cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.04m3v
title: Data from: Heterozygote deficits in cyst plant parasitic nematodes: possible causes and consequences

description: Deviations of genotypic frequencies from Hardy–Weinberg equilibrium (HWE)
 expectations could reveal important aspects of the biology of populations.
 Deviations from HWE due to heterozygote deficits have been recorded for
 three plant-parasitic nematode species. However, it has never been
 determined whether the observed deficits were due (i) to the presence of
 null alleles, (ii) to a high level of consanguinity and/or (iii) to a
 Wahlund effect. The aim of the present work was, while taking into the
 possible confounding effect of null alleles, to disentangle consanguinity
 and Wahlund effect in natural populations of those three economically
 important cyst nematodes using microsatellite markers: Globodera pallida,
 G. tabacum and Heterodera schachtii, pests of potato, tobacco and sugar
 beet, respectively. The results show a consistent pattern of heterozygote
 deficiency in the three nematode species sampled at the spatial scale of
 the host plant. We demonstrate that the prevalence of null alleles is weak
 and that heterozygote deficits do not have a single origin. Our results
 suggested that it is restricted dispersal that leads to heterozygote
 deficits through both consanguinity and substructure, which effects can be
 linked to soil movement, cyst density, and the number of generations per
 year. We discuss potential implications for the durability of plant
 resistances that are used to protect crops against parasites in which
 mating between relatives occur. While consanguineous mating leads to
 homozygosity at all loci, including loci governing avirulence/virulence,
 which favours the expression of virulence when recessive, the Wahlund
 effect is expected to have no particular effect on the adaptation of
 nematodes to resistances.
description: G_pallidaGenotypic data (Genepop format) for the species Globodera pallidaG_tabacumGenotypic data (Genepop format) for the species Globodera tabacumH_schachtiiGenotypic data (Genepop format) for the species Heterodera schachtii
DOI: 10.5061/dryad.q8r422h
title: Data from: Melanin-based sexual dichromatism in the Western Palearctic avifauna implies darker males and lighter females

description: Melanins are the most common pigments providing coloration in the plumage
 and bare skin of birds and other vertebrates. Numerous species are
 dichromatic in the adult or definitive plumage, but the direction of this
 type of sexual dichromatism (i.e., whether one sex tends to be darker than
 the other ones) has not been thoroughly investigated. Using color plates,
 we analysed the presence of melanin-based color patches in 666 species
 belonging to 69 families regularly breeding in the Western Palearctic.
 Sexual dichromatism based on melanins in at least one integumentary part
 involved 205 (30.7%) species. The body parts contributing more frequently
 to dichromatism were the dorsal areas, head and breast, whereas the less
 dichromatic body parts were the belly and the exposed integumentary parts
 (i.e., bill and legs). Regarding the phylogenetic spread of dichromatisms,
 37 (53.6%) families contained at least one species with melanin-based
 sexual dimorphism in the definitive adult plumage. As for the direction of
 the color difference, males are darker than females in a majority of
 species, meaning that males tend to produce more eumelanin and females
 tend to synthesize more pheomelanin. This survey has revealed the high
 prevalence of melanins in the emergence of sexual dichromatism in birds,
 at least in the Western Palearctic. Whether the described pattern is due
 to sexual selection promoting more conspicuous males or to natural
 selection for more cryptic females remains to be determined. Given that
 pheomelanin synthesis concurrently consumes the antioxidant glutathione
 but also reduces toxic cysteine, sex-biased physiological factors should
 also be given consideration in the evolution of bird plumages.
description: dichromatism by body
 area in species of the Western PalearcticColor descriptions of
 both male and females considering 7 body parts (see headings). Only
 dichromatic species. Monochromatic species not
 included.dichromatismbybodypart-WP.xlsSpecies for phylogenyBird species of the Western Palearctic considering whether or not they are dichromatic for melanins in at least one body part.
DOI: 10.5061/dryad.3ng7p
title: Data from: Niche divergence versus neutral processes: combined environmental and genetic analyses identify contrasting patterns of differentiation in recently diverged pine species

