cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vf807sd
title: Data from: Divergence in female damselfly sensory structures is consistent with a species recognition function but shows no evidence of reproductive character displacement

description: Males and females transmit and receive signals prior to mating that convey
 information such as sex, species identity, or individual condition. In
 some animals, tactile signals relayed during physical contact between
 males and females before and during mating appear to be important for mate
 choice or reproductive isolation. This is common among odonates, when a
 male grasps a female’s thorax with his terminal appendages prior to
 copulation, and the female subsequently controls whether copulation occurs
 by bending her abdomen to complete intromission. It has been hypothesized
 that mechanosensory sensilla on the female thoracic plates mediate mating
 decisions, but is has been difficult to test this idea. Here, we use North
 American damselflies in the genus Enallagma (Odonata: Coenagrionidae) to
 test the hypothesis that variation in female sensilla traits is important
 for species recognition. Enallagma anna and E. carunculatum hybridize in
 nature, but experience strong reproductive isolation as a consequence of
 divergence in male terminal appendage morphology. We quantified several
 mechanosensory sensilla phenotypes on the female thorax among multiple
 populations of both species and compared divergence in these traits in
 sympatry versus allopatry. Although these species differed in features of
 sensilla distribution within the thoracic plates, we found no strong
 evidence of reproductive character displacement among the sensilla traits
 we measured in regions of sympatry. Our results suggest that
 species‐specific placement of female mechanoreceptors may be sufficient
 for species recognition, although other female sensory phenotypes might
 have diverged in sympatry to reduce interspecific hybridization.
description: Individual female
 damselfly dataData associated with
 individual female damselfly specimens. Measurement methods are described
 in the accompanying paper. Units of measurement are included in column
 headings.IndividualFemaleData.csvPopulation meansMean trait values for each damselfly population, calculated from individual data in "IndividualFemaleData.txt." Measurement methods are described in the accompanying paper. Units of measurement are included in column headings. When a population only included one sample, this value was used as the population mean.PopulationMeans.csvSensilla and plate outline coordinatesX and y coordinates describing locations of sensilla and perimeter of mesostigmal plate.Concatenated_sensilla_and_plate_coordinates.zip
DOI: 10.5061/dryad.sb68v
title: Data from: High levels of effective long-distance dispersal may blur ecotypic divergence in a rare terrestrial orchid

description: Background: Gene flow and adaptive divergence are key aspects of
 metapopulation dynamics and ecological speciation. Long-distance dispersal
 is hard to detect and few studies estimate dispersal in combination with
 adaptive divergence. The aim of this study was to investigate effective
 long-distance dispersal and adaptive divergence in the fen orchid (Liparis
 loeselii (L.) Rich.). We used amplified fragment length polymorphism
 (AFLP)-based assignment tests to quantify effective long-distance
 dispersal at two different regions in Northwest Europe. In addition,
 genomic divergence between fen orchid populations occupying two
 distinguishable habitats, wet dune slacks and alkaline fens, was
 investigated by a genome scan approach at different spatial scales
 (continental, landscape and regional) and based on 451 AFLP loci. Results:
 We expected that different habitats would contribute to strong divergence
 and restricted gene flow resulting in isolation-by-adaptation. Instead, we
 found remarkably high levels of effective long-distance seed dispersal and
 low levels of adaptive divergence. At least 15% of the assigned
 individuals likely originated from among-population dispersal events with
 dispersal distances up to 220 km. Six (1.3%) ‘outlier’ loci, potentially
 reflecting local adaptation to habitat-type, were identified with high
 statistical support. Of these, only one (0.22%) was a replicated outlier
 in multiple independent dune-fen population comparisons and thus possibly
 reflecting truly parallel divergence. Signals of adaptation in response to
 habitat type were most evident at the scale of individual populations.
 Conclusions: The findings of this study suggest that the homogenizing
 effect of effective long-distance seed dispersal may overwhelm divergent
 selection associated to habitat type in fen orchids in Northwest Europe.
description: AFLP
 dataThe file AFLP data.txt
 includes the binary matrix of AFLP band presence (1) – absence (0) for 451
 AFLP-markers and 422 individuals of Liparis loeselii sampled in 38
 populations. The matrix also include the spatial coordinates of each
 sampled population, given in the two last columns. The markers are
 numbered M1 to M451. The description of each marker (size in base pairs,
 primer combination) is given in the file readme.txt.
DOI: 10.5061/dryad.7sq2j
title: Data from: A reconsideration of the classification of the spider infraorder Mygalomorphae based on three nuclear genes and morphology (Arachnida: Araneae)

