cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5cp20
title: Data from: Mutant invasions and adaptive dynamics in variable environments

description: The evolution of natural organisms is ultimately driven by the invasion
 and possible fixation of mutant alleles. The invasion process is highly
 stochastic, however, and the probability of success is generally low, even
 for advantageous alleles. Additionally, all organisms live in a stochastic
 environment, which may have a large influence on what alleles are
 favorable, but also contributes to the uncertainty of the invasion
 process. We calculate the invasion probability of a beneficial, mutant
 allele in a monomorphic, large population subject to stochastic
 environmental fluctuations, taking into account density- and
 frequency-dependent selection, stochastic population dynamics and temporal
 autocorrelation of the environment. We treat both discrete and continuous
 time population dynamics, and allow for overlapping generations in the
 continuous time case. The results can be generalized to diploid, sexually
 reproducing organisms embedded in communities of interacting species. We
 further use these results to derive an extended canonical equation of
 adaptive dynamics, predicting the rate of evolutionary change of a
 heritable trait on long evolutionary time scales.
description: Fig2This file contains the
 Matlab m-files necessary to produce Fig 2 of the main
 articleFig3This contains the Matlab
 m-files necessary to generate Fig. 3 of the main
 article.FigsC1_C2_C3This contains the Matlab m-files necessary to generate Figs. C1, C2 and C3 of the online supplement.FigsC4_C5This contains the Matlab m-files necessary to generate Figs. C4 and C5 of the online supplement.
DOI: 10.5061/dryad.fb782
title: Data from: Adaptive evolution during an ongoing range expansion: the invasive bank vole (Myodes glareolus) in Ireland.

description: Range expansions are extremely common, but have only recently begun to
 attract attention in terms of their genetic consequences. As populations
 expand, demes at the wave front experience strong genetic drift, which is
 expected to reduce genetic diversity and potentially cause 'allele
 surfing', where alleles may become fixed over a wide geographic area
 even if their effects are deleterious. Previous simulation models show
 that range expansions can generate very strong selective gradients on
 dispersal, reproduction, competition and immunity. To investigate the
 effects of range expansion on genetic diversity and adaptation, we studied
 the population genomics of the bank vole (Myodes glareolus) in Ireland.
 The bank vole was likely introduced in the late 1920s and is expanding its
 range at a rate of ̴2.5 km yr-1. Using Genotyping by Sequencing (GBS), we
 genotyped 281 bank voles at 5,979 SNP loci. Fourteen sample sites were
 arranged in three transects running from the introduction site to the wave
 front of the expansion. We found significant declines in genetic diversity
 along all three transects. However, there was no evidence that sites at
 the wave front had accumulated more deleterious mutations. We looked for
 outlier loci with strong correlations between allele frequency and
 distance from the introduction site, where the direction of correlation
 was the same in all three transects. Amongst these outliers, we found
 significant enrichment for genic SNPs, suggesting the action of selection.
 Candidates for selection included several genes with immunological
 functions and several genes that could influence behavior.
description: SNP
 DATAGenotypes of 5979 SNPs
 for the 281 bank voles described in the manuscript. Bank voles were
 collected in Ireland. SNPs were identified using GBS (genotyping by
 sequencing), in conjunction with the UNEAK pipeline (part of Tassel) and a
 Perl script to call genotypes in a max likelihood
 framework.FOR_DRYAD.xlsx
DOI: 10.5061/dryad.gv06d
title: Data from: Mammals across the K/Pg boundary in northeastern Montana, U.S.A.: dental morphology and body-size patterns reveal extinction selectivity and immigrant-fueled ecospace filling

