cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.ebqv8k
title: Occurrence Download

description: A dataset containing 3012 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Emmelichthys nitidus",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 3012 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001601-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.c5310
title: Data from: Delimiting tropical mountain ecoregions for conservation

description: Ecological regions aggregate habitats with similar biophysical
 characteristics within well-defined boundaries, providing spatially
 consistent platforms for monitoring, managing and forecasting the health
 of interrelated ecosystems. A major obstacle to the implementation of this
 approach is imprecise and inconsistent boundary placement. For globally
 important mountain regions such as the Eastern Arc (Tanzania and Kenya),
 where qualitative definitions of biophysical affinity are well
 established, rule-based methods for landform classification provide a
 straightforward solution to ambiguities in region extent. The method
 presented in this paper encompasses the majority of both contemporary and
 estimated preclearance forest cover within strict topographical limits.
 Many of the species here tentatively considered 'near-endemic'
 could be reclassified as strictly endemic according to the derived
 boundaries. LandScan and census data show population density inside the
 ecoregion to be higher than in rural lowlands, and lowland settlement to
 be most probable within 30 km. This definition should help to align
 landscape scale conservation strategies in the Eastern Arc and promote new
 research in areas of predicted, but as yet undocumented, biological
 importance. Similar methods could work well in other regions where
 mountain extent is poorly resolved. Spatial data accompany the online
 version of this article.
description: Shapefiles for the
 Eastern Arc Mountains in Tanzania and KenyaForest and mountain
 extent for the 13 mountain blocs/ranges that comprise the Eastern Arc
 chain. Provided in WGS1984 and UTM zone 37S coordinate reference systems.
 For metadata, see the published article (open access) - mountain limits
 relate to version 9 in the SOMEastern Arc
 Mountains.zip
DOI: 10.5061/dryad.md545
title: Data from: Isolation and characterization of microsatellite loci for the isopod crustacean Armadillidium vulgare and transferability in terrestrial isopods

description: Armadillidium vulgare is a terrestrial isopod (Crustacea, Oniscidea) which
 harbors Wolbachia bacterial endosymbionts. A. vulgare is the major model
 for the study of Wolbachia-mediated feminization of genetic males in
 crustaceans. As a consequence of their impact on host sex determination
 mechanisms, Wolbachia endosymbionts are thought to significantly influence
 A. vulgare evolution on various grounds, including population genetic
 structure, diversity and reproduction strategies. To provide molecular
 tools for examining these questions, we isolated microsatellite loci
 through 454 pyrosequencing of a repeat-enriched A. vulgare genomic
 library. We selected 14 markers and developed three polymorphic
 microsatellite multiplex kits. We tested the kits on two A. vulgare
 natural populations and found high genetic variation, thereby making it
 possible to investigate the impact of Wolbachia endosymbionts on A.
 vulgare nuclear variation at unprecedented resolution. In addition, we
 tested the transferability of these kits by cross-species amplification in
 five other terrestrial isopod species harboring Wolbachia endosymbionts.
 The microsatellite loci showed good transferability in particular in
 Armadillidium nasatum and Chaetophiloscia elongata, for which these
 markers represent promising tools for future genetic studies.
description: Armadillidium_vulgare_454reads.fasFasta file containing 18511 reads from Armadillidium vulgare (Crustacea, Isopoda). The reads were generated by 454 pyrosequencing of a microsatellite-enriched genomic library derived from a pool of 8 individuals.
DOI: 10.5061/dryad.3k31s
title: Data from: Interaction rules underlying group decisions in homing pigeons

