. 3. With
 knowledge from the simulated data, we applied these models to daily counts
 of staging migratory shorebirds and estimated daily abundances accounting
 for variation in the detection and immigration rates. Daily counts of
 ruddy turnstones (Arenaria interpres) staging at Westhampton Island, New
 York, were collected during northward migration (1997–1999). We tested the
 effects of weather and tides on detection probability, and we modeled
 within-season variation in immigration rates as a function of time. 4.
 Covariates affecting the detection probability differed among years, but
 tide height consistently was correlated with detection probability.
 Accounting for detection and immigration rates, the predicted maximum
 single-day populations of ruddy turnstones were 172%, 165%, and 129% of
 the observed counts for each year. 5. Synthesis and applications.
 Management and conservation plans for migratory species require abundance
 estimates that are near the true population size though they are difficult
 to obtain. Our study is the first empirical application of the generalized
 N-mixture model that incorporates temporal trends in immigration and
 estimates daily abundance of a staging unmarked migratory population.
 Correct estimation of population sizes and the environmental factors
 affecting them can aid the conservation prioritization of species and
 staging sites. Moreover, the use of generalized N-mixture models can
 improve our understanding of the environmental factors that shape
 migratory movements.
description: Kwon_JAPPL_2018_00216.R3_dataRepeated counts of ruddy turnstones surveyed at Westhampton Island, New York, during the northward migration of 1997–1999, accompanied with environmental covariates.
DOI: 10.5061/dryad.g0b2c
title: Data from: Individual quality and age but not environmental or social conditions modulate costs of reproduction in a capital breeder

description: Costs associated with reproduction are widely known to play a role in the
 evolution of reproductive tactics with consequences to population and
 eco-evolutionary dynamics. Evaluating these costs as they pertain to
 species in the wild remains an important goal of evolutionary ecology.
 Individual heterogeneity, including differences in individual quality
 (i.e., among-individual differences in traits associated with survival and
 reproduction) or state, and variation in environmental and social
 conditions can modulate the costs of reproduction; however, few studies
 have considered effects of these factors simultaneously. Taking advantage
 of a detailed, long-term dataset for a population of feral horses (Sable
 Island, Nova-Scotia, Canada), we address the question of how intrinsic
 (quality, age), environmental (winter severity, location), and social
 conditions (group size, composition, sex ratio, density) influence the
 costs of reproduction on subsequent reproduction. Individual quality was
 measured using a multivariate analysis on a combination of four static and
 dynamic traits expected to depict heterogeneity in individual performance.
 Female quality and age interacted with reproductive status of the previous
 year to determine current reproductive effort, while no effect of social
 or environmental covariates was found. High quality females showed higher
 probabilities of giving birth and weaning their foal regardless of their
 reproductive status the previous year, while those of lower quality showed
 lower probabilities of producing foals in successive years. Middle-aged
 (prime) females had the highest probability of giving birth when they had
 not reproduced the year before but no such relationship with age was found
 among females that had reproduced the previous year, indicating that
 prime-aged females bear higher costs of reproduction. We show that
 individual quality and age were key factors modulating the costs of
 reproduction in a capital breeder but that environmental or social
 conditions were not, highlighting the importance of considering multiple
 factors when studying costs of reproduction.
description: data_MS_ECE-2016-11-01203Full data used for the analysesdata-SHORT_MS_ECE-2016-11-01203.csv
DOI: 10.5061/dryad.t7g8f
title: Data from: Assortative mating and the maintenance of population structure in a natural hybrid zone

