cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jb268
title: Data from: Pathogen richness and abundance predict patterns of adaptive MHC variation in insular amphibians

description: The identification of the factors responsible for genetic variation and
 differentiation at adaptive loci can provide important insights into the
 evolutionary process, and is crucial for the effective management of
 threatened species. We studied the impact of environmental viral richness
 and abundance on functional diversity and differentiation of the MHC class
 Ia locus in populations of the black-spotted pond frog (Pelophylax
 nigromaculatus), an IUCN-listed species, on 24 land-bridge islands of the
 Zhoushan Archipelago and 3 nearby mainland sites. We found a high
 proportion of private MHC alleles in mainland and insular populations,
 corresponding to 32 distinct functional supertypes, and strong positive
 selection on MHC antigen-binding sites in all populations. Viral pathogen
 diversity and abundance was reduced at island sites relative to the
 mainland, and islands housed distinctive viral communities. Standardized
 MHC diversity at island sites exceeded that found at neutral
 microsatellites, and the representation of key functional supertypes was
 positively correlated with the abundance of specific viruses in the
 environment (Frog virus 3 and Ambystoma tigrinum virus). These results
 indicate that pathogen-driven diversifying selection can play an important
 role in maintaining functionally-important MHC variation following island
 isolation, highlighting the importance of considering functionally
 important genetic variation and host-pathogen associations in conservation
 planning and management.
description: Submit
 MSMS
 dataSubmit
 Datasequential
 dataSubmit
 data.txtPathogenic
 dataTable S1 and
 S6Supporting information
 for Table S1 and S6
DOI: 10.5061/dryad.93481g3
title: Data from: Patterns of genetic differentiation in Colorado potato beetle correlate with contemporary, not historic, potato land cover

description: Changing landscape heterogeneity can influence connectivity and alter
 genetic variation in local populations, but there can be a lag between
 ecological change and evolutionary responses. Temporal lag effects might
 be acute in agroecosystems, where land cover has changed substantially in
 the last two centuries. Here, we evaluate how patterns of an insect
 pest's genetic differentiation are related to past and present
 agricultural land cover change over a 150-year period. We quantified
 change in the amount of potato, Solanum tuberosum L., land cover since
 1850 using county-level agricultural census reports, obtained allele
 frequency data from 7,408 single-nucleotide polymorphism loci, and
 compared effects of historic and contemporary landscape connectivity on
 genetic differentiation of Colorado potato beetle, Leptinotarsa
 decemlineata Say, in two agricultural landscapes in the USA. We found that
 potato land cover peaked in Wisconsin in the early 1900’s, followed by
 rapid decline and spatial concentration, whereas it increased in amount
 and extent in the Columbia Basin of Oregon and Washington beginning in the
 1960’s. In both landscapes, we found small effect sizes of landscape
 resistance on genetic differentiation, but a 20x to 1,000x larger effect
 of contemporary relative to historic landscape resistances. Demographic
 analyses suggest population size trajectories were largely consistent
 among regions, and therefore are not likely to have differentially
 impacted the observed patterns of population structure in each region..
 Weak landscape genetics associations might instead be related to the
 coarse resolution of our historical land cover data. Despite rapid changes
 in agricultural landscapes over the last two centuries, genetic
 differentiation among L. decemlineata populations appears to reflect
 ongoing landscape change. The historical landscape genetics framework
 employed in this study is broadly applicable to other agricultural pests,
 and might reveal general responses of pests to agricultural land use
 change.
description: shapefile -
 Oregon/WashingtonPotato land cover data
 at the county level for Oregon and Washington (1840-2012), generated from
 the Census of Agriculture. Values of potato land cover are represented as
 a proportion of total county area.CB_potato_shapefile.tar.gzshapefile - WisconsinPotato land cover data at the county level for Wisconsin (1840-2012), generated from the Census of Agriculture. Values of potato land cover are represented as a proportion of total county area.WI_potato_shapefile.tar.gzGBS barcodesBarcodes associated with GBS data for Colorado potato beetle samples in the Columbia Basin (OR and WA). This file can be used to demultiplex raw reads which have been deposited on the NCBI SRA.CPB4_barcodes.txt
DOI: 10.15468/eabryj
title: Virginia Tech University, Massey Herbarium - Fungi

