cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tc07j
title: Data from: A worldwide molecular phylogeny provides new insight on cryptic diversity within the moonworts (Botrychium s. s., Ophioglossaceae)

description: The moonwort genus, Botrychium s. s., includes diploid and polyploid taxa
 that occur primarily in the northern hemisphere. Their evolutionary
 history, morphologically cryptic taxa and deep divergence of the family in
 the phylogeny of ferns has long fascinated pteridologists. Previous
 molecular studies did not include a complete taxonomic sampling of the
 taxa in the genus, nor multiple specimens from throughout the known
 geographical range of each taxon. Therefore, to investigate evolutionary
 relationships of the major clades of Botrychium s. s., we increased both
 taxonomic representativeness (multiple accessions per taxa), as well as
 phylogenetic resolution by including additional new chloroplast markers.
 To confirm identification and provide evidence from both maternal and
 paternal parentage of allopolyploids, we also included specimens that have
 been characterized by allozyme profiles determined by electrophoretic
 analysis of 20 nuclear enzyme loci for each taxon. We analyzed four
 chloroplast regions (matK intron, trnHGUG —psbA, andtrnLUAA —trnFGAA
 intergenic spacers, and rpL16 intron region) of 365 specimens fromAsia,
 Europe, North America, Oceania, and South America, sampling the
 geographical range of 34 of 35 accepted Botrychium s. s. taxa and thirteen
 putatively new taxa. We conducted a phylogenetic analysis of maternal
 lineages based on 2,385 aligned nucleotides using maximum likelihood and
 Bayesian inference to explore genetic diversity and phylogenetic
 relationships among taxa. We found strong support for themonophyly of
 three major clades: Lanceolatum, Lunaria, and Simplex-Campestre, and
 resolved 15 subclades. Our results suggest multiple origins for at least
 four polyploid taxa (B. boreale, B. michiganense, B. yaaxudakeit, and B.
 watertonense). The Simplex-Campestre clade had the largest number of
 species, despite having a similar total number of haplotypes as the
 Lunaria clade (62 and 59, respectively), which has the broadest worldwide
 distribution. In total, our new molecular phylogeny comprises 47 taxa, of
 which thirteen are discussed for possible taxonomic recognition.
description: S1_Botrychium_matK_368_sequencesnon-coding chloroplast locus matK intronS1_matK_368_sequences.nexusS2_Botrychium_rpL16_367_sequencesnon-coding chloroplast locus rpL16 intronS2_rpL16_367_sequences.nexusS3_Botrychium_trnLF_368_sequencesnon-coding chloroplast locus trnL-trnF intergenic spacerS3_trnLF_368_sequences.nexusS4_Botrychium_trnHpsbA_368_sequencesnon-coding chloroplast locus trnH–psbA intergenic spacerS4_trnHpsbA_368_sequences.nexus
DOI: 10.5061/dryad.926pq
title: Data from: Ecology has contrasting effects on genetic variation within species versus rates of molecular evolution across species in water beetles

