cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q968v83
title: Data from: Genomic analysis and prediction within a US public collaborative winter wheat regional testing nursery

description: The development of inexpensive, whole-genome profiling enables a
 transition to allele-based breeding using genomic prediction models. These
 models consider alleles shared between lines to predict phenotypes and
 select new lines based on estimated breeding values. This approach can
 leverage highly-unbalanced datasets common to breeding programs. The
 Southern Regional Performance Nursery (SRPN) is a public nursery
 established by the USDA-ARS in 1931 to characterize performance and
 quality of near-release wheat varieties from breeding programs in the US
 Central Plains. New entries are submitted annually and can be reentered
 only once. The trial is grown at more than 30 locations each year and
 lines are evaluated for grain yield, disease resistance, and agronomic
 traits. Overall genetic gain is measured across years by including common
 check cultivars for comparison. We have generated whole-genome profiles
 via genotyping-by-sequencing for 939 SPRN entries dating back to 1992. We
 measured the diversity within the nursery and have explored its potential
 use as a GS training population. GS prediction models across years
 (average r= 0.33) outperformed year-to-year phenotypic correlation for
 yield (r=0.27) for a majority of the years evaluated, suggesting that
 genomic selection has the potential to outperform low heritability
 selection on yield in these highly variable environments. We also examined
 the predictability of programs using both program-specific and whole-set
 training populations. Generally, the predictability of a program was
 similar with both approaches. These results suggest that wheat breeding
 programs can collaboratively leverage the immense datasets that are
 generated from regional testing networks.
description: Southern Regional
 Performance Nursery phenotypic data 1992-2015Zip file containing the
 entry data used for the publication Genomic analysis and prediction within
 a US public collaborative winter wheat regional testing nursery. The ZIP
 file comprises of a list of all entries used, the raw phenotypes for all
 entries, a key for location codes, and a key for state
 codes.srpn_phenotypic_data.zip
DOI: 10.5061/dryad.99ch097
title: Data from: Mycorrhizal feedbacks generate positive frequency dependence accelerating grassland succession

description: 1. Plant mutualists including arbuscular mycorrhizal (AM) fungi have been
 postulated as being important drivers of plant community diversity and
 succession. Late successional plants have been shown to be more responsive
 to AM fungi and more sensitive to AM fungal species identity, which could
 generate positive feedback and potentially accelerate succession. 2. We
 test the effect of AM fungi on plant diversity and on frequency dependence
 predicted by positive plant‐AM fungi feedback across a successional
 gradient. We created prairie mesocosms comprised of a majority
 early‐successional, equal abundance and a majority late successional plant
 species. We inoculated these mesocosms and a field restoration experiment
 with 14 different communities of AM fungi from late successional prairies
 that varied in levels of species richness. 3. Overall, we found that AM
 fungi increased plant diversity and this was driven by the response of
 late successional plant species to mycorrhizae. Our results indicate that
 AM fungal composition is more important than AM fungal diversity per se.
 We found that the effect of inoculation with a single species or groups of
 AM fungi depended on whether those fungi benefited late successional plant
 species. Early successional plants consistently exhibited negative
 frequency dependent growth regardless of fungal composition, while late
 successional plants demonstrated positive frequency dependent growth in
 our mesocosms—but only in the presence of beneficial AM fungal species.
 These results are consistent with positive plant‐mycorrhizal feedbacks
 accelerating plant community successional trajectories once late
 successional plants establish. Mesocosm results were mirrored with field
 inoculation assays where we found that beneficial AM fungi facilitated
 late successional plant establishment. 4. Synthesis. Our results provide
 support for beneficial AM fungi being a primary mechanism for positive
 plant‐soil feedback driving plant community succession, as late
 successional seedlings grew faster and larger when their neighbors were
 also late successional plant species when they were associated with
 beneficial AM fungi. We found that this positive feedback thereby
 accelerated succession in mesocosms and in the field.
description: All
 dataWe have organized the
 zipped file to include several files. The titles of these files contain
 the relevant data sheets and code used to analyze the data. There are
 folders for the field and the mesocosm study
 separately.DRYAD DATA JoE Koziol
 Bever.zip
DOI: 10.5061/dryad.dq28j
title: Data from: Cryptic elevational zonation in trapdoor spiders (Araneae, Antrodiaetidae, Aliatypus janus complex) from the California southern Sierra Nevada

