cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8727
title: Data from: The evolutionary genetics of acquisition and allocation in the wing dimorphic cricket, Gryllus firmus.

description: The evolutionary trajectories of trade-offs are ultimately governed by the
 evolution of the underlying physiological processes of the acquisition and
 subsequent allocation of resources. In this study, we focused directly on
 acquisition and allocation as traits and estimated their genetic
 architecture in the trade-off between flight capability and reproduction
 in the cricket, Gryllus firmus. To determine the evolutionary genetics of
 acquisition and allocation both within and between resource environments
 we performed a large-scale quantitative genetic breeding experiment in
 which families were split over several resource levels. Our findings were
 fourfold: 1) there was substantial genetic variance in acquisition and
 allocation; 2) contrary to the assumption of independence between
 acquisition and allocation, there was a significant genetic correlation
 between them; 3) the genetic covariance between acquisition and allocation
 was significantly different in the different food environments, 4) the
 trade-off, as measured by the genetic correlation between flight muscle
 mass and ovary mass, was only significant in the food restriction
 environments. However, when measured directly as the genetic correlation
 between reproductive allocation and flight allocation, we found a
 consistent strong negative genetic correlation, demonstrating that when
 allocation is measured independently of acquisition we find evidence for
 the trade-off.
description: Half-Sib
 DataThis data is from a
 half-sibling breeding experiment done in the lab using Gryllus firmus
 females at 7 days of age. All masses are dry masses. Energy values were
 calculated as described in King et al. 2010. Column headings are: Animal:
 individual number, Sire: male parent number, Dam: female parent number,
 Bucket: cage number, Wing Morph: long-wing (L), short wing (S), Food: Low,
 Medium (Med), Ad libitum (AD), State of DLM (0=histolyzed, 1=partially
 histolyzed, 2=intact), DLM Mass (mg), Ovary Mass (mg), Remaining Mass
 (Body mass-DLM and Ovary Mass), Acquisition (total energy content, J), DLM
 Energy (J), Ovary Energy (J).Kingetal2011.xls
DOI: 10.5061/dryad.8729
title: Data from: Measuring population differentiation using GST or D? A simulation study with microsatellite DNA markers under a finite island model and nonequilibrium conditions

description: Genetic differentiation of populations is a key question in population
 genetic investigations. Wright’s FST (and its relatives such as GST) has
 been a standard measure of differentiation. However, the deficiencies of
 these indexes and their significance have been increasing realized in
 recent years, leading to some new measures being proposed, such as Jost’s
 (2008) D. This has also stimulated some considerable debate which, in
 certain sense, makes empirical biologists even more confused, for example,
 on statistics which should be used for estimating population
 differentiation. Here we report a simulation study with neutral
 microsatellite DNA loci under a finite island model to compare the
 performance of GST and D, under non-equilibrium conditions, in particular.
 Our results suggest that there exist fundamental differences between the
 two statistics and neither GST nor D operate satisfactorily in all
 situations for quantifying differentiation. D is very sensitive to
 mutation models but GST noticeably less so ...
description: origin .obj files for
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 of Origin, a widely-used painting software. You can process this
 compressed file with Winrar and then open it with
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 compressed file with Winrar and then open it with
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DOI: 10.5061/dryad.8733
title: Data from: Habitat specialization of birds in the Czech Republic: comparison of objective measures with expert opinion