description: Travelling in groups gives animals opportunities to share route
 information by following cues from each other's movement. The outcome
 of group navigation will depend on how individuals respond to each other
 within a flock, school, swarm, or herd. Despite the abundance of modelling
 studies, only recently have researchers developed techniques to determine
 the interaction rules among real animals. Here we use high-resolution GPS
 (global positioning system) tracking to study these interactions in pairs
 of pigeons flying home from a familiar site. Momentary changes in velocity
 indicate alignment with the neighbour's direction, as well as
 attraction or avoidance depending on distance. Responses were stronger
 when the neighbour was in front. From the flocking behaviour, we develop a
 model to predict features of group navigation. Specifically, we show that
 the interactions between pigeons stabilise a side-by-side configuration,
 promoting bidirectional information transfer and reducing the risk of
 separation. However, if one bird gets in front it will lead directional
 choices. Our model further predicts, and observations confirm, that a
 faster bird (as measured from solo flights) will fly slightly in front and
 thus dominate the choice of homing route. Our results explain how group
 decisions emerge from individual differences in homing flight behaviour.
description: GPS tracks of homing
 pigeonsGPS_tracks.zip
DOI: 10.5061/dryad.t8f5m
title: Data from: Independent acquisition of sodium selectivity in bacterial and animal sodium channels

description: Electrical signaling in animal nerves and muscles is largely carried out
 by proteins in the superfamily of voltage-gated ion channels. These
 proteins are based on a single homologous domain, but different types
 exist as single-domain tetramers, two-domain dimers, or four-domain
 proteins that comprise the whole pore-forming structure. Four-domain
 channels are hypothesized to have evolved from a single-domain ancestor by
 two rounds of internal duplication. The role that a channel plays in a
 cell’s physiology is largely determined by its selectivity for specific
 ion species and by the stimulus that opens the channel — its method of
 ‘gating’. The voltage-gated sodium (Nav) and calcium channels (Cav), which
 drive the upstroke of action potentials and transduce electrical signals
 into cellular signals, respectively, both have the four-domain
 architecture, whereas voltage-gated potassium channels (Kv) have only one
 domain. Crystallographic studies have led to important discoveries about
 ion permeation and gating in the single domain Kv channels, but structural
 studies of the four-domain Nav and Cav channels have not achieved the same
 level of precision, leaving the atomic details of these important proteins
 in the dark. The recent discovery of and subsequent crystallographic work
 on a voltage-gated, sodium-selective, single-domain channel in bacteria
 (BacNav) was therefore greeted with excitement as a potential model of
 four-domain Nav channels.
description: Supplemental_Data.tarThis archive contains datasets used for the analyses in the paper and several stability analyses conducted to verify the results. Motivations for these can be found in the supplemental material of the paper.
DOI: 10.5061/dryad.h7v76
title: Data from: The Hemiptera type-material housed in the "Museu de Ciencias Naturais, Fundação Zoobotanica do Rio Grande do Sul" of Porto Alegre, Brazil

description: We provide a commented and referenced list on the type material deposited
 in the “Museu de Ciencias Naturais, Fundação Zoobotânica do Rio Grande do
 Sul”, Porto Alegre, Brazil. Geographic coordinates are available on a
 digital repository for free access. High-resolution images of the
 specimens are available under request.
description: Specimens
 LabelsThis file contains
 photos for all the labels of the type-material deposited in the Museu de
 Ciências Naturais (MCNZ) listed in the paper. In the main folder you will
 find a spreadsheet (*.ods and *.xls available), with the photo file names
 for each specimen number. One species may have more than one specimen, one
 specimen may have more than one label photo and one photo may represent
 more than one specimen. By using autofilter, you will be able to search
 for a determined species, specimen or photo. Species are organized into
 separate folders containing their respective photos. The labels photos
 were taken with the same equipment used for the holotype photos presented
 in the paper.Ruschel_etal_2013_-_Specimens_Labels.zipGeographic CoordinatesThis file contains a spreadsheet (*.ods and *.xls available) with geographical coordinates for all the geographic data in the Hemiptera type-collection of Museu de Ciências Naturais (MCNZ). We used Google Earth for searching coordinates, but was added only when the labels provided enough information to recognize the correct locality with a minimum level of reliability. The toponyms were corrected using global gazetteers, such as Global Gazetteer Version 2.2 (available online at http://www.fallingrain.com/world/index.html). It is possible find more than one locality and coordinates for each species. By using autofilter, you will be able to search for species and/or localities.Ruschel_etal_2013_-_Coordinates.zip
DOI: 10.5061/dryad.b0qn5
title: Data from: Are habitat fragmentation, local adaptation and isolation by distance driving population divergence in wild rice Oryza rufipogon?

