cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6r12h
title: Data from: The impact of reconstruction methods, phylogenetic uncertainty and branch lengths on inference of chromosome number evolution in American daisies (Melampodium, Asteraceae)

description: Chromosome number change (polyploidy and dysploidy) plays an important
 role in plant diversification and speciation. Investigating chromosome
 number evolution commonly entails ancestral state reconstruction performed
 within a phylogenetic framework, which is, however, prone to uncertainty,
 whose effects on evolutionary inferences are insufficiently understood.
 Using the chromosomally diverse plant genus Melampodium (Asteraceae) as
 model group, we assess the impact of reconstruction method (maximum
 parsimony, maximum likelihood, Bayesian methods), branch length model
 (phylograms versus chronograms) and phylogenetic uncertainty (topological
 and branch length uncertainty) on the inference of chromosome number
 evolution. We also address the suitability of the maximum clade
 credibility (MCC) tree as single representative topology for chromosome
 number reconstruction. Each of the listed factors causes considerable
 incongruence among chromosome number reconstructions. Discrepancies
 between inferences on the MCC tree from those made by integrating over a
 set of trees are moderate for ancestral chromosome numbers, but severe for
 the difference of chromosome gains and losses, a measure of the
 directionality of dysploidy. Therefore, reliance on single trees, such as
 the MCC tree, is strongly discouraged and model averaging, taking both
 phylogenetic and model uncertainty into account, is recommended. For
 studying chromosome number evolution, dedicated models implemented in the
 program ChromEvol and ordered maximum parsimony may be most appropriate.
 Chromosome number evolution in Melampodium follows a pattern of
 bidirectional dysploidy (starting from x = 11 to x = 9 and x = 14,
 respectively) with no prevailing direction.
description: Dataset ITS-B (alignment
 and phylogenetic trees used for analyses)Nexus file containing
 sequence alignment of nuclear ITS sequences and 4,500 phylogenetic trees
 (obtained using BEAST) used for chromosome number
 reconstructiondataset_ITS_BEAST.nexDataset ITS-MB (alignment and phylogenetic trees used for analyses)Nexus file containing sequence alignment of nuclear ITS sequences and 4,500 phylogenetic trees (obtained using MrBayes; out-groups removed) used for chromosome number reconstructiondataset_ITS_MrBayes.nexDataset matK-B (alignment and phylogenetic trees used for analyses)Nexus file containing sequence alignment of plastid matK sequences and 4,500 phylogenetic trees (obtained using BEAST) used for chromosome number reconstructiondataset_matK_BEAST.nexDataset matK-MB (alignment and phylogenetic trees used for analyses)Nexus file containing sequence alignment of plastid matK sequences and 4,500 phylogenetic trees (obtained using MrBayes; out-groups removed) used for chromosome number reconstructiondataset_matK_MrBayes.nex
DOI: 10.5061/dryad.f5r7f
title: Data from: Feeding ecology of Northeast Atlantic mackerel, Norwegian spring-spawning herring and blue whiting in the Norwegian Sea

description: The Norwegian spring-spawning (NSS) herring (Clupea harengus), blue
 whiting (Micromesistius poutassou) and Northeast Atlantic (NEA) mackerel
 (Scomber scombrus) are extremely abundant pelagic planktivores that feed
 in the Norwegian Sea (NS) during spring and summer. This study
 investigated the feeding ecology and diet composition of these
 commercially important fish stocks on the basis of biological data,
 including an extensive set of stomach samples in combination with
 hydrographical data, zooplankton samples and acoustic abundance data from
 12 stock monitoring surveys carried out in 2005-2010. Mackerel were absent
 during the spring, but had generally high feeding overlap with herring in
 the summer, with a diet mainly based on calanoid copepods, especially
 Calanus finmarchicus, as well as a similar diet width. Stomach fullness in
 herring diminished from spring to summer and feeding incidence was lower
 than that of mackerel in summer. However, stomach fullness did not differ
 between the two species, indicating that herring maintain an equally
 efficient pattern of feeding as mackerel in summer, but on a diet that is
 less dominated by copepods and is more reliant on larger prey. Blue
 whiting tended to have a low dietary overlap with mackerel and herring,
 with larger prey such as euphausiids and amphipods dominating, and stomach
 fullness and feeding incidence increasing with length. For all the species
 feeding incidence increased with decreasing temperature, and for mackerel
 so did stomach fullness, indicating that feeding activity is highest in
 areas associated with colder water masses. Significant annual effects on
 diet composition and feeding-related variables suggested that the three
 species are able to adapt to different food and environmental conditions.
 These annual effects are likely to have an important impact on the
 predation pressure on different plankton groups and the carrying capacity
 of individual systems, and emphasise the importance of regular monitoring
 of pelagic fish diets.
description: CTD and fish sampling
 data used in the msCTD, fishing stations,
 biological sampling of fish and stomach content data from Ecosystem
 Surveys carried out in the Norwegian Sea in May and July from 2005 to
 2010.ms_data.zip
DOI: 10.5061/dryad.cb437
title: Data from: Ecomorphological determinations in the absence of living analogs: the predatory behavior of the marsupial lion (Thylacoleo carnifex) as revealed by elbow-joint morphology