description: CAPSULE: Expert-based classification of bird species as habitat
 specialists and as generalists agrees with objective measures of species’
 habitat requirements based on large-scale monitoring data. AIMS: To
 compare habitat specialization of 137 common bird species breeding in the
 Czech Republic using three different measures and to test their
 relationships to species’ abundance and habitat associations. METHODS:
 Data on bird abundance and surveyed habitats were collected through a
 standardized monitoring scheme of common breeding species in the Czech
 Republic. From these data we calculated a quantitative species
 specialization index (SSI). Canonical correspondence analysis (CCA) was
 applied to calculate species’ habitat niche breadth and the level of
 association of each species to the main habitats. A panel of 11 local bird
 experts classified each species as habitat generalist or habitat
 specialist. RESULTS: Species classified as habitat specialists by expert
 opinion showed higher habitat specialization according to the SSI, as well
 as according to CCA-based habitat niche breadth. These species were also
 more closely associated with one of the main habitat types. These
 relationships were significant even after controlling for abundance.
 CONCLUSIONS: As expert opinion accords with the level of species’ habitat
 specialization expressed using two quantitative objective measures, we
 suggest that these characteristics reflect real interspecific variation in
 the breadth of habitat requirements in birds. Interspecific differences in
 habitat specialization are not caused solely by the variability in
 abundance among species.
description: Czech Bird Data
 (managers: Reif and Vermouzek)Abundance of breeding
 bird species counted two times in eight habitats in 2006-2008 within a
 large-scale breeding bird monitoring scheme covering the Czech
 Republic.Czech Bird Data (managers- Reif
 and Vermouzek.txt
DOI: 10.5061/dryad.23s51
title: Data from: Hybridization in headwater regions, and the role of rivers as drivers of speciation in Amazonian birds

description: Many understory birds and other groups form genetically differentiated
 subspecies or closely related species on opposite sides of major rivers of
 Amazonia, but are proposed to come into geographic contact in headwater
 regions where narrower river widths may present less of a dispersal
 barrier. Whether such forms hybridize in headwater regions is generally
 unknown, but has important implications to our understanding of the role
 of rivers as drivers of speciation. We used a dataset of several thousand
 SNPs to show that seven taxon pairs which differentiate across a major
 Amazonian river come into geographic contact and hybridize in headwater
 regions. All taxon pairs possessed hybrids with low numbers of loci in
 which alleles were inherited from both parental species, suggesting they
 are backcrossed with parentals, and indicating gene flow between parental
 populations. Ongoing gene flow challenges rivers as the sole cause of in
 situ speciation, but is compatible with the view that the wide river
 courses in the heart of Amazonia may have driven interfluvial divergence
 during episodes of wet forest retraction away from headwater regions. Taxa
 as old as 4 Ma in our Amazonian dataset continue to hybridize at contact
 zones, suggesting reproductive isolation evolves at a slow pace.
description: SNP_dataset_for_DryadSNP data
DOI: 10.5061/dryad.392t9
title: Data from: Multiple glacial refugia for cool-temperate deciduous trees in northern East Asia: the Mongolian oak as a case study

description: In East Asia, temperate forests are predicted to have retracted southward
 to c. 30° N during the last glacial maximum (LGM) based on fossil pollen
 data, whereas phylogeographic studies have often suggested glacial in situ
 survival of cool-temperate deciduous trees in their modern northern
 ranges. Here we report a study of the genetic diversity and structure of
 29 natural Mongolian oak (Quercus mongolica) populations using 19 nuclear
 simple sequence repeat (nSSR) loci and four chloroplast DNA fragments.
 Bayesian clustering analysis with nSSRs revealed five groups, which were
 inferred by approximate Bayesian computation (ABC) to have diverged in
 multiple refugia through multiple glacial–interglacial cycles. Analysis of
 chloroplast DNA variation revealed four lineages that were largely but
 incompletely geographically disjunct. Ecological niche modelling (ENMs)
 indicated a southward range shift of the oak's distribution at the
 LGM, although high suitability scores were also evident in the Changbai
 Mts. (Northeast China), the Korean Peninsula, areas surrounding the Bohai
 Sea, and along the coast of the Russian Far East. In addition, endemic
 chloroplast DNA haplotypes and nuclear lineages occurred in high-latitude
 northern areas where the ENM predicted no suitable habitat. The combined
 evidence from nuclear and chloroplast DNA, and the results of the ENM
 clearly demonstrate that multiple northern refugia, including cryptic
 ones, were maintained across the current distributional range of the
 Mongolian oak during the LGM or earlier glacial periods. Though spatially
 limited, postglacial expansions from these refugia have led to a pattern
 of decreased genetic diversity with increasing latitude.
description: nuclear SSR
 dataSample
 locationssample
 locations.txtThe aligned cpDNA
 sequences for all individualsThe aligned cpDNA
 sequences for each of 324 individuals,which is concatenated from four
 cpDNA fragments, trnH-psbA (1-541 bp), rpL14-rpL36 (542-1704 bp),
 trnQ-trnS (1705-2657) and trnS-trnT (2658-3979).cpDNA_seq3979_324.fasFiles used for MAXENT analysisENM_data includes distribution records of Mongolian oak and climate data used for MAXENT analysisENM data.raroutlier list by lositan.txtOutlier list identified by Lositan software for 19 nuclear SSR markersInput file for structure analysisStructure input file based on 19 nuclear SSR markers, -9 is used for missing data.ssr_19_780.str
DOI: 10.5061/dryad.pt532
title: Data from: Three-dimensional camouflage: exploiting photons to conceal form