description: Habitat fragmentation weakens the connection between populations and is
 accompanied with isolation by distance (IBD) and local adaptation
 (isolation by adaptation, IBA), both leading to genetic divergence between
 populations. To understand the evolutionary potential of a population and
 to formulate proper conservation strategies, information on the roles of
 IBD and IBA in driving population divergence is critical. The putative
 ancestor of Asian cultivated rice (Oryza sativa) is endangered in China
 due to habitat loss and fragmentation. We investigated the genetic
 variation in 11 Chinese Oryza rufipogon populations using 79
 microsatellite loci to infer the effects of habitat fragmentation, IBD and
 IBA on genetic structure. Historical and current gene flows were found to
 be rare (mh = 0.0002–0.0013, mc = 0.007–0.029), indicating IBD and
 resulting in a high level of population divergence (FST = 0.343). High
 within-population genetic variation (HE = 0.377–0.515), relatively large
 effective population sizes (Ne = 96–158), absence of bottlenecks and
 limited gene flow were found, demonstrating little impact of recent
 habitat fragmentation on these populations. Eleven gene-linked
 microsatellite loci were identified as outliers, indicating local
 adaptation. Hierarchical AMOVA and partial Mantel tests indicated that
 population divergence of Chinese O. rufipogon was significantly correlated
 with environmental factors, especially habitat temperature. Common garden
 trials detected a significant adaptive population divergence associated
 with latitude. Collectively, these findings imply that IBD due to
 historical rather than recent fragmentation, followed by local adaptation,
 has driven population divergence in O. rufipogon.
description: microsatellites data for
 genepopinput file of genepop
 (11pops,79loci,384 samples)genepop input
 file.txtmicrosatellites data for
 Structureinput file for Structure
 (11pops,79loci, 384samples, missdata=-9)structure
 inputfile.txtmicrosatellites data for
 MSAinput data of MSA
 (11pops+1pop(outgroup, 7 samples), 79loci, 391samples)MSA input
 file.datmicrosatellites data for
 migrateinput file of
 migrate(11pops, 30 neutral loci, 384samples)migrate
 inputfile.datmicrosatellites data for
 Bayesassinput file of bayesass
 (neutral loci)bayesass
 inputfile.txtmicrosatellites data for
 DIYABCinput file of DIYABC
 (neutral loci, 3 groups+1outgroup)DIYABCinputfile.txtDIYABC settingsThe scenarios, parameters and settings of DIYABC (6 different scenarios are including)DIYABC scenarios settings.txt
DOI: 10.5061/dryad.59g56
title: Data from: Molecular identification of cryptic bumblebee species from degraded samples using PCR-RFLP approach

description: The worldwide decline and local extinctions of bumblebees has raised a
 need for fast and accurate tools for species identification. Morphological
 characters are often not sufficient and molecular methods have been
 increasingly used for reliable identification of bumblebee species.
 Molecular methods often require high quality DNA which makes them less
 suitable for analysis of low quality or older samples. We developed an
 efficient PCR-RFLP identification method for four bumblebee species of the
 subgenus Bombus s. str. (B. lucorum, B. terrestris, B. magnus, B.
 cryptarum) from degraded samples using a partial mitochondrial COI
 fragment (446 bp) and three diagnostic restriction enzymes (Hinf I, Hae
 III, Hinc II). This approach allowed us to efficiently determine the
 correct species from all degraded DNA samples while only a subset of
 samples 64.6% (31 out of 48) resulted in successful amplification of a
 longer COI fragment (1064 bp) using the previously described method. This
 protocol can be applied for conservation and management of bumblebees
 within this subgenus and is especially useful for fast species
 identification from degraded samples.
description: Bumblebee trapping
 samplesBumblebee (Bombus sensu
 stricto-group) trapping sample ID numbers, collecting dates, and trap
 locations from two trapping areas (S and T) in Kemiönsaari, Finland.
 Sequenced samples have been included in a separate alignment file except
 for samples with nuclear copies of mtDNA.Vesterlund et al
 1.xlsxSample information for
 sequenced bumblebeesCollection locations of
 sequenced bumblebee samples, castes, and the presence of nuclear copies of
 mtDNA (NUMTS).Vesterlund et al
 2.xlsxSequenced bumblebee
 samples aligned with Apis mellifera liqustica genomeBioEdit alignment file
 containing the sequenced bumblebee samples aligned with Apis mellifera
 liqustica genome. Samples containing nuclear copies of mtDNA or incomplete
 sequence data have been removed.Vesterlund
 alignment.bio
DOI: 10.5061/dryad.6n94m
title: Data from: An integrative approach to detect subtle trophic niche differentiation in the sympatric trawling bat species Myotis dasycneme and Myotis daubentonii

