cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v7g2k
title: Data from: Resolving basal lamiid phylogeny and the circumscription of Icacinaceae with a plastome-scale data set

description: PREMISE OF THE STUDY: Major relationships within Lamiidae, an asterid
 clade with ∼40000 species, have largely eluded resolution despite two
 decades of intensive study. The phylogenetic positions of Icacinaceae and
 other early-diverging lamiid clades (Garryales, Metteniusaceae, and
 Oncothecaceae) have been particularly problematic, hindering
 classification and impeding our understanding of early lamiid (and
 euasterid) character evolution. METHODS: To resolve basal lamiid
 phylogeny, we sequenced 50 plastid genomes using the Illumina sequencing
 platform and combined these with available asterid plastome sequence data
 for more comprehensive phylogenetic analyses. KEY RESULTS: Our analyses
 resolved basal lamiid relationships with strong support, including the
 circumscription and phylogenetic position of the enigmatic Icacinaceae.
 This greatly improved basal lamiid phylogeny offers insight into character
 evolution and facilitates an updated classification for this clade, which
 we present here, including phylogenetic definitions for 10 new or
 converted clade names. We also offer recommendations for applying this
 classification to the Angiosperm Phylogeny Group (APG) system, including
 the recognition of a reduced Icacinaceae, an expanded Metteniusaceae, and
 two orders new to APG: Icacinales (Icacinaceae + Oncothecaceae) and
 Metteniusales (Metteniusaceae). CONCLUSIONS: The lamiids possibly radiated
 from an ancestry of tropical trees with inconspicuous flowers and large,
 drupaceous fruits, given that these morphological characters are
 distributed across a grade of lineages (Icacinaceae, Oncothecaceae,
 Metteniusaceae) subtending the core lamiid clade (Boraginales,
 Gentianales, Lamiales, Solanales, Vahlia). Furthermore, the presence of
 similar morphological features among members of Aquifoliales suggests
 these characters might be ancestral for the Gentianidae (euasterids) as a
 whole.
description: 73 gene data set for 112
 asterids73 plastid genes for 112
 accessions of asterids focusing on the lamiids73genes112taxa.nexGene partitionsList of the starting and stopping positions of the concatenated 73 plastid genes.GenePart
DOI: 10.5061/dryad.nq648
title: Data from: Seasonal changes in the altitudinal distribution of nocturnally migrating birds during autumn migration

description: Wind plays a significant role in the flight altitudes selected by
 nocturnally migrating birds. At mid-latitudes in the Northern Hemisphere,
 atmospheric conditions are dictated by the polar-front jet stream, whose
 amplitude increases in the autumn. One consequence for migratory birds is
 that the region’s prevailing westerly winds become progressively stronger
 at higher migration altitudes. We expect this seasonality in wind speed to
 result in migrants occupying progressively lower flight altitudes, which
 we test using density estimates of nocturnal migrants at 100 m altitudinal
 intervals from 12 weather surveillance radar stations located in the
 northeastern USA. Contrary to our expectations, median migration altitudes
 deviated little across the season, and the variance was lower during the
 middle of the season and higher during the beginning and especially the
 end of the season. Early-season migrants included small- to
 intermediate-sized long-distance migrants in the orders Charadriiformes
 and Passeriformes, and late-season migrants included large-bodied and
 intermediate-distance migrants in the order Anseriformes. Therefore,
 seasonality in the composition of migratory species, and related variation
 in migration strategies and behaviours, resulted in a convex–concave
 bounded distribution of migration altitudes. Our results provide a basis
 for assessing the implications for migratory bird populations of changes
 in mid-latitude atmospheric conditions probably occurring under global
 climate change.
description: STEM_probability-of-occurrenceWeekly estimates of probability of occurrence for 142 migratory species within 37.5 km radius circles centered on 12 weather surveillance radar stations located in the northeastern USA . Estimates are derived from spatiotemporal exploratory models (STEM) with occurrence information from the eBird citizen science dataset for the combined period 2004 to 2011.WSR_station_reflectivityDaily total effective scattering area (reflectivity) of birds (square centimeters) per unit volume (cubic km) estimated at 12 weather surveillance radar (WSR) stations in the northeastern USA during the autumn of 2010 and 2011 within 37.5 km radius of each WSR station and within 100-m altitudinal bins.
DOI: 10.5061/dryad.5590q
title: Data from: Inflation of molecular clock rates and dates: molecular phylogenetics, biogeography, and diversification of a global cicada radiation from Australasia (Hemiptera: Cicadidae: Cicadettini)