description: Understanding the factors that give rise to natural hybrid zones and
 govern their dynamics and structure is important to predicting the
 evolutionary consequences of hybridization. Here we use a combination of
 multi-generational population genetic data, mating patterns from a natural
 population, behavioral assays, and mark-recapture data within clinal
 hybrid zones of the genus Xiphophorus to test the role of assortative
 mating in maintaining population structure and the potential for ongoing
 genetic exchange between heterospecifics. Our data demonstrate that
 population structure is temporally robust and driven largely by
 assortative mating stemming from pre-copulatory isolation between pure
 species. Furthermore, mark-recapture data revealed that rates of migration
 within the same stream reach are far below the level needed to support
 population structure. Contrasting with many empirical studies of natural
 hybrid zones, there appeared to be no hybrid male dysfunction nor
 discrimination against hybrid males by pure parental females, and hybrid
 females mated and associated with pure species and hybrid males at random.
 Despite strong isolation between pure parentals, hybrids therefore can act
 as a conduit for genetic exchange between heterospecifics, which has been
 shown to increase the tempo of evolutionary change. Additionally, our
 findings highlight the complexity of natural hybrid zone dynamics,
 demonstrating that multivariate selection can give rise to patterns that
 do not fit classical models of hybrid zone evolution.
description: Social Association Data
 Culumber et al.X-Y coordinates of fish
 positions in the assays of social association reported in Culumber et al.
 "Assortative mating and the maintenance of population structure in a
 natural hybrid zone". American Naturalistdata.xls
DOI: 10.5061/dryad.6d4n6
title: Data from: Social structure varies with elevation in an alpine ant

description: Insect societies vary greatly in social organization, yet the relative
 roles of ecological and genetic factors in driving this variation remain
 poorly understood. Identifying how social structure varies along
 environmental gradients can provide insights into the ecological
 conditions favouring alternative social organizations. Here, we
 investigate how queen number variation is distributed along elevation
 gradients within a socially polymorphic ant, the Alpine silver ant Formica
 selysi. We sampled low and high elevation populations in multiple Alpine
 valleys. We show that populations belonging to different drainage basins
 are genetically differentiated. In contrast, there is little genetic
 divergence between low and high elevation populations within the same
 drainage basin. Thus, elevation gradients in each of the drainage basins
 represent independent contrasts. Whatever the elevation, all well-sampled
 populations are socially polymorphic, containing both monogynous (= one
 queen) and polygynous (= multiple queen) colonies. However, the proportion
 of monogynous colonies per population increases at higher elevation, while
 the effective number of queens in polygynous colonies decreases, and this
 pattern is replicated in each drainage basin. The increased prevalence of
 colonies with a single queen at high elevation is correlated with summer
 and winter average temperature, but not with precipitation. The colder,
 unpredictable, and patchy environment encountered at higher elevations may
 favour larger queens with the ability to disperse and establish incipient
 monogynous colonies independently, while the stable and continuous habitat
 in the lowlands may favour large, fast-growing polygynous colonies. By
 highlighting differences in the environmental conditions favouring
 monogynous or polygynous colonies, this study sheds light on the
 ecological factors influencing the distribution and maintenance of social
 polymorphism.
description: Purcell et al.
 Environmental VariablesColony position, social
 structure, and environmental variables.Purcell_etal_Ant_Elev_Gradients_envi.csvPurcell et al. Microsat DataMicrosatellite results for each individual and each colony. 'NA' represents missing data. Individuals with poor quality results were removed.Purcell_etal_2014_MicrosatData.csvFormica_selysi_COI_MolEcol.fasAligned COI sequences of Formica selysi individuals.
DOI: 10.5061/dryad.63r07
title: Data from: Relationship among medical student resilience, educational environment and quality of life