description: Comparative analysis is a potentially powerful approach to study the
 effects of ecological traits on genetic variation and rate of evolution
 across species. However, the lack of suitable datasets means that
 comparative studies of correlates of genetic traits across an entire clade
 have been rare. Here, we use a large DNA-barcode dataset (5062 sequences)
 of water beetles to test the effects of species ecology and geographical
 distribution on genetic variation within species and rates of molecular
 evolution across species. We investigated species traits predicted to
 influence their genetic characteristics, such as surrogate measures of
 species population size, latitudinal distribution and habitat types,
 taking phylogeny into account. Genetic variation of cytochrome oxidase I
 in water beetles was positively correlated with occupancy (numbers of
 sites of species presence) and negatively with latitude, whereas
 substitution rates across species depended mainly on habitat types, and
 running water specialists had the highest rate. These results are
 consistent with theoretical predictions from nearly-neutral theories of
 evolution, and suggest that the comparative analysis using large databases
 can give insights into correlates of genetic variation and molecular
 evolution.
description: Supplementary Data A.
 Table of haplotype, habitat and localityAccession numbers,
 geographic locations and habitat types of CO1 samples of water
 beetlesSupplementaryDataA.haplotype_habitat_locality.txtSupplementary Data B. Table of gmyc species traitsEcological and genetic traits of GMYC groupsSupplementaryDataB.gmycspecies_traits.txtSupplementary Data C. Accession numbers of CO1-16S-18SAccession numbers of downloaded sequences of CO1, 16S and 18SSupplementaryDataC.accessionCO1-16S-18S.txtGMYC Beast MCC treeAn MCC tree of GMYC groups in Newick formatgmyc.beast.rellognorm.re.treSupplementary Data A. Table of haplotype, habitat and locality (with corrected names)Accession numbers, geographic locations and habitat types of CO1 samples of water beetles (with corrected species names)SupplementaryDataA.haplotype_habitat_locality.revised.txtGMYC Beast MCC tree (with corrected names)An MCC tree of GMYC groups in Newick format with corrected species namesgmyc.beast.rellognorm.revised.tre
DOI: 10.5061/dryad.rh686
title: Data from: Disentangling the role of phenotypic plasticity and genetic divergence in contemporary ecotype formation during a biological invasion

description: The occurrence of contemporary ecotype formation through adaptive
 divergence of populations within the range of an invasive species
 typically requires standing genetic variation but can be facilitated by
 phenotypic plasticity. The relative contributions of both of these to
 adaptive trait differentiation have rarely been simultaneously quantified
 in recently diverging vertebrate populations. Here we study a case of
 intraspecific divergence into distinct lake and stream ecotypes of
 threespine stickleback that evolved in the past 140 years within the
 invasive range in Switzerland. Using a controlled laboratory experiment
 with full-sib crosses and treatments mimicking a key feature of ecotypic
 niche divergence, we test if the phenotypic divergence that we observe in
 the wild results from phenotypic plasticity or divergent genetic
 predisposition. Our experimental groups show qualitatively similar
 phenotypic divergence as those observed among wild adults. The relative
 contribution of plasticity and divergent genetic predisposition differs
 among the traits studied, with traits related to the biomechanics of
 feeding showing a stronger genetic predisposition, whereas traits related
 to locomotion are mainly plastic. These results implicate that phenotypic
 plasticity and standing genetic variation interacted during contemporary
 ecotype formation in this case.
description: MorphologyGeometric morphometric landmarks and linear measurements for experimental F1 threespine stickleback, their parents, wild type adults and young of the year individuals. Wild caught fish derive either from a lake or a stream site whereas experimental families were split and raised either under a benthic or limnetic diet.
DOI: 10.5061/dryad.n8963
title: Data from: Mechanisms of kin discrimination inferred from pedigrees and the spatial distribution of mates

description: Where animals avoid inbreeding, different mechanisms of kin discrimination
 can leave different “signatures” in the patterns of observed mate
 relationship. For example, consider a species with no paternal care. If
 females avoid mating with familiar individuals, one would expect a deficit
 of offspring whose parents are maternal half-siblings, but paternal
 half-siblings would be unfamiliar with each other and thus mate at the
 frequency expected by chance. If spatial cues are used to avoid
 inbreeding, females would be expected to produce few offspring with males
 (even unrelated males) living near the female’s birth site. We searched
 for these and other signatures with data from a long-term study of
 bannertailed kangaroo rats Dipodomys spectabilis in Arizona, USA, using a
 combination of intensive censusing, mapping of available dens,
 microsatellite-based parentage determination, and a randomization routine
 that determines the numbers of offspring expected if females in the
 population mate indiscriminately among the males available to them. The
 data are consistent with the hypothesis that kangaroo rats discriminate
 kin by association, rather than by using spatial cues or self-referential
 phenotype matching. Our randomization routine also demonstrates that in
 this species, dispersal alone is not particularly effective at eliminating
 opportunities for inbreeding. Our approach can be applied wherever the
 spatial distribution of individual mates and their pedigree relationships
 are known, and should be widely applicable as a means of assessing the
 degree to which both kin recognition and dispersal influence inbreeding.
description: Dipodomys_spectabilis_kinrecDistances and kin relationships between known mothers and possible fathers of all bannertailed kangaroo rat offspring whose parents were determined by microsatellite genotyping, 1990-2008, Arizona: see Readme file.
DOI: 10.5061/dryad.m0n46
title: Data from: Micro- and macroevolutionary trade-offs in plant-feeding insects