description: Many animals have a gradation of body color, termed “countershading,”
 where the areas that are typically exposed to more light are darker. One
 hypothesis is that this patterning enhances visual camouflage by making
 the retinal image of the animal match that of the background, a
 fundamentally two-dimensional theory. More controversially, countershading
 may also obliterate cues to three-dimensional (3D) shape delivered by
 shading. Despite relying on distinct cognitive mechanisms, these two
 potential functions hitherto have been amalgamated in the literature. It
 has previously not been possible to validate either hypothesis
 empirically, because there has been no general theory of optimal
 countershading that allows quantitative predictions to be made about the
 many environmental parameters involved. Here we unpack the logical
 distinction between using countershading for background matching and using
 it to obliterate 3D shape. We use computational modeling to determine the
 optimal coloration for the camouflage of 3D shape. Our model of 3D
 concealment is derived from the physics of light and informed by
 perceptual psychology: we simulate a 3D world that incorporates
 naturalistic lighting environments. The model allows us to predict
 countershading coloration for terrestrial environments, for any body shape
 and a wide range of ecologically relevant parameters. The approach can be
 generalized to any light distribution, including those underwater.
description: am_nat_2015_3D_camouflageData, model, Matlab code for reproducing the figures in the manuscript.
DOI: 10.5061/dryad.8743
title: Data from: The coupling hypothesis: why genome scans may fail to map local adaptation genes

description: Genomic scans of multiple populations often reveal marker loci with
 greatly increased differentiation between populations. Often this
 differentiation coincides in space with contrasts in ecological factors,
 forming a genetic–environment association (GEA). GEAs imply a role for
 local adaptation, and so it is tempting to conclude that the strongly
 differentiated markers are themselves under ecologically based divergent
 selection, or are closely linked to loci under such selection. Here, we
 highlight an alternative and neglected explanation: intrinsic (i.e.
 environment-independent) pre- or post-zygotic genetic incompatibilities
 rather than local adaptation can be responsible for increased
 differentiation. Intrinsic genetic incompatibilities create endogenous
 barriers to gene flow, also known as tension zones, whose location can
 shift over time. However, tension zones have a tendency to become trapped
 by, and therefore to coincide with, exogenous barriers due to ecological
 selection. This coupling of endogenous and exogenous barriers can occur
 easily in spatially subdivided populations, even if the loci involved are
 unlinked. The result is that local adaptation explains where genetic
 breaks are positioned, but not necessarily their existence, which can be
 best explained by endogenous incompatibilities. More precisely, we show
 that (i) the coupling of endogenous and exogenous barriers can easily
 occur even when ecological selection is weak; (ii) when environmental
 heterogeneity is fine-grained, GEAs can emerge at incompatibility loci,
 but only locally, in places where habitats and gene pools are sufficiently
 intermingled to maintain linkage disequilibria between genetic
 incompatibilities, local-adaptation genes and neutral loci. Furthermore,
 the association between the locally adapted and intrinsically incompatible
 alleles (i.e. the sign of linkage disequilibrium between endogenous and
 exogenous loci) is arbitrary and can form in either direction. Reviewing
 results from the literature, we find that many predictions of our model
 are supported, including endogenous genetic barriers that coincide with
 environmental boundaries, local GEA in mosaic hybrid zones, and inverted
 or modified GEAs at distant locations. We argue that endogenous genetic
 barriers are often more likely than local adaptation to explain the
 majority of Fst-outlying loci observed in genome scan approaches – even
 when these are correlated to environmental variables.
description: Coupling endogenous and
 exogenous selectionCoupling.zip
DOI: 10.5061/dryad.j151j
title: Data from: Exogenous restoration of TUSC2 expression induces responsiveness to erlotinib in wildtype epidermal growth factor receptor (EGFR) lung cancer cells through context specific pathways resulting in enhanced therapeutic efficacy