description: The Cretaceous/Tertiary (K/Pg) mass extinction has long been viewed as a
 pivotal event in mammalian evolutionary history, in which the extinction
 of non-avian dinosaurs allowed mammals to rapidly expand from
 small-bodied, generalized insectivores to a wide array of body sizes and
 ecological specializations. Many studies have used global- or
 continental-scale taxonomic databases to analyze this event on coarse
 temporal scales, but few studies have documented morphological diversity
 of mammalian paleocommunities on fine spatiotemporal scales in order to
 examine ecomorphological selectivity and ecospace filling across this
 critical transition. Focusing on well-sampled and temporally
 well-constrained mammalian faunas across the K/Pg boundary in northeastern
 Montana, I quantified dental-shape disparity and morphospace occupancy via
 landmark- and semilandmark-based geometric morphometrics and mean body
 size, body-size disparity, and body-size structure via body-mass
 estimates. My results reveal several key findings: (1) latest Cretaceous
 mammals, particularly metatherians and multituberculates, had a greater
 ecomorphological diversity than is generally appreciated, occupying
 regions of the morphospace that are interpreted as strict carnivory,
 plant-dominated omnivory, and herbivory; (2) the decline in dental-shape
 disparity and body-size disparity across the K/Pg boundary shows a pattern
 of constructive extinction selectivity against larger-bodied dietary
 specialists, particularly strict carnivores and taxa with plant-based
 diets, that suggests the kill mechanism was related to depressed primary
 productivity rather than a globally instantaneous event; (3) the
 ecomorphological recovery in the earliest Paleocene was fueled by
 immigrants, namely three multituberculate families (taeniolabidids,
 microcosmodontids, eucosmodontids) and to a lesser extent archaic
 ungulates; and (4) despite immediate increases in the taxonomic richness
 of eutherians, their much-celebrated post-K/Pg ecomorphological expansion
 had a slower start than is generally perceived and most likely only began
 400,000 to 1 million years after the extinction event.
description: Wilson_suppmaterial_Dec172012
DOI: 10.5061/dryad.53j31
title: Data from: Genetic diversity, linkage disequilibrium and selection signatures in Chinese and Western pigs revealed by genome-wide SNP markers

description: To investigate population structure, linkage disequilibrium (LD) pattern
 and selection signature at the genome level in Chinese and Western pigs,
 we genotyped 304 unrelated animals from 18 diverse populations using
 porcine 60 K SNP chips. We confirmed the divergent evolution between
 Chinese and Western pigs and showed distinct topological structures of the
 tested populations. We acquired the evidence for the introgression of
 Western pigs into two Chinese pig breeds. Analysis of runs of homozygosity
 revealed that historical inbreeding reduced genetic variability in several
 Chinese breeds. We found that intrapopulation LD extents are roughly
 comparable between Chinese and Western pigs. However, interpopulation LD
 is much longer in Western pigs compared with Chinese pigs with average
 r20.3 values of 125 kb for Western pigs and only 10.5 kb for Chinese pigs.
 The finding indicates that higher-density markers are required to capture
 LD with causal variants in genome-wide association studies and genomic
 selection on Chinese pigs. Further, we looked across the genome to
 identify candidate loci under selection using FST outlier tests on two
 contrast samples: Tibetan pigs versus lowland pigs and belted pigs against
 non-belted pigs. Interestingly, we highlighted several genes including
 ADAMTS12, SIM1 and NOS1 that show signatures of natural selection in
 Tibetan pigs and are likely important for genetic adaptation to high
 altitude. Comparison of our findings with previous reports indicates that
 the underlying genetic basis for high-altitude adaptation in Tibetan pigs,
 Tibetan peoples and yaks is likely distinct from one another. Moreover, we
 identified the strongest signal of directional selection at the EDNRB loci
 in Chinese belted pigs, supporting EDNRB as a promising candidate gene for
 the white belt coat color in Chinese pigs. Altogether, our findings
 advance the understanding of the genome biology of Chinese and Western
 pigs.
description: Data from: Genetic
 Diversity, Linkage Disequilibrium and Selection Signatures in Chinese and
 Western Pigs Revealed by Genome-Wide SNP MarkersDataset corresponds to
 the article: "Genetic Diversity, Linkage Disequilibrium and Selection
 Signatures in Chinese and Western Pigs Revealed by Genome-Wide SNP
 Markers" Huashui Ai, Lusheng Huang, Jun Ren. For any correspondence,
 please address Lusheng Huang (lushenghuang@hotmail.com) Complete dataset
 contains 52,556 SNP genotypes for 304 individuals. Info_sample.txt file
 contains information about location (Origin) and population (POPname) for
 each sample. 304IDs.maf0.05.geno0.1.* files contains genotypes for samples
 included for all analyses in the paper (PLINK format).304IDs.tar.gz
DOI: 10.5061/dryad.k7c1m
title: Data from: Mediation of seed provisioning in the transmission of environmental maternal effects in Maritime pine (Pinus pinaster Aiton)