description: The mycological collections at Virginia Tech include primarily Basidiomycetes with emphases on the Agaricales, Boletales, Gasteromycetes, and the Aphyllophorales. In addition, a small Ascomycete collection with emphasis on Discomycetes is present. The collection has been a pivotal part of the program of teaching and research in mycology over the past from 1970 through 2005. With the retirement of Dr. Orson K. Miller, the mycological collection entered a static stage in terms of growth. In 2012, the bulk of the collection was transferred to the New York Botanical Garden with 5400 specimens from the Southeastern United States remaining at VPI. Many collections are complemented by fresh notes, color transparencies and black and white negatives. A Microsoft Access database contains nearly 15,000 records, including all specimens currently housed at VPI. The mycological herbarium is participated in the Macrofungi Collections Consortium Digitization Project during 2013-2014 and is now available online. Prior to being moved to the New York Botanical Garden, the collection contained an estimated 29,500 specimens. Geographical coverage included major collections from Virginia and the Appalachian region, central Idaho and northwestern Montana. In addition, an Alaskan collection numbered more than 6000 with emphasis on arctic and alpine tundra fungi. Major foreign collection were from Europe, Western Australia, Republic of Korea and from The Greater Antilles, especially Puerto Rico, the Dominican Republic, and Jamaica. Additional collections came from Canada, Japan, South Africa, and Thailand. Those interested in consulting specimens from outside the SE United States region should contact the New York Botanical Garden.
DOI: 10.5061/dryad.5025v
title: Data from: Bayesian analysis of a morphological supermatrix sheds light on controversial fossil hominin relationships

description: The phylogenetic relationships of several hominin species remain
 controversial. Two methodological issues contribute to the uncertainty—use
 of partial, inconsistent datasets and reliance on phylogenetic methods
 that are ill-suited to testing competing hypotheses. Here, we report a
 study designed to overcome these issues. We first compiled a supermatrix
 of craniodental characters for all widely accepted hominin species. We
 then took advantage of recently developed Bayesian methods for building
 trees of serially sampled tips to test among hypotheses that have been put
 forward in three of the most important current debates in hominin
 phylogenetics—the relationship between Australopithecus sediba and Homo,
 the taxonomic status of the Dmanisi hominins, and the place of the
 so-called hobbit fossils from Flores, Indonesia, in the hominin tree.
 Based on our results, several published hypotheses can be statistically
 rejected. For example, the data do not support the claim that Dmanisi
 hominins and all other early Homo specimens represent a single species,
 nor that the hobbit fossils are the remains of small-bodied modern humans,
 one of whom had Down syndrome. More broadly, our study provides a new
 baseline dataset for future work on hominin phylogeny and illustrates the
 promise of Bayesian approaches for understanding hominin phylogenetic
 relationships.
description: Character_matrixList_of_fossil_hypodigmsList_of_CharactersCharacter_matrix_coded
DOI: 10.5061/dryad.7ck7r
title: Data from: The last bastion? X chromosome genotyping of Anopheles gambiae species pair males from a hybrid zone reveals complex recombination within the major candidate ‘genomic island of speciation’