description: Background and Aims: Solving relationships of recently diverged taxa,
 poses a challenge due to shared polymorphism and weak reproductive
 barriers. Multiple lines of evidence are needed to identify independently
 evolving lineages. This is especially true of long-lived species with
 large effective population sizes, and slow rates of lineage sorting. North
 American pines are an interesting group to test this multiple approach.
 Our aim is to combine cytoplasmic genetic markers with environmental
 information to clarify species boundaries and relationships of the species
 complex of Pinus flexilis, Pinus ayacahuite, and Pinus strobiformis.
 Methods: Mitochondrial and chloroplast sequences were combined with
 previously obtained microsatellite data and contrasted with environmental
 information to reconstruct phylogenetic relationships of the species
 complex. Ecological niche models were compared to test if ecological
 divergence is significant among species. Key Results and Conclusion:
 Separately, both genetic and ecological evidence support a clear
 differentiation of all three species but with different topology, but also
 reveal an ancestral contact zone between P. strobiformis and P.
 ayacahuite. The marked ecological differentiation of P. flexilis suggests
 that ecological speciation has occurred in this lineage, but this is not
 reflected in neutral markers. The inclusion of environmental traits in
 phylogenetic reconstruction improved the resolution of internal branches.
 We suggest that combining environmental and genetic information would be
 useful for species delimitation and phylogenetic studies in other recently
 diverged species complexes.
description: Sequence Key for
 populationsThis file has the
 identification keys for all sequences in the mitochondrial and chloroplast
 alignments.PopulationKey.docAlignment of concatenated chloroplast sequencesConcatenated sequences of the atpB-rbcL and trnL-trnF spacerscp_atpb_rbcl_trnLF.nexAlignment of mitochondrial sequencesSecond intron of the nad5 mitochondrial gene.mt_nad5d.nex
DOI: 10.5061/dryad.s631d
title: Data from: Bayesian tests of topology hypotheses with an example from diving beetles

description: We review Bayesian approaches to model testing in general and to the
 assessment of topological hypotheses in particular. We show that the
 standard way of setting up Bayes factor tests of the monophyly of a group,
 or the placement of a sample sequence in a known reference tree, can be
 misleading. The reason for this is related to the well-known dependency of
 Bayes factors on model-specific priors. Specifically, when testing tree
 hypotheses it is important that each hypothesis is associated with an
 appropriate tree space in the prior. This can be achieved by using
 appropriately constrained searches or by filtering trees in the posterior
 sample, but in a more elaborate way than typically implemented. If it is
 difficult to find the appropriate tree sets to be contrasted, then the
 posterior model odds may be more informative than the Bayes factor. We
 illustrate the recommended techniques using an empirical test case
 addressing the issue of whether two genera of diving beetles (Coleoptera:
 Dytiscidae), Suphrodytes and Hydroporus, should be synonymized. Our
 refined Bayes factor tests, in contrast to standard analyses, show that
 there is strong support for Suphrodytes nesting inside Hydroporus, and the
 genera are therefore synonymized.
description: Supplementary
 TablesSupplementary Table 1.
 Primers used for PCR amplification and sequencing.Supplementary Table 2.
 General properties of the DNA matrix. Invar = number of invariant sites.
 Var = number of variable sites. PI = number of parsimony informative
 sites. A, T, C, G = proportion of respective base.Supplementary
 File.pdfDNA dataset
 matrixDNA dataset matrix in
 nexus format with four genes (COI, H3, 16S, 18S), 2111 characters and 38
 taxa.Bergsten_etal_dataset.nexPhylogeny from Bayesian analysisMajority-rule consensus tree from bayesian analysis with MrBayes 3.2 in nexus format.Bergsten_etal_tree.tre
DOI: 10.5061/dryad.76bv3
title: Data from: Seasonality and temperature-dependent flight dispersal of Triatoma infestans (Hemiptera: Reduviidae) and other vectors of Chagas disease in western Argentina

