cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.83bk3j9p0
title: Scripts in C for simulating the wave of gene advance under diverse systems of mating

description: This dataset includes 4 programs coded in C for simulating the wave of
 gene advance under diverse systems of mating. Program 1 was used for
 simulation under unifor density based on Equations (1) and (2) in the main
 text. Program 2 was used for simulation under uniform density based on
 Equations (5)-(11).  Program 3 was used for Monte Carlo (MC)
 simulation under uniform density. Program 4 was used for MC simulation
 under logistic growth model. Variable and parameter symbols within these
 programs are self-explanatory. You may simulate different cases by
 changing parameter settings.
DOI: 10.5061/dryad.b8gtht79c
title: Data from: Genetic and environmental canalization are not correlated among altitudinally varying populations of Drosophila melanogaster

description: Organisms are exposed to environmental and mutational effects influencing
 both mean and variance of phenotypes.  Potentially deleterious
 effects arising from this variation can be reduced by the evolution of
 buffering (canalizing) mechanisms, ultimately reducing phenotypic
 variability. There has been interest regarding the conditions enabling the
 evolution of canalization. Under some models, the circumstances under
 which genetic canalization evolves is limited, despite apparent empirical
 evidence for it. It has been argued that genetic canalization evolves as a
 correlated response to environmental canalization (congruence model). Yet,
 empirical evidence has not consistently supported predictions of a
 correlation between genetic and environmental canalization. In a recent
 study, a population of Drosophila adapted to high altitude showed evidence
 of genetic decanalization relative to those from low altitudes. Using
 strains derived from these populations, we tested if they varied for
 multiple aspects of environmental canalization We observed the expected
 differences in wing size, shape, cell (trichome) density and mutational
 defects between high- and low-altitude populations. However, we observed
 little evidence for a relationship between measures of environmental
 canalization with population or with defect frequency. Our results do not
 support the predicted association between genetic and environmental
 canalization.
description: Please see the associated paper for detailed description of
 sampling. All wings were dissected and then mounted in
 70% glycerol/PBS and digital images were captured as described in the
 paper. The raw digitial images (not part of the DRYAD
 collection, which is the flat text files including size and landmark for
 all specimens) for the first set of experiments can be found on
 figshare https://doi.org/10.6084/m9.figshare.1449060
description: Please see the file readme_code_new.txt in this data repository
 for detailed information on all the data and scripts.
DOI: 10.5061/dryad.v41ns1rsp
title: Eco-evolutionary outsiders: establishing in a distantly related neighbourhood delays and reorganizes nutrient recycling

description: Rapid environmental change forces long-lived plants like trees to
 immigrate into zones still occupied by phylogenetically distantly related
 species. Does such phylogenetic isolation (PI) change the trees’ ecosystem
 functioning such as litter decomposition? We studied oaks (Quercus
 petraea) of low and high PI, reciprocally transplanting their litters to
 identify effect of aboveground litter quality and belowground decomposer
 biota. Across 8 and 14 months we quantified decomposition (mass loss,
 C-loss and N-loss), decomposer biota (Acari, Collembola, microbes)
 and 13C/12C ratio. Across 14 months, aboveground PI retarded
 decomposition (mass and C loss). Across 8 and 14 months, above- and
 belowground PI extensively altered relationships between decomposition and
 abundances/diversities of different soil biota, reduced microbial activity
 and 13C/12C ratios. Overall, coexistence of trees with distant
 relatives impedes and severely re-organizes C and N recycling. Such
 negative ecosystem feedback might prevent trees from tracking and
 conserving abiotic niches under environmental change.
DOI: 10.5061/dryad.c59zw3r4n
title: Cryptic diversity across the Trans-Mexican Volcanic Belt of Mexico in the montane bunchgrass lizard Sceloporus subniger (Squamata: Phrynosomatidae)