description: Speciation with gene flow may be aided by reduced recombination helping to
 build linkage between genes involved in the early stages of reproductive
 isolation. Reduced recombination on chromosome X has been implicated in
 speciation within the Anopheles gambiae complex, species of which
 represent the major Afrotropical malaria vectors. The most recently
 diverged, morphologically indistinguishable, species pair, A. gambiae and
 Anopheles coluzzii, ubiquitously displays a ‘genomic island of divergence’
 spanning over 4 Mb from chromosome X centromere, which represents a
 particularly promising candidate region for reproductive isolation genes,
 in addition to containing the diagnostic markers used to distinguish the
 species. Very low recombination makes the island intractable for
 experimental recombination studies, but an extreme hybrid zone in Guinea
 Bissau offers the opportunity for natural investigation of X-island
 recombination. SNP analysis of chromosome X hemizygous males revealed: (i)
 strong divergence in the X-island despite a lack of autosomal divergence;
 (ii) individuals with multiple-recombinant genotypes, including likely
 double crossovers and localized gene conversion; (iii)
 recombination-driven discontinuity both within and between the molecular
 species markers, suggesting that the utility of the diagnostics is
 undermined under high hybridization. The largely, but incompletely
 protected nature of the X centromeric genomic island is consistent with a
 primary candidate area for accumulation of adaptive variants driving
 speciation with gene flow, while permitting some selective shuffling and
 removal of genetic variation.
description: Caputo et al 2016 Data
 S1Information on the two
 Sequenom iPLEX® multiplexes used to genotype the X-centromeric region of
 An.gambiae and An.coluzzii specimens from Guinea Bissau and Burkina Faso
 as described in the paper. The two iPLEX assays were designed to genotype
 a total of 35 X-pericentromeric species-specific SNPs, yielding a density
 of 1 SNP per 0.12 Mb across the 4 Mb region targeted.Caputo et al 2016 Data
 S2Genotyping results
 obtained for 61 males from Guinea Bissau (Safim) and 33 males from Burkina
 Faso which were Illumina -genotyped at 711 SNPs (43 on chromosome-X; 411
 on chromosome-2; 257 on chromosome-3) as described in the
 paper.
DOI: 10.5061/dryad.k4p7d
title: Data from: Male risk-taking is related to number of mates in a polygynous bird.

description: Evolutionary theory predicts that when intrasexual competition is intense,
 risky behaviors can evolve if they enhance reproductive success. Here we
 tested the idea that polygynous males exhibit predictable variation in
 risk-taking during intense competition for mates. We conducted an
 observational study of a village weaverbird (Ploceus cucullatus) breeding
 colony, and video recorded synchronous fleeing events, a common predator
 avoidance behavior. Males adjusted their flight from the colony according
 to the amplitude (loudness) and Wiener entropy (harshness) of conspecific
 alarm calls during a perceived threat. Males also varied in how often they
 fled the colony. Specifically, in line with predictions based on the value
 of a male’s territory, males with more nesting females were less likely to
 flee, and returned sooner if they did flee, compared to males with fewer
 nesting females. Males with a nest under construction also returned to
 their nests sooner than males without constructions in progress,
 consistent with predictions based on nest sabotage by conspecifics. These
 results suggest that male weavers perform a cost-benefit analysis in real
 time in order to decide how to respond to a perceived threat, with
 self-protection trading off with the security of one’s territory and
 mates.
description: visibility_dataNumber of visible males and females before, during, and after a synchronous fleeing event.fleeing_probability_dataPredictors of fleeing probability in male weaversorder_of_return_dataPredictors of male order of return following a synchronous fleeing event in male weaverbirds.
DOI: 10.5061/dryad.g2r87
title: Data from: Decades of field data reveal that turtles senesce in the wild

description: Lifespan and aging rates vary considerably across taxa; thus,
 understanding the factors that lead to this variation is a primary goal in
 biology and has ramifications for understanding constraints and
 flexibility in human aging. Theory predicts that senescence—declining
 reproduction and increasing mortality with advancing age—evolves when
 selection against harmful mutations is weaker at old ages relative to
 young ages or when selection favors pleiotropic alleles with beneficial
 effects early in life despite late-life costs. However, in many long-lived
 ectotherms, selection is expected to remain strong at old ages because
 reproductive output typically increases with age, which may lead to the
 evolution of slow or even negligible senescence. We show that, contrary to
 current thinking, both reproduction and survival decline with adult age in
 the painted turtle, Chrysemys picta, based on data spanning &gt;20 y
 from a wild population. Older females, despite relatively high
 reproductive output, produced eggs with reduced hatching success.
 Additionally, age-specific mark–recapture analyses revealed increasing
 mortality with advancing adult age. These findings of reproductive and
 mortality senescence challenge the contention that chelonians do not age
 and more generally provide evidence of reduced fitness at old ages in
 nonmammalian species that exhibit long chronological lifespans.
description: Warner et al. 2016
 (PNAS) painted turtle recapture historiesRecapture histories for
 adult female Chrysemys pictaWarner et al. 2016 (PNAS)
 recapture histories.xlsxWarner et al. 2016
 (PNAS) reproductive data REVISEDReproductive data for
 adult female Chrysemys pictaWarner_RevisedReproData
 _11NOV2016.csv
DOI: 10.18160/n7d3-ew9f
title: Biogenic in-situ observations (L2), Munich PAR, 2023-03-23–2024-12-31