description: The relative roles of ecological niche conservatism versus niche
 divergence in promoting montane speciation remains an important topic in
 biogeography. Here, our aim was to test whether lineage diversification in
 a species complex of trapdoor spiders corresponds with riverine barriers
 or with an ecological gradient associated with elevational tiering.
 Aliatypus janus was sampled from throughout its range, with emphasis on
 populations in the southern Sierra Nevada Mountains of California. We
 collected multi-locus genetic data to generate a species tree for A. janus
 and its close relatives. Coalescent based hypothesis tests were conducted
 to determine if genetic breaks within A. janus conform to riverine
 barriers. Ecological niche models (ENM) under current and Last Glacial
 Maximum (LGM) conditions were generated and hypothesis tests of niche
 conservatism and divergence were performed. Coalescent analyses reveal
 deeply divergent genetic lineages within A. janus, likely corresponding to
 cryptic species. Two primary lineages meet along an elevational gradient
 on the western slopes of the southern Sierra Nevada Mountains. ENMs under
 both current and LGM conditions indicate that these groups occupy largely
 non-overlapping niches. ENM hypothesis testing rejected niche identity
 between the two groups, and supported a sharp ecological gradient
 occurring where the groups meet. However, the niche similarity test
 indicated that the two groups may not inhabit different niches from their
 backgrounds. The Sierra Nevada Mountains provide a natural laboratory for
 simultaneously testing ecological niche divergence and conservatism and
 their role in speciation across a diverse range of taxa. Aliatypus janus
 represents a species complex with cryptic lineages that may have diverged
 due to parapatric speciation along an ecological gradient, or been
 maintained by the evolution of ecological niche differences following
 allopatric speciation.
description: Aliatypus_COI_dryadCytochrome oxidase I alignment nexus fileAliatypus_28S_dryad28S ribosomal DNA nexus file. Aligned with MAFFT, ambiguously aligned regions removed using GBLOCKS with default conditions.Aliatypus_E9E10_39S_dryad39S ribosomal protein L44, putative, alignment nexus fileAliatypus_F1F2_ribonuclease_dryadribonuclease P/MRP protein subunit POP5, putative, alignment file, nexus formatAliatypus_F9F10_tartan_dryadtartan protein, putative, alignment file, nexus formatAliatypus_G1G2_Sdccag1_dryadSdccag1 protein, putative, alignment file, nexus formatAliatypus_H1H2_Sushi_dryadSushi, von Willebrand factor type A, EGF and pentraxin domain-containing protein 1, putative, alignment file, nexus formatAliatypus_H9H10_ribosome_dryadribosome biogenesis protein, putative, alignment file, nexus format
DOI: 10.5061/dryad.hf305
title: Data from: Diversification practices reduce organic to conventional yield gap

description: Agriculture today places great strains on biodiversity, soils, water and
 the atmosphere, and these strains will be exacerbated if current trends in
 population growth, meat and energy consumption, and food waste continue.
 Thus, farming systems that are both highly productive and minimize
 environmental harms are critically needed. How organic agriculture may
 contribute to world food production has been subject to vigorous debate
 over the past decade. Here, we revisit this topic comparing organic and
 conventional yields with a new meta-dataset three times larger than
 previously used (115 studies containing more than 1000 observations) and a
 new hierarchical analytical framework that can better account for the
 heterogeneity and structure in the data. We find organic yields are only
 19.2% (±3.7%) lower than conventional yields, a smaller yield gap than
 previous estimates. More importantly, we find entirely different effects
 of crop types and management practices on the yield gap compared with
 previous studies. For example, we found no significant differences in
 yields for leguminous versus non-leguminous crops, perennials versus
 annuals or developed versus developing countries. Instead, we found the
 novel result that two agricultural diversification practices,
 multi-cropping and crop rotations, substantially reduce the yield gap (to
 9 ± 4% and 8 ± 5%, respectively) when the methods were applied in only
 organic systems. These promising results, based on robust analysis of a
 larger meta-dataset, suggest that appropriate investment in agroecological
 research to improve organic management systems could greatly reduce or
 eliminate the yield gap for some crops or regions.
description: DataForSubmittingMeta-dataset of studies comparing organic and conventional yields.
DOI: 10.5061/dryad.v7h47
title: Data from: Evolutionary relationships within the Triops (Notostraca: Branchiopoda) using complete mitochondrial genomes

