cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ns7gp
title: Data from: Genetic identification of endangered North African ungulates using noninvasive sampling

description: North African ungulates include several threatened and emblematic species,
 yet are poorly studied mainly due to their remoteness and elusiveness.
 Noninvasive sampling provides a useful approach to obtain ecological and
 genetic information essential to guide conservation actions. The very
 first and most important step in conservation planning is to accurately
 identify species, and molecular genetics has been proved to be a useful
 tool. Several molecular genetics protocols are available for species
 identification, even for samples with poor quality DNA, such as faeces,
 hairs or bones. Most of these protocols use mitochondrial DNA for
 barcoding despite this marker being especially prone to problems,
 including mtDNA introgression, nuclear insert copies, high intraspecific
 diversity or heteroplasmy. In this work, we developed a molecular method
 based on polymorphisms in small fragments of the mitochondrial cytochrome
 b (cytb, mtDNA) and the nuclear kappa casein genes (KCAS, nDNA) for
 identifying endangered North African ungulates. These fragments revealed
 polymorphisms, including species-specific variation, which allowed species
 identification of nine ungulate species that co-occur in North Africa. The
 method was validated across more than 400 samples, including different
 types of noninvasive samples collected in the field. The simplicity, high
 reliability and relative low cost of the described method make it a
 promising tool to improve ecological studies of the North African
 ungulates and consequently, the implementation of more efficient
 management and conservation plans for these endangered ungulates.
description: Bayesian inference tree
 for the cytb fragmentData Set of Figure 2 -
 Bayesian inference tree for the cytb fragment showing the phylogenetic
 relationship of all endangered North African ungulates and the domestic
 species. Posterior probabilities of major nodes are indicated. Tragulus
 napu was used as outgroup.treetree.nexBayesian inference tree for the cytb and KCAS concatenated fragmentsData Set of Figure S1 - Bayesian inference tree for the cytb and KCAS concatenated fragments showing the phylogenetic relationship of all endangered North African ungulates and the domestic species. Posterior probabilities of major nodes are indicated. Oreotragus oreotragus was used as outgroup. The Bayesian tree inference for cytb was performed using the GTR+I+G model.TreeConcatMrB.nex
DOI: 10.5061/dryad.16rr4
title: Data from: A highly social, land-dwelling fish defends territories in a constantly fluctuating environment

description: The Pacific leaping blenny (Alticus arnoldorum) is a marine fish that has
 made a highly successful transition to land. We report an extensive field
 study on the behavior of this remarkable fish and how it has coped with
 life on land. The fish occurs in great abundance above the waterline along
 the rocky coastlines of Micronesia. We found them to be terrestrial in all
 aspects of their adult daily life, but heavily constrained by large
 fluctuations in both tide and temperature with almost all activity limited
 to a brief period at mid-tide. Despite this, the fish were highly social
 and data were consistent with males defending exclusive territories on
 land. A variety of metrics – the use of visual displays, the allometry of
 ornaments, and sexual dimorphism – further imply sexual selection on both
 sexes was strong. Despite being restricted to an extremely narrow
 habitable zone in which conditions change constantly, the Pacific leaping
 blenny is remarkably adapted to life on land and rarely returned to water.
 The genus is unique among the living fishes in its degree of
 terrestriality and serves as a useful model of the constraints and
 adaptations that accompany major ecological transitions.
description: Ord_TJ-ETH-110199_readmeData descriptionOrd_TJ_ETH-11-0199_BehavMorph_dataBehavior, morphological and environmental dataOrd_TJ_ETH-11-0199_Transect_dataData from transect estimates of density
DOI: 10.5061/dryad.3gv78
title: Data from: Broad-scale variation in sexual dichromatism in songbirds is not explained by sex differences in exposure to predators during incubation