description: BACKGROUND: The infraorder Mygalomorphae (i.e., trapdoor spiders,
 tarantulas, funnel web spiders, etc.) is one of three main lineages of
 spiders. Comprising 15 families, 325 genera, and over 2,600 species, the
 group is a diverse assemblage that has retained a number of features
 considered primitive for spiders. Despite an evolutionary history dating
 back to the lower Triassic, the group has received comparatively little
 attention with respect to its phylogeny and higher classification. The few
 phylogenies published all share the common thread that a stable
 classification scheme for the group remains unresolved. METHODS AND
 FINDINGS: We report here a reevaluation of mygalomorph phylogeny using the
 rRNA genes 18S and 28S, the nuclear protein-coding gene EF-1γ, and a
 morphological character matrix. Taxon sampling includes members of all 15
 families representing 58 genera. The following results are supported in
 our phylognetic analyses of the data: (1) the Atypoidea (i.e.,
 antrodiaetids, atypids, and mecicobothriids) is a monophyletic group
 sister to all other mygalomorphs; and (2) the families Mecicobothriidae,
 Hexathelidae, Cyrtaucheniidae, Nemesiidae, Ctenizidae, and Dipluridae are
 not monophyletic. The Microstigmatidae is likely to be subsumed into
 Nemesiidae. Nearly half of all mygalomorph families require reevaluation
 of generic composition and placement. The polyphyletic family
 Cyrtaucheniidae is most problematic, representing no fewer than four
 unrelated lineages. CONCLUSIONS: Based on these analyses we propose the
 following nomenclatural changes: (1) the establishment of the family
 Euctenizidae (NEW RANK); (2) establishment of the subfamily Apomastinae
 within the Euctenizidae; and (3) the transfer of the cyrtaucheniid genus
 Kiama to Nemesiidae. Additional changes include relimitation of
 Domiothelina and Theraphosoidea, and the establishment of the
 Euctenizoidina clade (Idiopidae + Euctenizidae). In addition to these
 changes, we propose a “road map” for future sampling across the infraorder
 with the aim of solving many remaining vexing questions that plague
 mygalomorph systematics.
description: Bondetal_dataMesquite generated NEXUS file of aligned DNA sequences and morphological character matrix and associated tree files for all combined and independent analyses.
DOI: 10.5061/dryad.292q34fp
title: Data from: The evolutionary enigma of mixed mating systems in plants: occurrence, theoretical explanations, and empirical evidence

description: Mixed mating, in which hermaphrodite plant species reproduce by both self-
 and cross-fertilization, presents a challenging problem for evolutionary
 biologists. Theory suggests that inbreeding depression, the main selective
 factor opposing the evolution of selfing, can be purged with
 self-fertilization, a process that is expected to yield pure strategies of
 either outcrossing or selfing. Here we present updated evidence suggesting
 that mixed mating systems are frequent in seed plants. We outline the
 floral and pollination mechanisms that can lead to intermediate
 outcrossing, review the theoretical models that address the stability of
 intermediate outcrossing, and examine relevant empirical evidence. A
 comparative analysis of estimated inbreeding coefficients and outcrossing
 rates suggests that mixed mating often evolves despite strong inbreeding
 depression. The adaptive significance of mixed mating has yet to be fully
 explained for any species. Recent theoretical and empirical work suggests
 that future progress will come from a better integration of studies of
 floral mechanisms, genetics, and ecology, and recognition of how selective
 pressures vary in space and time.
description: Mixed mating outcrossing
 rate databaseThis Excel file contains
 data on outcrossing rates and the inbreeding coefficient for plants
 species collected from published literature. Column headings in the file
 are described in the associated ReadMe file.
DOI: 10.5061/dryad.7sq32
title: Data from: Patterns of mating and generation of diversity in a Geum hybrid swarm