description: Dated phylogenetic trees are important for studying mechanisms of
 diversification, and molecular clocks are important tools for studies of
 organisms lacking good fossil records. However, studies have begun to
 identify problems in molecular clock dates caused by uncertainty of the
 modeled molecular substitution process. Here we explore Bayesian
 relaxed-clock molecular dating while studying the biogeography of ca. 200
 species from the global cicada tribe Cicadettini. Because the available
 fossils are few and uninformative, we calibrate our trees in part with a
 cytochrome oxidase I (COI) clock prior encompassing a range of literature
 estimates for arthropods. We show that tribe-level analyses calibrated
 solely with the COI clock recover extremely old dates that conflict with
 published estimates for two well-studied New Zealand subclades within
 Cicadettini. Additional subclade analyses suggest that COI relaxed-clock
 rates and maximum-likelihood branch lengths become inflated relative to
 EF-1α intron and exon rates and branch lengths as clade age increases. We
 present corrected estimates derived from (1) an extrapolated EF-1α exon
 clock derived from COI-calibrated analysis within the largest New Zealand
 subclade, (2) post-hoc scaling of the tribe-level chronogram using results
 from subclade analyses, and (3) exploitation of a geological calibration
 point associated with New Caledonia. We caution that considerable
 uncertainty is generated due to dependence of substitution estimates on
 both the taxon sample and the choice of model, including gamma category
 number and the choice of empirical versus estimated base frequencies. Our
 results suggest that diversification of the tribe Cicadettini commenced in
 the early- to mid-Cenozoic and continued with the development of open,
 arid habitats in Australia and worldwide. We find that Cicadettini is a
 rare example of a global terrestrial animal group with an Australasian
 origin, with all non-Australasian genera belonging to two distal clades.
 Within Australia, we show that Cicadettini is more widely distributed than
 any other cicada tribe, diverse in temperate, arid and monsoonal habitats,
 and nearly absent from rainforests. We comment on the taxonomic
 implications of our findings for thirteen cicada genera.
description: Marshall et al.
 Cicadettini data files and treefilesContains main genetic
 dataset (COI, COII, and EF1a) and the MRK genus-level genetic dataset (COI
 and Ef1a) plus the MRK tree and tribe-level trees that were used for ML
 optimization of COI data.Marshall et al. Cicadettini
 genetic datasets and
 treefiles.zipMarshall et al. Syst.
 Biol. in press 2015 Cicadettini Supplementary MaterialsThis PDF file contains
 all of the Supplementary Figures and Tables, the Online Appendix, and the
 Supplementary Results (extended phylogenetic results and Lagrange
 output)Marshall et al. Cicadettini
 Supplementary 16 Sept 2015.pdf
DOI: 10.6084/m9.figshare.30763751
title: Niskanen et al. Agaricineae data files

description: Genomic-level data have enabled us to create better resolved phylogenies and revolutionized our views on fungal relationships. <i>Agaricineae</i> is the largest suborder of <i>Agaricales</i> and mainly comprises the brown- and dark-spored <i>Agaricales</i> with thick-walled and pigmented basidiospores. Our study is the most extensive phylogenomic study of the suborder <i>Agaricineae</i> to date including 54 genera and 86 species. For 21 of them shallow whole genome sequence data were produced in this study from dried fungarium specimens. A total of 24 families is recognized including five that are proposed as new: <i>Agrocybaceae</i>, <i>Galerinaceae</i>, <i>Hemipholiotaceae</i>, <i>Kuehneromycetaceae</i>, and <i>Phaeocollybiaceae</i>. In addition, <i>Battarreaceae</i> is accepted at family level based on previous phylogenetic studies bringing the total number of accepted families in the suborder <i>Agaricineae </i>to 25. The families are further grouped into eight informal “superfamilies”: Agaricacea, Bolbitiacea, Cortinariacea, Galeropsidacea, Inocybacea, Nidulariacea, Psathyrellacea and Strophariacea. Several families have been emended based on the current study and recent phylogenetic studies and as a result, a total of 184 genera is listed as accepted in suborder <i>Agaricineae</i>. Based on our analysis, most of the families are estimated to have originated and/or diversified in the mid to late Cretaceous or early Paleogene.
DOI: 10.6084/m9.figshare.30763751.v2
title: Niskanen et al. Agaricineae data files

