cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pm1r2
title: Data from: Phylogeography of Petrolisthes armatus, an invasive species with low dispersal ability

description: Theoretically, species with high population structure are likely to expand
 their range, because marginal populations are free to adapt to local
 conditions; however, meta-analyses have found a negative relation between
 structure and invasiveness. The crab Petrolisthes armatus has a wide
 native range, which has expanded in the last three decades. We sequenced
 1718 bp of mitochondrial DNA from native and recently established
 populations to determine the population structure of the former and the
 origin of the latter. There was phylogenetic separation between Atlantic
 and eastern Pacific populations, and between east and west Atlantic ones.
 Haplotypes on the coast of Florida and newly established populations in
 Georgia and South Carolina belong to a different clade from those from
 Yucatán to Brazil, though a few haplotypes are shared. In the Pacific,
 populations from Colombia and Ecuador are highly divergent from those from
 Panamá and the Sea of Cortez. In general, populations were separated
 hundreds to million years ago with little subsequent gene flow. High
 genetic diversity in the newly established populations shows that they
 were founded by many individuals. Range expansion appears to have been
 limited by low dispersal rather than lack of ability of marginal
 populations to adapt to extreme conditions.
description: armatus_COIHL_AllHaplosAlignment of partial DNA sequences of the mitochondrial COI gene (fragment COIHL)armatus_Concat_AllHaplosAlignment of concatenated partial DNA sequences of the mitochondrial genes COI and 16S rDNA
DOI: 10.5061/dryad.35k1n3m
title: Data from: Phenological mismatch drives selection on elevation, but not on slope, of breeding time plasticity in a wild songbird

description: Phenotypic plasticity is an important mechanism for populations to respond
 to fluctuating environments, yet may be insufficient to adapt to a
 directionally changing environment. To study whether plasticity can evolve
 under current climate change, we quantified selection and genetic
 variation in both the elevation (RNE) and slope (RNS) of the breeding time
 reaction norm in a long-term (1973–2016) study population of great tits
 (Parus major). The optimal RNE (the caterpillar biomass peak date
 regressed against the temperature used as cue by great tits) changed over
 time, whereas the optimal RNS did not. Concordantly, we found strong
 directional selection on RNE, but not RNS, of egg-laying date in the
 second third of the study period; this selection subsequently waned,
 potentially due to increased between-year variability in optimal laying
 dates. We found individual and additive genetic variation in RNE but,
 contrary to previous studies on our population, not in RNS. The predicted
 and observed evolutionary change in RNE were, however, marginal, due to
 low heritability and the sex limitation of laying date. We conclude that
 adaptation to climate change can only occur via micro-evolution of RNE,
 but this will necessarily be slow and potentially hampered by increased
 variability in phenotypic optima.
description: Data_for_GxEData (phenotypes) necessary for calculating the G matrix for the laying date – temperature reaction normPedigree_for_GxEPedigree necessary for calculating the G matrixData_PeriodSpecificReactionNorm_and_SelectionData necessary to construct the period-specific reaction norm (RN), as well as the lifetime reproducive success necessary to estimate selection on RNData_for_annual_selectiongradientsdata necessary to calculate selection gradientsSelectionGradients_for_evolutionary_predictionsSelection gradients, temperatures and annual proportion of recruits to predict the evolutionary responseRscript_SimulationR script used to simulate the effect of the residual structure in the random regression model on the estimates of IxE and the power to detect it.
DOI: 10.5061/dryad.10pv6
title: Data from: Association mapping of morphological traits in wild and captive zebra finches: reliable within but not between populations