description: To understand the evolutionary consequences of hybridization between the
 outcrossing plant Geum rivale and the selfer G. urbanum we tested the
 predictions of two simple models which assume either A). low or B). high
 pollen fitness in hybrids. Model A predicts only four genotypic classes
 (G. rivale, G. rivale backcross (BCR), F1 and G. urbanum) and asymmetric
 introgression from inbreeding to outbreeding species. Model B predicts
 additional genotypic classes and potential generation of novel inbreeding
 lines in the hybrid swarm. AFLP analysis of adults revealed only the four
 genotypes predicted by model A. However, microsatellite analysis of
 parent-progeny arrays demonstrated production of selfed offspring by F1
 and BCR maternal parents and contribution of these genotypes to outcross
 pollen pools, as predicted by model B. Moreover AFLP and morphological
 analysis showed that the offspring generation comprised genotypes and
 phenotypes covering the entire spectrum of variation between the two
 parental species, in line with model B. A common garden experiment
 indicated no systematic reduction in fitness of offspring derived from
 hybrid parents. The genetic structure of the adults in the Geum hybrid
 swarm cannot be explained by restricted mating patterns but may result
 from ecological selection acting on a diverse offspring population.
description: AFLP, Microsatellite,
 Morphology and Fitness dataThe data file contains
 the raw data for 30 adults from a Geum urbanum x G. rivale hybrid swarm
 plus their open pollinated offspring (collected outside Edinburgh,
 Scotland). AFLP tab: scoring sheet for 202 AFLP markers of 30 adults and 5
 of their open pollinated offspring each, 12 reference samples each from
 pure Geum urbanum and G. rivale populations and 15 controlled F1 crosses.
 The Microsatellite tab contains the scoring for 3 SSR loci of the same 30
 adults plus 10 of their open pollinated offspring. The Morphology tab
 contains 9 morphological measurements taken in a common garden environment
 for the same samples used in the AFLP file apart from reference and
 controlled F1 samples. The Fitness tab contains the number of seed heads
 and leaf volume produced in a common garden environment for the same
 offspring samples used in the AFLP file.Dryad.xls
DOI: 10.5061/dryad.sr534
title: Data from: Parsimonious inference of hybridization in the presence of incomplete lineage sorting

description: Hybridization plays an important evolutionary role in several groups of
 organisms. A phylogenetic approach to detect hybridization entails
 sequencing multiple loci across the genomes of a group of species of
 interest, reconstructing their gene trees, and taking their differences as
 indicators of hybridization. However, methods that follow this approach
 mostly ignore population effects, such as incomplete lineage sorting
 (ILS). Given that hybridization occurs between closely related organisms,
 ILS may very well be at play and, hence, must be accounted for in the
 analysis framework. To address this issue, we present a parsimony
 criterion for reconciling gene trees within the branches of a phylogenetic
 network, and a local search heuristic for inferring phylogenetic networks
 from collections of gene-tree topologies under this criterion. This
 framework enables phylogenetic analyses while accounting for both
 hybridization and ILS. Further, we propose two techniques for
 incorporating information about uncertainty in gene-tree estimates. Our
 simulation studies demonstrate the good performance of our framework in
 terms of identifying the location of hybridization events, as well as
 estimating the proportions of genes that underwent hybridization. Also,
 our framework shows good performance in terms of efficiency on handling
 large data sets in our experiments. Further, in analysing a yeast data
 set, we demonstrate issues that arise when analysing real data sets.
 Although a probabilistic approach was recently introduced for this
 problem, and although parsimonious reconciliations have accuracy issues
 under certain settings, our parsimony framework provides a much more
 computationally efficient technique for this type of analysis. Our
 framework now allows for genome-wide scans for hybridization, while also
 accounting for ILS.
description: Supplementary
 MaterialSOM.pdf
DOI: 10.5061/dryad.pb04q
title: Data from: Historical citizen science to understand and predict climate-driven trout decline

