cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.s11b6
title: Data from: Genomic and phenotypic architecture of a spruce hybrid zone (Picea sitchensis x P. glauca)

description: Interspecific hybridization may enhance the capacity of populations to
 adapt to changing environments, and has practical implications for
 reforestation. We use genomewide estimates of admixture and phenotypic
 traits for trees in a common garden to examine the extent and direction of
 gene flow across a Picea hybrid zone, testing assumptions of the bounded
 hybrid superiority and tension zone models of hybrid zone maintenance.
 Seeds were collected from the ecological transition zone spanning from
 maritime to continental climates across the Picea sitchensis-P. glauca
 contact zone, and 721 trees were planted in a common garden experiment
 within the hybrid zone. Individuals were genotyped using a panel of 384
 candidate-gene single nucleotide polymorphisms (SNPs) putatively
 associated with adaptive traits in Picea, and phenotyped at age ten for
 height and autumn cold hardiness. Low interspecific heterozygosity in
 hybrids indicated intrinsic reproductive barriers were too weak to prevent
 widespread recombination, although introgression appeared asymmetric with
 P. sitchensis dominating the zone. While marker-based hybrid index was
 strongly correlated with climate and geography, phenotypic traits
 exhibited weak or no significant clines. Our results indicated that
 exogenous selection appeared to play a strong role in the distribution and
 structure of this hybrid zone, indicative of an environmentally determined
 bounded hybrid superiority model of hybrid zone maintenance, although
 endogenous mechanisms could not be ruled out. This study provides insight
 into the mechanisms underlying adaptation across ecologically transitional
 hybrid zones that will ultimately provide an additional tool in managing
 these economically important tree species.
description: DataDryad_PopulationDataIndividual (GenotypeID) and Population data for individuals genotyped and phenotyped from common garden experiment. TenYR_Height is height at 10 years of age (mm) and ColdInjury.8 and ColdInjury.18 is a proportion of injury at -8C and -18C. respectively
DOI: 10.5061/dryad.180n7
title: Data from: Systematics of the blindsnakes (Serpentes: Scolecophidia: Typhlopoidea) based on molecular and morphological evidence

description: The blindsnake superfamily Typhlopoidea (Gerrhopilidae, Typhlopidae, and
 Xenotyphlopidae) is a diverse, widespread part of the global snake fauna.
 A recent systematic revision based on molecular phylogenetic analyses and
 some morphological evidence presented a preliminary solution to the
 non-monophyly of many previously recognized genera, but additional
 clarification is needed regarding the recognition of some species and
 genera. We rectify these problems here with a new molecular phylogenetic
 analysis including 95 of the 275 currently recognized, extant typhlopoids,
 incorporating both nuclear and mitochondrial loci. We supplement this with
 data on the external, visceral, and hemipenial morphology of nearly all
 species to generate a revised classification for Typhlopoidea. Based on
 morphological data, we re-assign Cathetorhinus from Typhlopidae to
 Gerrhopilidae. Xenotyphlopidae maintains its current contents
 (Xenotyphlops). In Typhlopidae, one monotypic genus is synonymized with
 its larger sister-group as it cannot be unambiguously diagnosed
 morphologically (Sundatyphlops with Anilios), and two genera are
 synonymized with Typhlops (Antillotyphlops and Cubatyphlops), as they are
 not reciprocally monophyletic. The genus Asiatyphylops is renamed
 Argyrophis, the senior synonym for the group. We erect one new genus
 (Lemuriatyphlops) for a phylogenetically distinct species-group in
 Asiatyphlopinae. Fourteen of eighteen recognized typhlopid genera are
 maintained in four subfamilies: Afrotyphlopinae (Afrotyphlops,
 Grypotyphlops [re-assigned from Asiatyphlopinae], Letheobia, and
 Rhinotyphlops), Asiatyphlopinae (Acutotyphlops, Anilios, Cyclotyphlops,
 Indotyphlops, Malayotyphlops, Ramphotyphlops, and Xerotyphlops),
 Madatyphlopinae (Madatyphlops), and Typhlopinae (Amerotyphlops and
 Typhlops), some with altered contents. Diagnoses based on morphology are
 provided for all 19 typhlopoid genera, accounting for all 275 species.
 This taxonomy provides a robust platform for future revisions and
 description of new species.
description: Typhlopidae_10_5DNA Sequence Matrix. See partitions in README.partsRAxML_bipartitionsRAxML Tree.
DOI: 10.5061/dryad.cc47h
title: Data from: Island Biogeography, the effects of taxonomic effort and the importance of island niche diversity to single island endemic species