description: A long-standing hypothesis asserts that plant-feeding insects specialize
 on particular host plants because of negative interactions (trade-offs)
 between adaptations to alternative hosts, yet empirical evidence for such
 trade-offs is scarce. Most studies have looked for microevolutionary
 performance trade-offs within insect species, but host use could also be
 constrained by macroevolutionary trade-offs caused by epistasis and
 historical contingency. Here we used a phylogenetic approach to estimate
 the micro- and macroevolutionary correlations between use of alternative
 host-plant taxa within two major orders of plant-feeding insects:
 Lepidoptera (caterpillars) and Hemiptera (true bugs). Across 1,604
 caterpillar species, we found both positive and negative pairwise
 correlations between use of 11 host-plant orders, with overall network
 patterns suggesting that different host-use constraints act over micro-
 and macroevolutionary timescales. In contrast, host-use patterns of 955
 true bug species revealed uniformly positive correlations between use of
 the same 11 host plant orders over both timescales. The lack of consistent
 patterns across timescales and insect orders indicates that host-use
 trade-offs are historically contingent rather than universal constraints.
 Moreover, we observed few negative correlations overall despite the wide
 taxonomic and ecological diversity of the focal host-plant orders,
 suggesting that positive interactions between host-use adaptations, not
 trade-offs, dominate the long-term evolution of host use in plant-feeding
 insects.
description: Host-use data and
 phylogenies for plant-feeding Hemiptera and LepidopteraWe have included
 host-use information (in link form) for plant-feeding Hemiptera and
 Lepidoptera. There are 4 data files for each insect order, presenting the
 host-use information categorized by host plant genus, family and order.
 The fourth file is by plant order again, but this time a link is only
 included if that insect was observed on two genera in that plant order. We
 have also included molecular phylogenies for each insect order, produced
 using PHLAWD and the sequences available on genbank.Dryad_Data.tar
DOI: 10.5061/dryad.t608580
title: Data from: Distribution and genetic diversity of the rare plant Veratrum woodii (Liliales: Melanthiaceae) in Georgia: a preliminary study with AFLP fingerprint data

description: Veratrum woodii, a long-lived herbaceous perennial species, has a
 fragmented distribution with populations scattered in the southeastern and
 lower midwestern USA. In Georgia, the species has a protection status of
 rare. This preliminary study focused on verifying historic and/or
 unvouchered populations in Georgia and characterizing variation and
 genetic structure within and among all populations in the state. We
 analyzed AFLP (amplified fragment length polymorphism) data as dominantly
 inherited markers for 16 populations sampled from Georgia, Florida, and
 Missouri. Our results suggest that this species overall has relatively low
 levels of genetic diversity and that differentiation among populations is
 comparable to species with similar life history traits. Measures of
 genetic diversity, such as mean He, indicate that variation of populations
 has some partitioning between disjunct northern and southern Georgia (and
 Florida) populations. However, our analyses imply that watershed
 assignment, rather than geographic distance, provides a better explanation
 for variation and population structure. We hypothesize that southern
 relict populations in Georgia may have served as refugia during
 Pleistocene glaciations. We conclude that life-history characteristics,
 low levels of genetic variation, and suppression of ecological disturbance
 collectively jeopardize populations of Veratrum woodii in Georgia.
description: Data from: Distribution
 and genetic diversity of the rare plant Veratrum woodii (Liliales:
 Melanthiaceae) in Georgia: A preliminary study with AFLP fingerprint
 dataconcatenated AFLP
 dataZomlefer20Feb2018concatdata.xlsx
DOI: 10.5061/dryad.f1858
title: Data from: Fasting glucose and risk of colorectal cancer in the Korean Multi-center Cancer Cohort