description: The evolution of sexual dichromatism provoked one of the greatest
 disagreements between Charles Darwin and Alfred Russel Wallace. According
 to Darwin the main driving force is sexual selection, whereby choosy
 females prefer showy males, leading to the evolution of conspicuous male
 plumage. On the other hand, Wallace suggested that dichromatism may arise
 because nest predation favors more cryptic females. To test the role of
 natural selection in the evolution of dichromatism we combined
 quantitative data on differences in parental share in nest attentiveness
 (representing the strength of natural selection on males vs. females) with
 spectrophotometric measurements of dichromatism in 412 species of
 songbirds from 69 families. We expected to find stronger dichromatism in
 open-nesting species with more divergent parental roles and in body parts
 exposed during incubation. Dichromatism was not related to the differences
 in parental share during incubation, but it was most pronounced in lekking
 species, migrants, and small species. Our results thus suggest that
 Wallace's hypothesis is not able to explain broad-scale variation in
 the dichromatism of songbirds, but point to a role for sexual selection,
 mutual mate choice, and migration strategy in shaping the extraordinary
 variation in dichromatism exhibited by songbirds.
description: Dryad
 data_sex.dichromatismData used in the
 analyses of sexual dichromatism in songbirdsdata_dichr_Dryad.xls
DOI: 10.5061/dryad.q3g70
title: Data from: Competition induces increased toxin production in toad larvae without allelopathic effects on heterospecific tadpoles

description: 1. Inducible defences are a form of phenotypic plasticity by which
 organisms respond to and mitigate the threat posed by predators, parasites
 and competitors. While anti-predatory defences are often in trade-off with
 anti-competitor responses, chemicals that deter predators may have
 negative effects on competitors as well. Allelopathy is well known in
 plants and plant-like animals, but whether the toxins of mobile,
 behaviourally and morphologically complex animals are induced by and exert
 allelopathic effects on competitors is poorly known. 2. Common toads Bufo
 bufo synthesize bufadienolides which make them unpalatable or toxic to
 many predators. However, bufadienolide content of toad tadpoles correlates
 positively with the density of competitors in natural populations,
 suggesting that they may upregulate their toxin production to inhibit
 their competitors, such as heterospecific tadpoles that may be vulnerable
 to toad toxins. 3. We conducted a microcosm experiment with tadpoles of
 common toads and agile frogs Rana dalmatina, in which we manipulated the
 density of conspecific and heterospecific competitors. We measured the
 bufadienolide content of toad tadpoles to test for competitor-induced
 changes in toxin production, and we assessed the growth and development of
 agile frog tadpoles to test for allelopathy. 4. We found that toad
 tadpoles contained higher amounts of bufadienolides at higher densities;
 however, heterospecific competitors did not have a stronger effect than
 conspecifics. Furthermore, the presence or density of toad tadpoles had no
 effect on the body mass and development rate of agile frog tadpoles. 5.
 Our results demonstrate competitor-induced plasticity in toxin production,
 but we found no support for an allelopathic function of bufadienolides.
 Instead, we suggest that inducible changes in bufadienolide production may
 serve to mitigate risks posed by competitors, including aggression,
 cannibalism or disease. Therefore, bufadienolides are intriguing
 candidates for multi-purpose defences that may provide protection not only
 against predators but also against competitors.
description: All data of Bókony et
 al. 2017. Functional EcologyExcel file containing 3
 data sheets: 1) total biomass per tub, 2) Bufo data, 3) Rana data; plus a
 "Notes" sheet for README.Bokony_et_al_2017_Functional_Ecology_data.xls
DOI: 10.5061/dryad.8807
title: Data from: Reinforcement selection acting on the European house mouse hybrid zone

description: Behavioural isolation may lead to complete speciation when partial
 postzygotic isolation acts in the presence of divergent specific mate
 recognition systems. These conditions exist where Mus musculus musculus
 and M. m. domesticus come into contact and hybridize. We studied two mate
 recognition signal systems, based on urinary and salivary proteins, across
 a Central European portion of the mouse hybrid zone. Introgression of the
 genomic regions responsible for these signals: the major urinary proteins
 (MUPs) and androgen binding proteins (ABPs) respectively, was compared to
 introgression at loci assumed to be nearly neutral and those under
 selection against hybridization. The preference of individuals taken from
 across the zone regarding these signals was measured in Y mazes, and we
 develop a model for the analysis of the transition of such traits under
 reinforcement selection. The strongest assortative preferences were found
 in males for urine and females for ABP. Clinal analyses confirm nearly
 neutral introgression of an Abp locus and two loci closely linked to the
 Abp gene cluster whereas two markers flanking the Mup gene region reveal
 unexpected introgression. Geographic change in the preference traits
 matches our reinforcement selection model significantly better than
 standard cline models. Our study confirms that behavioural barriers are
 important components of reproductive isolation between the house mouse
 subspecies.
description: Table_S1_onlineFrequencies of M. m. musculus alleles for each locus and sampling site. Distance along the transect and effective number of alleles (Ne) are also given. h = hybrid index expressed as the frequency of musculus alleles averaged across the six diagnostic allozyme loci.
DOI: 10.5061/dryad.p8n5kb15
title: Data from: Diversification and phylogeographic structure in widespread Azteca plant-ants from the northern Neotropics