description: Island biogeography theory is fundamentally reliant on measuring the
 number of species per island and hence has taxonomy at its foundation. Yet
 as a metric used in tests of the theory, island species richness (S) has
 varied with time according to the level of taxonomic effort (a function of
 the rate of finding and describing species). Studies using a derivative of
 S, single-island endemic species richness (SIE S), may be prone to change
 in taxonomic effort. Decreases or increases in species numbers resulting
 from taxonomic revision or increased sampling are likely to have a large
 effect on values of SIE S, as they tend to be smaller than total S for the
 same island. Using simple biogeography models, we analysed estimates of
 SIE S in plants, land snails, beetles, and fungi from comprehensive data
 sets for eight island groups, produced species accumulation curves and
 applied Bayesian regression over five time periods. Explanatory power
 differed across taxa, but area and island age were not always the best
 explanatory variables, and niche diversity appeared to be important.
 Changing levels of SIE S over time had different effects on models with
 different taxa and between island archipelagos. The results indicated that
 the taxonomic effort that determines SIE S is important. However, as this
 cannot often be quantified, we suggest Bayesian approaches should be more
 useful than frequentist methods in evaluating SIE S in island biogeography
 theory. Fundamentally, the article highlights the importance of taxonomy
 to theoretical biogeography.
description: Island Biogeography
 Supporting Information
DOI: 10.5061/dryad.2pb57
title: Data from: Genetic structure across broad spatial and temporal scales: Rocky Mountain tailed frogs (Ascaphus montanus; Anura: Ascaphidae) in the inland temperate rainforest

description: Contemporary and historical processes interact to structure genetic
 variation, however discerning between these can be difficult. Here, we
 analyze range-wide variation at 13 microsatellite loci in 2098 Rocky
 Mountain tailed frogs, Ascaphus montanus, collected from 117 streams
 across the species distribution in the Inland Northwest (INW) and
 interpret that variation in light of historical phylogeography,
 contemporary landscape genetics, and the reconstructed paleodistribution
 of the species. Further, we project species distribution models (SDMs) to
 predict future changes in the range as a function of changing climate.
 Genetic structure has a strong spatial signature that is precisely
 congruent with a deep (~1.8 MY) phylogeographic split in mtDNA when we
 partition populations into 2 clusters (K = 2), and is congruent with
 refugia areas inferred from our paleorange reconstructions. There is a
 hierarchical pattern of geographic structure as we permit additional
 clusters, with populations clustering following mountain ranges.
 Nevertheless, genetic diversity is the highest in populations at the
 center of the range and is attenuated in populations closer to the range
 edges. Similarly, geographic distance is the single best predictor of
 pairwise genetic differentiation, but connectivity also is an important
 predictor. At intermediate and local geographic scales, deviations from
 isolation-by-distance are more apparent, at least in the northern portion
 of the distribution. These results indicate that both historical and
 landscape factors are contributing to the genetic structure and diversity
 of tailed frogs in the Inland Northwest.
description: Collection
 LocalitiesLocalities of streams
 that were surveyed, including those where we collected tailed frogs and
 those where we found none.SupplementalTable1.pdfMultilocus genotypesGenotypes at 13 microsattelite loci for 2118 Rocky Mountain tailed frogs.Ascaphus.genotypes.xls
DOI: 10.5061/dryad.r37sj
title: Data from: Geographical parthenogenesis and population genetic structure in the alpine species Ranunculus kuepferi (Ranunculaceae)