description: Identifying causal genetic variants underlying heritable phenotypic
 variation is a longstanding goal in evolutionary genetics. We previously
 identified several quantitative trait loci (QTL) for five morphological
 traits in a captive population of zebra finches (Taeniopygia guttata) by
 whole-genome linkage mapping. We here follow up on these studies with the
 aim to narrow down on the quantitative trait variants (QTN) in one wild
 and three captive populations. First, we performed an association study
 using 672 single nucleotide polymorphisms (SNPs) within candidate genes
 located in the previously identified QTL regions in a sample of 939
 wild-caught zebra finches. Then, we validated the most promising
 SNP-phenotype associations (n = 25 SNPs) in 5,228 birds from four
 populations. Genotype-phenotype associations were generally weak in the
 wild population, where linkage disequilibrium (LD) spans only short
 genomic distances. In contrast, in captive populations, where LD blocks
 are large, apparent SNP-effects on morphological traits (i.e.
 associations) were highly repeatable with independent data from the same
 population. Most of those SNPs also showed significant associations with
 the same trait in other captive populations, but the direction and
 magnitude of these effects varied among populations. This suggests that
 the tested SNPs are not the causal QTN but rather physically linked to
 them, and that LD between SNPs and causal variants differs between
 populations due to founder effects. While the identification of QTN
 remains challenging in non-model organisms, we illustrate that it is
 indeed possible to confirm the location and magnitude of QTL in a
 population with stable linkage between markers and causal variants.
description: data_phenotypes_BodyMassBody mass data used for the initial linkage analysis. A detailed description of the file is in the README.data_phenotypes_TarsusDigitRatioTarsus length, body size and digit ratio data used for the initial linkage analysis. A detailed description of the file is in the README.data_phenotypes_TarsusBodySizeDigitRatio.txtdata_genotypes_SequenomGenotypic data for all individuals from the wild and multiple captive populations used for the validation study. A detailed description of the file is in the README.data_snp_annotationAdditional information for all SNPs used for the validation study. A detailed description of the file is in the README.
DOI: 10.5061/dryad.21723
title: Data from: Shedding light on bird egg color: pigment as parasol and the dark car effect

description: The vibrant colors of many birds’ eggs, particularly those that are blue
 to blue-green, are extraordinary in that they are striking traits present
 in hundreds of species that have nevertheless eluded evolutionary
 functional explanation. We propose that egg pigmentation mediates a
 trade-off between two routes by which solar radiation can harm bird
 embryos: transmittance through the eggshell and overheating through
 absorbance. We quantitatively test four components of this hypothesis on
 variably colored eggs of the village weaverbird (Ploceus cucullatus) in a
 controlled light environment: (1) damaging ultraviolet radiation can
 transmit through bird eggshells, (2) infrared radiation at natural
 intensities can heat the interior of eggs, (3) more intense egg coloration
 decreases light transmittance (“pigment as parasol”), and (4) more intense
 egg coloration increases absorbance of light by the eggshell and heats the
 egg interior (“dark car effect”). Results support all of these
 predictions. Thus, in sunlit nesting environments, less pigmentation will
 increase the detrimental effect of transmittance, but more pigmentation
 will increase the detrimental effect of absorbance. The optimal
 pigmentation level for a bird egg in a given light environment, all other
 things being equal, will depend on the balance between light transmittance
 and absorbance in relation to embryo fitness.
description: LahtiArdia16
 Data+FiguressData underlying analyses
 and figures in our paper.LahtiArdia16_Data+Figs.xlsx
DOI: 10.5061/dryad.7rf84
title: Data from: Extreme prescribed fire during drought reduces survival and density of woody resprouters