description: Previous cohort studies have demonstrated a positive association between
 diabetes mellitus (DM) and colorectal cancer (CRC). However, there are few
 comparisons between groups with controlled DM and uncontrolled DM. This
 study examined associations between diabetes as defined by fasting serum
 glucose (FSG) levels and self-reported history of DM and CRC risk among
 Korean adults. Data from the Korean Multi-center Cancer Cohort between
 1993 and 2005 were analyzed. The study population comprised 14,570
 participants aged 20 years or older. Participants were followed until
 December 31, 2012 (median follow-up: 11.9 years). Among participants with
 high FSG (≥126mg/dL), the risk of developing CRC was significantly higher
 (HR: 1.51 [1.02-2.25]) than among participants with low FSG
 (&lt;126mg/dL). Risk was not significantly higher among participants
 with self-reported history of DM (HR: 1.34 [0.78-2.31]). When both FSG and
 history of DM were considered together, the risk of CRC was higher among
 participants with both high FSG and no history of DM (HR: 1.54
 [0.97-2.43]), but was not significantly higher among participants with
 both high FSG and a history of DM (HR: 1.50 [0.73-3.05]). When the first 5
 years of follow-up were excluded, among participants with high FSG, the
 risk of developing CRC was significantly higher (HR: 1.61 [1.02-2.56])
 than among participants with low FSG. Risk of CRC was also significantly
 higher among participants with high FSG and no history of DM (HR: 1.69
 [1.01-2.84]). High FSG and self-reported history of DM were associated
 with increased risk of CRC in this Korean population.
description: Diabetes mellitus and
 risk of colorectal cancerThe Korean Multi-center
 Cancer Cohort is a population-based prospective cohort study designed to
 investigate the relationship between exposures to environmental factors,
 lifestyle factors, and the risk of cancer in Korea. A total of 20,636
 participants (8,235 men and 12,401 women) were recruited from six
 geographic areas of Korea from 1993 to 2005. For these analyses, we
 excluded participants who had no information on age at cohort recruitment
 (1,182 men and 1,792 women), whose FSG level information was incomplete or
 who had no information about history of diabetes mellitus (1,007 men and
 1,575 women), who were aged 20 years or younger (156 men and 334 women),
 who had a prior diagnosis of colorectal cancer (6 men and 13 women), or
 who were censored within one month from the baseline survey (1 man). After
 these exclusions, 14,570 participants (5,883 men and 8,687 women) were
 included in the final analysis. Data were created using SAS software
 version 9.4 (SAS Institute Inc., Cary, North Carolina, United
 States).Data
 instruction.xlsxKMCC DM
 CRC.csv
DOI: 10.5061/dryad.s136dc8
title: Data from: Lichens: a limit to peat growth?