description: Photosynthetically Active Radiation (PAR)  data from Munich, Germany. Measurement locations are indicated in the map. Details of the measurements, file contents etc are described in ICOS Cities deliverable report D3.13.
DOI: 10.5061/dryad.sc30g
title: Data from: Nest size is predicted by female identity and the local environment in the blue tit, but is not related to genetic or foster mother's nest size

description: The potential for animals to respond to changing climates has sparked
 interest in intraspecific variation in avian nest structure since this may
 influence nest microclimate and protect eggs and offspring from inclement
 weather. However, there have been relatively few large-scale attempts to
 examine variation in nests or the determinates of individual variation in
 nest structure within populations. Using a set of mostly pre-registered
 analyses, we studied potential predictors of variation in the size of a
 large sample (803) of blue tit (Cyanistes caeruleus) nests across three
 breeding seasons at Wytham Woods, UK. Whilst our pre-registered analyses
 found that individual females built very similar nests across years, there
 was no evidence in follow-up (post hoc) analyses that their nest size
 correlated to that of their genetic mother or, in a cross-fostering
 experiment, to the nest where they were reared. In further pre-registered
 analyses, spatial environmental variability explained nest size
 variability at relatively broad spatial scales, and especially strongly at
 the scale of individual nestboxes. Our study indicates that nest structure
 is a characteristic of individuals, but is not strongly heritable,
 indicating that it will not respond rapidly to selection. Explaining the
 within-individual and within-location repeatability we observed requires
 further study.
description: Final blue tit nest size
 dataNest sizes recorded by
 SCG in Wytham Woods, UK 2001-2003. Nest sizes were recorded as fraction of
 standardised nest box filled. Blue tits were identified using uniquely
 marked metal rings to give identities. Zone is the woodland compartment in
 Wytham Woods where the nest is.Final BT nest data LON
 2018-2-6.csvBlue tit nest sizes for
 genetic mother-daughter pairsNest sizes (recorded as
 fraction of standardised nest box filled) of blue tit daughters and their
 genetic mothers, as recorded by SCG in Wytham Woods, Oxfordshire, UK in
 2001-2003genetic
 depth2.csvBlue tit nest sizes for
 foster mother-daughter pairs 2Nest sizes (recorded as
 fraction of standardised nest box filled) of daughters and their foster
 mothers, as recorded by SCG in Wytham Woods, UK during 2001-2003 breeding
 seasons. Rrearing
 depth2.csvFinal R code used for
 analysis 2The R code that I wrote
 to analyse different factors controlling the nest size of blue tits in
 Wytham Woods, UK during the 2001-2003 breeding seasons using the data
 files attachedFinal BT nest size analysis
 code.R
DOI: 10.5061/dryad.ng720
title: Data from: Perceptual expertise in forensic facial image comparison

description: Forensic facial identification examiners are required to match the
 identity of faces in images that vary substantially, owing to changes in
 viewing conditions and in a person's appearance. These
 identifications affect the course and outcome of criminal investigations
 and convictions. Despite calls for research on sources of human error in
 forensic examination, existing scientific knowledge of face matching
 accuracy is based, almost exclusively, on people without formal training.
 Here, we administered three challenging face matching tests to a group of
 forensic examiners with many years' experience of comparing face
 images for law enforcement and government agencies. Examiners outperformed
 untrained participants and computer algorithms, thereby providing the
 first evidence that these examiners are experts at this task. Notably,
 computationally fusing responses of multiple experts produced near-perfect
 performance. Results also revealed qualitative differences between expert
 and non-expert performance. First, examiners' superiority was
 greatest at longer exposure durations, suggestive of more entailed
 comparison in forensic examiners. Second, experts were less impaired by
 image inversion than non-expert students, contrasting with face memory
 studies that show larger face inversion effects in high performers. We
 conclude that expertise in matching identity across unfamiliar face images
 is supported by processes that differ qualitatively from those supporting
 memory for individual faces.
description: Fusion simulation
 analysis aROC dataThis file contains a tab
 for each group in each condition of the EFCT. In each tab are the
 individual group aROC scores used to compute the mean aROC scores that are
 plotted in Figure 4.whiteEtAl_EFCTaROCfusionData.xlsxTest performance by subjectPercent correct on the GFMT; aROC scores for EFCT and PICTwhiteEtAl_subjectPerformanceDataFinal.xlsx
DOI: 10.5061/dryad.vd6k4b2
title: Data from: Genetic dissection of hybrid male sterility across stages of spermatogenesis