description: Management intervention in ecosystems with degraded environmental services
 requires innovative resource management strategies that go beyond
 conventional restoration and conservation practices. We established a
 unique study that experimentally targeted extreme fire conditions during
 drought in humid subtropical and semiarid ecoregions. In the southern
 Great Plains of North America, conventional restoration and conservation
 practices have been either historically ineffective or economically cost
 prohibitive at restoring grass-dominated ecosystems following conversion
 to resprouting shrublands. Our aim was to assess the potential for extreme
 fire during drought to force the system along an alternate ecological
 trajectory from its current progression toward closed-canopy resprouting
 shrubland, something conventional fire prescriptions have been unable to
 accomplish. We first tested the potential for high intensity fires
 exhibiting extreme behaviour to disrupt the progression from grassland to
 shrubland. In both ecoregions, significant levels of mortality were
 observed for mature woody resprouters. As a result, densities were either
 maintained or reduced three years following extreme fire treatments,
 whereas resprouter densities continued to increase in areas that were not
 burned. A second interventionist approach involving extreme fire and
 herbicide treatment combinations was not supported. Interactions between
 prescribed extreme fire and herbicide did not significantly reduce
 resprouter densities more than using herbicide alone at either site.
 Synthesis and applications: Extreme fires during drought resulted in
 exceptionally high levels of mortality across all sizes of woody
 resprouters and limited recruitment, resulting in 35–55% lower densities
 of resprouters than in areas not burned. These findings counter prevailing
 scientific and management expectations, which are based largely on studies
 that impose tight controls over prescribed fire conditions and avoid
 extreme fire behaviour. Future interventions for controlling woody
 resprouters with fire may require rethinking the present ideology that
 extreme fire behaviour has no place in modern social-ecological
 landscapes.
description: Data
 file
DOI: 10.5061/dryad.1pv891t
title: Data from: Variance in reproductive success is driven by environmental factors not mating system in Bonytail

description: Studying the reproductive ecology of aggregate broadcast spawning fishes
 is difficult because it generally is not feasible to sample all potential
 parents and unambiguously assign their offspring. We used molecular‐based
 parentage analysis to gain insights into the reproductive ecology of the
 endangered Bonytail, and to evaluate whether protected off‐channel
 habitats could be used as an alternative to hatchery production. By
 genotyping adults and offspring stocked (n = 4130) into two experimental
 backwaters across three years, we determined that most adults (82‐97%)
 contributed to progeny production across years and backwaters, with one
 exception. Both sexes mated multiply and the number of mates and family
 size were positively correlated. There was also a positive correlation
 between adult size and metrics of reproductive success. There were strong
 interactions between sample years and backwaters suggesting that
 environmental factors are the primary driver of variance in reproductive
 success. Knowledge of mating systems and sources of variance in
 reproductive success is important for management of endangered fish
 because high variance in reproductive success leads to substantial losses
 of genetic variation when few individuals reproduce successfully. Although
 variance in reproductive success was observed, most adults contributed to
 genetically diverse progeny in experimental backwaters. These results
 support the use of predator‐free, but otherwise natural, backwaters as an
 effective conservation tool for reintroducing Bonytail to its native
 habitat.
description: Dryad_Bt14_16_UsatsMicrosatellite genotypes for Bonytail (Gila elegans) for 18 loci. Data is included for two backwaters (Nine Mile and Nevada Egg) and three years (2014, 2015, 2016) for adults and their offspring. Data was used to conduct parentage analyses.
DOI: 10.5061/dryad.q4jv0
title: Data from: The first flea with fully distended abdomen from the Early Cretaceous of China

description: Background: Fleas, the most notorious insect ectoparasites of human, dogs,
 cats, birds, etc., have recently been traced to its basal and primitive
 ancestors during the Middle Jurassic. Compared with extant fleas, these
 large basal fleas have many different features. Although several fossil
 species with transitional morphologies filled the evolutionary blank, the
 early evolution of these ectoparasites is still poorly known. Results:
 Here we report a new flea with transitional morphology, Pseudopulex tanlan
 sp. nov., assigned to Pseudopulicidae, from the Lower Cretaceous Yixian
 Formation of Liaoning Province, China. Different from the previously
 described pseudopulicids, P. tanlan has relatively small body size but
 lacking any ctenidia on the tibiae or body, while the male with
 comparatively small and short genitalia. On the other hand, P. tanlan has
 some characters similar to the transitional fleas of saurophthirids, such
 as, a small head, short compacted antennae, small pygidium and the body
 covered with many stiff setae. Conclusions: Even though other
 possibilities can not be ruled out, the female specimen with extremely
 distended abdomen suggest that it might have consumed its last meal before
 its demise. Compared with other reported female flea fossils, we calculate
 and estimate that P. tanlan sp. nov. might have been able to consume 0.02
 milliliter (ml) of blood, which is about 15 times of the intake volume by
 extant fleas. These new findings further support that fleas had evolved a
 broad diversity by the Early Cretaceous.
description: Table S1. Measurements
 for all the known female Mesozoic fleasMeasurements for all the
 known female Mesozoic fleasTable
 S1.docFigure S1. Illustration
 of calculating the intake volume by holotype Pseudopulex tanlan sp.
 nov.(A and B) Selected parts
 of the fully distended abdomen; (C and D) Selected parts of the
 pseudomorph of non-swelling condition.Figure
 S1.tif
DOI: 10.5061/dryad.746k3
title: Data from: Low genetic diversity and strong population structure shaped by anthropogenic habitat fragmentation in a critically endangered primate, Trachypithecus leucocephalus