description: The tadpole shrimp (Notostraca: Triops) have been called living fossils
 with conserved morphology, but subtle morphological variations within and
 between species has yielded confused taxonomic assignments. To aid in
 cryptic species detection of tadpole shrimp from southern New Mexico, USA,
 the first complete mitochondrial genomes for three putative species (T.
 longicaudatus “long,” T. l. “short,” T. newberryi) are reported. The
 genomes ranged in length from 15,058 bp to 15,060 bp with 13 coding genes,
 22 tRNA genes, 2 rRNA genes and a control region. Phylogenetic trees were
 constructed using previously sequenced Triops-genomes to assess genetic
 relationships within the genus. The T. longicaudatus-genomes from Genbank
 were consistent with our genomes for T. newberryi and T. l. “short.”
 Variation in mitochondrial genes were identified that will aid future
 identification of cryptic lineages of tadpole shrimp. Genetic
 differentiation among the genomes of Triops in New Mexico support
 elevation to species status.
description: Triopslongicaudatus-long_454Reads_mtGenomeAssemblyThe reads in this FASTA file were generated by a Roche 454 Life Sciences GS FLX genome sequencer at New Mexico State University, NM, USA. The sequence reads were used to assembly the mitochondrial genome from Triops longicaudatus "long".Triopslongicaudatus-short_454Reads_MtGenomeAssemblyThe reads in this FASTA file were generated by a Roche 454 Life Sciences GS FLX genome sequencer at New Mexico State University, NM, USA. The sequence reads were used to assembly the mitochondrial genome from Triops longicaudatus "short".Triopsnewberryi_454Reads_mtGenomeAssemblyThe reads in this FASTA file were generated by a Roche 454 Life Sciences GS FLX genome sequencer at New Mexico State University, NM, USA. The sequence reads were used to assembly the mitochondrial genome from Triops newberryi.
DOI: 10.5061/dryad.73k6g
title: Data from: Locomotory abilities and habitat of the Cretaceous bird Gansus yumenensis inferred from limb length proportions

description: The relative length proportions of the three bony elements of the pelvic
 (femur, tibiotarsus and tarsometatarsus) and pectoral (humerus, ulna and
 manus) limbs of the early Cretaceous bird Gansus yumenensis, a
 well-represented basal ornithuromorph from China are investigated and
 compared to those of extant taxa. Ternary plots show that the pectoral
 limb length proportions of Gansus are most similar to Apodiformes (swifts
 and hummingbirds), which plot away from all other extant birds. In
 contrast, the pelvic limb length proportions of Gansus fall within the
 extant bird cluster and show similarities with the neornithine families
 Podicipedidae (grebes), Diomedeidae (albatross) and Phalacrocoracidae
 (cormorants). Although it does have some of the pelvic limb features of
 grebes and cormorants, the femur of Gansus is more gracile and is thus
 more consistent with an albatross like shallow diving mode-of-life than a
 strong-foot-propelled diving movement pattern. The position of Gansus in
 pectoral limb ternary morphospace is largely due to its elongated manus.
 In contrast to apodiformes, where the humerus and ulna are short and
 robust, an adaptation, which provides a stiff wing for their demanding
 fast agile and hovering flight (respectively), the wing-bones of Gansus
 are slender, indicating a less vigorous flapping flight style. The suite
 of characters exhibited by Gansus mean it is difficult to completely
 interpret its likely ecology. Nevertheless, our analyses suggest that it
 is probable that this bird was both volant and capable of diving to some
 degree using either foot-propelled or, perhaps, both its wings and its
 feet for underwater locomotion.
description: Limb_length_dataThe file contains 4 tables containing pelvic and pectoral limb length measurements of fossil birds and extant birds measured in mm. The data were collected from museum specimens.Nudds_et_al_JEB-2012-00481.R1_data.pdf
DOI: 10.5061/dryad.5jf41k5
title: Data from: The ghost of introduction past: spatial and temporal variability in the genetic diversity of invasive smallmouth bass