description: Although maternal environmental effects are increasingly recognized as an
 important source of phenotypic variation with relevant impacts in
 evolutionary processes, their relevance in long-lived plants such as pine
 trees is largely unknown. Here, we used a powerful sample size and a
 strong quantitative genetic approach to analyse the sources of variation
 of early seedling performance and to identify seed mass (SM)-dependent and
 -independent maternal environmental effects in Maritime pine. We measured
 SM of 8924 individual seeds collected from 10 genotypes clonally
 replicated in two environments of contrasting quality (favourable and
 stressful), and we measured seedling growth rate and biomass allocation to
 roots and shoots. SM was extremely variable (up to 14-fold) and strongly
 determined by the maternal environment and the genotype of the mother
 tree. The favourable maternal environment led to larger cones, larger
 seeds and reduced SM variability. The maternal environment also determined
 the offspring phenotype, with seedlings coming from the favourable
 environment being 35% larger and with greater root/shoot ratio.
 Transgenerational plasticity appears, thus, to be a relevant source of
 phenotypic variation in the early performance of this pine species. Seed
 provisioning explained most of the effect of the maternal environment on
 seedling total biomass. Environmental maternal effects on seedling biomass
 allocation were, however, determined through SM-independent mechanisms,
 suggesting that other epigenetic regulation channels may be involved.
description: HDY-12-OR0394R
 DATAOriginal data analyzed
 in the manuscript. Data is organized at three different leves: cone, seed
 and seedling.
DOI: 10.5061/dryad.c4d3j
title: Data from: The tree of life and a new classification of bony fishes

description: The tree of life of fishes is in a state of flux because we still lack a
 comprehensive phylogeny that includes all major groups. The situation is
 most critical for a large clade of spiny-finned fishes, traditionally
 referred to as percomorphs, whose uncertain relationships have plagued
 ichthyologists for over a century. Most of what we know about the
 higher-level relationships among fish lineages has been based on
 morphology, but rapid influx of molecular studies is changing many
 established systematic concepts. We report a comprehensive molecular
 phylogeny for bony fishes that includes representatives of all major
 lineages. DNA sequence data for 21 molecular markers (one mitochondrial
 and 20 nuclear genes) were collected for 1410 bony fish taxa, plus four
 tetrapod species and two chondrichthyan outgroups (total 1416 terminals).
 Bony fish diversity is represented by 1093 genera, 369 families, and all
 traditionally recognized orders. The maximum likelihood tree provides
 unprecedented resolution and high bootstrap support for most backbone
 nodes, defining for the first time a global phylogeny of fishes. The
 general structure of the tree is in agreement with expectations from
 previous morphological and molecular studies, but significant new clades
 arise. Most interestingly, the high degree of uncertainty among
 percomorphs is now resolved into nine well-supported supraordinal groups.
 The order Perciformes, considered by many a polyphyletic taxonomic waste
 basket, is defined for the first time as a monophyletic group in the
 global phylogeny. A new classification that reflects our phylogenetic
 hypothesis is proposed to facilitate communication about the newly found
 structure of the tree of life of fishes. Finally, the molecular phylogeny
 is calibrated using 60 fossil constraints to produce a comprehensive time
 tree. The new time-calibrated phylogeny will provide the basis for and
 stimulate new comparative studies to better understand the evolution of
 the amazing diversity of fishes.
description: Alignment in nexus
 formatConcat_Three_Plus.nexRAxML tree - 3+ dataset with 24 partitionsRAxMLThree_Plus_24_part.treTABLE_S1Table S1. List of material examined, catalog numbers, and genetic coverage for each taxon. EToL numbers E0001­–E1184 indicate taxa targeted and sequenced for this study; for some genes/taxa the corresponding sequence was retrieved from NCBI). EToL numbers G1185–G1534 indicate sequences retrieved from NCBI or other genomic databases. Composite taxa include the two species names on labels (Genus_species1_species2).
DOI: 10.5061/dryad.467g5
title: Data from: Stage and size structure of three species of oaks in central coastal California