description: Sceloporus subniger Poglaygen & Smith is a montane bunchgrass
 lizard distributed across pine-oak forests of central Mexico. Prompted by
 the discovery of a new population of this lizard in far western Mexico,
 and by recent studies suggesting S. subniger may be a composite of several
 distinct species, we examined in more detail the genetic structure of S.
 subniger. We generated a mitochondrial DNA (mtDNA) dataset from 81
 specimens and an ultraconserved elements (UCE) dataset representing
 thousands of genomic regions from 12 specimens to specifically evaluate
 the genetic distinctiveness of populations from western Michoacán and
 adjacent Jalisco along with the newly discovered population in the Sierra
 de Mascota in western Jalisco. We also recorded morphological data from 47
 museum specimens to compare to our genetic data. Results from our analyses
 of the genetic data, augmented by specimen measurements and scale counts,
 support the notion that S. subniger is indeed a composite of distinct
 species. Montane bunchgrass lizards from western Michoacán and adjacent
 Jalisco, and from the Sierra de Mascota in western Jalisco, each represent
 distinct new species, which we describe and name here.
description: file: <strong>subnigerND4.nex</strong><br>
 Nexus file with aligned ND4 sequences. See ReadMe_mtDNA file to match
 sample names with species and locality. file:
 <strong>subniger_tRNAs.txt</strong><br> Nexus file with
 aligned tRNA sequences. See ReadMe_mtDNA file to match sample names with
 species and locality. file:
 <strong>subnigerSTRUCTURE.txt</strong><br> Input file
 with SNPs for STRUCTURE analyses. See ReadMe_SNPs file to match sample
 names with species and locality. file:
 <strong>subnigerSNAPP.nex</strong><br> Nexus file with
 SNPs for BFD* analyses in SNAPP. See ReadMe_SNPs file to match sample
 names with species and locality.
DOI: 10.5061/dryad.jm63xsj7k
title: Data from: Environmental change, if unaccounted, prevents detection of cryptic evolution in a wild population

description: Detecting contemporary evolution requires demonstrating that genetic
 change has occurred. Mixed-effects models allow estimation of quantitative
 genetic parameters and are widely used to study evolution in wild
 populations. However, predictions of evolution based on these parameters
 frequently fail to match observations. Furthermore, such studies often
 lack an independent measure of evolutionary change against which to verify
 predictions. Here, we applied three commonly used quantitative genetic
 approaches to predict the evolution of size at maturity in a wild
 population of Trinidadian guppies. Crucially, we tested our predictions
 against evolutionary change observed in common garden experiments
 performed on samples from the same population. We show that standard
 quantitative genetic models underestimated or failed to detect the cryptic
 evolution of this trait as demonstrated by the common garden experiments.
 The models failed because: 1) size at maturity and fitness both decreased
 with increases in population density, 2) offspring experienced higher
 population densities than their parents, and 3) selection on size was
 strongest at high densities. When we accounted for environmental change,
 predictions better matched observations in the common garden experiments,
 although substantial uncertainty remained. Our results demonstrate that
 predictions of evolution are unreliable if environmental change is not
 appropriately captured in models.
description: This dataset includes: guppy_data.csv -
 individual phenotypic, fitness and environmental data from the study
 population<br> guppy_ped.csv - pedigree for the study
 population<br> common_garden.csv - phenotypic data from the common
 garden experiments In addition, we include code for
 performing the analyses described in the manuscript as well as model
 output objects.
description: Please read the manuscript and supplementary material, and the
 READ_ME file included with this dataset.
DOI: 10.15468/dl.w5fypq
title: Occurrence Download

description: A dataset containing 124 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Baikiaea plurijuga",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 124 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002405-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.93nsj3
title: Occurrence Download

description: A dataset containing 2243871 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is COL.20_2",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 2243871 records from 688 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002381-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.mcvdncjxw
title: Data from: The dynamic transmission of positional information in stau-mutants during Drosophila embryogenesis.