description: Hybrid sterility is a common form of reproductive isolation between
 nascent species. Although hybrid sterility is routinely documented and
 genetically dissected in speciation studies, its developmental basis is
 rarely examined, especially in generations beyond the F1. To identify
 phenotypic and genetic determinants of hybrid male sterility from a
 developmental perspective, we characterized testis histology in 312 F2
 hybrids generated by intercrossing inbred strains of Mus musculus
 domesticus and M. m. musculus, two subspecies of house mice. Hybrids
 display a range of histologic abnormalities that indicate defective
 spermatogenesis. Among these abnormalities, we quantified decreased testis
 size, reductions in spermatocyte and spermatid number, increased apoptosis
 of meiosis I spermatocytes, and more multinucleated syncytia.
 Collectively, our phenotypic data point to defects in meiosis I as a
 primary barrier to reproduction. We identified seven quantitative trait
 loci (QTL) controlling five histologic traits. A region of chromosome 17
 that contains Prdm9, a gene known to confer F1 hybrid male sterility,
 affects multinucleated syncytia and round spermatids, potentially
 extending the phenotypic outcomes of this incompatibility. The X
 chromosome also plays a key role, with loci affecting multinucleated
 syncytia, apoptosis of round spermatids, and round spermatid numbers. We
 detected an epistatic interaction between QTL on chromosomes 17 and X for
 multinucleated syncytia. Our results refine the developmental basis of a
 key reproductive barrier in a classic model system for speciation
 genetics.
description: Testis histology
 phenotypesphenotypes.xlsxF2 genotypesF2genotypes.xlsxGenomic positions of SNP markersmarkers.xlsxRead me
DOI: 10.5061/dryad.jr77n
title: Data from: Bet-hedging as a mechanism for the evolution of polyandry, revisited

description: Females that mate with multiple males (polyandry) may reduce the risk that
 their eggs are fertilized by a single unsuitable male. About 25 years ago
 it was hypothesized that bet-hedging could function as a mechanism
 favoring the evolution of polyandry, but this idea is controversial
 because theory indicates that bet-hedging via polyandry can compensate the
 costs of mating only in small populations. Nevertheless, populations are
 often spatially structured, and even in the absence of spatial structure,
 mate choice opportunity can be limited to a few potential partners. We
 examined the effectiveness of bet-hedging in such situations with
 simulations carried out under two scenarios; (1) intrinsic male quality,
 with offspring survival determined by male phenotype (male's ability
 to generate viable offspring), and (2) genetic incompatibility (offspring
 fitness determined non-additively by parental genotypes). We find higher
 fixation probabilities for a polyandrous strategy compared to a monandrous
 strategy if complete reproductive failure due to male effects or parental
 incompatibility is pervasive in the population. Our results also indicate
 that bet-hedging polyandry can delay the extinction of small demes. Our
 results underscore the potential for bet-hedging to provide benefits to
 polyandrous females and have valuable implications for conservation
 biology.
description: Yasui and
 Garcia-Gonzalez polyandry bet-hedging raw dataAll simulation results
 described in the paperintrinsic male quality
 scenario (binomial quality distribution)Fujitsu F-BASIC for
 Windows V6.0 program source code for the intrinsic male quality scenario
 (binomial quality distribution)intrinsic male quality
 scenario (continuous quality distribution with SD0.167)Fujitsu F-BASIC for
 Windows V6.0 program source code for the intrinsic male quality scenario
 (continuous quality distribution)gametophytic genetic
 compatibility scenarioFujitsu F-BASIC for
 Windows V6.0 program source code for the genetic incompatibility scenario
 (gametophytic incompatibility)Instruction manual for
 simulation programsInstruction manual for 3
 program filesInstruction_manual_for_simulation_programs.txt