description: Flight dispersal of Triatominae is affected by climatic conditions and
 determines the spatiotemporal patterns of house invasion and transmission
 of Trypanosoma cruzi Chagas (Kinetoplastida: Trypanosomatidae). We
 investigated the detailed time structure and temperature dependencies of
 flight occurrence of Triatoma infestans Klug (Hemiptera: Reduviidae) and
 other triatomine species in a rural village of western Argentina by taking
 advantage of the attraction of adult triatomines to artificial light
 sources. Most of the village’s streetlight posts were systematically
 inspected for triatomines twice between sunset and midnight over 425
 nights in the spring–summer seasons of 1999–2002, an unprecedented
 light-trap sampling effort for any triatomine species. In total, 288
 adults were captured, including 122 Triatoma guasayana Wygodzinsky and
 Abalos, 89 T. infestans, 72 Triatoma eratyrusiformis Del Ponte, and 5
 Triatoma garciabesi Carcavallo et al. Adult sex ratios were balanced in T.
 infestans and strongly male-biased in other species. Nearly all
 flight-dispersing triatomines were caught when temperatures at sunset were
 &gt;20 °C (range, 16.6–31.7 °C), suggesting a putative threshold
 around 17–18 °C. Triatomine catches were rare on rainy days. Logistic
 regression analysis revealed that the proportion of nights in which at
 least an adult T. infestans was caught increased highly significantly with
 increasing temperature at sunset and was modified by collection month,
 with greater catches in early spring and no sex differential. This study
 confirms that spring represents a previously overlooked, important
 dispersal period of T. infestans, and shows large variations among and
 within Triatominae in their temporal patterns of flight occurrence,
 abundance, and sex ratio.
description: DiIorio_Gurtler_flight_dataThe data set contains the presence/absence and number of triatomine adults by sex collected at public streetlight posts on given dates, temperature at sunset and presence/absence of rain
DOI: 10.5061/dryad.g0295
title: Data from: Climate change and bird reproduction: warmer springs benefit breeding success in boreal forest grouse

description: Global warming is predicted to adversely affect reproduction of birds,
 especially in northern latitudes. A recent study in Finland inferred that
 declining populations of black grouse Tetrao tetrix could be attributed to
 advancement of the time of mating and chicks hatching too early – a
 support of the mismatch hypothesis. Here, we examine the breeding success
 of sympatric capercaillie T. urogallus and black grouse over a 38-year
 period in southeast Norway. Breeding season temperatures increased, being
 most pronounced in April. Although the onset of spring advanced nearly 3
 weeks, peak of mating advanced only 4-5 days. Contrasting the result of
 the Finnish study, breeding success increased markedly in both species
 (capercaillie: 62%, black grouse: 38%). Both brood frequency and brood
 size increased during the study period, but significantly so only for
 brood frequency in capercaillie. Whereas the frequency of capercaillie
 broods was positively affected by rising temperatures, especially during
 the pre-hatching period, this was not the case in black grouse. Brood
 size, on the other hand, increased with increasing post-hatching
 temperatures in both species. Contrary to the prediction that global
 warming will adversely affect reproduction in boreal forest grouse, our
 study shows that breeding success was enhanced in warmer springs.
description: Background grouse census
 and climate dataGrouse census and
 climate data during 1979-2016 at the Varaldskogen study area, southeast
 Norway, including list of variables.Wegge-Rolstad_Grouse-Climate_data.xlsx
DOI: 10.15468/dl.3bxbgc
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Mexico",
 "TaxonKey is Ficimia streckeri",
 "Year 1960-2026"
 ]
}

 The dataset includes 28 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000768-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.12rj7fr
title: Data from: Lizards at the peak: physiological plasticity does not maintain performance in lizards transplanted to high altitude