description: Oaks are foundational species in much of California, and many oak
 populations in the state may be in jeopardy due to a lack of recruitment
 of young trees. Despite considerable interest in this problem, there have
 been few comprehensive surveys of all stages of oak development. We
 surveyed all stages of three oaks: Quercus lobata, Q. douglasii, and Q.
 agrifolia in a forest plot with mixed land-use in central coastal
 California. We found abundant seedlings of all oak species, but an
 apparent paucity of Q. lobata and Q. douglasii saplings. First year
 seedlings of all species were less abundant in parts of the study site
 with cattle grazing, but later-stage seedlings of Q. lobata and Q.
 douglasii were equally abundant across land-use types. Quercus agrifolia
 seedlings were associated with non-grazed areas; Quercus agrifolia
 late-stage seedlings in the grazed area were smaller and less abundant
 than in non-grazed areas. Quercus agrifolia seedlings of all stages tended
 to be clustered around conspecific mature trees. Quercus lobata late-stage
 seedlings, and to a lesser degree those of Q. douglasii, were often
 distant from any potential parent tree. These data indicate that young
 stages of the three species of oak have different spatial distributions
 and occur in different abundances at two sites with different grazing
 regimes. They are also consistent with a relative lack of regeneration in
 Q. lobata and Q. douglasii, although it remains to be determined that the
 small number of saplings of these species observed is insufficient to
 replace mortality of mature trees. This survey provides a baseline from
 which future resampling can assess the long-term demographic success of
 three Californian oak species.
description: oak localities, size,
 habitatthe complete database
 used for all analyses in paper.expanded_oaks.csv
DOI: 10.5061/dryad.14214
title: Data from: Complete chloroplast genome of the genus Cymbidium: lights into the species identification, phylogenetic implications and population genetic analyses

description: Background: Cymbidium orchids, including some 50 species, are the famous
 flowers, and they possess high commercial value in the floricultural
 industry. Furthermore, the values of different orchids are great
 differences. However, species identification is very difficult. To a
 certain degree, chloroplast DNA sequence data are a versatile tool for
 species identification and phylogenetic implications in plants. Different
 chloroplast loci have been utilized for evaluating phylogenetic
 relationships at each classification level among plant species, including
 at the interspecies and intraspecies levels. However, there is no evidence
 that a short sequence can distinguish all plant species from each other in
 order to infer phylogenetic relationships. Molecular markers derived from
 the complete chloroplast genome can provide effective tools for species
 identification and phylogenetic resolution. Results: The complete
 nucleotide sequences of eight individuals from a total of five Cymbidium
 species’ chloroplast (cp) genomes were determined using Illumina
 sequencing technology of the total DNA via a combination of de novo and
 reference-guided assembly. The length of the Cymbidium cp genome is about
 155 kb. The cp genomes contain 123 unique genes, and the IR regions
 contain 24 duplicates. Although the genomes, including genome structure,
 gene order and orientation, are similar to those of other orchids, they
 are not evolutionarily conservative. The cp genome of Cymbidium evolved
 moderately with more than 3% sequence divergence, which could provide
 enough information for phylogeny. Rapidly evolving chloroplast genome
 regions were identified and 11 new divergence hotspot regions were
 disclosed for further phylogenetic study and species identification in
 Orchidaceae. Conclusions: Phylogenomic analyses were conducted using 10
 complete chloroplast genomes from seven orchid species. These data
 accurately identified the individuals and established the phylogenetic
 relationships between the species. The results reveal that phylogenomics
 based on organelle genome sequencing lights the species
 identification—organelle-scale “barcodes”, and is also an effective
 approach for studying whole populations and phylogenetic characteristics
 of Cymbidium.
description: Cymbidium_CP
 genomesCymbidium_Coding
 regionsCymbidium_Introns and
 spacersCymbidium_IR
 regionCymbidium_LSCCymbidium_SSC
DOI: 10.5061/dryad.b5m0j
title: Data from: Ancient DNA complements microfossil record in deep-sea subsurface sediments