description: Geographical parthenogenesis describes the enigmatic phenomenon that
 asexual organisms have larger distribution areas than their sexual
 relatives, especially in previously glaciated areas. Classical models
 suggest temporary advantages to asexuality in colonization scenarios
 because of uniparental reproduction and clonality. We analyzed population
 genetic structure and self-fertility of the plant species Ranunculus
 kuepferi on 59 populations from the whole distribution area (European
 Alps, Apennines and Corsica). Amplified fragment length polymorphisms
 (AFLPs) and five microsatellite loci revealed individual genotypes for all
 populations and mostly insignificant differences between diploid sexuals
 and tetraploid apomicts in all measures of genetic diversity. Low
 frequencies of private AFLP fragments/simple sequence repeat alleles, and
 character incompatibility analyses suggest that facultative recombination
 explains best the unexpectedly high genotypic diversity of apomicts.
 STRUCTURE analyses using AFLPs revealed a higher number of partitions and
 a stronger geographical subdivision for diploids than for tetraploids,
 which contradicts expectations of standard gene flow models, but indicates
 a reduction of genetic structure in asexuals. Apomictic populations
 exhibited high admixture near the sexual area, but appeared rather uniform
 in remote areas. Bagging experiments and analyses of pollen tube growth
 confirmed self-fertility for pollen-dependent apomicts, but self-sterility
 for diploid sexuals. Facultative apomixis combines advantages of both
 modes of reproduction: uniparental reproduction allows for rapid
 colonization of remote areas, whereas facultative sexuality and polyploidy
 maintains genetic diversity within apomictic populations. The density
 dependence of outcrossing limits range expansions of sexual populations.
description: raw matrix
 AFLP_Geographical parthenogenesis and population genetic structure in the
 alpine species Ranunculus kuepferi (Ranunculaceae)AFLP matrix which
 contains in the first row the cytoytpe + population + sample number within
 the population and in the second row the population ID.
DOI: 10.5281/zenodo.18381470
title: Taxonomic revision of Hydrogaster (Malvaceae; Grewioideae), an endemic and monospecific genus of Brazil
DOI: 10.5281/zenodo.18381469
title: Taxonomic revision of Hydrogaster (Malvaceae; Grewioideae), an endemic and monospecific genus of Brazil
DOI: 10.5061/dryad.m717n
title: Data from: Nitrogen fertilization effects on productivity and nitrogen loss in three grass-based perennial bioenergy cropping systems

description: Nitrogen (N) fertilization can greatly improve plant productivity but
 needs to be carefully managed to avoid harmful environmental impacts.
 Nutrient management guidelines aimed at reducing harmful forms of N loss
 such as nitrous oxide (N2O) emissions and nitrate (NO3-) leaching have
 been tailored for many cropping systems. The developing bioenergy industry
 is likely to make use of novel cropping systems, such as polycultures of
 perennial species, for which we have limited nutrient management
 experience. We studied how a switchgrass (Panicum virgatum) monoculture, a
 5-species native grass mixture and an 18-species restored prairie
 responded to annual fertilizer applications of 56 kg N ha-1 in a
 field-scale agronomic trial in south-central Wisconsin over a 2-year
 period. We observed greater fertilizer-induced N2O emissions and
 sub-rooting zone NO3- concentrations in the switchgrass monoculture than
 in either polyculture. Fertilization increased aboveground net primary
 productivity in the polycultures, but not in the switchgrass monoculture.
 Switchgrass was generally more productive, while the two polycultures did
 not differ from each other in productivity or N loss. Our results
 highlight differences between polycultures and a switchgrass monoculture
 in responding to N fertilization.
description: Main
 tablePrimary data supporting
 analyses in Duran et al., principally Figure 1, Tables 1 and 2, and S1 and
 S2 Tables.main.csvDaily temperature and precipitationDaily temperature and precipitation data for 2011 and 2012 from an automated weather station located on one switchgrass plot from the experiment. Support S1 Figure.climate.csvHarvest dataPlot level harvest information. Supporting Figure 2.harvest.csvSeasonal soil nitrateSoil nitrate concentrations measured throughout the growing season. Supporting S2 Figure.nitrate.csvHourly soil temperature and water contentHourly automated soil measurements from a single switchgrass plot in 2011 and 2012. Supporting S1 Figure.soils.csv
DOI: 10.5061/dryad.k5mp137
title: Data from: A multi-state dynamic occupancy model to estimate local colonization-extinction rates and patterns of co-occurrence between two or more interacting species