description: Understanding the demographic history of introduced populations is
 essential for unravelling their invasive potential and adaptability to a
 novel environment. To this end, levels of genetic diversity within the
 native and invasive range of a species are often compared. Most studies,
 however, focus solely on contemporary samples, relying heavily on the
 premise that the historic population structure within the native range has
 been maintained over time. Here, we assess this assumption by conducting a
 three-way comparison of the genetic diversity of native (historic and
 contemporary) and invasive (contemporary) smallmouth bass (Micropterus
 dolomieu) populations. Analyses of a total of 572 M. dolomieu samples,
 representing the contemporary invasive South African range, contemporary
 and historical native USA range (dating back to the 1930s when these fish
 were first introduced into South Africa), revealed that the historical
 native range had higher genetic diversity levels when compared to both
 contemporary native and invasive ranges. These results suggest that both
 contemporary populations experienced a recent genetic bottleneck.
 Furthermore, the invasive range displayed significant population
 structure, whereas both historical and contemporary native USA populations
 revealed higher levels of admixture. Comparison of contemporary and
 historical samples showed both a historic introduction of M. dolomieu, as
 well as a more recent introduction, thereby demonstrating that
 undocumented introductions of this species have occurred. Although
 multiple introductions might have contributed to the high levels of
 genetic diversity in the invaded range, we discuss alternative factors
 that may have been responsible for the elevated levels of genetic
 diversity and highlight the importance of incorporating historic specimens
 into demographic analyses.
description: Microsatellite genotypes
 for contemporary invasive (CI), contemporary native (CN) and historical
 native (HN) populationsMicrosatellite genotypes
 for smallmouth bass (Micropterus dolomieu) collected in a contemporary
 invasive range (CI- South Africa) and contemporary and historical native
 range (CN & HN - USA).Dryad submission_Microsatellite
 genotypes.xlsxcytb mtDNA
 sequencescytb mtDNA sequences for
 Micropterus dolomieu in an invasive (South Africa) and native (USA)
 rangeSA_USA_cytb.fasControl Region sequences for Micropterus dolomieuCR mtDNA sequences for Micropterus dolomieu in an invasive (South Africa) and native (USA) rangeSA_USA_cr.fas
DOI: 10.5061/dryad.322q2
title: Data from: Contrasts in the marine ecosystem of two Macaronesian islands: a comparison between the remote Selvagens Reserve and Madeira Island