description: Genomic-level data have enabled us to create better resolved phylogenies and revolutionized our views on fungal relationships. <i>Agaricineae</i> is the largest suborder of <i>Agaricales</i> and mainly comprises the brown- and dark-spored <i>Agaricales</i> with thick-walled and pigmented basidiospores. Our study is the most extensive phylogenomic study of the suborder <i>Agaricineae</i> to date including 54 genera and 86 species. For 21 of them shallow whole genome sequence data were produced in this study from dried fungarium specimens. A total of 24 families is recognized including five that are proposed as new: <i>Agrocybaceae</i>, <i>Galerinaceae</i>, <i>Hemipholiotaceae</i>, <i>Kuehneromycetaceae</i>, and <i>Phaeocollybiaceae</i>. In addition, <i>Battarreaceae</i> is accepted at family level based on previous phylogenetic studies bringing the total number of accepted families in the suborder <i>Agaricineae </i>to 25. The families are further grouped into eight informal “superfamilies”: Agaricacea, Bolbitiacea, Cortinariacea, Galeropsidacea, Inocybacea, Nidulariacea, Psathyrellacea and Strophariacea. Several families have been emended based on the current study and recent phylogenetic studies and as a result, a total of 184 genera is listed as accepted in suborder <i>Agaricineae</i>. Based on our analysis, most of the families are estimated to have originated and/or diversified in the mid to late Cretaceous or early Paleogene.
DOI: 10.6084/m9.figshare.30763751.v3
title: Niskanen et al. Agaricineae data files

description: Genomic-level data have enabled us to create better resolved phylogenies and revolutionized our views on fungal relationships. <i>Agaricineae</i> is the largest suborder of <i>Agaricales</i> and mainly comprises the brown- and dark-spored <i>Agaricales</i> with thick-walled and pigmented basidiospores. Our study is the most extensive phylogenomic study of the suborder <i>Agaricineae</i> to date including 54 genera and 86 species. For 21 of them shallow whole genome sequence data were produced in this study from dried fungarium specimens. A total of 24 families is recognized including five that are proposed as new: <i>Agrocybaceae</i>, <i>Galerinaceae</i>, <i>Hemipholiotaceae</i>, <i>Kuehneromycetaceae</i>, and <i>Phaeocollybiaceae</i>. In addition, <i>Battarreaceae</i> is accepted at family level based on previous phylogenetic studies bringing the total number of accepted families in the suborder <i>Agaricineae </i>to 25. The families are further grouped into eight informal “superfamilies”: Agaricacea, Bolbitiacea, Cortinariacea, Galeropsidacea, Inocybacea, Nidulariacea, Psathyrellacea and Strophariacea. Several families have been emended based on the current study and recent phylogenetic studies and as a result, a total of 184 genera is listed as accepted in suborder <i>Agaricineae</i>. Based on our analysis, most of the families are estimated to have originated and/or diversified in the mid to late Cretaceous or early Paleogene.
DOI: 10.5061/dryad.c2n5j
title: Data from: Hybrid ‘superswarm’ leads to rapid divergence and establishment of populations during a biological invasion

description: Understanding the genetic background of invading species can be crucial
 information clarifying why they become invasive. Intraspecific genetic
 admixture among lineages separated in the native ranges may promote the
 rate and extent of an invasion by substantially increasing standing
 genetic variation. Here, we examined the genetic relationships among
 threespine stickleback that recently colonized Switzerland. This invasion
 results from several distinct genetic lineages that colonized multiple
 locations and have since undergone range expansions, where they coexist
 and admix in parts of their range. Using 17 microsatellites genotyped for
 634 individuals collected from 17 Swiss and two non-Swiss European sites,
 we reconstruct the invasion of stickleback and investigate the potential
 and extent of admixture and hybridization among the colonizing lineages
 from a population genetic perspective. Specifically, we test for an
 increase in standing genetic variation in populations where multiple
 lineages coexist. We find strong evidence of massive hybridization early
 on, followed by what appears to be recent increased genetic isolation and
 the formation of several new genetically distinguishable populations,
 consistent with a hybrid ‘superswarm’. This massive hybridization and
 population formation event(s) occurred over approximately 140 years and
 likely fuelled the successful invasion of a diverse range of habitats. The
 implications are that multiple colonizations coupled with hybridization
 can lead to the formation of new stable genetic populations potentially
 kick-starting speciation and adaptive radiation over a very short
 timescale.
description: MEC-15-690-DryadThis zip file extracts data used in Roy et al MEC-15-0690. The ".txt" file is the raw microsatellite scores in number of repeats formatted for the Convert.exe program. The different forlders contain the data and results (Lositan and Bayescan) for various tests and analyses performed in the MS cited above. ".in" files are for structurama 2.0 input (Mac format), ".u" files are for IMa2 input (also accompanied by ".priors" files), while structure inputs list only "Project_data" files (and should be renamed as such prior to use).
DOI: 10.5061/dryad.51v22
title: Data from: Integrating phylogenomic and morphological data to assess candidate species-delimitation models in brown and red-bellied snakes (Storeria)

