cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j4r13dc
title: Data from: Functional attributes of ungulate migration: landscape features facilitate movement and access to forage

description: Long-distance migration by terrestrial mammals is a phenomenon critical to
 the persistence of populations, but such migrations are declining globally
 because of over-harvest, habitat loss, and movement barriers.
 Increasingly, there is a need to improve existing routes, mitigate route
 segments affected by anthropogenic disturbance and in some instances,
 determine if alternative routes are available. Using a hypothesis-driven
 approach, we identified landscape features associated with the primary
 functional attributes, stopovers and movement corridors, of spring
 migratory routes for mule deer in 2 study areas using resource selection
 functions. Patterns of selection for landscape attributes of movement
 corridors and stopovers mostly were similar, however landscape features
 associated with movement corridors aligned better with areas that
 facilitated movement, whereas selection of stopovers was consistent with
 sites offering early access to spring forage. For movement corridors, deer
 selected for dry sites, low elevation, and low anthropogenic disturbance.
 For stopovers, deer selected for dry sites, with consistently early
 green-up across years, south-southwesterly aspects, low elevation, and low
 anthropogenic disturbance. Stopovers and movement corridors of a migratory
 route presumably promote different functions, but for a terrestrial
 migrant, patterns of habitat selection indicate that the same general
 habitat attributes may facilitate both movement and foraging in spring.
 Our findings emphasize the roles of topographical wetness, vegetation
 phenology, and anthropogenic disturbance in shaping use of the landscape
 during migration for this large herbivore. Avoiding human disturbance and
 tracking ephemeral forage resources appear to be a consistent pattern
 during migration, which reinforces the notion that movement during
 migration has a nutritional underpinning and disturbance potentially
 alters the net benefits of migration.
description: Monteith_FuncMigDataThe zip file contains two folders labeled AR (Atlantic Rim) and UG (Upper Green). Inside each is a shapefile of the corridors and stopovers used in the analyses.
DOI: 10.5061/dryad.5vv1dj8
title: Data from: Habitat or temporal isolation: unravelling herbivore-parasitoid speciation patterns using double digest RADseq

description: Ecological speciation is often observed in phytophagous insects and their
 parasitoids due to divergent selection caused by host-associated or
 temporal differences. Most previous studies have utilized limited genetic
 markers or distantly related species to look for reproductive barriers of
 speciation. In our study we focus on closely related species of Lygus bugs
 and two sister species of Peristenus parasitoid wasps. Using mitochondrial
 DNA COI and genome wide SNPs generated using ddRADseq, we tested for
 potential effects of host-associated differentiation (HAD) or temporal
 isolation in this system. While three species of Lygus are clearly
 delineated with both COI and SNPs, no evidence of HAD or temporal
 differentiation was detected. Two Peristenus sister species were supported
 by both sets of markers and separated temporally with P. mellipes emerging
 early in June and attacking the first generation of Lygus, and P. howardi
 emerging later in August and attacking the second generation of their
 hosts. This is one of the few studies to examine closely related hosts and
 parasitoids to examine drivers of diversification. Given the results of
 this study, the Lygus-Peristenus system demonstrates temporal isolation as
 a potential barrier to reproductive isolation for parasitoids, which could
 indicate higher parasitoid diversity in regions of multivoltine hosts.
 This study also demonstrates that incorporating systematics improves
 studies of parasitoid speciation, particularly by obtaining accurate host
 records through rearing, carefully delimiting cryptic species, and
 examining population level differences with genomic scale data among
 closely related taxa.
description: Zhang et al 2018 -
 Habitat or Temporal Isolation: Unravelling herbivore-parasitoid speciation
 patterns using double digest RADseq-VCF files for all raw
 SNP data sets -Input files for MrBayes (Nexus format), RAxML (PHYLIP
 format), STRUCTURE (.str format) -R scripts for AMOVA and
 ggtree.Zhang et al
 2018.zip
DOI: 10.5061/dryad.pm71k02
title: Data from: Development of a PCR-RFLP assay to identify Drosophila melanogaster among field-collected larvae