description: Bats are well known for species richness and ecological diversity thus
 they provide a good opportunity to study relationships and interaction
 between species. To assess interactions we consider distinct traits which
 are likely to be triggered by niche shape and evolutionary processes. We
 present data on the trophic niche differentiation between two sympatric
 European trawling bat species, Myotis dasycneme and M. daubentonii,
 incorporating a wide spectrum of methodological approaches. We measure
 morphological traits involved in foraging and prey handling performance
 including bite force, weight lifting capacity and wing morphology. We then
 measure resulting prey consumption using both morphological and molecular
 diet analysis. These species closely resemble each other in morphological
 traits however, subtle but significant differences were apparent in bite
 force and lift capacity which are related to differences in basic body and
 head size. Both morphological and molecular diet analyses show strong
 niche overlap. We detected subtle differences in less frequent prey items,
 as well as differences in the exploitation of terrestrial and
 aquatic-based prey groups. M. dasycneme feeds more on aquatic prey, like
 Chironomidae and their pupal stages, or the aquatic moth Acentria
 ephemerella. M. daubentonii feeds more on terrestrial prey, like
 Brachycera, or Coleoptera. This suggests that these bats use different
 micro-habitats within the habitat where they co-occur.
description: BiteForceMdasMdautxt-file with bite force data collected in the field. abbreviations: FA=forearm length; Species: 1= male; 2= femal; Sex: f = female; m= male; mean bite force = mean; maximal bite force= max; upper toothrow length= CM³.Morphology data Mdas Mdautxt file containing morphological data on wings of Mdasycneme and Mdaubentonii collected in the field. Species: 1= Myotis dasycneme, 2= Myotis daubentonii. Sex: 1= male, 2= female. Status: 1= juvenile, 2= subadult, 3= adult. FA= forearm length. Lhw= length hand wing. Law= length arm wing. S= wing area. Tl= tip length ratio, Ts= tip area ratio, I= wing tip shape index.weight lifting performanceexcel file with weight lifting performance data collected from bats in the lab. FA= forearm length.Myotis_Molecular Diet Data_ClippedFasta file containing sequences from ion torrent sequencing faecal samples of Myotis dasycneme and Myotis daubentonii.Myotis_Data_Clipped.fastamorphological diet dataexcel file containing the presence absence data of prey from faecal samples of Myotis dasycneme and Myotis daubentonii.
DOI: 10.5061/dryad.80ph2
title: Data from: Multilocus analyses reveal little evidence for lineage wide adaptive evolution within major clades of soft pines (Pinus subgenus Strobus)