description: Habitat fragmentation may strongly impact population genetic structure and
 reduce the genetic diversity and viability of small and isolated
 populations. The white-headed langur (Trachypithecus leucocephalus) is a
 critically endangered primate species living in a highly fragmented and
 human-modified habitat in southern China. We examined the population
 genetic structure and genetic diversity of the species and investigated
 the environmental and anthropogenic factors that may have shaped its
 population structure. We used 214 unique multi-locus genotypes from 41
 social groups across the main distribution area of T. leucocephalus, and
 found strong genetic structure and significant genetic differentiation
 among local populations. Our landscape genetic analyses using a causal
 modelling framework suggest that a large habitat gap and geographical
 distance represent the primary landscape elements shaping genetic
 structure, yet high levels of genetic differentiation also exist between
 patches separated by a small habitat gap or road. This is the first
 comprehensive study that has evaluated the population genetic structure
 and diversity of T. leucocephalus using nuclear markers. Our results
 indicate strong negative impacts of anthropogenic land modifications and
 habitat fragmentation on primate genetic connectivity between forest
 patches. Our analyses suggest that two management units of the species
 could be defined, and indicate that habitat continuity should be enforced
 and restored to reduce genetic isolation and enhance population viability.
description: Genotype
 DataMicrosatellite genotype,
 sex and haplotype data of 214 unique individualsLandscape
 DataLandscape data
 (geographical distance, large habitat gap, small habitat gap, and roads)
 of 214 unique individuals
DOI: 10.5061/dryad.m02v7
title: Data from: Coordinated rates of evolution between interacting plastid and nuclear genes in Geraniaceae

description: Although gene coevolution has been widely observed within individuals and
 between different organisms, rarely has this phenomenon been investigated
 within a phylogenetic framework. The Geraniaceae is an attractive system
 in which to study plastid-nuclear genome coevolution due to the highly
 elevated evolutionary rates in plastid genomes. In plants, the
 plastid-encoded RNA polymerase (PEP) is a protein complex composed of
 subunits encoded by both plastid (rpoA, rpoB, rpoC1, and rpoC2) and
 nuclear genes (sig1-6). We used transcriptome and genomic data for 27
 species of Geraniales in a systematic evaluation of coevolution between
 genes encoding subunits of the PEP holoenzyme. We detected strong
 correlations of dN (nonsynonymous substitutions) but not dS (synonymous
 substitutions) within rpoB/sig1 and rpoC2/sig2, but not for other
 plastid/nuclear gene pairs, and identified the correlation of dN/dS ratio
 between rpoB/C1/C2 and sig1/5/6, rpoC1/C2 and sig2, and rpoB/C2 and sig3
 genes. Correlated rates between interacting plastid and nuclear sequences
 across the Geraniales could result from plastid-nuclear genome
 coevolution. Analyses of coevolved amino acid positions suggest that
 structurally mediated coevolution is not the major driver of
 plastid-nuclear coevolution. The detection of strong correlation of
 evolutionary rates between SIG and RNAP genes suggests a plausible
 explanation for plastome-genome incompatibility in Geraniaceae.
description: Supplemental Data
 FilesSupplemental Data File
 1: sequence alignments. Supplemental Data File 2: accessions of reference
 genes used. Supplemental Data File 3: Python scripts in this
 study.
DOI: 10.5061/dryad.4f16h
title: Data from: Quantitative genetics of plumage color: lifetime effects of early nest environment on a colorful sexual signal

