cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t1r37b7v
title: Data from: A phylogeny and evolutionary natural history of Mesoamerican toads (Anura: Bufonidae: Incilius) based on morphology, life history, and molecular data

description: We combine mitochondrial and nuclear DNA sequence data with non-molecular
 (morphological and natural history) data to conduct phylogenetic analyses
 and generate an evolutionary hypothesis for the relationships among nearly
 every species of Mesoamerican bufonid in the genus Incilius. We collected
 a total of 5,898 aligned base-pairs (bp) of sequence data from
 mitochondrial (mtDNA: 12S–16S, cyt b, ND2–CO1, including tRNAsTRP–TYR and
 the origin of light strand replication; total 4,317 bp) and nuclear (CXCR4
 and RAG1; total 1,581 bp) loci from 52 individuals representing 37
 species. For the non-molecular data, we collected 44 characters from 29
 species. We also include Crepidophryne, a genus that has not previously
 been included in molecular analyses. We present results of parsimony and
 Bayesian analyses for these data separately and combined. Relationships
 based on the non-molecular data were poorly supported and did not resolve
 a monophyletic Incilius (Rhinella marina was nested within). Our molecular
 data provide significant support to most of the relationships. Our
 combined analyses demonstrate that inclusion of a considerably smaller
 dataset (44 vs. 5,898 characters) of non-molecular characters can provide
 significant support where the molecular relationships were lacking
 support. Our combined results indicate that Crepidophryne is nested within
 Incilius; therefore, we place the former in the synonymy of the latter
 taxon. Our study provides the most comprehensive evolutionary framework
 for Mesoamerican bufonids (Incilius), which we use as a starting point to
 invoke discussion on the evolution of their unique natural history traits.
description: Mendelson_etal_Inc52_MrBMrBayes file for all molecular data (see Table 1 for voucher information). See Appendix I for GenBank numbers).Mendelson_etal_Inc37MrBCombined non-molecular and molecular MrBayes file (see Table 1 for voucher information, Appendix I for GenBank numbers, and Appendix III for Non-molecular character descriptions).
DOI: 10.5061/dryad.450dp
title: Data from: Historical biogeography of the fern genus Deparia (Athyriaceae) and its relation with polyploidy

description: The wide geographical distribution of many fern species is related to
 their high dispersal ability. However, very limited studies surveyed
 biological traits that could contribute to colonization success after
 dispersal. In this study, we applied phylogenetic approaches to infer
 historical biogeography of the fern genus Deparia (Athyriaceae, Eupolypod
 II). Because polyploids are suggested to have better colonization
 abilities and are abundant in Deparia, we also examined whether polyploidy
 could be correlated to long-distance dispersal events and whether
 polyploidy could play a role in these dispersals/establishment and range
 expansion. Maximum likelihood and Bayesian phylogenetic reconstructions
 were based on a four-region combined cpDNA dataset (rps16-matK IGS,
 trnL-L-F, matK and rbcL; a total of 4,252 characters) generated from 50
 ingroup (ca. 80% of the species diversity) and 13 outgroup taxa. Using the
 same sequence alignment and maximum likelihood trees, we carried out
 molecular dating analyses. The resulting chronogram was used to
 reconstruct ancestral distribution using Lagrange and ancestral ploidy
 level using ChromEvol. We found that Deparia originated around 27.7 Ma in
 continental Asia/East Asia. A vicariant speciation might account for the
 disjunctive distribution of East Asia–northeast North America. There were
 multiple independent long-distance dispersals to Africa/Madagascar (at
 least once), Southeast Asia (at least once), south Pacific islands (at
 least twice), Australia/New Guinea/New Zealand (at least once), and the
 Hawaiian Islands (at least once). In particular, the long-distance
 dispersal to the Hawaiian Islands was associated with polyploidization,
 and the dispersal rate was slightly higher in the polyploids than in
 diploids. Moreover, we found five species showing recent infraspecific
 range expansions, all of which took place concurrently with
 polyploidization. In conclusion, our study provides the first
 investigation using phylogenetic and biogeographic analyses trying to
 explore the link between historical biogeography and ploidy evolution in a
 fern genus and our results imply that polyploids might be better
 colonizers than diploids.
description: Deparia_matK+rbcLmatK + rbcL alignment includes Deparia and Eupolypod II outgroups (the partitions are detailed in the nexus file)Deparia_four_cpDNA_regionstrnL-L-F + rps16-matK IGS + matK + rbcL alignment includes Deparia, Athyriaceae, Onocleaceae, and Blechnaceae outgroups (the partitions are detailed in the nexus file)Deparia_CRY2_first_intronalignment of Deparia CRY2 first intron
DOI: 10.5061/dryad.p513f
title: Data from: Differences in endophyte communities of introduced trees depend on the phylogenetic relatedness of the receiving forest