description: Systematics at the species level is still marked by theoretical and
 empirical tensions amongst the desires to identify geographical lineages,
 delimit species, and estimate their relationships. These goals are often
 confounded because each relies, at least to some extent, on the others
 being known. However, recently developed methods can simultaneously
 address all three. Furthermore, next-generation genomic sequencing allows
 us to generate large-scale molecular data sets to examine variation within
 species at a fine scale. Finally, a renaissance in morphological species
 validation allows us to integrate historical species definitions with
 coalescent models for species delimitation. Here, we investigate the
 applicability of these methods in an empirical case, in the Nearctic snake
 genus Storeria. Integrating trait data into species delimitation reduces
 the number of species delimited from molecular data alone. Whereas
 molecular data support eight distinct species-level lineages, including
 morphological data reduces this to four. The taxa Storeria dekayi,
 Storeria occipitomaculata, Storeria storerioides, and Storeria victa are
 considered distinct, monotypic species, with no subspecies recognized. We
 highlight the need for careful assessment of species delimitation,
 combining both computational genetic methods as well as traditional
 character-based descriptions. It is now possible to identify
 phylogeographical lineages, delimit species using molecular and
 morphological data, and estimate their relationships in a single coherent
 set of analyses. Moving forward, this will allow for more rapid and
 objective assessments of cryptic diversity at the species level.
description: Anchored_PhylogenomicsIncludes all analyses, data, methods, and code for the Anchored Phylogenomics assembly of Storeria.
DOI: 10.5061/dryad.46qm6
title: Data from: Non-monotonic temporal-weighting indicates a dynamically modulated evidence-integration mechanism

description: Perceptual decisions are thought to be mediated by a mechanism of
 sequential sampling and integration of noisy evidence whose temporal
 weighting profile affects the decision quality. To examine temporal
 weighting, participants were presented with two brightness-fluctuating
 disks for 1, 2 or 3 seconds and were requested to choose the overall
 brighter disk at the end of each trial. By employing a signal-perturbation
 method, which deploys across trials a set of systematically controlled
 temporal dispersions of the same overall signal, we were able to quantify
 the participants’ temporal weighting profile. Results indicate that, for
 intervals of 1 or 2 sec, participants exhibit a primacy-bias. However, for
 longer stimuli (3-sec) the temporal weighting profile is non-monotonic,
 with concurrent primacy and recency, which is inconsistent with the
 predictions of previously suggested computational models of perceptual
 decision-making (drift-diffusion and Ornstein-Uhlenbeck processes). We
 propose a novel, dynamic variant of the leaky-competing accumulator model
 as a potential account for this finding, and we discuss potential neural
 mechanisms.
description: AllData_Exp1Behavioral data Exp.1 in .mat formatAllData_Exp2AllData_Exp3AllData_Exp4
DOI: 10.5061/dryad.20t14
title: Data from: HExT, a software supporting tree-based screens for hybrid taxa in multilocus datasets, and an evaluation of the homoplasy excess test

