cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.s270f
title: Data from: Complex constraints on allometry revealed by artificial selection on the wing of Drosophila melanogaster

description: Precise exponential scaling with size is a fundamental aspect of
 phenotypic variation. These allometric power laws are often invariant
 across taxa and have long been hypothesized to reflect developmental
 constraints. Here we test this hypothesis by investigating the
 evolutionary potential of an allometric scaling relationship in
 drosophilid wing shape that is nearly invariant across 111 species
 separated by at least 50 million years of evolution. In only 26
 generations of artificial selection in a population of Drosophila
 melanogaster, we were able to drive the allometric slope to the outer
 range of those found among the 111 sampled species. This response was
 rapidly lost when selection was suspended. Only a small proportion of this
 reversal could be explained by breakup of linkage disequilibrium, and
 direct selection on wing shape is also unlikely to explain the reversal,
 because the more divergent wing shapes produced by selection on the
 allometric intercept did not revert. We hypothesize that the reversal was
 instead caused by internal selection arising from pleiotropic links to
 unknown traits. Our results also suggest that the observed selection
 response in the allometric slope was due to a component expressed late in
 larval development and that variation in earlier development did not
 respond to selection. Together, these results are consistent with a role
 for pleiotropic constraints in explaining the remarkable evolutionary
 stability of allometric scaling.
description: Morphological wing
 measurements of Drosophila melanogasterData from selection
 experiment on allometry. See README fileData_Selection_on_Allometry_Experiment.csvMorphological wing measurements of 111 drosophilid speciesContent of datafile (repeated from README.txt): Species: species identifier hopefully self explanatory, normally [first letter in genus]_[species or subspecies, abbreviated], see table S6 in Bolstad et al. 2015 for the scientific name; ID: individual fly ID in the form of the picture name; Date: the date the image of the fly was taken (day_month_year); Sex: the sex of each fly, where F codes for female and M codes for male; WingSize: the size of each fly's wing in log(mm) (square root of area on the natural logarithmic scale); L2Length: length of vein L2 in log(mm), where log is the natural logarithmData_Allometry_Comparative.csv
DOI: 10.18167/dvn1/7zc8yn
title: SNP data and phenotypes for oil palm training and test sets, and associated script for genomic predictions with multi-layer perceptron

description: The data come from two experimental designs located on the SOCFINDO estate in North Sumatra, Indonesia. One is used to train genomic prediction models, the other as test set. The SNP genotypes were obtained with a custom Affymetrix Axiom® SNP array. The phenotypes are fresh fruit bunch production (FFB) corresponding to annual cumulative bunch (kg), bunch number (BN) corresponding to annual cumulative bunch number, and annual average bunch weight (BW, in kg). The python script implements genomic prediction with the multi-layer perceptron artificial neural network.
description: Beagle for final imputation of SNP data, 5.4
DOI: 10.5061/dryad.v6k91
title: Data from: Effective number of breeders provides a link between interannual variation in stream flow and individual reproductive contribution in a stream salmonid

description: The effective number of breeders that give rise to a cohort (Nb) is a
 promising metric for genetic monitoring of species with overlapping
 generations; however, more work is needed to understand factors that
 contribute to variation in this measure in natural populations. We tested
 hypotheses related to interannual variation in Nb in two long-term studies
 of brook trout populations. We found no supporting evidence for our
 initial hypothesis that inline image reflects inline image (defined as the
 number of adults in a population at the time of reproduction). inline
 image was stable relative to inline image and did not follow trends in
 abundance (one stream negative, the other positive). We used stream flow
 estimates to test the alternative hypothesis that environmental factors
 constrain Nb. We observed an intermediate optimum autumn stream flow for
 both inline image (R2 = 0.73, P = 0.02) and full-sibling family evenness
 (R2 = 0.77, P = 0.01) in one population and a negative correlation between
 autumn stream flow and full-sib family evenness in the other population (r
 = −0.95, P = 0.02). Evidence for greater reproductive skew at the lowest
 and highest autumn flow was consistent with suboptimal conditions at flow
 extremes. A series of additional tests provided no supporting evidence for
 a related hypothesis that density-dependent reproductive success was
 responsible for the lack of relationship between Nb and NC (so-called
 genetic compensation). This work provides evidence that Nb is a useful
 metric of population-specific individual reproductive contribution for
 genetic monitoring across populations and the link we provide between
 stream flow and Nb could be used to help predict population resilience to
 environmental change.
description: Brook trout data from
 West Brook, MassachusettsIndividual information
 for fish from each of the 2001 to 2009 brook trout cohorts from West
 Brook, Massachusetts. Information includes: sample location, length, sex,
 full-sib family assignment, 12 microsatellite genotypes. See ReadMe file
 for more information.WB 2001-2009 no
 IS.txtBrook trout data from
 Fridley Gap, VirginiaIndividual information
 for brook trout from Fridley Gap, Virginia. Information includes cohort,
 full-sib family assignments, and genotypes at 8 microsatellite
 loci.FG
 2004-2011.txt
DOI: 10.5061/dryad.7s4h1
title: Data from: Biodiversity comparison among phylogenetic diversity metrics and between three North American prairies