description: 1. Although ecology is rife with theory that explores how multiple species
 co-occur through space and time, the ﬁeld lacks robust statistical models
 to parameterize this theory with empirical data, particularly when species
 are detected imperfectly and data are collected as a time-series. 2. We
 address this need by developing an occupancy model that estimates local
 colonization and extinction rates for two or more interacting species when
 data are collected across multiple sampling occasions. This model
 estimates how community composition at a site may change across sampling
 occasions by assuming the latent occupancy state is a categorical random
 variable. We used a multinomial-logit model to parameterize
 species-speciﬁc parameters and pairwise interactions between species, both
 of which can be made a function of covariates. These transition
 probabilities between community states can then be converted to occupancy
 or co-occurrence probabilities to determine how community composition
 varies along an environmental gradient or through time. 3. As an example,
 we estimate patterns of co-occurrence between coyote (Canis latrans),
 Virginia opossum (Didelphis virginiana), and raccoon (Procyon lotor) in
 Chicago, Illinois, USA with data from a multi-year camera trapping study.
 Models with pairwise interactions between species greatly out performed
 models that assumed independence between species. Opossum and raccoon, for
 example, were far less likely to go extinct in habitat patches where
 coyotes were present. 4. Community composition at a site depends on
 species interactions and the local environment. Our model can separate
 such eﬀects by estimating the underlying processes that deﬁne species
 occurrence patterns. As a result, our model can more explicitly quantify a
 wide range of ecological dynamics and therefore be used to empirically
 test ecological theory, such as estimating priority eﬀects at a site or
 turnover rates between species, both of which can be made to vary as a
 function of covariates.
description: Fidino_MEESee README for description of contents.
DOI: 10.5061/dryad.rn5pt
title: Data from: Eating down the food chain: generalism is not an evolutionary dead end for herbivores

description: The role of trophic specialisation in taxonomic diversification remains
 unclear. Plant specialists diversify faster than omnivores and
 animalivores, but at shorter macroevolutionary scales this pattern
 sometimes reverses. Here, we estimate the effect of diet diversification
 on speciation rates in noctilionoid bats, controlling for tree shape, rate
 heterogeneity and macroevolutionary regimes. We hypothesise that niche
 subdivision among herbivores positively relates to speciation rates,
 differing between macroevolutionary regimes. We found the rate at which
 new herbivorous lineages originate decreases as rates of diet evolution
 increase. Herbivores experience higher speciation rates, but generalist
 herbivores and predominantly herbivorous omnivores speciate faster than
 specialised herbivores, omnivores and animalivores. Generalised herbivory
 is not a dead end. We show that analysing ecological traits and
 diversification requires accounting for macroevolutionary regimes and
 within- and between-clade variation in evolutionary rates. Our approach
 overcomes the high false-positive rates of other methods and illuminates
 the roles of herbivory and specialisation in speciation.
description: Diet and evolutionary
 rates in NoctilionoideaDiet, trophic level
 index, and path-wise rates of speciation and trophic level evolution for
 192 species of noctilionoid bats.Noctilionoidea.data.csvMaximum clade credibility tree of NoctilionoideaTime-calibrated molecular phylogeny of 192 species of noctilionoid bats.Noctilionoidea.mcctree.nexSample of phylogenies of NoctilionoideaSample of 100 time-calibrated molecular phylogenies of noctilionoid bats.Noctilionoidea.100trees.nexR script for QuaSSE simulationsScript to test the performance of the quantitative state speciation and extinction (QuaSSE) model in phylogenies that include a shift in the speciation rate.testing.QuaSSE.RR script for split QuaSSE simulationsScript to test the performance of the quantitative state speciation and extinction model in phylogenies that are partitioned to explicitly accommodate a shift in the speciation rate (split QuaSSE).testing.splitQuaSSE.R
DOI: 10.5061/dryad.1580
title: Data from: Genealogy and palaeodrainage basins in Yunnan Province: phylogeography of the Yunnan spiny frog, Nanorana yunnanensis (Dicroglossidae)