description: The Neotropical myrmecophytic tree Cordia alliodora hosts symbiotic Azteca
 ants in most of its widespread range. The taxonomy of the genus Azteca is
 notoriously difficult, which has frequently obscured species identity in
 ecological studies. We used sequence data from one mitochondrial and four
 nuclear loci to infer phylogenetic relationships, patterns of geographic
 distribution, and timing of diversification for 181 colonies of Azteca
 from Mexico to Colombia. We identified at least eight lineages of C.
 alliodora-dwelling Azteca, including at least five lineages within the
 most abundant and specialized species, Azteca pittieri. Mitochondrial and
 nuclear data were concordant at the species level, but not within species;
 comparison of the two datasets suggested that both introgression and
 incomplete lineage sorting contributed to these inconsistencies.
 Divergence time analyses estimated that C. alliodora-dwelling Azteca
 shared a common ancestor approximately 9-18 million years ago, coinciding
 with arid climatic conditions that favored their primary habitat,
 seasonally dry tropical forests. Significant differentiation not
 correlated with geographic distance was found among the five lineages of
 A. pittieri, which suggests limited historical gene flow among
 geographically restricted populations. This contrasts with the previously
 reported lack of phylogeographic structure in the host tree. Climatic
 niches, and particularly precipitation-related variables, did not overlap
 between the sites occupied by northern and southern lineages of A.
 pittieri. Together, these results suggest that restricted gene flow among
 ant populations may facilitate local adaptation to environmental
 heterogeneity. Differences in evolvability between the ants and their host
 trees may affect the evolutionary stability of this widespread ant-plant
 mutualism.
description: Azteca_dataAlignments, haplotype assignments, distance matrices, analysis code, and bioclimatic variables associated with collection sites, plus a ReadMe file that explains each file in more detail.PringleDryad.zip
DOI: 10.5061/dryad.sd845
title: Data from: Determining population structure and hybridization for two iris species

description: Identifying processes that promote or limit gene flow can help define the
 ecological and evolutionary history of a species. Furthermore, defining
 those factors that make up “species boundaries” can provide a definition
 of the independent evolutionary trajectories of related taxa. For many
 species, the historic processes that account for their distribution of
 genetic variation remain unresolved. In this study, we examine the
 geographic distribution of genetic diversity for two species of Louisiana
 Irises, Iris brevicaulis and Iris fulva. Specifically, we asked how
 populations are structured and if population structure coincides with
 potential barriers to gene flow. We also asked whether there is evidence
 of hybridization between these two species outside Louisiana hybrid zones.
 We used a genotyping-by-sequencing approach and sampled a large number of
 single nucleotide polymorphisms across these species' genomes. Two
 different population assignment methods were used to resolve population
 structure in I. brevicaulis; however, there was considerably less
 population structure in I. fulva. We used a species tree approach to infer
 phylogenies both within and between populations and species. For I.
 brevicaulis, the geography of the collection locality was reflected in the
 phylogeny. The I. fulva phylogeny reflected much less structure than
 detected for I. brevicaulis. Lastly, combining both species into a
 phylogenetic analysis resolved two of six populations of I. brevicaulis
 that shared alleles with I. fulva. Taken together, our results suggest
 major differences in the level and pattern of connectivity among
 populations of these two Louisiana Iris species.
description: Ibrev_IfulvaData provided here are diploid Single nucleotide polymorphisms (SNPs) used in the analysis to determine population structure and hybridization for two iris species. In addition, to the SNP calls, collection information is also provided.
DOI: 10.5061/dryad.m27k2
title: Data from: Nest shape explains variation in sexual dichromatism in New World blackbirds