description: The fruit fly Drosophila melanogaster is a model organism to study several
 aspects of metazoan biology. Most of the work has been conducted in adult
 fruit flies, including laboratory and field-derived specimens, but
 Drosophila melanogaster larvae recently became a valuable model to better
 understand animal physiology, development or host-microbe interactions.
 While adult flies can be easily assigned to a given Drosophila species
 based on morphological characteristics, such visual identification is more
 intricate at the larval stage. This could explain the limited number of
 studies focusing on larvae, especially field-derived samples. Here, we
 developed a Polymerase Chain Reaction-Restriction Fragment Length
 Polymorphism (PCR-RFLP) assay that discriminates D. melanogaster from
 other ecologically relevant Drosophila species at the larval stage. The
 method, which targets the cytochrome oxidase I (COI) gene, was validated
 using laboratory-derived larvae from seven D. melanogaster populations
 originating from different geographic areas as well as six Drosophila
 species. We further validated this PCR-RFLP assay in a natural context, by
 identifying wild larvae collected in two locations in France. Notably,
 among all PCR-RFLP profiles that matched the D. melanogaster species, 100%
 were correctly identified, as confirmed by COI sequencing. In summary, our
 work provides a rapid, simple and accurate molecular tool to identify D.
 melanogaster from field-collected larvae.
description: Development of a
 PCR-RFLP assay to identify Drosophila melanogaster among field-collected
 larvaeSanger sequencing of COI
 PCR fragment from wild Drosophila larvaeDeposit.zip
DOI: 10.5061/dryad.1450520
title: Data from: The oldest sigmodontine rodent revisited and the age of the first South American cricetids

description: New fossil material of Auliscomys formosus Reig 1978 allows restudy of the
 oldest known South American representative of the subfamily Sigmodontinae,
 Auliscomys formosus was based on a fragmentary dentary exhumed from the
 Monte Hermoso Formation of central Argentina. Previous studies allocated
 A. formosus to the early Pliocene. A revaluation of dental and cranial
 morphology, including for the first time the upper dentition, and the
 inclusion of A. formosus in a phylogenetic analysis of the tribe
 Phyllotini, indicates that A. formosus represents a new genus,
 Kraglievichimys. Kraglievichimys shares a mosaic of characters with the
 living Auliscomys Osgood, 1915 and Loxodontomys Osgood, 1947. The
 taxonomic reassignment of A. formosus and the possibility that the Monte
 Hermoso Formation may be younger than Early Pliocene in age provides a new
 understanding of cricetid diversification in South America. Estimates of
 sigmodontine ancestry by molecular approaches are biased toward older
 ages, whereas this new interpretation of the history of K. formosus
 suggests that the South American history of sigmodontines spans less than
 4 million years.
description: Suppl_data_1
 Morphological measurements of the taxa used for the linear
 modelLength and width of
 upper and lower molars of the taxa used for the linear model. Measurement
 are provided in millimeters and correspond to the mean of the number of
 measured individuals (N). geoU and geoL represent the geometric mean
 calculated respectively for upper and lower toothrows.Suppl_data_1.xlsxSuppl_Data_2 Matrix used for phylogenetic analysisMatrix used for the phylogenetic analysis formatted for use in TNT software. It comprises 27 taxa, Abrothrix andina =Chroeomys andinus) as outgroup and 98 unordered charactersSuppl_Data_2.tntSuppl_Data_3 Results of the linear model1. Graph of the linear model showing the correlation between geoU and geoL; black circles represent the measured taxa used for comparison; red line represents the regression line; green area represents the prediction interval of the linear model; red dot represents the measured values for Kraglievichimys formosus. 2. Validation tests of the linear modelSuppl_Data_3.tif
DOI: 10.5061/dryad.sv74pj2
title: Data from: Archaeogenomic evidence from the southwestern US points to a pre-Hispanic scarlet macaw breeding colony