description: Historical species records offer an excellent opportunity to test the
 predictive ability of range forecasts under climate change, but
 researchers often consider that historical records are scarce and
 unreliable, besides the datasets collected by renowned naturalists. Here,
 we demonstrate the relevance of biodiversity records developed through
 citizen-science initiatives generated outside the natural sciences
 academia. We used a Spanish geographical dictionary from the
 mid-nineteenth century to compile over 10 000 freshwater fish records,
 including almost 4 000 brown trout (Salmo trutta) citations, and
 constructed a historical presence–absence dataset covering over 2 000 10 ×
 10 km cells, which is comparable to present-day data. There has been a
 clear reduction in trout range in the past 150 years, coinciding with a
 generalized warming. We show that current trout distribution can be
 accurately predicted based on historical records and past and present
 values of three air temperature variables. The models indicate a
 consistent decline of average suitability of around 25% between 1850s and
 2000s, which is expected to surpass 40% by the 2050s. We stress the
 largely unexplored potential of historical species records from
 non-academic sources to open new pathways for long-term global change
 science.
description: HISTORICAL TROUT
 DISTRIBUTION IN SPAINPresence (=1) or absence
 (=0) of brown trout (Salmo trutta) in 5427 localities in Spain during the
 mid-19th century, as informed by the geographical dictionary edited by
 Pascual Madoz [Madoz P. 1845-1850 Diccionario Geográfico, Estadístico y
 Histórico de España, y sus Posesiones de Ultramar. 16 vols. Madrid,
 Spain]. Absence localities are those in which the dictionary identified
 freshwater fish species but did not mention the trout. Latitude and
 longitude are given in decimal degreesHISTORICAL_TROUT_DATA.xls
DOI: 10.5061/dryad.nt615
title: Data from: Performance of TaqMan Array Card to detect TB drug resistance on direct specimens

description: Culture based phenotypic drug susceptibility testing (DST) for
 Mycobacterium tuberculosis (TB) is time consuming therefore rapid
 genotypic methods are increasingly being utilized. We previously developed
 and evaluated on TB isolates a rapid genotypic TaqMan array card (TAC)
 that detects mutations in several resistance-associated genes using dozens
 of primer pairs, probes, and high resolution melt analysis, with
 &gt;96% accuracy versus Sanger sequencing. In this study we examined
 the performance of TAC on sputum, comparing results between 71 paired
 sputum and multi drug resistant TB isolates. We also adapted the TAC to
 include wild-type probes and broadened coverage for rpoB and gyrA
 mutations. TAC was 89% successful at detecting wild-type or mutations
 within inhA, katG, rpoB, eis, gyrA, rplC, and pncA on smear positive sputa
 and 33% successful on smear negative sputa. The overall accuracy of these
 detections as compared to the TAC results of the paired isolate was 95% ±
 7 (average sensitivity 98% ± 3; specificity 92% ± 14). Accuracy of sputum
 TAC results versus phenotypic DST for isoniazid, rifampin,
 amikacin/kanamycin, ofloxacin/moxifloxacin, and pyrazinamide was 87% ± 11.
 This was similar to that of the paired isolate TAC results (accuracy 90% ±
 12) and inaccuracies primarily reflected intrinsic genotypic-phenotypic
 discordance. The TAC is a rapid, modular, comprehensive, and accurate TB
 DST for the major first and second line TB drugs on smear positive sputum.
description: Raw
 data
DOI: 10.5061/dryad.6qr6j
title: Data from: Evaluating carbon storage, timber harvest, and habitat possibilities for a western Cascades (US) forest landscape