description: Protection of Earth's ecosystems requires identification of
 geographical areas of greatest biodiversity. Assessment of biodiversity
 begins with knowledge of the evolutionary histories of species in a
 geographic area. Multiple phylogenetic diversity (PD) metrics have been
 developed to describe biodiversity beyond species counts, but sufficient
 empirical studies, particularly at fine phylogenetic scales, have not been
 conducted to provide conservation planners with evidence for incorporating
 PD metrics into selection of priority regions. We review notable studies
 that are contributing to a growing database of empirical results, we
 report on the effect of using high-throughput sequencing to estimate the
 phylogenies used to calculate PD metrics, and we discuss difficulties in
 selecting appropriate diversity indices. We focused on two of the most
 speciose angiosperm families in prairies—Asteraceae and Fabaceae—and
 compared 12 PD metrics and four traditional measures of biodiversity
 between three North American prairie sites. The varying results from the
 literature and from the current data reveal the wide range of applications
 of PD metrics and the necessity for many more empirical studies. The
 accumulation of results from further investigations will eventually lead
 to a scientific understanding upon which conservation planners can make
 informed decisions about where to apply limited preservation funds.
description: Asteraceae-matK-rbcLSequence alignment of Asteraceae matK + rbcL plastid genes for 29 taxaAsteraceae-rbcLSequence alignment of Asteraceae rbcL plastid genes for 29 taxaFabaceae-71 genesSequence alignment of 71 concatenated Fabaceae plastid genes for 20 taxaAsteraceae-76 genesSequence alignment of 76 concatenated Asteraceae plastid genes for 29 taxaAsteraceae-matK-rbcLSequence alignment of concatenated Asteraceae matK + rbcL plastid genes for 29 taxaFabaceae-matK-rbcLSequence alignment of concatenated Fabaceae matK + rbcL plastid genes for 20 taxaFabaceae-matKSequence alignment of Fabaceae matK plastid genes for 20 taxaFabaceae-rbcLSequence alignment of Fabaceae rbcL plastid genes for 20 taxa
DOI: 10.5061/dryad.5b568
title: Data from: Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