description: Expression of the tumor suppressor gene TUSC2 is reduced or absent in most
 lung cancers and is associated with worse overall survival. In this study,
 we restored TUSC2 gene expression in several wild type EGFR non-small cell
 lung cancer (NSCLC) cell lines resistant to the epidermal growth factor
 receptor (EGFR) tyrosine kinase inhibitor erlotinib and analyzed their
 sensitivity to erlotinib in vitro and in vivo. A significant inhibition of
 cell growth and colony formation was observed with TUSC2 transient and
 stable expression. TUSC2-erlotinib cooperativity in vitro could be
 reproduced in vivo in subcutaneous tumor growth and lung metastasis
 formation lung cancer xenograft mouse models. Combination treatment with
 intravenous TUSC2 nanovesicles and erlotinib synergistically inhibited
 tumor growth and metastasis, and increased apoptotic activity.
 High-throughput qRT-PCR array analysis enabling multi-parallel expression
 profile analysis of eighty six receptor and non-receptor tyrosine kinase
 genes revealed a significant decrease of FGFR2 expression level,
 suggesting a potential role of FGFR2 in TUSC2-enhanced sensitivity to
 erlotinib. Western blots showed inhibition of FGFR2 by TUSC2 transient
 transfection, and marked increase of PARP, an apoptotic marker, cleavage
 level after TUSC2-erlotinb combined treatment. Suppression of FGFR2 by
 AZD4547 or gene knockdown enhanced sensitivity to erlotinib in some but
 not all tested cell lines. TUSC2 inhibits mTOR activation and the latter
 cell lines were responsive to the mTOR inhibitor rapamycin combined with
 erlotinib. These results suggest that TUSC2 restoration in wild type EGFR
 NSCLC may overcome erlotinib resistance, and identify FGFR2 and mTOR as
 critical regulators of this activity in varying cellular contexts. The
 therapeutic activity of TUSC2 could extend the use of erlotinib to lung
 cancer patients with wildtype EGFR.
description: A549-siRNA-FGFR2-ERRaw dataAZD4547-Erlotinib combinaiton in A549 cells repeatRaw dataAZD4547-Erlotinib combination in A549, H1299 H1650Raw dataCopy of heatmap-rawdata-normdataRaw dataCopy of result-heatmap-GeneExpRaw dataCopy of result-heatmap-RPPARaw dataH1299 h322 h460 rapa-er combinationRaw dataraw fig 3cRaw data - in vivo effect of TUSC2 + ERraw fig4Raw data - TUSC2 repressed FGFR2 expression in H1299 cellsraw figure 1Raw data - TUSC2 expression
DOI: 10.5061/dryad.mr73c
title: Data from: Ants adjust their pheromone deposition to a changing environment and their probability of making errors

description: Animals must contend with an ever-changing environment. Social animals,
 especially eusocial insects such as ants and bees, rely heavily on
 communication for their success. However, in a changing environment
 communicated information can become rapidly outdated. This is a particular
 problem for pheromone-trail using ants, as once deposited pheromones
 cannot be removed. Here we study the response of ant foragers to an
 environmental change. Ants were trained to one feeder location, and the
 feeder was then moved to a different location. We found that ants
 responded to an environmental change by strongly up-regulating pheromone
 deposition immediately after experiencing the change. This may help
 maintain the colony’s foraging flexibility, and allow multiple food
 locations to be exploited simultaneously. Our treatment also caused
 uncertainty in the foragers, by making their memories less reliable. Ants
 returning to the nest after eventually finding the food source
 up-regulated pheromone deposition if they had made a wrong choice.
 Intriguingly, ants on their way towards the food source down-regulated
 pheromone deposition if they were going to make an error. This may suggest
 that individual ants can measure the reliability of their own memories and
 respond appropriately.
description: complete
 datasetThe complete dataset
 used in this study. The workbook has three tabs: the raw data as it was
 imputted, a cleaned version, and a version in which the data is stacked by
 pheromone treatment, to allow testing the pheromone treatment
 effect.ESM
 3 - raw data.xlsx
DOI: 10.5061/dryad.1bf13
title: Data from: Varroa destructor changes cuticular hydrocarbons to mimic its new host.