description: Hundreds of scarlet macaw (Ara macao cyanoptera) skeletons have been
 recovered from archaeological contexts in the southwestern United States
 and northwestern Mexico (SW/NW). The location of these skeletons,
 &gt;1,000 km outside their Neotropical endemic range, has suggested a
 far-reaching pre-Hispanic acquisition network. Clear evidence for scarlet
 macaw breeding within this network is only known from the settlement of
 Paquimé in NW dating between 1250 and 1450 CE. Although some scholars have
 speculated on the probable existence of earlier breeding centers in the
 SW/NW region, there has been no supporting evidence. In this study, we
 performed an ancient DNA analysis of scarlet macaws recovered from
 archaeological sites in Chaco Canyon and the contemporaneous Mimbres area
 of New Mexico. All samples were directly radiocarbon dated between 900 and
 1200 CE. We reconstructed complete or near-complete mitochondrial genome
 sequences of 14 scarlet macaws from five different sites. We observed
 remarkably low genetic diversity in this sample, consistent with breeding
 of a small founder population translocated outside their natural range.
 Phylogeographic comparisons of our ancient DNA mitogenomes with
 mitochondrial sequences from macaws collected during the last 200 years
 from their endemic Neotropical range identified genetic affinity between
 the ancient macaws and a single rare haplogroup (Haplo6) observed only
 among wild macaws in Mexico and northern Guatemala. Our results suggest
 that people at an undiscovered pre-Hispanic settlement dating between 900
 and 1200 CE managed a macaw breeding colony outside their endemic range
 and distributed these symbolically important birds through the SW.
description: Ancient scarlet macaw
 bam files, revised A. m. macao reference, and consensus
 filesThis dataset includes 1)
 aligned bam files for 17 ancient scarlet macaws, 2) aligned and masked bam
 files for 17 ancient scarlet macaws, 3) the revised A. m. macao reference
 sequence, and the consensus sequence fasta files.macaw_q30.zip
DOI: 10.5061/dryad.29kb682
title: Data from: Examining the interglacial high-elevation refugia scenario in East Asian subtropical mountain systems with the frog species Leptobrachium liui

description: The effects of Quaternary climatic oscillations on the distributions of
 organisms in different parts of the world are not equally well understood,
 limiting the ability to understand the determinants of biodiversity.
 Compared with the mountain regions in southern Europe and southwestern
 North America, such effects on high-elevation species in the East Asian
 subtropical mountain systems located in southern and southeastern China
 have seldom been addressed. In this study, using Leptobrachium liui
 (Megophryidae), we made one of the earliest attempts to examine the
 interglacial high-elevation refugia scenario in these Asian mountains.
 Based on our current understanding of the study system, we formulated a
 hypothesis that these frogs of western origin were distributed more widely
 and continuously during glacial phases, allowing eastward dispersal, and
 that they are currently isolated in interglacial refugia at higher
 elevations. Microsatellite data and mitochondrial and nuclear sequence
 data were obtained with extensive sampling followed by the synthesis of
 phylogeographic and population genetic analyses and modeling of the
 species distribution. The analyses revealed a sequential eastward
 divergence of microsatellite clusters and gene lineages accompanied by a
 decline in genetic diversity. Molecular dating estimates revealed
 divergence events in the Pleistocene, and a reduction in local populations
 was inferred to have occurred at a time comparable to the end of the last
 glacial. Strong genetic isolation by distance reflecting a more continuous
 historical distribution was detected. Furthermore, environmental niche
 models inferred a wide planar distribution during the last glacial
 maximum, providing further support for the hypothesis.
description: L. liui + L.
 leishanense, 909 mtDNA sequencesA 745-bp mitochondrial
 locus containing regions of the tRNA-Leu (16 bp) and NADH dehydrogenase
 subunit 1 genes; 799 individuals from 22 sampling sites of Leptobrachium
 liui and 108 individuals from 3 sites of L. leishanense; 2 individuals of
 L. boringii as the outgroup; alignment in fasta format.ND1-745bp-909seq.fasL. liui + L. leishanense, 201 rag1 sequencesAn 800-bp partial sequence of the recombinase activating protein 1 gene; 199 sequences from 22 sampling sites of Leptobrachium liui and 3 sites of L. leishanense; 2 sequences of L. ngoclinhense and L. xanthospilum as outgroups; alignment in fasta format.RAG1-800bp-201seq.fasL. liui + L. leishanense, 832 individuals' STR832 individuals from 21 populations of Leptobrachium liui and 3 populations of L. leishanense; 8-14 microsatellite loci each population; data in genepop format.STR-24pop-14Loci.txt
DOI: 10.5061/dryad.r2f59f0
title: Data from: Enhanced virus filtration in hybrid membranes with MWCNT nanocomposite