description: It has been suggested that Staufen (Stau) is key in controlling the
 variability of the posterior boundary of the Hb anterior domain (xHb).
 However, its underlying mechanism is elusive. Here, we quantified the
 dynamic 3D expression of segmentation genes in Drosophila embryos. With
 improved control of measurement errors, we show xHb of stau- mutants
 reproducibly moves posteriorly by 10% of the embryo length (EL) to the
 wild type (WT) position in the nuclear cycle (nc) 14, and its variability
 at short time windows is comparable as that of the WT. Moreover, for stau-
 mutants, the upstream Bicoid (Bcd) gradients show equivalent relative
 intensity noise to that of the WT in nc12-nc14, and the downstream
 Even-skipped (Eve) and cephalic furrow (CF) show the same positional
 errors as the WT. Our results indicate that threshold-dependent activation
 and self-organized filtering are not mutually exclusive but could both be
 implemented in early Drosophila embryogenesis.
description: <strong>Raw Figure</strong> Images
 of an immunostained Drosophila embryo of the fly line stauHL54
 (w;stauHL54) acquired by a Zeiss Z1 light-sheet microscope (1920*1920
 pixels, 16 bits and a pixel size of 0.286 micrometer). The embryo age is
 32 minutes during n.c.14. Images were taken with a W Plan Apo 20*/1.0
 water immersion objective and with sequential excitation wavelengths of
 638, 561, and 405 nm for  Hb, Kr, and DAPI, respectively. Two z-stack of
 images with 1 micrometer spacing were taken from two opposite sides by
 rotating the embryos 180 degree.  
 <strong>Result Display</strong>
 The image analysis results in the process of source code. Three
 parts including the images after combining, after projection at different
 angles and Hb profile extracting. 
description: This dataset is a set of raw data and the processed results for
 reference. It could be used as an example for testing the 3D imaging
 analsyis code, which can be dowloaded from the corrosponding published
 paper.   <strong>Raw
 Figure</strong> Folder <em>1</em> and
 <em>2</em> are two z-stack of images with 1 micrometer spacing
 were taken from two opposite sides by rotating the embryos 180
 degree.   <strong>Result
 Display</strong> Folder
 <em>kfuC3</em>: the  raw images after imaging combining
 (Hb); Folder <em>Angelfigure</em>: the raw
 images after projection at different angles; Folder
 <em>HbProfile</em>: the anlysis results.
   Note there are three channels in our raw
 data but four channels setting in source code initially, please adjust the
 parameters setting when running.
DOI: 10.5061/dryad.00000001t
title: Spatial environmental complexity mediates sexual conflict and sexual selection in Drosophila melanogaster

description: Sexual selection is an important agent of evolutionary change, but the
 strength and direction of selection often vary over space and time. One
 potential source of heterogeneity may lie in the opportunity for male–male
 and/or male–female interactions imposed by the spatial environment. It has
 been suggested that increased spatial complexity permits sexual selection
 to act in a complementary fashion with natural selection (hastening the
 loss of deleterious alleles and/or promoting the spread of beneficial
 alleles) via two (not mutually exclusive) pathways. In the first scenario,
 sexual selection potentially acts more strongly on males in complex
 environments, allowing males of greater genetic “quality” a greater chance
 of outcompeting rivals, with benefits manifested indirectly in offspring.
 In the second scenario, increased spatial complexity reduces opportunities
 for males to antagonistically harm females, allowing females (especially
 those of greater potential fecundities) to achieve greater reproductive
 success (direct fitness benefits). Here, using Drosophila melanogaster ,
 we explore the importance of these mechanisms by measuring direct and
 indirect fitness of females housed in simple vial environments or in vials
 in which spatial complexity has been increased. We find strong evidence in
 favor of the female conflict‐mediated pathway as individuals in complex
 environments remated less frequently and produced more offspring than
 those housed in a simpler spatial environment, but no difference in the
 fitness of sons or daughters. We discuss these results in the context of
 other recent studies and what they mean for our understanding of how
 sexual selection operates.
description: There are three files associated with this data set.
 Remating Offpsring.csv contains counts of the number of red-eyed
 and brown-eyed offspring produced individual female flies housed in vials
 that offered either a simple (control, C) or spatially complex
 (experiental, E) environment. The presence of red-eyes indicates
 remating. sonsfitness.csv contains estimates of the
 reproductive success of male flies whose mother had been housed in either
 a simple (control, C) or spatially complex (experiental, E) environment
 for varying numbers of days. From a bundle of test-tubes, we counted the
 number of females (1 female per test-tube) that had mated with the target
 son (presence of red-eyed offpsring produced). The total number of
 offspring sired by the target male is also recorded.
 agg_daughters.csv contains the mean number of offspring produced
 by females whose mother had been housed in either a simple (control, C) or
 spatially complex (experiental, E) environment for varying numbers of
 days.
DOI: 10.5061/dryad.jq2bvq86t
title: Data from: Genetic differentiation between two varieties of Oreocharis benthamii (Gesneriaceae) in sympatric and allopatric regions