description: Varroa destructor (Vd) is a honeybee ectoparasite. Its original host is
 the Asian honeybee, Apis cerana, but it has also become a severe, global
 threat to the European honeybee, Apis mellifera. Previous studies have
 shown that Varroa can mimic a host's cuticular hydrocarbons (HC),
 enabling the parasite to escape the hygienic behaviour of the host
 honeybees. By transferring mites between the two honeybee species, we
 further demonstrate that Vd is able to mimic the cuticular HC of a novel
 host species when artificially transferred to this new host. Mites
 originally from A. cerana are more efficient than mites from A. mellifera
 in mimicking HC of both A. cerana and A. mellifera. This remarkable
 adaptability may explain their relatively recent host-shift from A. cerana
 to A. mellifera.
description: GC-MS traces for two
 honey bee samples (1st page) and relative amount of each chemical per bee
 or mites sample. .The first page are two
 TICS (total ion chromatograms or GC-MS chromatograms) of the 2 Apis bees.
 The first is a BCC, an Apis cerana that received a mite from A. cerana.
 The second is a BMM, an Apis mellifera that received a mite from A.
 mellifera. Pages after that are the relative proportions of each compound
 for each bee or mite sample.rawdataLeConte
 eta_v33.pdf
DOI: 10.5061/dryad.h5971
title: Data from: The implications of stratigraphic compatibility for character integration among fossil taxa

description: Two characters are stratigraphically compatible if some phylogenies
 indicate that their combinations (state-pairs) evolved without homoplasy
 and in an order consistent with the fossil record. Simulations assuming
 independent character change indicate that we expect approximately 95% of
 compatible character pairs to also be stratigraphically compatible over a
 wide range of sampling regimes and general evolutionary models. However,
 two general models of rate heterogeneity elevate expected stratigraphic
 incompatibility: “early burst” models, where rates of change are higher
 among early members of a clade than among later members of that clade, and
 “integration” models, where the evolution of characters is correlated in
 some manner. Both models have important theoretical and methodological
 implications. Therefore, we examine 259 metazoan clades for deviations
 from expected stratigraphic compatibility. We do so first assuming
 independent change with equal rates of character change through time. We
 then repeat the analysis assuming independent change with separate “early”
 and “late” rates (with “early” = the first third of taxa in a clade), with
 the early and late rates chosen to maximize the probability of the
 observed compatibility among the early taxa and then the whole clade. We
 single out Cambrian trilobites as a possible “control” group because
 morphometric studies suggest that integration patterns are not conserved
 among closely related species. Even allowing for early bursts, we see
 excess stratigraphic incompatibility (i.e., negative deviations) in
 significantly more clades than expected at 0.50, 0.25, and 0.05 P values.
 This pattern is particularly strong in chordates, echinoderms, and
 arthropods. However, stratigraphic compatibility among Cambrian trilobites
 matches the expectations of integration studies, as they (unlike
 post-Cambrian trilobites) do not deviate from the expectations of
 independent change with no early bursts. Thus, these results suggest that
 processes such as integration strongly affect the data that
 paleontologists use to study phylogeny, disparity, and rates.
description: Data from: The
 Implications of Stratigraphic Compatibility for Character Integration
 among Fossil TaxaThese include the data
 matrices, first and last appearances, and character-ordering files
 analyzed within this paper.Stratigraphic Compatibilty Test
 Code.zipSOM
 AppendixWagner_&_Estabrook_Data_2014