description: Following Charles Darwin, research on sexual dichromatism has long focused
 on sexual selection driving ornamentation in males. However, Alfred Russel
 Wallace proposed another explanation – that dichromatism evolves as a
 result of selection favoring crypsis in incubating females. Many recent
 studies suggest that evolutionary changes in sexual dichromatism often
 result from changes in female, in addition to male, plumage, yet the
 evolutionary mechanisms driving changes in female plumage remain largely
 unexplained. To test Wallace's hypothesis, we examined variation in
 sexual dichromatism and nest shape, a proxy for predation risk, among New
 World blackbirds (Aves: Icteridae). Phylogenetic models reveal an
 evolutionary correlation between sexual dichromatism and nest exposure.
 Specifically, we found that transitions in monochromatic lineages with
 exposed nests toward either concealed nests or dichromatism were common.
 Although this evidence supports Wallace's hypothesis that female
 incubation leads to selection for crypsis or concealment, we also found
 that transitions to monomorphism were common, even in lineages with
 exposed nests – a result suggestive of a role for positive selection on
 female ornamentation. These patterns of plumage evolution support a
 growing body of work emphasizing the importance of developing and testing
 hypotheses to explain evolutionary changes in female, as well as male,
 ornamentation.
description: dataset
 1Main
 dataset describing the coverage for each tree and designations of nest
 shape and dichromatism for each species.bayestraits
 filesFiles required for
 running RJ-MCMC analyses
DOI: 10.5061/dryad.3472nk1
title: Data from: The niches of nuthatches affect their lineage evolution differently across latitude

description: Ecological niche evolution can promote or hinder the differentiation of
 taxa and determine their distribution. Niche‐mediated evolution may differ
 among climatic regimes, and thus species that occur across a wide
 latitudinal range offer a chance to test these heterogeneous evolutionary
 processes. In this study, we examine (1) how many lineages have evolved
 across the continent‐wide range of the Eurasian nuthatch (Sitta europaea),
 (2) whether the lineages’ niches are significantly divergent or conserved,
 and (3) how their niche evolution explains their geographic distribution.
 Phylogenetic reconstruction and ecological niche models (ENMs) showed that
 the Eurasian nuthatch contained six parapatric lineages that diverged
 within two million years and did not share identical climatic niches.
 However, the niche discrepancy between these distinct lineages was
 relatively conserved compared with the environmental differences between
 their ranges and thus was unlikely to drive lineage divergence. The ENMs
 of southern lineages tended to cross‐predict with their neighboring
 lineages whereas those of northern lineages generally matched with their
 abutting ranges. The coalescence‐based analyses revealed more stable
 populations for the southern lineages than the northern ones during the
 last glaciation cycle. In contrast to the overlapping ENMs, the smaller
 parapatric distribution suggests that the southern lineages might have
 experienced competitive exclusion to prevent them from becoming sympatric.
 On the other hand, the northern lineages have expanded their ranges and
 their current abutting distribution might have resulted from lineages
 adapting to different climatic conditions in allopatry. This study
 suggests that niche evolution may affect lineage distribution in different
 ways across latitude.
description: Presence
 PointsThis folder contains two
 occurrence point datasets, First approach_Presence Points.xlsx and Second
 Approach_Presence Points.xlsx, used for ENM analyses.E_spaceThis folder contains R scripts used for ENM E_space analyses for this study.MMRRThis folder contains the data and script used for MMRR tests for this study.DNA sequencesDNA sequences of one mtDNA and seven introns used in this studyReadMe for DRYAD deposit_Chen et al. (ME)A README file describing the files deposited in the database.
DOI: 10.5061/dryad.cc145b6
title: Data from: Irreproducible text-book 'knowledge': the effects of color bands on zebra finch fitness