description: Membrane separation is proved to be a powerful tool for several
 applications such as wastewater treatment or the elimination of various
 microorganisms from drinking water. In this study, the efficiency of
 inorganic composite based multi-walled carbon nanotube hybrid membranes
 was investigated in the removal of MS2 bacteriophages from contaminated
 water. With this object multi-walled carbon nanotubes were coated with
 copper(I) oxide, titanium(IV) oxide and iron(III) oxide nanoparticles,
 respectively, and their virus removal capability was tested in both batch
 and flow experiments. Considering the possible pH range of drinking water,
 the filtration tests were carried out at pH 5.0, 7.5 and 9.0 as well. The
 extent of MS2 removal strongly depended on the pH values for each
 composite, which can be due to electrostatic interactions between the
 membrane and the virus. The highest removal (≥99.99%) was obtained with
 the Cu2O-coated MWCNT water membrane in the whole pH range. The fabricated
 nanocomposites were characterized by X-ray diffraction, specific surface
 area measurement, dynamic light scattering, zeta potential measurement,
 Raman spectroscopy, transmission electron microscopy and scanning electron
 microscopy techniques. This study presents a simple route to design novel
 and effective nanocomposite-based hybrid membranes for virus removal.
description: DATAFile_RSOS_ZNAnalysis of MWCNT nanocomposite samples and results of MS2 filtration
DOI: 10.5061/dryad.40vp30d
title: Data from: Bursts of amino acid replacements in protein evolution

description: Evolution can occur both gradually and through alternating episodes of
 stasis and rapid changes. However, the prevalence and magnitude of
 fluctuations of the rate of evolution remains obscure. Detecting a rapid
 burst of changes requires a detailed record of past evolution, so that
 events that occurred within a short time interval can be identified. Here,
 we use the phylogenies of the Baikal Lake amphipods and of Catarrhini,
 which contain very short internal edges facilitating this task. We detect
 6 radical bursts of evolution of individual proteins during such short
 time periods, each involving between 6 and 38 amino acid substitutions.
 These bursts were extremely unlikely to have occurred neutrally, and were
 apparently caused by positive selection. On average, in the course of a
 time interval required for one synonymous substitution per site, a protein
 undergoes a strong burst of rapid evolution with probability at least
 ~0.01.
description: Eulimno clade tree
 (nwk)eulimno.nwkHyall clade tree (nwk)hyall.nwkAcantho clade tree (nwk)acantho.nwkMicro clade tree (nwk)micro.nwkPallasea clade tree (nwk)pallasea.nwkEulimno clade substitution statisticsColumn names: cog, branch, #nonsyn_subst, #syn_subst, #nonsyn_sites, #syn_sitessn_Eulimno.outAcantho clade substitutions statisticsColumn names: cog, branch, #nonsyn_subst, #syn_subst, #nonsyn_sites, #syn_sitessn_Acantho.outHyall ckade substitution statisticsColumn names: cog, branch, #nonsyn_subst, #syn_subst, #nonsyn_sites, #syn_sitessn_Hyall.outMicro clade substitution statisticsColumn names: cog, branch, #nonsyn_subst, #syn_subst, #nonsyn_sites, #syn_sitessn_Micro.outPallasea clase substitution statisticsColumn names: cog, branch, #nonsyn_subst, #syn_subst, #nonsyn_sites, #syn_sitessn_Pallasea.outcog05361_NOP16NOP16 gene alignment in Pallaseacog05414_DNAJC11DNAJC11 gene alignment in Pallaseacog05812_MRPL22MRPL22 gene alignment in Pallaseacog06250_AKR1AKR1 gene alignment in Eulimnocog06257_MRPS25MRPS25 gene alignment in EulimnoPKRPKR gene alignment in Catarrhini
DOI: 10.5061/dryad.t775334
title: Data from: Biophysical dependences among functional wood traits