description: The islands of Madeira and Selvagens are less than 300 km apart but offer
 a clear contrast between a densely populated and highly developed island
 (Madeira), and a largely uninhabited and remote archipelago (Selvagens)
 within Macaronesia in the eastern Atlantic. The Madeira Archipelago has
 ~260,000 inhabitants and receives over six million visitor days annually.
 The Selvagens Islands Reserve is one of the oldest nature reserves in
 Portugal and comprises two islands and several islets, including the
 surrounding shelf to a depth of 200 m. Only reserve rangers and a small
 unit of the maritime police inhabit these islands. The benthic community
 around Selvagens was dominated by erect and turf algae, while the
 community at Madeira was comprised of crustose coralline and turf algae,
 sessile invertebrates, and sea urchin barrens. The sea urchin Diadema
 africanum was 65% more abundant at Madeira than at Selvagens. Total fish
 biomass was 3.2 times larger at Selvagens than at Madeira, and biomass of
 top predators was more than 10 times larger at Selvagens. Several
 commercially important species (e.g., groupers, jacks), which have been
 overfished throughout the region, were more common and of larger size at
 Selvagens than at Madeira. Important sea urchin predators (e.g.,
 hogfishes, triggerfishes) were also in higher abundance at Selvagens
 compared to Madeira. The effects of fishing and other anthropogenic
 influences are evident around Madeira. This is in stark contrast to
 Selvagens, which harbors healthy benthic communities with diverse algal
 assemblages and high fish biomass, including an abundance of large
 commercially important species. The clear differences between these two
 island groups highlights the importance of expanding and strengthening the
 protection around Selvagens, which harbors one of the last intact marine
 ecosystems in the North Atlantic, and the need to increase management and
 protection around Madeira.
description: Selvagens_Madeira_fish_dataCollected in the field, Excel, abbreviations in Readme fileSelvagens_Madeira_benthic_datacollected in the field, Excel, abbreviations in Readme fileSelvagens_Madeira_mobile_invertscollected in the field, Excel, abbreviations in Readme file
DOI: 10.5061/dryad.q810f
title: Data from: Ecological and evolutionary diversification within the genus Carex (Cyperaceae): consequences for community assembly in subarctic fens

description: The concept of limiting similarity predicts that closely related taxa are
 less likely to co-occur than expected by chance. The degree to which the
 phylogenetic relatedness in plant communities is in accord with limiting
 similarity has been little tested at the scale where the consequences of
 adaptive differentiation during speciation should be most evident: the
 scale of neighboring, congeneric plants within a community. To quantify
 species co-occurrence patterns in relation to environment, we sampled
 sedge species, their rooting level relative to the water table, and the
 water pH in 2,124 0.25 m² quadrats distributed across 29 subarctic fens in
 the central Labrador Peninsula. We estimated phylogenetic relationships
 using four DNA regions (ETS, ITS, matK, trnL-trnF) for all species of
 Carex (42), Eriophorum (6), and Trichophorum (2) in the region, of which
 21, four, and two, respectively, occurred in the sampled fens. We
 demonstrate that closely related species of Carex are less likely to
 co-occur than expected by chance using 1) a probabilistic method to test
 the significance of pairwise co-occurrence patterns of species, and 2)
 linear mixed modeling to relate these patterns to phylogenetic
 relationships and ecological tolerances along gradients of substrate pH
 and rooting level in relation to the water table. The results also
 indicate that suites of species with significant mutual pairwise
 co-occurrence belong to distant lineages within the
 Cariceae-Dulichieae-Scirpeae clade of Cyperaceae and have stabilizing
 niche differences. We suggest that niche differentiation during the
 evolution and diversification of a clade of wetland Carex species over the
 past few million years, especially during the dynamic glacial cycles of
 the Pleistocene, has resulted in diverse sedge communities that share
 space and resources in harsh northern peatland habitats.
description: Supplemental Table
 1csv
 file with field sampling data for species co-occurences, rooting level and
 pH values in each of the 0.25 m2 quadrats sampled in the Schefferville
 fens, with accompanying READ_ME.rtf file giving details of sampling method
 and defining abbreviationsSupplemental_Table_1_Quadrat_by_species_env_matrix.csvSupplemental_Table_2csv file giving co-occurrence results for all pairwise combinations of Cyperaceae species in Schefferville fens, with accompanying READ_ME.rtf file giving details of column headings and abbreviations used.DNA alignmentAlignment of sequence data for ETS, ITS, matK, trnL-trnF regions for species of Cyperaceae in Schefferville fensSupplemental_Figure_1Summary tree of BEAST results for alternative analysis using two secondary calibrations for dating the phylogenetic tree of Cyperaceae species from Schefferville fensSupplemental_Figure_2Summary tree from BEAST analysis using a secondary calibration for the root and Carex colwellensis to data the crown node of Carex