description: The pattern of genetic differentiation between diverging species receives
 much attention as one of the key observable features of speciation. It has
 often been suggested that introgression between closely related species
 occurs commonly where their distributions overlap, leading to their
 becoming more morphologically and genetically similar, but there are a few
 opposite results. However, most of these studies have been carried out
 with animals and separate species; few have looked at intraspecific cases,
 especially in plants. Here, we conduct a comparative study on patterns of
 genetic differentiation among populations of two varieties of Oreocharis
 benthamii in allopatry and sympatry based on ISSR data for 754 individuals
 from 26 populations, in order to understand the processes leading to
 speciation. Contrary to expectations, the facultative xenogamy (mixed
 mating) species O. benthamii has a relatively low genetic diversity within
 populations (H=0.1014, I=0.1528) and high genetic differentiation among
 populations (GST=0.5867, ФST=0.659), as is typically found for selfing
 species. Genetic variance between the two varieties in sympatric
 populations (44%, ФST=0.444) is significantly more than that in allopatric
 populations (14%, ФST=0.138). Consistent with the taxonomical delimitation
 of the two varieties, all sampled individuals of O. benthamii clustered
 into two genetic groups. Moreover, the genetic structures of populations
 of both varieties is correlated with their different geographical origins.
 Our studies show that significant divergence between sympatric populations
 of the two varieties could be attributed primally to reinforcement by
 genetic divergent selection in sympatry where secondary contact had
 occurred. The major proportion of the genetic variation in outcrossing and
 mixed mating plants may exist among populations when the populations are
 distributed in fragmented habitats, due to the paucity of suitable habitat
 combined with inefficient seed dispersal mechanism and limited pollinator
 foraging area that may limit the gene flow.
DOI: 10.5061/dryad.jh9w0vt88
title: Data from: Behavioural red-light sensitivity in fish according to the optomotor response

description: Various procedures have been adopted to investigate spectral sensitivity
 of animals, e.g., absorption spectra of visual pigments,
 electroretinography, optokinetic response, optomotor response (OMR), and
 phototaxis. These works have led to various conclusions about animal
 vision. However, visual sensitivity should be evaluated consistently for a
 reliable comparison. In this study, we retrieved behavioural data of
 several fish species that used a unified procedure for the OMR test and
 compared the sensitivities to near-infrared light. Besides cavefish that
 lack eyes, some species were not appropriate for the OMR test because they
 either stayed still or changed swimming direction frequently. Eight fish
 species out of 13 species tested were OMR positive. Detailed analyses
 using goldfish, zebrafish, guppy, medaka, stickleback, and cichlid
 revealed that all the fish were sensitive to light at λ ≥ 750 nm, where
 the threshold wavelengths varied from 750 nm to 880 nm. Fish opsin
 repertoire enabled the perception of red light. In contrast, the copy
 number of long-wave-sensitive (LWS) genes did not necessarily improve
 red-light sensitivity. The duplication of LWS and other cone opsin genes
 that have occurred extensively during fish evolution might not aid
 increasing spectral sensitivity, but provide some other ophthalmic
 function, such as enhanced spectral discrimination.
description: <b>Fig3 </b> OMR data sets of Nile
 tilapia under light of 720, 750, 800, 810, 820, 830, 840, 850 and
 860nm. OMR data sets of Mexican cavefish under light
 of 720, 750, 800, 820 and 860 nm. Fig3.zip
 <strong>Fig4</strong> OMR data
 sets of medaka, goldfish, zebrafish, guppy, three-spined stickleback,
 mbuna under light of 700, 750, 800, 850, 900, 950 and 1000 nm.
 Fig4.zip
 <strong>Fig5</strong> OMR data
 sets of medaka, goldfish, zebrafish, guppy, three-spined stickleback,
 mbuna under light of 780, 800, 820, 840, 860 and 880 nm.
 Fig5.zip <strong>OMR data sets of
 goldfish for Steel's test</strong> OMR data
 sets of goldfish under light of 780, 800, 820, 840, 860, 880 and 950
 nm. SteelsComparison_Goldfish.zip
 ND: not determined,  NA: data not available (fish did not show
 positive OMR)
DOI: 10.15468/dl.wx8x6m
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "CatalogNumber" : [
 "is one of (PDD 90221, PDD 90225, PDD 90231, PDD 90269, PDD 90325, PDD 90333, PDD 90429, PDD 90473, PDD 90477, PDD 90535, PDD 90579, PDD 90586, PDD 90707, PDD 90948)"
 ]
}