description: Thylacoleo carnifex, or the "pouched lion" (Mammalia:
 Marsupialia: Diprotodontia: Thylacoleonidae) was a carnivorous marsupial
 that inhabited Australia during the Pleistocene. Although today all
 authors agree that Thylacoleo had a hypercarnivorous diet, the way in
 which it killed its prey remains uncertain. Here we use geometric
 morphometrics to capture the shape of the elbow joint (i.e., the posterior
 articular surface of the distal humerus) in a wide sample of extant
 mammals of known behavior to determine how elbow anatomy reflects forearm
 use. We then employ this information to investigate the predatory behavior
 of Thylacoleo. A Principal Components Analysis indicates that Thylacoleo
 is the only carnivorous mammal to cluster with extant taxa that have an
 extreme degree of forearm maneuverability, such as primates and arboreal
 xenarthrans (pilosans). A Canonical Variates Analysis confirms that
 Thylacoleo had forearm maneuverability intermediate between wombats
 (terrestrial) and arboreal mammals, and a much greater degree of
 maneuverability than any living carnivoran placental. A Linear
 Discriminant Analysis computed to separate the elbow morphology of
 arboreal mammals from terrestrial ones shows that Thylacoleo was primarily
 terrestrial but with some climbing abilities. We infer from our results
 that Thylacoleo used its forelimbs for grasping or manipulating prey to
 much higher degree than its supposed extant placental counterpart, the
 African lion (Panthera leo). The use of the large and retractable claw on
 the semi-opposable thumb of Thylacoleo for potentially slashing and
 disemboweling prey is discussed in the light of this new evidence.
description: Supp.
 info.Supplementary Table1,
 Supplementary Figure 1, Supplementary Figure 2, Supplementary Figure 3,
 Supplementary Figure 4.
DOI: 10.5061/dryad.g0m5s
title: Data from: Assessing models of speciation under different biogeographic scenarios; an empirical study using multi-locus and RNA-seq analyses

description: Evolutionary biology often seeks to decipher the drivers of speciation,
 and much debate persists over the relative importance of isolation and
 gene flow in the formation of new species. Genetic studies of closely
 related species can assess if gene flow was present during speciation,
 because signatures of past introgression often persist in the genome. We
 test hypotheses on which mechanisms of speciation drove diversity among
 three distinct lineages of desert tortoise in the genus Gopherus. These
 lineages offer a powerful system to study speciation, because different
 biogeographic patterns (physical vs. ecological segregation) are observed
 at opposing ends of their distributions. We use 82 samples collected from
 38 sites, representing the entire species' distribution and generate
 sequence data for mtDNA and four nuclear loci. A multilocus phylogenetic
 analysis in *BEAST estimates the species tree. RNA-seq data yield 20,126
 synonymous variants from 7665 contigs from two individuals of each of the
 three lineages. Analyses of these data using the demographic inference
 package ∂a∂i serve to test the null hypothesis of no gene flow during
 divergence. The best-fit demographic model for the three taxa is
 concordant with the *BEAST species tree, and the ∂a∂i analysis does not
 indicate gene flow among any of the three lineages during their
 divergence. These analyses suggest that divergence among the lineages
 occurred in the absence of gene flow and in this scenario the genetic
 signature of ecological isolation (parapatric model) cannot be
 differentiated from geographic isolation (allopatric model).
description: EdwardsEtAl_Ecology&Evolution2015_ArchivedDataTranscriptome assembly .fasta file, SNP data .vcf, and shared genotype information used in Edwards et al. 2015
DOI: 10.5061/dryad.ps04c
title: Data from: Combined DNA, toxicological and heavy metal analyses provides an auditing toolkit to improve pharmacovigilance of traditional Chinese medicine (TCM).