description: 1. The fruticose lichens Cladina stellaris and Cladina rangiferina, form
 thick mats that can cover large areas of northern peatlands (above ~ 50°
 latitude), including the extensive peatlands of the Hudson Bay Lowland
 (HBL) in Canada, where lichens may cover up to 50 % of the landscape.
 Despite the abundance of lichens in northern peatlands, our understanding
 of their role within peatland ecosystems, and peat accumulation in
 particular, is limited. 2. We investigate the potential effect of these
 mat-forming lichens on peat production and decomposition processes, using
 field data from an ombrogenous bog in the HBL and laboratory analyses. We
 hypothesise that (a) production in lichen-shrub hummocks is less than in
 Sphagnum-shrub hummocks; (b) the decay of lichen litter is faster than
 that of Sphagnum moss so the mass litter input to the peat profile is
 reduced; and (c) faster decomposition of the underlying peat is stimulated
 by lichen leachates, resulting in greater mass loss. 3. We found that
 thick lichen mats alter vegetation composition in peatlands, reducing
 Sphagnum cover and inhibiting the growth of small shrubs. Coupled with low
 lichen productivity that is constrained by moisture conditions, production
 for lichen-shrub hummocks is significantly smaller than for Sphagnum-shrub
 hummocks, confirming hypothesis (a). Our data also support hypothesis (b),
 with chemical analyses of lichen mats and leachates from lichen mats
 indicating faster decay of lichens compared to Sphagnum moss, and
 therefore reduced mass litter input to the peat profile in
 lichen-dominated hummocks. Although we found no evidence to suggest
 leachates from lichens enhance decomposition processes in peatlands
 (hypothesis c), larger dry bulk densities for peat under lichen mats
 indicate a loss of structural integrity and potential collapse of the peat
 column. 4. Synthesis: As production of new material added to the peat
 column is less in lichen-dominated hummocks, local peat accumulation slows
 or ceases, representing a potential temporary limit to peat growth. Our
 results highlight the importance of lichens as a vegetation feedback in
 peatland development, with thick mats probably constraining or reducing
 hummock height relative to adjacent, lichen-free hollows.
description: CO2_fluxVegetationLeachatesFTIRBulk_density
DOI: 10.5061/dryad.b06f3s2
title: Data from: Species diversity rises exponentially with the number of available resources in a multi-trait competition model

description: Theoretical studies of ecosystem models have generally concluded that
 large numbers of species will not stably co-exist if the species are all
 competing for the same limited set of resources. Here we describe a simple
 multi-trait model of competition where the presence of $N$ resources will
 lead to the stable co-existence of up to $2^N$ species. Our model also
 predicts that the long-term dynamics of the population will lie on a
 neutral attractor hyperplane. When the population shifts within the
 hyperplane, its dynamics will behave neutrally, while shifts which occur
 perpendicular to the hyperplane will be subject to restoring forces. This
 provides a potential explanation of why complex ecosystems might exhibit
 both niche-like and neutral responses to perturbations. Like the neutral
 theory of biodiversity, our model generates good fits to species abundance
 distributions in several datasets but does so without needing to evoke
 inter-generational stochastic effects, continuous species creation or
 immigration dynamics. Additionally, our model is able to explain species
 abundance correlations between independent but similar ecosystems
 separated by more than 1400 km inside the Amazonian forests.
description: Code for the
 figuresThe zip file contains
 seven folders containing the MATLAB code needed to reproduce the two
 figures and five supplementary figures presented in the paper. The code
 for each figure is contained within a separate and appropriately numbered
 folder, with the letter S denoting supplementary figures. Each code folder
 contains a main file named either plot X or Figure X which can be run to
 reproduce the figures with the help of auxiliary functions. The code files
 contain added comments and documentation to explain their organization
 further.Code.zip
DOI: 10.5061/dryad.14c6b
title: Data from: Opportunities for biodiversity gains under the world’s largest reforestation programme

description: Reforestation is a critical means of addressing the environmental and
 social problems of deforestation. China’s Grain-for-Green Program (GFGP)
 is the world’s largest reforestation scheme. Here we provide the first
 nationwide assessment of the tree composition of GFGP forests and the
 first combined ecological and economic study aimed at understanding GFGP’s
 biodiversity implications. Across China, GFGP forests are overwhelmingly
 monocultures or compositionally simple mixed forests. Focusing on birds
 and bees in Sichuan Province, we find that GFGP reforestation results in
 modest gains (via mixed forest) and losses (via monocultures) of bird
 diversity, along with major losses of bee diversity. Moreover, all current
 modes of GFGP reforestation fall short of restoring biodiversity to levels
 approximating native forests. However, even within existing modes of
 reforestation, GFGP can achieve greater biodiversity gains by promoting
 mixed forests over monocultures; doing so is unlikely to entail major
 opportunity costs or pose unforeseen economic risks to households.
description: Data for Hua et al
 Nature CommunicationsAll data for the field
 component of the article.Data, Hua et
 al.xlsx