description: Historical drainage patterns adjacent to the Qinghai-Tibetan Plateau
 differed markedly from those of today. We examined the relationship
 between drainage history and geographic patterns of genetic variation in
 the Yunnan spiny frog, Nanorana yunnanensis, using approximately 981 base
 pairs of mitochondrial DNA (mtDNA) partial sequences from encoding genes
 ND1 and ND2, and intervening areas including complete tRNA Ile, tRNA Gln,
 and tRNA Met. Two null hypotheses were tested, including (1) that genetic
 patterns do not correspond to the development of drainage systems and (2)
 that populations had been stable and not experienced population expansion,
 bottlenecking and selection. Genealogical analyses identified three,
 major, well-supported maternal lineages, each of which had two
 sublineages. These divergent lineages were completely concordant with six
 geographical regions. Genetic structure and divergence were strongly
 congruent with historical rather than contemporary drainage patterns. Most
 lineages and sublineages were formed through population fragmentation
 events during the rearrangement of paleodrainage basins in the early
 Pliocene and early Pleistocene. Sympatric lineages occurred only in
 localities at the boundaries of major drainages, likely reflecting
 secondary contact of previously allopatric populations. Extensive
 population expansion probably occurred early in the Middle Pleistocene
 accompanying dramatic climatic oscillations.
description: sequence file for
 Nanorana yunnanensis.txtThe sequences were
 obtained for all samples collected in the field, and the data file was
 created using the software MEGA 3.1. The column heading for each sequence
 is comprised of GenBank Accession No. and sequence description which
 include the species name and gene componants et al.sequencefileforNanoranayunnanensis.txt
DOI: 10.5061/dryad.8dd3n
title: Data from: Can long-range PCR be used to amplify genetically divergent mitochondrial genomes for comparative phylogenetics? A case study within spiders (Arthropoda: Araneae).

description: The development of second generation sequencing technology has resulted in
 the rapid production of large volumes of sequence data for relatively
 little cost, thereby substantially increasing the quantity of data
 available for phylogenetic studies. Despite these technological advances,
 assembling longer sequences, such as that of entire mitochondrial genomes,
 has not been straightforward. Existing studies have been limited to using
 only incomplete or nominally intra-specific datasets resulting in a
 bottleneck between mitogenome amplification and downstream high-throughput
 sequencing. Here we assess the effectiveness of a wide range of targeted
 long-range PCR strategies, encapsulating single and dual fragment primer
 design approaches to provide full mitogenomic coverage within the Araneae
 (Spiders). Despite extensive rounds of optimisation, full mitochondrial
 genome PCR amplifications were stochastic in most taxa, although 454 Roche
 sequencing confirmed the successful amplification of 10 mitochondrial
 genomes out of the 33 trialled species. The low success rates of
 amplification using long-Range PCR highlights the difficulties in
 consistently obtaining genomic amplifications using currently available
 DNA polymerases optimised for large genomic amplifications and suggests
 that there may be opportunities for the use of alternative amplification
 methods.
description: Supplementary
 table1Taxonomic  information
  and   primer  sequences  for  specimensSupplementary table
 2Taxonomic  information 
 and   primer  properties  for  specimensSliding window analysis
 of nucleotide diversitySliding  window  plots 
 of  nucleotide  diversity  (pi)  across  all  13  mitochondrial  protein 
 coding  genes  and  both  ribosomal  RNA  genes  of  six  Araneae
  taxa. Sliding_window_spider_genes.pdfRoche 454 sequence quality plotFrequency plot of phred quality scores from the total number of reads obtained from 454 sequencing454_Quality_plot.pdf454 assembled contigsFasta files of contigs assembled from 454 GS FLX sequencing data
DOI: 10.15468/dl.uqp9sk
title: Occurrence Download

description: A dataset containing 6688 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Senna hirsuta"
 ]
}

 The dataset includes 6688 records from 380 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000532-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.