description: Globally, there has been an increase in the use of herbal remedies
 including traditional Chinese medicine (TCM). There is a perception that
 products are natural, safe and effectively regulated, however, regulatory
 agencies are hampered by a lack of a toolkit to audit ingredient lists,
 adulterants and constituent active compounds. Here, for the first time, a
 multidisciplinary approach to assessing the molecular content of 26 TCMs
 is described. Next generation DNA sequencing is combined with
 toxicological and heavy metal screening by separation techniques and mass
 spectrometry (MS) to provide a comprehensive audit. Genetic analysis
 revealed that 50% of samples contained DNA of undeclared plant or animal
 taxa, including an endangered species of Panthera (snow leopard). In 50%
 of the TCMs, an undeclared pharmaceutical agent was detected including
 warfarin, dexamethasone, diclofenac, cyproheptadine and paracetamol. Mass
 spectrometry revealed heavy metals including arsenic, lead and cadmium,
 one with a level of arsenic &gt;10 times the acceptable limit. The
 study showed 92% of the TCMs examined were found to have some form of
 contamination and/or substitution. This study demonstrates that a
 combination of molecular methodologies can provide an effective means by
 which to audit complementary and alternative medicines.
description: Coghlan et al 2015 fasta
 filesFasta files for
 mitochondrial and plant chloroplast DNA sequenced in this
 study
DOI: 10.5061/dryad.hq50s
title: Data from: Transcriptome profiling of immune tissues reveals habitat-specific gene expression between lake and river sticklebacks

description: The observation of habitat-specific phenotypes suggests the action of
 natural selection. The three-spined stickleback (Gasterosteus aculeatus)
 has repeatedly colonized and adapted to diverse freshwater habitats across
 the northern hemisphere since the last glaciation, while giving rise to
 recurring phenotypes associated with specific habitats. Parapatric lake
 and river populations of sticklebacks harbour distinct parasite
 communities, a factor proposed to contribute to adaptive differentiation
 between these ecotypes. However, little is known about the transcriptional
 response to the distinct parasite pressure of those fish in a natural
 setting. Here, we sampled wild-caught sticklebacks across four
 geographical locations from lake and river habitats differing in their
 parasite load. We compared gene expression profiles between lake and river
 populations using 77 whole-transcriptome libraries from two
 immune-relevant tissues, the head kidney and the spleen. Differential
 expression analyses revealed 139 genes with habitat-specific expression
 patterns across the sampled population pairs. Amongst the 139
 differentially expressed genes, 8 are annotated with an immune function
 and 42 have been identified as differentially expressed in previous
 experimental studies in which fish have been immune challenged. Together
 these findings reinforce the hypothesis that parasites contribute to
 adaptation of sticklebacks in lake and river habitats.
description: Raw expression count by
 HTSeqRaw expression count
 data of each library for each Ensembl genes generated by HTSeq. Each
 column represents a library and each row represents an annotated
 stickleback gene from Ensembl. Description of the libraries (tissue types,
 habitat types, sampling locations and sex of the samples) are given in the
 README.txt file.count_htseq.txtEdgeR results for head kidney librariesDifferential gene expression analysis results for head kidney libraries from EdgeR, including all genes in the analysis. This file contains information on log-fold-changes (logFC) between lake and river ecotypes (positive values indicate higher expression in river and vice versa), log of average count per million reads (logCPM), likelihood ratio (LR), raw p values as well as adjusted p values (FDR).edgeR_results_hk.txtEdgeR results for spleen librariesDifferential gene expression analysis results for spleen libraries from EdgeR, including all genes in the analysis. This file contains information on log-fold-changes between lake and river ecotypes (positive values indicate higher expression in river and vice versa), log of average count per million reads (logCPM), likelihood ratio (LR), raw p values as well as adjusted p values (FDR).edgeR_results_sp.txtGO enrichment analyses in head kidneyResults of Gene Ontology (GO) enrichment analyses among DE genes in the head kidney.topGO_hk.xlsxGO enrichment analyses in spleenResults of Gene Ontology (GO) enrichment analyses among DE genes in the spleen.topGO_sp.xlsx
DOI: 10.5061/dryad.7n8gc
title: Data from: Detecting and quantifying introgression in hybridized populations: simplifying assumptions yield overconfidence and uncertainty