description: Warming climates are facilitating the range expansion of many taxa to
 habitats that were formerly thermally inhospitable, including to higher
 latitudes and elevations. The potential for such colonization, however,
 varies widely among taxa. Since environmental factors may interact to
 affect colonization potential, an understanding of underlying
 physiological and behavioural mechanisms is necessary to predict how
 species will respond to potentially suitable habitats. For example,
 temperature and oxygen availability will interact to shape physiological
 and performance traits. Our model species, the wall lizard Podarcis
 muralis, is a widely distributed ectotherm that continues to expand its
 range in Europe despite being limited by cold temperatures at high
 elevations and latitudes. To test the potential for organisms to expand to
 warming high-altitude environments, we conducted a transplant experiment
 to quantify the within-individual effects of high-altitude hypoxia on
 physiological and performance traits. Transplanted lizards maintained
 individual differences in physiological traits related to oxygen capacity
 and metabolism (haemoglobin concentration, haematocrit, and peak
 post-exhaustion metabolic rate) as well as performance traits tied to
 fitness (sprint speed and running endurance). Although lizards altered
 blood biochemistry to increase oxygen-carrying capacity, their performance
 was reduced at high altitude. Furthermore, lizards at high altitude
 suffered a rapid loss of body condition over the six-week experiment,
 potentially indicating an energetic cost to hypoxia. Taken together, this
 demonstrates a limited potential for within-individual plasticity to
 facilitate colonization of novel high-altitude environments.
description: Primary data associated
 with Gangloff et al. 2018Provides experimental
 data on lizard (Podarcis muralis) morphometrics, physiology, and
 performance. Used for all analyses in manuscript except sprint
 speed.Gangloffetal2019_PBZ_PrimaryData.csvSprint speed data associated with Gangloff et al. 2018Provides experimental data on lizard (Podarcis muralis) sprint speed.Gangloffetal2019_PBZ_SprintData.csv
DOI: 10.5061/dryad.sk013
title: Data from: Genetic structure in a dynamic baboon hybrid zone corroborates behavioral observations in a hybrid population

description: Behavior and genetic structure are intimately related: mating patterns and
 patterns of movement between groups or populations influence the movement
 of genetic variation across the landscape and from one generation to the
 next. In hybrid zones, the behavior of the hybridizing taxa can also have
 an important impact on the incidence and outcome of hybridization events.
 Hybridization between yellow baboons and anubis baboons has been
 well-documented in the Amboseli basin of Kenya, where more anubis-like
 individuals tend to experience maturational and reproductive advantages.
 However, it is unknown whether these advantages are reflected in the
 genetic structure of populations surrounding this area. Here, we used
 nuclear microsatellite genotype data to evaluate the geographic structure
 and composition of baboon populations in southern Kenya, up to the border
 of Tanzania. Our results indicate that, unlike for mitochondrial DNA,
 microsatellite-based measures of genetic structure are in concordance with
 phenotypically based taxonomic distinctions, and that the currently active
 hybrid zone is relatively narrow. Interestingly, isolation with migration
 analysis revealed asymmetric gene flow in this region from anubis
 populations into yellow populations, in support of the anubis-biased
 phenotypic advantages observed in Amboseli. Populations that are primarily
 yellow but that are the recipients of anubis gene flow exhibit higher
 levels of genetic diversity than yellow populations far from the
 introgression front. Our results support previous work that indicates a
 long history of hybridization and male-mediated genetic introgression
 among East African baboons. In particular, it suggests that anubis baboons
 are in the process of gradual range expansion into the historic range of
 yellow baboon populations, a pattern that could be mechanistically
 explained by behavioral and life history advantages that correlate with
 anubis ancestry.
description: Data_Charpentier_et_alGenotypes
DOI: 10.5061/dryad.2hp4hq3
title: Data from: Risk factors for suicidality in Huntington's disease: an analysis of the 2CARE clinical trial

description: Most suicidality literature in HD is based on natural history studies or
 retrospective reviews, but reports on risk factors from clinical trials
 are limited. We analyzed 609 participants from 2CARE, a randomized,
 double-blind, placebo controlled clinical trial with up to 5 years of
 follow-up, for risk factors related to suicidality. The primary outcome
 variable was the time from randomization until the first occurrence of
 either suicidal ideation or attempt. We also considered time from
 randomization until the first suicide attempt as a secondary outcome
 variable. Depression, anxiety, bipolar disorder, antidepressant or
 anxiolytic use, and prior suicide attempt at baseline were associated with
 time to ideation or attempt. Baseline employment status, marital status,
 CAG repeat length, tetrabenazine use, and treatment assignment (coenzyme
 Q10 or placebo) were not associated with suicidality. Time-dependent
 variables from the UHDRS Behavioral Assessment were associated with time
 to suicidal ideation or attempt, driven mainly by items related to
 depressed mood, low self-esteem/guilt, anxiety, suicidal thoughts,
 irritability, and compulsions. Variables associated with time to suicide
 attempt alone were generally similar. These data suggest psychiatric
 co-morbidities in HD are predictive of suicidal behavior while
 participating in clinical trials, reinforcing the importance of clinical
 surveillance and treatment towards lessening risk during participation and
 perhaps beyond. Designing a composite algorithm for early prediction of
 suicide attempts in HD may be of value, particularly given anticipated
 trials aimed at disease modification are likely to be long-term.
description: McGarry et al
 Suicidality in HD Supplementary Material 10.31.18
DOI: 10.5061/dryad.f0824
title: Data from: Incipient habitat race formation in an amphibian