description: Phenotypic differences among individuals are often linked to differential
 survival and mating success. Quantifying the relative influence of genetic
 and environmental variation on phenotype allows evolutionary biologists to
 make predictions about the potential for a given trait to respond to
 selection and various aspects of environmental variation. In particular,
 the environment individuals experience during early development can have
 lasting effects on phenotype later in life. Here, we used a natural
 full-sib/half-sib design as well as within-individual longitudinal
 analyses to examine genetic and various environmental influences on
 plumage color. We find that variation in melanin-based plumage color – a
 trait known to influence mating success in adult North American barn
 swallows (Hirundo rustica erythrogaster) – is influenced by both genetics
 and aspects of the developmental environment, including variation due to
 the maternal phenotype and the nest environment. Within individuals,
 nestling color is predictive of adult color. Accordingly, these early
 environmental influences are relevant to the sexually selected plumage
 color variation in adults. Early environmental conditions appear to have
 important lifelong implications for individual reproductive performance
 through sexual signal development in barn swallows. Our results indicate
 that feather color variation conveys information about developmental
 conditions and maternal care alleles to potential mates in North American
 barn swallows. Melanin-based colors are used for sexual signaling in many
 organisms, and our study suggests that these signals may be more sensitive
 to environmental variation than previously thought.
description: Quantitative genetics of
 plumage colorThis is an excel file
 with 5 worksheets containing datasets used for different analyses shown in
 the paper. 1) Comparing color between sexes and developmental stages, 2)
 Frequency of extra-pair young (EPY) across years, 3) Comparing color of
 recruited vs. non-recruited individuals, 4) Within-individual color
 comparison of recruited individuals, and 5) data used in the animal model
 analysis. See the ReadMe file for more details.Dryad data
 submission.xlsx
DOI: 10.5061/dryad.75g1b55
title: Data from: An evaluation of the methods to estimate effective population size from measures of linkage disequilibrium

description: In 1971, John Sved derived an approximate relationship between linkage
 disequilibrium and effective population size for an ideal finite
 population. This seminal work was extended by Sved and Feldman (1973) and
 Weir and Hill (1980) who derived additional equations with the same
 purpose. These equations yield useful estimates of effective population
 size, as they require a single sample in time. As these estimates of
 effective population size are now commonly used on a variety of genomic
 data, from arrays of single nucleotide polymorphisms to whole genome data,
 some authors have investigated their bias through simulation studies and
 proposed corrections for different mating systems. However, the cause of
 the bias remains elusive. Here we show the problems of using linkage
 disequilibrium as a statistical measure and, analogously, the problems in
 estimating effective population size from such measure. For that purpose,
 we compare three commonly used approaches with a transition probability
 based method that we develop here. It provides an exact computation of
 linkage disequilibrium. We show here that the bias in the estimates of
 linkage disequilibrium and effective population size are partly due to low
 frequency markers, tightly linked markers or to a small total number of
 crossovers per generation. These biases, however, do not decrease when
 increasing sample size or using unlinked markers. Our results show the
 issues of such measures of effective population based on linkage
 disequilibrium, and suggest which of the method here studied should be
 used in empirical studies as well as the optimal distance between markers
 for such estimates.
description: Simulation Codes and
 DataCodes to generate the
 results obtained in the paper, as well as the file r2_multi.txt which is
 the multinomial approximation to the exact transition probability matrix.
 r2_multi.txt has three columns: N, c and r^2.LDNe.tar.gz