description: 1. Wood properties and especially wood density have been used as
 functional traits organized along major axes of species life history and
 strategy. Beyond statistical analyses, a better mechanistic understanding
 of relationships among wood traits is essential for ecologically relevant
 interpretation of wood trait variations. 2. A set of theoretical
 relationships mechanistically linking wood basic density with some other
 wood traits is derived from cellular material physics. These theoretical
 models picture basic physical constraints and thus provide null-hypotheses
 for further ecological studies. Analysis is applied to data from two
 original datasets and several datasets extracted from literature. 3.
 Results emphasize the strong physical constraint behind the link between
 basic density and maximal storable water on the one hand, and elastic
 modulus on the other hand. Beyond these basic physical constraints, the
 developed framework reveals physically less expected trends: the amount of
 free water available for physiological needs increases in less dense wood
 of fast growing species, the cell wall stiffness decreases with density in
 temperate species and is higher in sapling stages in the rainforest
 understorey where competition for light is associated to high mechanical
 risk. 4. We emphasize the use of theoretically independent traits derived
 from models of cellular material physics to investigate the functional
 variation of wood traits together with their environmental and
 phylogenetic variations. Although the current study is limited to basic
 density, green wood lumen saturation and wood specific modulus, we further
 emphasize the identification of complementary independent wood traits
 representing other biomechanical functions, nutrient storage, hydraulic
 conductance and resistance to drought.
description: Appendix_S2_DatasetsFile contains two dataset each presented in a separated sheet accompanied with a readme sheet.
DOI: 10.5061/dryad.qq6hv63
title: Data from: Origin and macroevolution of micro-moths on sunken Hawaiian islands

description: The origins and evolution of Hawaiian biodiversity are a matter of
 controversy, and the mechanisms of lineage diversification for many
 organisms on this remote archipelago remain unclear. Here we focus on the
 poorly-known endemic leaf-mining moth genus Philodoria (Lepidoptera,
 Gracillariidae), whose species feed on a diversity of Hawaiian plant
 lineages, many of which are critically endangered. We use anchored hybrid
 enrichment to assemble the first phylogenomic dataset (507 loci) for any
 Hawaiian animal taxon. To uncover the timing and pattern of
 diversification of these moths, we apply two frequently used dating
 calibration strategies, biogeographic calibrations and secondary
 calibrations. Island calibrations on their own resulted in much younger
 and unrealistic dates compared to strategies that relied on secondary
 calibrations. Our dating results indicate that Philodoria is among the
 oldest known Hawaiian arthropod lineages. Philodoria likely originated on
 the now partially sunken islands of Laysan or Lisianski, approximately 21
 million years ago, and were associated with host plants in the families
 Ebenaceae, Malvaceae, or Primulaceae. Major feeding groups associated with
 specific host plant families originated soon after the plants colonize the
 islands. Allopatric isolation and host shifts, in concert and
 independently, likely play major roles in the diversification of
 Philodoria.
description: Dataset1_FcC_supermatrix_507_nucFinal nucleotide alignment for 507 loci (Dataset 1, probe region only) used in phylogenetic analyses.ESM3-Dataset1_FcC_supermatrix_507_nuc.nexDataset1_FcC_supermatrix_507_AAFinal amino acid alignment for 507 loci (Dataset 1, probe region only) used in phylogenetic analyses.ESM4-Dataset1_FcC_supermatrix_507_AA.nexDataset2_FcC_supermatrix_D60E15_FULL_LENGTH_FINALFinal nucleotide alignment for 507 loci (Dataset 2, probe and flanking regions) used in phylogenetic analyses.ESM5-Dataset2_FcC_supermatrix_D60E15_FULL_LENGTH_FINAL.fasA3_MCC_BEASTMaximum Clade Credibility tree from most likely divergence time estimate (Table 2 - Analysis A3).ESM15-A3_MCC_BEAST.treesA3_MCC_BEAST_infileBEAST infile for most likely divergence time estimate (Table 2 - Analysis A3).ESM16-A3_MCC_BEAST_infile.xmlGene_CoverageGene coverage information for nucleotide dataset for 507 loci (probe region only).ESM19-Gene_Coverage.xlsx