description: Estimates from molecular data for the fraction of new nonsynonymous
 mutations that are adaptive vary strongly across plant species. Much of
 this variation is due to differences in life-history strategies as they
 influence the effective population size (Ne). Ample variation for these
 estimates, however, remains even when comparisons are made across species
 with similar values of Ne. An open question thus remains as to why the
 large disparity for estimates of adaptive evolution exists among plant
 species. Here, we have estimated the distribution of deleterious fitness
 effects (DFE) and the fraction of adaptive nonsynonymous substitutions (α)
 for 11 species of soft pines (subgenus Strobus) using DNA sequence data
 from 167 orthologous nuclear gene fragments. Most newly arising
 nonsynonymous mutations were inferred to be so strongly deleterious that
 they would rarely become fixed. Little evidence for long-term adaptive
 evolution was detected, as all 11 estimates for α were not significantly
 different from zero. Nucleotide diversity at synonymous sites, moreover,
 was strongly correlated with attributes of the DFE across species, thus
 illustrating a strong consistency with the expectations from the Nearly
 Neutral Theory of molecular evolution. Application of these patterns to
 genome-wide expectations for these species, however, was difficult as the
 loci chosen for analysis were a biased set of conserved loci which greatly
 influenced estimates of the DFE and α. This implies that genome-wide
 parameter estimates will need truly genome-wide data, so that many of
 existing patterns documented previously for forest trees (e.g. little
 evidence for signature of selection) may need revision.
description: Eckert_et_al_pairwise_alignmentsThe file named Eckert_et_al_pairwise_alignments.zip contains 11 directories corresponding to pairwise alignments between loblolly pine and one of the eleven focal species. Within each directory are 192 fasta formatted alignment files (except for Pinus strobiformis which contains 191 alignment files). Alignment files are named by locus as defined in the manuscript associated with this Dryad entry. Within each alignment file are aligned sequences for the focal species and Pinus taeda (= loblolly pine). Sequences are identified to species using the following codes: Pial: Pinus albicaulis, Piar: Pinus aristata, Piay: Pinus ayacahuite, Pibf: Pinus balfouriana, Pifl: Pinus flexilis, Pila: Pinus lambertiana, Pilo: Pinus longaeva, Pimn: Pinus monticola, Pimo: Pinus monophylla, Pisb: Pinus strobiformis, Pist: Pinus strobus, Pita: Pinus taeda. Please note that a subset of 167 alignments was used in the final analysis. These can be identified using the online supplemental file available at the journal website.
DOI: 10.5061/dryad.mh50q
title: Data from: Does genetic distance between parental species influence outcomes of hybridisation among coral reef butterflyfishes?

description: Christmas Island is located at the overlap of the Indian and Pacific Ocean
 marine provinces and is a hot spot for marine hybridization. Here, we
 evaluate the ecological framework and genetic consequences of
 hybridization between butterflyfishes Chaetodon guttatissimus and
 Chaetodon punctatofasciatus. Further, we compare our current findings to
 those from a previous study of hybridization between Chaetodon
 trifasciatus and Chaetodon lunulatus. For both species groups, habitat and
 dietary overlap between parental species facilitate frequent
 heterospecific encounters. Low abundance of potential mates promotes
 heterospecific pair formation and the breakdown of assortative mating.
 Despite similarities in ecological frameworks, the population genetic
 signatures of hybridization differ between the species groups.
 Mitochondrial and nuclear data from C. guttatissimus × C.
 punctatofasciatus (1% divergence at cyt b) show bidirectional maternal
 contributions and relatively high levels of introgression, both inside and
 outside the Christmas Island hybrid zone. In contrast, C. trifasciatus ×
 C. lunulatus (5% cyt b divergence) exhibit unidirectional mitochondrial
 inheritance and almost no introgression. Back-crossing of hybrid C.
 guttatissimus × C. punctatofasciatus and parental genotypes may eventually
 confound species-specific signals within the hybrid zone. In contrast,
 hybrids of C. trifasciatus and C. lunulatus may coexist with and remain
 genetically distinct from the parents. Our results, and comparisons with
 hybridization studies in other reef fish families, indicate that genetic
 distance between hybridizing species may be a factor influencing outcomes
 of hybridization in reef fish, which is consistent with predictions from
 terrestrially derived hybridization theory.
description: 20130905_DRYADdata_GPTLThe .zip file contains all ecological/behavioural data as well as microsatellite genotypes for the C. guttatissimus group. Please see the READ-ME file for more information and doi to C. trifasciatus group genotypes.mtDNA alignmentmtDNA 566bp cytochrome b alignment of 88 individualsALIGNMENT_gut_punct.nexPhylogenetic treesNJ, MP, ML and BI trees used to provide support on the MST in Figure 3.Phylo_trees_GP.zip
DOI: 10.5281/zenodo.18390605
title: LINF_320011300

description: Protein of unknown function - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.5281/zenodo.18390606
title: LINF_320011300

description: Protein of unknown function - conserved; Leishmania infantum (strain JPCM5)