description: Background: The use of transcriptomic and genomic datasets for
 phylogenetic reconstruction has become increasingly common as researchers
 attempt to resolve recalcitrant nodes with increasing amounts of data. The
 large size and complexity of these datasets introduce significant
 phylogenetic noise and conflict into subsequent analyses. The sources of
 conflict may include hybridization, incomplete lineage sorting, or
 horizontal gene transfer, and may vary across the phylogeny. For
 phylogenetic analysis, this noise and conflict has been accommodated in
 one of several ways: by binning gene regions into subsets to isolate
 consistent phylogenetic signal; by using gene-tree methods for
 reconstruction, where conflict is presumed to be explained by incomplete
 lineage sorting (ILS); or through concatenation, where noise is presumed
 to be the dominant source of conflict. The results provided herein
 emphasize that analysis of individual homologous gene regions can greatly
 improve our understanding of the underlying conflict within these
 datasets. Results: Here we examined two published transcriptomic datasets,
 the angiosperm group Caryophyllales and the aculeate Hymenoptera, for the
 presence of conflict, concordance, and gene duplications in individual
 homologs across the phylogeny. We found significant conflict throughout
 the phylogeny in both datasets and in particular along the backbone. While
 some nodes in each phylogeny showed patterns of conflict similar to what
 might be expected with ILS alone, the backbone nodes also exhibited low
 levels of phylogenetic signal. In addition, certain nodes, especially in
 the Caryophyllales, had highly elevated levels of strongly supported
 conflict that cannot be explained by ILS alone. Conclusion: This study
 demonstrates that phylogenetic signal is highly variable in phylogenomic
 data sampled across related species and poses challenges when conducting
 species tree analyses on large genomic and transcriptomic datasets.
 Further insight into the conflict and processes underlying these complex
 datasets is necessary to improve and develop adequate models for sequence
 analysis and downstream applications. To aid this effort, we developed the
 open source software phyparts (https://bitbucket.org/blackrim/phyparts),
 which calculates unique, conflicting, and concordant bipartitions, maps
 gene duplications, and outputs summary statistics such as internode
 certainy (ICA) scores and node-specific counts of gene duplications.
description: cary_rooted_bootstrap_at-least-60-taxa.tarHomolog trees for Caryophyllales. Names can be found in the cary_name_dict.txt file.HYM_bootstrap_rr_extract_clades.tarHymenoptera homolog files. The names for the taxa can be found in the hym_name_dict.txt file.cary_name_dictNames translations for the tips in the homolog trees.hym_name_dictHymentopera names in the homolog trees.
DOI: 10.5061/dryad.bn038
title: Data from: PoMo: an allele frequency-based approach for species tree estimation

description: Incomplete lineage sorting can cause incongruencies of the overall
 species-level phylogenetic tree with the phylogenetic trees for individual
 genes or genomic segments. If these incongruencies are not accounted for,
 it is possible to incur several biases in species tree estimation. Here,
 we present a simple maximum likelihood approach that accounts for
 ancestral variation and incomplete lineage sorting. We use a
 POlymorphisms-aware phylogenetic MOdel (PoMo) that we have recently shown
 to efficiently estimate mutation rates and fixation biases from within and
 between-species variation data. We extend this model to perform efficient
 estimation of species trees. We test the performance of PoMo in several
 different scenarios of incomplete lineage sorting using simulations and
 compare it with existing methods both in accuracy and computational speed.
 In contrast to other approaches, our model does not use coalescent theory
 but is allele frequency based. We show that PoMo is well suited for
 genome-wide species tree estimation and that on such data it is more
 accurate than previous approaches.
description: DeMaio_Kosiol_SysBio_2014_online_SupplementOnline Supplementary Material
DOI: 10.5061/dryad.63pm5
title: Data from: An efficient independence sampler for updating branches in Bayesian Markov chain Monte Carlo sampling of phylogenetic trees

description: Sampling tree space is the most challenging aspect of Bayesian
 phylogenetic inference. The sheer number of alternative topologies is
 problematic by itself. In addition, the complex dependency between branch
 lengths and topology increases the difficulty of moving efficiently among
 topologies. Current tree proposals are fast but sample new trees using
 primitive transformations or re-mappings of old branch lengths. This
 reduces acceptance rates and presumably slows down convergence and mixing.
 Here, we explore branch proposals that do not rely on old branch lengths
 but instead are based on approximations of the conditional posterior.
 Using a diverse set of empirical data sets, we show that most conditional
 branch posteriors can be accurately approximated via a Γ distribution. We
 empirically determine the relationship between the logarithmic conditional
 posterior density, its derivatives, and the characteristics of the branch
 posterior. We use these relationships to derive an independence sampler
 for proposing branches with an acceptance ratio of ∼90% on most data sets.
 This proposal samples branches between 2× and 3× more efficiently than
 traditional proposals with respect to the effective sample size per unit
 of runtime. We also compare the performance of standard topology proposals
 with hybrid proposals that use the new independence sampler to update
 those branches that are most affected by the topological change. Our
 results show that hybrid proposals can sometimes noticeably decrease the
 number of generations necessary for topological convergence. Inconsistent
 performance gains indicate that branch updates are not the limiting factor
 in improving topological convergence for the currently employed set of
 proposals. However, our independence sampler might be essential for the
 construction of novel tree proposals that apply more radical topology
 changes.
description: suppl-datacontains the alignments of all the 15 datasets under examination in this studysupplementcontains supplementary figures referenced in the main text; contains mathematical details as well as additional information on datasets
DOI: 10.5061/dryad.q66s5
title: Data from: Strong selection significantly increases epistatic interactions in the long-term evolution of a protein