description: The homoplasy excess test (HET) is a tree-based screen for hybrid taxa in
 multilocus nuclear phylogenies. Homoplasy between a hybrid taxon and the
 clades containing the parental taxa reduces bootstrap support in the tree.
 The HET is based on the expectation that excluding the hybrid taxon from
 the data set increases the bootstrap support for the parental clades,
 whereas excluding non-hybrid taxa has little effect on statistical node
 support. To carry out a HET, bootstrap trees are calculated with
 taxon-jackknife data sets, that is excluding one taxon (species,
 population) at a time. Excess increase in bootstrap support for certain
 nodes upon exclusion of a particular taxon indicates the hybrid (the
 excluded taxon) and its parents (the clades with increased support). We
 introduce a new software program, hext, which generates the
 taxon-jackknife data sets, runs the bootstrap tree calculations, and
 identifies excess bootstrap increases as outlier values in boxplot graphs.
 hext is written in r language and accepts binary data (0/1; e.g. AFLP) as
 well as co-dominant SNP and genotype data. We demonstrate the usefulness
 of hext in large SNP data sets containing putative hybrids and their
 parents. For instance, using published data of the genus Vitis (˜6,000 SNP
 loci), hext output supports V. × champinii as a hybrid between V.
 rupestris and V. mustangensis. With simulated SNP and AFLP data sets,
 excess increases in bootstrap support were not always connected with the
 hybrid taxon (false positives), whereas the expected bootstrap signal
 failed to appear on several occasions (false negatives). Potential causes
 for both types of spurious results are discussed. With both empirical and
 simulated data sets, the taxon-jackknife output generated by hext provided
 additional signatures of hybrid taxa, including changes in tree topology
 across trees, consistent effects of exclusions of the hybrid and the
 parent taxa, and moderate (rather than excessive) increases in bootstrap
 support. hext significantly facilitates the taxon-jackknife approach to
 hybrid taxon detection, even though the simple test for excess bootstrap
 increase may not reliably identify hybrid taxa in all applications.
description: Tropheus AFLP
 dataA
 nexus-format file with the AFLP data of Tropheus spp. sampled from Lake
 Tanganyika. Sampling information is given in Egger et al. (2007; BMC
 Evolutionary Biology, 7, 137).Canidae_SNPdataThis file contains SNP genotype data of North American canids used in a homoplasy excess test for hybrid signal. The data were collected by vonHoldt et al. (2011; Genome Research 21, 1294-1305). The first line contains sample names. Row names indicate SNP loci. SNP genotypes are scored as 0 (homozygous for one allele), 1 (heterozygous), 2 (homozygous for the other allele).
DOI: 10.5061/dryad.6361n
title: Data from: Speciation genomics and a role for the Z chromosome in the early stages of divergence between Mexican ducks and mallards

description: Speciation is a continuous and dynamic process, and studying organisms
 during the early stages of this process can aid in identifying speciation
 mechanisms. The mallard (Anas platyrhynchos) and Mexican duck (A. [p.]
 diazi) are two recently diverged taxa with a history of hybridization and
 controversial taxonomy. To understand their evolutionary history, we
 conducted genomic scans to characterize patterns of genetic diversity and
 divergence across the mitochondrial DNA (mtDNA) control region, 3523
 autosomal loci and 172 Z-linked sex chromosome loci. Between the two taxa,
 Z-linked loci (ΦST = 0.088) were 5.2 times more differentiated than
 autosomal DNA (ΦST = 0.017) but comparable to mtDNA (ΦST = 0.092). This
 elevated Z differentiation deviated from neutral expectations inferred
 from simulated data that incorporated demographic history and differences
 in effective population sizes between marker types. Furthermore, 3% of
 Z-linked loci, compared to &lt;0.1% of autosomal loci, were detected
 as outlier loci under divergent selection with elevated relative (ΦST) and
 absolute (dXY) estimates of divergence. In contrast, the ratio of Z-linked
 and autosomal differentiation among the seven Mexican duck sampling
 locations was close to 1:1 (ΦST = 0.018 for both markers). We conclude
 that between mallards and Mexican ducks, divergence at autosomal markers
 is largely neutral, whereas greater divergence on the Z chromosome (or
 some portions thereof) is likely the product of selection that has been
 important in speciation. Our results contribute to a growing body of
 literature indicating elevated divergence on the Z chromosome and its
 likely importance in avian speciation.
description: BAYESCAN.FILESInput structure-like and BayeScan files for analyzing 3,523 autosomal and 172 Z-linked markers between Mexican ducks and mallards, as well as within Mexican ducks.FASTA & NEXUS.FILESFinal genotypes for 17 mallards and 105 Mexican ducks in fasta format. For fasta files, we provide individual files per locus across 3,523 autosomal and 172 Z-linked markers, as well as, concatenated files across all markers, autosomal-only, and Z-linked only. Additionally, concatenated files for autosomal and Z-linked are provided in nexus formatFASTA.NEXUS.FILES.zipMALLvMEDU.IMRun-ready IM input file with 1 mitochondrial and 17 nuclear introns (geometric mean of locus length = 215.8 bp) sequenced across 25 mallards and 25 Mexican ducks (attained from Lavretsky et al. 2014, The Auk. 131:524–538).PCA.ADMIXTURE.INPUT.FILESRun-ready files for PCA and ADMIXTURE (includes *.ped and *.map) analyses are provided for 3,523 autosomal and 172 Z-linked markers.