 The dataset includes 14 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002406-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.vx0k6djp6
title: Traces of air and body temperature in six hummingbird species in the Andes

description: Torpor is thought to be particularly important for small endotherms
 occupying cold environments and with limited fat reserves to fuel
 metabolism. It remains mysterious why, among birds, torpor is both rare
 and variable in extent. We investigated torpor in a hummingbird community
 at ~3,800 m a.s.l. in the tropical Andes by monitoring body temperature
 (Tb) in 26 individuals of six species held captive overnight and
 experiencing natural air temperature (Ta) patterns. All species used
 pronounced torpor, with one Metallura phoebe reaching a minimum Tb of 3.26
 °C, the lowest value yet reported for any bird or non-hibernating mammal.
 The extent and duration of nocturnal torpor varied among species, with
 overnight body mass (Mb) loss negatively correlated with both minimum Tb
 and bout duration. We found a significant phylogenetic signal for minimum
 Tb and overnight Mb loss, consistent with evolutionarily conserved
 thermoregulatory traits. Our findings suggest deep torpor is routine for
 high Andean hummingbirds, but evolved species differences affect its
 depth.
description: Tb = body temperature in <sup>o</sup>C
 Tair = air temperature in <sup>o</sup>C
DOI: 10.5061/dryad.ngf1vhhrc
title: Modifying plant photosynthesis and growth via simultaneous chloroplast transformation of Rubisco large and small subunits

description: Engineering improved Rubisco poses a crucial strategy for enhancing
 photosynthesis but is challenged by the alternate locations of the
 plastome rbcL gene and nuclear RbcS genes. Here we develop a RNAi-RbcS
 Nicotiana tabacum (tobacco) master-line, tobRrΔS, amenable to rbcL-rbcS
 co-engineering by chloroplast transformation. Four tobacco genotypes
 coding alternative rbcS genes and adjoining 5ˈ-intergenic sequences
 revealed Rubisco production was highest in the lines incorporating a rbcS
 gene whose codon use and 5ˈUTR matched rbcL. These lines produced up to
 50% the wild-type Rubisco content. Additional tobacco lines coding potato
 rbcL-rbcS operons examined how the differing mesophyll made small subunits
 (pS1, pS2, pS3) or the trichome pST-25 subunit influenced Rubisco
 biogenesis, catalysis, leaf physiology and plant growth. Rubisco levels
 were ~15% lower in leaves expressing pS3 relative to those producing pS1,
 pS2, and pST. However, the pS3-subunit increased carboxylation rate
 (kcatC) by 13% and carboxylation efficiency (CE, kcatC divided by the Km
 for CO2) by 17% relative to the pS1 and pS2 subunits as a result of the
 βa-βb loop substitutions Asn-55-His and Lys-57-Ser. By contrast tobacco
 photosynthesis and growth were most impaired in lines producing the
 pST-subunit that reduced CE and CO2/O2 specificity of potato Rubisco by
 40% and 15% respectively.