description: Many fields of science currently experience a heated debate about the
 extent of publication bias against null-findings. Here, we show a case
 where putatively well-established text-book knowledge cannot be confirmed.
 Across four decades, zebra finch (Taeniopygia guttata) studies have
 reported effects of bands of certain colors on male or female
 attractiveness and further on behavior, physiology, life-history and
 fitness. Only 8 out of 39 publications presented exclusively
 null-findings. Here, we analyze the results of eight experiments in which
 we quantified the fitness of 730 color-banded individuals from four
 captive populations (two domesticated and two recently wild-derived). This
 sample size exceeds the combined sample size of all 23 publications that
 clearly support the “color-band effect” hypothesis. In our populations,
 band color explained no variance in fitness and there were no context- or
 population-specific band color effects. Analysis of unpublished data from
 three other laboratories strengthens our null finding. Finally, a
 meta-analysis of previously published results is indicative of selective
 reporting and suggests that the effect size approaches zero when sample
 size is large. We argue that our field would benefit from more effective
 means to counter confirmation bias and publication bias.
description: femaledata_for Table2
 & Fig2the raw relative fitness
 data of femalesmaledata_for Table3
 & Fig3the raw relative fitness
 data of male zebra finchesdata_for
 Fig4summary data for Figure
 4data_for
 Fig5data from other Labs,
 for Figure 5data_for
 Fig6data for the
 meta-analysis, Figure 6meta_rawdatathe original raw data extracted from literature for meta-analysis
DOI: 10.5061/dryad.3dm147p
title: Data from: Molecular phylogeny of Terniopsis (Podostemaceae) and contrasting molecular and morphological variations in two species

description: Podostemaceae show different patterns of morphological variation relative
 to molecular ones between genera and between species, but additional
 material was necessary to make the patterns clearer. Using new material
 collected from Cambodia, we compared the variations of Terniopsis
 chanthaburiensis and T. heterostaminata in Cambodia, Laos and Thailand,
 and conducted matK phylogenetic analysis with many samples and most
 species of the genus. In contrast to the narrow molecular variation, the
 morphological variation (e.g., in the length of the shoots and pedicels)
 is large and continuous. The results indicate that variation in the two
 species is intraspecific. A similar pattern exists in two pairs of other
 species of Terniopsis, in which the morphological variation is large and
 discontinuous, while there is little molecular difference. The opposite
 pattern is present in other cases (e.g., Dalzellia zeylanica and Tristicha
 trifaria). The variation in T. chanthaburiensis and T. heterostaminata
 does not appear to be a response to variation in the habitats, that is
 submerged rock surfaces in fast currents. Distributional and phylogenetic
 data indicate that Terniopsis diversified primarily in Laos and Thailand,
 then expanded into neighboring regions. A synopsis of the genus Terniopsis
 and its 14 species is given.
description: Fig. 1. data of
 localities of Terniopsis chanthaburiensis and T.
 heterostaminataThe data of localities
 are used for the distribution map.Fig. 1
 data.xlsxFig. 2. Sequence data
 used by phylogenetic analyses of TerniopsisThe sequence data are
 used for constructing the phylogenetic tree of
 Terniopsis.Fig. 2.
 170707allPodo7.fas
DOI: 10.5061/dryad.4r1k05t
title: Data from: Evolution of invasiveness by genetic accommodation

description: Invasion success of species introduced to novel environments may be
 facilitated by adaptive evolution and by phenotypic plasticity. Here we
 investigate the independent and joint contribution of both mechanisms as
 drivers of invasiveness in the perennial sunflower Helianthus tuberosus.
 We show that invasive genotypes have multiple origins, and that invasive
 spread was facilitated by the repeated evolution of extreme values in a
 single trait, clonality. In line with genetic accommodation theory, we
 establish that this evolutionary transition occurred by refining a
 preexisting plastic response of clonality to water availability. Further,
 we demonstrate that under the non-drought conditions typically experienced
 by this plant in its introduced range, invasive spread is mediated by
 hybrid vigor and/or two major additive-effect loci, and that these
 mechanisms are complementary. Thus, in H. tuberosus, evolution of
 invasiveness was facilitated by phenotypic plasticity, and involved the
 use of multiple genetic solutions to achieve the same invasiveness trait.
description: Common garden and
 greenhouse trait data for 305 H. tuberosus accessionsH_tuberosus_CG_GR_traits.csvData for the field invasiveness experimentfield_invasiveness_experiment.csvRhizome numbers from the greenhouse drought experimentgreenhouse_drought_experiment.csvAllelopathy estimates for the progenitor species of H. tuberosusallelopathy_progenitor_species.csvSoil water content measurements for the invasiveness field experimentwater_content_data.csv