description: Theory defines conditions under which sympatric speciation may occur, and
 several possible examples of the process in action have been identified.
 In most cases, organisms specialize onto habitats that fall into discrete
 categories, such as host species used by herbivores and parasites.
 Ecological specialization within a continuous habitat gradient is
 theoretically possible, but becomes less likely with increasing gene flow
 among clinal habitat types. Here, I show that habitat race formation is
 underway in a frog, Rana temporaria, along a continuous and spatially
 mosaic habitat gradient. Tadpoles from 23 populations raised in an outdoor
 mesocosm experiment showed adaptive phenotypic variation correlated with
 the predator density in their pond of origin. A survey of microsatellite
 markers in 48 populations found that neutral genetic divergence was
 enhanced between ponds with very different densities of predators. This
 represents a new example of habitat specialization along a continuous
 habitat gradient with no spatial autocorrelation in habitat.
description: Data for Van Buskirk
 (2013, JEB)Two worksheets in a
 single Excel file. One contains results of the mesocosm experiment, and
 the other contains the original microsatellite data.dryad
 data.xlsx
DOI: 10.5061/dryad.c7885
title: Data from: Maternal effects and population regulation: maternal density-induced reproduction suppression impairs offspring capacity in response to immediate environment in root voles Microtus oeconomus

description: 1. The hypothesis that maternal effects act as an adaptive bridge in
 translating maternal environments into offspring phenotypes and thereby
 affecting population dynamics has not been studied in the well-controlled
 fields. 2. In this study, the effects of maternal population-density on
 offspring stress axis, reproduction and population dynamics were studied
 in root voles (Microtus oeconomus). Parental enclosures for breeding
 offspring were established by introducing 6 adults per sex into each of 4
 (low density) and 30 adults per sex into each of another 4 (high density)
 enclosures. Live-trapping started 2 weeks after. Offspring captured at age
 of 10-20 days were removed to laboratory, housed under laboratory
 conditions until puberty, and subsequently used to establish offspring
 populations in these same enclosures, after parental populations had been
 removed. Offspring from each of the 2 parental sources were assigned into
 4 enclosures with 2 for each of the 2 density treatments used in
 establishing parental populations (referred to as LL and LH for
 maternally-unstressed offspring, assigned in low- and high-density, and HL
 and HH for maternally-stressed offspring, assigned in low- and
 high-density). Fecal corticosterone metabolites (FCM) levels, offspring
 reproduction traits and population dynamics were tested following repeated
 live-trapping over 2 seasons. 3. Differential fluctuations in population
 size were observed between maternally density-stressed and unstressed
 offspring. Populations in LL and LH groups changed significantly in
 responding to initial density, and reached the similar levels at beginning
 of the second trapping season. Populations in HL and HH groups, however,
 were remained relatively steady, and in HL group the low population size
 was sustained until end of experiment. Maternal density-stress was
 associated with FCM elevations, reproduction suppression, and body mass
 decrease at sexual maturity in offspring. The FCM elevations and
 reproduction suppression were independent of offspring population density
 and correlated with decreased offspring quality. 4. These findings
 indicate that intrinsic state alterations induced by maternal stress
 impair offspring capacity in response to immediate environment, and these
 alterations are likely mediated by maternal stress system. The maladaptive
 reproduction suppression seen in HL group suggests intrinsic population
 density as one of ecological factors generating delayed density-dependent
 effects.
description: Femal reproductive
 conditionMale reproductive
 conditionOffspring
 FCMofspring
 numberOverwinter
 survivalparental
 FCMparental
 numberrecruitmentSexualbody mass