description: Deep-sea subsurface sediments are the most important archives of marine
 biodiversity. Until now, these archives were studied mainly using the
 microfossil record, disregarding large amounts of DNA accumulated on the
 deep-sea floor. Accessing ancient DNA (aDNA) molecules preserved down-core
 would offer unique insights into the history of marine biodiversity,
 including both fossilized and non-fossilized taxa. Here, we recover aDNA
 of eukaryotic origin across four cores collected at abyssal depths in the
 South Atlantic, in up to 32.5 thousand-year-old sediment layers. Our study
 focuses on foraminifera and radiolaria, two major groups of marine
 microfossils also comprising diverse non-fossilized taxa. We describe
 their assemblages in down-core sediment layers applying both
 micropaleontological and environmental DNA sequencing approaches. Short
 fragments of the foraminiferal and radiolarian SSU rRNA gene recovered
 from sedimentary DNA extracts provide evidence that eukaryotic aDNA is
 preserved in deep-sea sediments encompassing the Last Glacial Maximum.
 Most aDNA were assigned to non-fossilized taxa that also dominate in
 molecular studies of modern environments. Our study reveals the potential
 of aDNA to better document the evolution of past marine ecosystems and
 opens new horizons for the development of deep-sea palaeogenomics.
description: RSBL-2012-0942_DeepSea_aDNA_IlluminaSeqsDNA sequences generated by cloning/Sanger sequencing and by Illumina sequencing (MiSeq instrument). In each sequence header, several '_'-separated fields that could be indexed indicate: [0] the technology ('cloning' or 'illumina'), [1] the sediment core of origin, [2] the sub-sample layer depth in centimetre, [3] a numeric identifier, and for the cloning sequences, [4] the lab of origin the DNA extract and [5] the primer combination.RSBL-2012-0942_DeepSea_aDNASeqs.fasta
DOI: 10.5061/dryad.cg873
title: Data from: The cross-bridge spring: can cool muscles store elastic energy?

description: Muscles not only generate force. They may act as springs, providing energy
 storage to drive locomotion. Although extensible myofilaments are
 implicated as sites of energy storage, we show that intramuscular
 temperature gradients may enable molecular motors (cross-bridges) to store
 elastic strain energy. Using time-resolved small-angle X-ray diffraction
 paired with in situ measurements of mechanical energy exchange in flight
 muscle of Manduca sexta we produced high-speed movies of X-ray equatorial
 reflections indicating cross-bridge association with myofilaments. A
 temperature gradient within the flight muscle leads to lower cross-bridge
 cycling in the cooler regions. Those cross-bridges could elastically
 return energy at the extrema of muscle lengthening and shortening, helping
 drive cyclic wing motions. These results suggest cross-bridges can perform
 functions other than contraction, acting as molecular links for elastic
 energy storage.
description: SummedDiffractionImagesSummed X-ray diffraction Images from the 5 points in the contraction cycleWorkLoopDataData generated from work-loops. In matrix "b" the columns are desingated as follows: column1=time, column2=force(voltage), column3=force(calibrated as Newtons), column4=length(voltage), column5=length(calibrated as meters), column6=actual length change (accounting for the displacement of the force transducer), column7=stimulus, column8=X-ray shutter signalxray_workloop_legendThis matrix identifies the Matlab work-loop file number with the moth number, temperature of the trial, and muscle location. Additionally it assigns the X-ray diffraction image number (0-4) with when in the contraction cycle the image was taken (represented as cycle fraction) since the X-ray shutter was triggered off of the stimulus signal.swounds.pyThis code opens the .npz files (compressed NumPy files). Use this code to access the summed X-ray diffraction images and find the intensity of the equatorial reflections.
DOI: 10.5061/dryad.2j77t
title: Data from: Disentangling genetic and prenatal sources of familial resemblance across ontogeny in a wild passerine.

description: Cross-fostering experiments are widely used by quantitative geneticists to
 study genetics and by behavioral ecologists to study the effects of
 prenatal in- vestment. Generally, the effects of genes and prenatal
 investment are confounded and the interpretation given to such experiments
 is largely dependent on the in- terests of the researcher. Using a
 large-scale well controlled experiment on a wild population of blue tits
 (Cyanistes caeruleus) we are able to partition variation in body mass
 across ontogeny into the effects of genes and the effects of between-
 clutch variation in egg characteristics. We show that although egg effects
 are important early in ontogeny they quickly dissipate, suggesting that
 the genetic interpretation of cross-fostering experiments may be
 preferable for many types of trait. However, the heritability of body mass
 is smaller than has previously been reported. Our results suggest that
 this is due to a combination of control- ling postnatal environmental
 effects more carefully and accounting for viability selection operating
 early in ontogeny.
description: Egg
 DatatEGGS_dryad.csvMorphometric DatatMORPH_dryad.csvWeight DatatWEIGHT_dryad.csvSurvival DatatSURV_dryad.csvPedigree DatatPED_dryad.csvR ScriptsR code for performing all analyses in Hadfield at al. (2013) `Disentangling genetic and prenatal sources of familial resemblance across ontogeny in a wild passerine'Hadfield.2013.R