description: A growing threat to the conservation of many native species worldwide is
 genetic introgression from non-native species. Although improved molecular
 genetic techniques are increasing the availability of species diagnostic
 markers for many species, efficient field sampling design and reliable
 data interpretation require accurate estimates of uncertainty associated
 with the detection of non-native alleles and the quantification of
 introgression in native populations. Using fish populations as examples,
 we developed a simulation model of an age-structured population that
 tracks the introduction and inheritance of non-native alleles across
 generations by simulating stochastic mating and survival of individual
 fish and the resulting transmission of diagnostic markers. To simulate
 detection and quantification of introgression, we sampled varying
 combinations of n fish and m diagnostic markers to detect and quantify
 introgression from thousands of virtual, independent fish populations for
 a wide range of hybridization scenarios. Using the results of simulated
 sampling, we quantified the extent to which common simplifying assumptions
 regarding population structure and inheritance mechanisms can lead to: 1)
 overconfidence in our ability to detect non-native alleles, and 2)
 unrealistically narrow confidence intervals for estimates of the
 proportion of non-native alleles present. Under many circumstances,
 commonly-used simplifying assumptions underestimate the probability of
 failing to detect ongoing introgression and the uncertainty associated
 with estimates of introgression by orders of magnitude. Such
 overconfidence in our ability to detect and quantify introgression can
 affect critical conservation and management decisions regarding native
 species undergoing or at risk of introgression from non-native species.
description: supporting_dataSimulation results supporting study finding (.RData file type)
DOI: 10.5061/dryad.6cn66
title: Data from: The phylogeny of Rickettsia using different evolutionary signatures: how tree-like is bacterial evolution?

description: Rickettsia is a genus of intracellular bacteria whose hosts and
 transmission strategies are both impressively diverse, and this is
 reflected in a highly dynamic genome. Some previous studies have described
 the evolutionary history of Rickettsia as non-tree-like, due to
 incongruity between phylogenetic reconstructions using different portions
 of the genome. Here, we reconstruct the Rickettsia phylogeny using
 whole-genome data, including two new genomes from previously unsampled
 host groups. We find that a single topology, which is supported by
 multiple sources of phylogenetic signal, well describes the evolutionary
 history of the core genome. We do observe extensive incongruence between
 individual gene trees, but analyses of simulations over a single topology
 and interspersed partitions of sites show that this is more plausibly
 attributed to systematic error than to horizontal gene transfer. Some
 conflicting placements also result from phylogenetic analyses of accessory
 genome content (i.e. gene presence/absence), but we argue that these are
 also due to systematic error, stemming from convergent genome reduction,
 which cannot be accommodated by existing phylogenetic methods. Our results
 show that, even within a single genus, tests for gene exchange based on
 phylogenetic incongruence may be susceptible to false positives.
description: Supplementary
 FiguresSupplementary
 Tables16S rRNA
 alignmentRickettsia symbiont of
 Adalia bipunctata scaffoldsCore genome alignment -
 1st & 2nd codon positionscore genome alignment - 1st
 & 2nd codon positions.nexCore genome alignment -
 3rd codon positionscore genome alignment - 3rd
 codon positions.nexCore genome alignment -
 indelscore
 genome alignment - indels.nexAccessory genes
 alignment - presence absence with truncated genes as
 presentaccessory genes alignment-
 presence absence with truncated genes as
 present.nexAccessory genes
 alignment - presence absence with truncated genes as
 absentaccessory genes alignment-
 presence absence with truncated genes as
 absent.nexRickettsia gene
 orthology groups - presence/absence dataRickettsia gene orthology
 groups.csvRepresentatives of
 orthology groups
DOI: 10.5061/dryad.s5812
title: Data from: Incorporating animal spatial memory in step selection functions