description: Context: Resilience is a capacity to face and overcome adversities, with
 personal transformation and growth. In medical education, it is critical
 to understand the determinants of a positive, developmental reaction in
 the face of stressful, emotionally demanding situations. We studied the
 association among resilience, quality of life (QoL) and educational
 environment perceptions in medical students. Methods: We evaluated data
 from a random sample of 1,350 medical students from 22 Brazilian medical
 schools. Information from participants included the Wagnild and Young’s
 resilience scale (RS-14), the Dundee Ready Educational Environment Measure
 (DREEM), the World Health Organization Quality of Life questionnaire –
 short form (WHOQOL-BREF), the Beck Depression Inventory (BDI) and the
 State-Trait Anxiety Inventory (STAI). Results: Full multiple linear
 regression models were adjusted for sex, age, year of medical course,
 presence of a BDI score ≥ 14 and STAI state or anxiety scores ≥ 50.
 Compared to those with very high resilience levels, individuals with very
 low resilience had worse QoL, measured by overall (β=-0.89; 95% confidence
 interval =-1.21 to -0.56) and medical-school related (β=-0.85; 95%CI=-1.25
 to -0.45) QoL scores, environment (β=-6.48; 95%CI=-10.01 to -2.95),
 psychological (β=-22.89; 95%CI=-25.70 to -20.07), social relationships
 (β=-14.28; 95%CI=-19.07 to -9.49), and physical health (β=-10.74;
 95%CI=-14.07 to -7.42) WHOQOL-BREF domain scores. They also had a worse
 educational environment perception, measured by global DREEM score
 (β=-31.42; 95%CI=-37.86 to -24.98), learning (β=-7.32; 95%CI=-9.23 to
 -5.41), teachers (β=-5.37; 95%CI=-7.16 to -3.58), academic self-perception
 (β=-7.33; 95%CI=-8.53 to -6.12), atmosphere (β=-8.29; 95%CI=-10.13 to
 -6.44) and social self-perception (β=-3.12; 95%CI=-4.11 to -2.12) DREEM
 domain scores. We also observed a dose-response pattern across resilience
 level groups for most measurements. Conclusions: Medical students with
 higher resilience levels had a better quality of life and a better
 perception of educational environment. Developing resilience may become an
 important strategy to minimize emotional distress and enhance medical
 training.
description: Dataset of individual
 values of self-evaluation of quality of life, resilience, WHPQOL-BREF and
 DREEMIndividual values of a
 random sample of 1,350 medical students from 22 medical schools in Brazil.
 Values are from self-evaluation of quality of life in general and quality
 of life in medical school, all domains of quality of life questionnaire
 (WHOQOL-BREF) and all domains of questionnaire of educational environment
 perception (DREEM).Dataset Resilience Educational
 Environment QoL.xlsx
DOI: 10.5061/dryad.k302g
title: Data from: Large-scale genetic panmixia in the blue shark (Prionace glauca): a single worldwide population, or a genetic lag-time effect of the “grey zone” of differentiation?

description: The blue shark Prionace glauca, among the most common and widely studied
 pelagic sharks, is a top predator, exhibiting the widest distribution
 range. However, little is known about its population structure and spatial
 dynamics. With an estimated removal of 10 to 20 million individuals per
 year by fisheries, the species is classified as “Near Threatened” by
 International Union for Conservation of Nature. We lack the knowledge to
 forecast the long-term consequences of such a huge removal on this top
 predator itself and on its trophic network. The genetic analysis of more
 than 200 samples collected at broad scale (from Mediterranean Sea, North
 Atlantic and Pacific Oceans) using mtDNA and nine microsatellite markers
 allowed to detect signatures of genetic bottlenecks but a nearly complete
 genetic homogeneity across the entire studied range. This apparent
 panmixia could be explained by a genetic lag-time effect illustrated by
 simulations of demographic changes that were not detectable through
 standard genetic analysis before a long transitional phase here introduced
 as the “population grey zone”. The results presented here can thus
 encompass distinct explanatory scenarios spanning from a single
 demographic population to several independent populations. This limitation
 prevents the genetic-based delineation of stocks and thus the ability to
 anticipate the consequences of severe depletions at all scales. More
 information is required for the conservation of population(s) and
 managements of stocks, which may be provided by large scale sampling not
 only of individuals worldwide, but also of loci genome-wide.
description: SSR dataset from P.
 glaucaFirst column:
 localisation (either Mediterranean Sea: Gulf of Lion/Malta/Greece,
 Atlantic Ocean: Azores/Spain or Pacific Ocean: Hawaii/Australia/New
 Zealand). Second column:individual (individual tag). Others columns: the 9
 SSR selected (BEF94, CY92Z, TB02, DZOXN, TB04, TB01, FV6T5, A2ASY and
 EWU1E). Missing loci are coded with "0".pg_9SSR.xlsxCytb sequences from Prionace glaucaP. glauca cytb sequences of 758 bp length.pg_cytb.fasta