description: Epistatic interactions between residues determine a protein’s adaptability
 and shape its evolutionary trajectory. When a protein experiences a
 changed environment, it is under strong selection to find a peak in the
 new fitness landscape. It has been shown that strong selection increases
 epistatic interactions as well as the ruggedness of the fitness landscape,
 but little is known about how the epistatic interactions change under
 selection in the long-term evolution of a protein. Here we analyze the
 evolution of epistasis in the protease of the human immunodeficiency virus
 type 1 (HIV-1) using protease sequences collected for almost a decade from
 both treated and untreated patients, to understand how epistasis changes
 and how those changes impact the long-term evolvability of a protein. We
 use an information-theoretic proxy for epistasis that quantifies the
 co-variation between sites, and show that positive information is a
 necessary (but not sufficient) condition that detects epistasis in most
 cases. We analyze the “fossils” of the evolutionary trajectories of the
 protein contained in the sequence data, and show that epistasis continues
 to enrich under strong selection, but not for proteins whose environment
 is unchanged. The increase in epistasis compensates for the information
 loss due to sequence variability brought about by treatment, and
 facilitates adaptation in the increasingly rugged fitness landscape of
 treatment. While epistasis is thought to enhance evolvability via
 valley-crossing early-on in adaptation, it can hinder adaptation later
 when the landscape has turned rugged. However, we find no evidence that
 the HIV-1 protease has reached its potential for evolution after 9 years
 of adapting to a drug environment that itself is constantly changing. We
 suggest that the mechanism of encoding new information into pairwise
 interactions is central to protein evolution not just in HIV-1 protease,
 but for any protein adapting to a changing environment.
description: protease_sequences_1998_to_2006HIV-1 protease sequences collected from HIV Stanford Database on 17th September 2013. The data spans 9 years (1998-2006) and sequences from treated (i.e. patients receiving one or more protease inhibitors) and untreated patients are in separate files.longitudinal_protease_sequencesHIV-1 protease sequences collected from HIV Stanford Database on 17 September 2013. The data represents HIV-1 protease sequences collected from same patients 'before' and 'after' a condition (i.e. 'treated' or 'untreated'). For example: sequences from patients who were initially untreated and then went on to receive treatment are titled "untreated_to_treated_protease_17SEP2013.src.blue.before.consensus_added" and "untreated_to_treated_protease_17SEP2013.src.blue.after.consensus_adde" respectively.scriptsPython and matlab scripts to analyse protease sequence dataFigure_generatoriPython notebook to parse files and generate figures.
DOI: 10.5061/dryad.d3675
title: Data from: Monitoring spawning activity in a southern California marine protected area using molecular identification of fish eggs