description: Memory is among the most important and neglected forces that shapes animal
 movement patterns. Research on the movement-memory interface is crucial to
 understand how animals use spatial learning to navigate across space
 because memory-biased navigation is directly linked to animals’ space use
 and home range behaviour; however, because memory cannot be measured
 directly, it is difficult to account for. Here, we incorporated spatial
 memory into Step Selection Functions (SSF) to understand how resource
 selection and spatial memory affect space use of feral hogs (Sus scrofa).
 We used Biased Random Bridge kernel estimates linked to residence time as
 a surrogate for memory and tested four conceptually different dynamic maps
 of spatial memory. We applied this memory-based SSF to a data set of hog
 relocations to evaluate the importance of land cover type, time of day,
 and spatial memory on the animals’ space use. Our approach has shown how
 the incorporation of spatial memory into animal movement models can
 improve estimates of habitat selection. Memory-based SSF provided a
 feasible way to gain insight into how animals use spatial learning to
 guide their movement decisions. We found that while hogs selected forested
 areas and water bodies and avoided grasslands during the day (primarily at
 noon), they had a strong tendency to select previously visited areas,
 mainly those held in recent memory. Beyond actively updating their memory
 with recent experiences, hogs were able to discriminate among spatial
 memories encoded at different circadian phases of their activity. Even
 though hogs are thought to have long memory retention, they likely relied
 on recent experiences because the local food resources are quickly
 depleted and slowly renewed, yielding an uncertain spatial distribution of
 resources.
description: Hog movement - raw
 dataHog movement data -
 individual trajectories of the GPS-tracked hogsmovement
 data.txtSSF-memory
 codeR
 code to run the Step Selection Function memory basedssf_memory_script.R
DOI: 10.5061/dryad.vt0j1
title: Data from: Phylotranscriptomic analysis uncovers a wealth of tissue inhibitor of metalloproteinases variants in echinoderms

description: Tissue inhibitors of metalloproteinases (TIMPs) help regulate the
 extracellular matrix (ECM) in animals, mostly by inhibiting matrix
 metalloproteinases (MMPs). They are important activators of mutable
 collagenous tissue (MCT), which have been extensively studied in
 echinoderms, and the four TIMP copies in humans have been studied for
 their role in cancer. To understand the evolution of TIMPs, we combined
 405 TIMPs from an echinoderm transcriptome dataset built from 41 specimens
 representing all five classes of echinoderms with variants from
 protostomes and chordates. We used multiple sequence alignment with
 various stringencies of alignment quality to cull highly divergent
 sequences and then conducted phylogenetic analyses using both nucleotide
 and amino acid sequences. Phylogenetic hypotheses consistently recovered
 TIMPs as diversifying in the ancestral deuterostome and these early
 lineages continuing to diversify in echinoderms. The four vertebrate TIMPs
 diversified from a single copy in the ancestral chordate, all other copies
 being lost. Consistent with greater MCT needs owing to body wall
 liquefaction, evisceration, autotomy and reproduction by fission,
 holothuroids had significantly more TIMPs and higher read depths per
 contig. Ten cysteine residues, an HPQ binding site and several other
 residues were conserved in at least 70% of all TIMPs. The conservation of
 binding sites and the placement of echinoderm TIMPs involved in MCT
 modification suggest that ECM regulation remains the primary function of
 TIMP genes, although within this role there are a large number of
 specialized copies.
description: Echinoderm TIMP
 SequencesThe file contains
 sequences that belong to the TIMP gene family (tissue inhibitors of
 metalloproteinases). Different alignments represent the results of
 successive culling procedures to remove possible non-homologues. The
 sequences were obtained from an echinoderm transcriptome data
 set.TIMP_sequences.nexus