description: Forest policymakers and managers have long sought ways to evaluate the
 capability of forest landscapes to jointly produce timber, habitat, and
 other ecosystem services in response to forest management. Currently,
 carbon is of particular interest as policies for increasing carbon storage
 on federal lands are being proposed. However, a challenge in joint
 production analysis of forest management is adequately representing
 ecological conditions and processes that influence joint production
 relationships. We used simulation models of vegetation structure, forest
 sector carbon, and potential wildlife habitat to characterize
 landscape-level joint production possibilities for carbon storage, timber
 harvest, and habitat for seven wildlife species across a range of forest
 management regimes. We sought to: (1) characterize the general
 relationships of production possibilities for combinations of carbon
 storage, timber, and habitat; and (2) identify management variables that
 most influence joint production relationships. Our 160,000-ha study
 landscape featured environmental conditions typical of forests in the
 western Cascade Mountains of Oregon (US). Our results indicate that
 managing forests for carbon storage involves tradeoffs among timber
 harvest and habitat for focal wildlife species, depending on the
 disturbance interval and utilization intensity followed. Joint production
 possibilities for wildlife species varied in shape, ranging from
 competitive to complementary to compound, reflecting niche breadth and
 habitat component needs of species examined. Managing Pacific Northwest
 forests to store forest sector carbon can be roughly complementary with
 habitat for Northern Spotted Owl, Olive-sided Flycatcher, and Red Tree
 Vole. However, managing forests to increase carbon storage potentially can
 be competitive with timber production and habitat for Pacific Marten,
 Pileated Woodpecker, and Western Bluebird, depending on the disturbance
 interval and harvest intensity chosen. Our analysis suggest that joint
 production possibilities under forest management regimes currently typical
 on industrial forest lands (e.g., 40- to 80-year rotations with some tree
 retention for wildlife) represent but a small fraction of joint production
 outcomes possible in the region. Although the theoretical boundaries of
 the production possibilities sets we developed are probably unachievable
 in the current management environment, they arguably define the long-term
 potential of managing forests to produce multiple ecosystem services
 within and across multiple forest ownerships.
description: Archived
 dataData used to create
 Figures 1 through 4. See file:
 Kline_EA_figure_dataTables_metadata.docxData_archive.zip
DOI: 10.5061/dryad.sk497
title: Data from: The shift from plant–plant facilitation to competition under severe water deficit is spatially explicit

description: The stress-gradient hypothesis predicts a higher frequency of facilitative
 interactions as resource limitation increases. Under severe resource
 limitation, it has been suggested that facilitation may revert to
 competition, and identifying the presence as well as determining the
 magnitude of this shift is important for predicting the effect of climate
 change on biodiversity and plant community dynamics. In this study, we
 perform a meta-analysis to compare temporal differences of species
 diversity and productivity under a nurse plant (Retama sphaerocarpa) with
 varying annual rainfall quantity to test the effect of water limitation on
 facilitation. Furthermore, we assess spatial differences in the herbaceous
 community under nurse plants in situ during a year with below-average
 rainfall. We found evidence that severe rainfall deficit reduced species
 diversity and plant productivity under nurse plants relative to open
 areas. Our results indicate that the switch from facilitation to
 competition in response to rainfall quantity is nonlinear. The magnitude
 of this switch depended on the aspect around the nurse plant. Hotter south
 aspects under nurse plants resulted in negative effects on beneficiary
 species, while the north aspect still showed facilitation. Combined, these
 results emphasize the importance of spatial heterogeneity under nurse
 plants for mediating species loss under reduced precipitation, as
 predicted by future climate change scenarios. However, the decreased water
 availability expected under climate change will likely reduce overall
 facilitation and limit the role of nurse plants as refugia, amplifying
 biodiversity loss.
description: Compiled_CommunityDataData of all the compiled years for Figure 2. Meta-data is in the second page of the file.2012_CommunityDataCompiled data at the plot level for Figure 3. Meta-data is in the second page.Individual_LevelDataRaw species level data for each plot from 2012. Meta-data on second page. Used to make Figure 3c.