description: In order to protect the diverse ecosystems of coastal California, a series
 of marine protected areas (MPAs) have been established. The ability of
 these MPAs to preserve and potentially enhance marine resources can only
 be assessed if these habitats are monitored through time. This study
 establishes a baseline for monitoring the spawning activity of fish in the
 MPAs adjacent to Scripps Institution of Oceanography (La Jolla, CA, USA)
 by sampling fish eggs from the plankton. Using vertical plankton net tows,
 266 collections were made from the Scripps Pier between 23 August 2012 and
 28 August 2014; a total of 21,269 eggs were obtained. Eggs were identified
 using DNA barcoding: the COI or 16S rRNA gene was amplified from
 individual eggs and sequenced. All eggs that were successfully sequenced
 could be identified from a database of molecular barcodes of California
 fish species, resulting in species-level identification of 13,249 eggs.
 Additionally, a surface transport model of coastal circulation driven by
 current maps from high frequency radar was used to construct probability
 maps that estimate spawning locations that gave rise to the collected
 eggs. These maps indicated that currents usually come from the north but
 water parcels tend to be retained within the MPA; eggs sampled at the
 Scripps Pier have a high probability of having been spawned within the
 MPA. The surface transport model also suggests that although larvae have a
 high probability of being retained within the MPA, there is also
 significant spillover into nearby areas outside the MPA. This study
 provides an important baseline for addressing the extent to which spawning
 patterns of coastal California species may be affected by future changes
 in the ocean environment.
description: Fish egg
 sequencesRaw (unedited) Sanger
 sequences (COI and 16S) obtained from fish eggs collected off the Scripps
 Pier over 2 years of sampling (Aug 2012- Aug 2014). Organized in columns
 by date sequenced with the date of collection next to each sequence
 name.sequences
 combined.xlsxHarada et al. Identified
 Fish EggsEgg identifications by
 date Aug 2012- Aug 2014
DOI: 10.5061/dryad.dt392
title: Data from: Floral reflectance, color, and thermoregulation: what really explains geographic variation in thermal acclimation ability of ectotherms?

description: Adaptive phenotypic plasticity in thermally sensitive traits, that is,
 thermal acclimation, generally increases with increasing latitude and
 altitude. The presumed explanation is that high-latitude/ altitude
 organisms have evolved greater acclimation ability because of exposure to
 greater temperature fluctuations. Using a conceptual model of the thermal
 environment during the reproductive season, we tested this hypothesis
 against an alternative that plasticity is greater because of increased
 exposure to specific temperatures that strongly select for thermal
 acclimation. We examined geographic variation in floral reflectance/color
 plasticity among 29 European populations of a widespread perennial herb,
 Plantago lanceolata. In- dividuals partially thermoregulate reproduction
 through tempera- ture-sensitive plasticity in floral reflectance/color.
 Plasticity was pos- itively correlated with latitude and altitude. Path
 analyses support the hypothesis that the thermal environment mediates
 these geo- graphic effects. Plasticity declined as seasonal temperature
 range in- creased, and it increased as duration of the growing season
 shortened and as the proportion of time exposed to temperatures favoring
 thermoregulation increased. Data provide evidence that floral re-
 flectance/color plasticity is adaptive and that it has evolved in re-
 sponse not to the magnitude of temperature variation during the
 reproductive season but rather to the relative exposure to low tem-
 peratures, which favor thermoregulation.
description: Spectral scans of
 reflectance for Pre-flowering spikes by popThis file shows the
 spectral scan results (362-850nm) for reflectance of spikes (clusters) of
 flowers just prior to stigma emergence in any flower. Spikes were
 collected from plants derived from 29 European populations and that were
 grown in growth chambers at a warm and cool temperature. File can be read
 with help from the ReadMe file.Lacey et al. 2010 Pre-flow
 spike refl by pop 30Jan07.xlsx
DOI: 10.24378/exe.31095430
title: London Urban Tree Species Classification Data

description: This dataset was created as part of the ongoing study on urban trees species classification in the UK. This study is a sub-project under the PhD programme titled 'Geospatial Data and AI for Enhanced Property Information Database in the UK'. The dataset includes multi-temporal spectral reflectance values of selected tree instances in the central London area. The dataset is in two parts. The first group contains spectral signatures derived from PlanetScope satellite images from 2021 to 2025, while the second group include multi-temporal spectral signatures derived from Sentinel 2A imagery from 2021 to 2025.The goal of releasing this dataset is to contribute to the remote sensing and ecological research community to advance research aimed at accurately classifying urban tree species using the multi-temporal spectral signatures approach.This dataset is released also to support the 2026 IGARSS Conference paper titled 'Towards Urban Tree Species Classification in the UK: A machine learning Instance Segmentation Approach to Multimodal Species-Classification Dataset Creation and Algorithms Development'. The International Geoscience and Remote Sensing Symposium (IGARSS) is the flagship conference of the IEEE Geoscience and Remote Sensing Society (GRSS).