description: Plant species sometimes perform extraordinarily well when introduced to
 new environments, through achieving higher growth rates, individual
 biomasses or higher densities in their receiving communities compared to
 their native range communities. One hypothesis proposed to explain
 enhanced performance in species’ new environments is that their soil
 microbial communities may be different and provide greater benefit than
 microbial communities encountered in species’ native environments.
 However, detailed descriptions of soil biota associated with species in
 both their native and introduced environments remain scarce. We
 established a global network of sites in regions where the tree species
 Pinus contorta has been introduced (Chile, New Zealand, Finland, Scotland
 and Sweden), as well as native range sites where the introduced
 populations originated (Canada and USA). We conducted pyrosequencing
 analysis to compare the root fungal endophyte communities associated with
 P. contorta in its native environments and in introduced environments with
 phylogenetically similar and dissimilar tree species (i.e. P. sylvestris
 in Europe and Nothofagus spp. in the Southern Hemisphere). Fungal
 communities associated with P. contorta consistently differed between its
 introduced and native environments. In Europe, P. contorta associated with
 the same community as P. sylvestris, where one particular species
 (Piloderma sphaerosporum) was particularly abundant relative to Canadian
 sites. In the Southern Hemisphere, P. contorta fungal communities were
 composed primarily of North American taxa and exhibited very little
 overlap with fungal communities associated with native Nothofagus spp.
 Synthesis. Our work shows that plants exhibit considerable plasticity in
 their interaction with fungi, by associating with different fungal
 communities across native and introduced environments. Our work also
 indicates that fungal communities associated with introduced plants can
 assemble through different mechanisms, that is by associating with
 existing fungal communities of phylogenetically close species, or through
 reassembly of co-introduced and co-invading fungi. The identification of
 different fungal communities in a plant species new environment provides
 an important step forward in understanding how soil biota may impact
 growth and invasion when a species is introduced to new environments.
description: Raw Data
 SummaryRaw data of fungal
 community OTUs, and OTU richness and abundance across 7 stand types,
 including Pinus contorta in: a) Canada, b) USA, c) Europe, d) Southern
 Hemisphere, and e) Pinus sylvestris in Europe, f) Nothofagus spp. in the
 Southern Hemisphere, and g) and Invading Pinus contorta individuals in
 Southern Hemisphere.
DOI: 10.5061/dryad.8s58v
title: Data from: Rare species contribute disproportionately to the functional structure of species assemblages

description: There is broad consensus that the diversity of functional traits within
 species assemblages drives several ecological processes. It is also widely
 recognized that rare species are the first to go extinct following
 human-induced disturbances. Surprisingly, however, the functional
 importance of rare species is still poorly understood, particularly in
 tropical species-rich assemblages where the majority of species are rare
 and the rate of species extinction can be high. Here we investigated the
 consequences of local and regional extinctions on the functional structure
 of species assemblages. We used three extensive datasets (stream fish from
 the Brazilian Amazon, rainforest trees from French Guiana, and birds from
 the Australian Wet Tropics) and built an integrative measure of species
 rarity vs. commonness, combining local abundance, geographic range, and
 habitat breadth. Using different scenarios of species loss, we found a
 disproportionate impact of rare species extinction for the three groups,
 with significant reductions in levels of functional richness,
 specialization and originality of assemblages, which may severely
 undermine the integrity of ecological processes. The whole breadth of
 functional abilities within species assemblages, which is
 disproportionately supported by rare species, is certainly critical in
 maintaining ecosystems particularly under the ongoing rapid environmental
 transitions.
description: Rarity index and
 functional traits for stream fishes, rainforest trees and
 birds.This file contains all
 data needed to reproduce the study, including the values of rarity metrics
 (i.e. local abundance, geographic range, habitat breadth, and the
 integrative measure of rarity vs. commonness - RIi) and functional traits
 for each species (i.e. 395 stream fish from the Brazilian Amazon, 262
 rainforest trees from French Guiana, and 86 birds from the Australian Wet
 Tropics). The file also includes data on species presence/absence across
 local assemblages. Description of abbreviations are provided as a metadata
 sheet.Datasets_Leitao_Rare_species_biodiversity.xlsx
DOI: 10.5061/dryad.8469
title: Data from: Metapopulation structure of a seed-predator weevil and its host plants in arms race coevolution

description: Although the importance of gene flow in the geographic structuring of
 host–parasite interactions has been well discussed, little is known about
 how dispersal drives the spatial dynamics of other types of coevolutionary
 interactions in nature. We evaluated the roles of gene flow in the
 geographically structured processes of a predator–prey arms race involving
 a seed-predatory weevil with a long mouthpart and its host camellia plant
 with a thick fruit coat. Molecular genetic analyses showed that both
 weevil and camellia populations were structured at a spatial scale of
 several kilometers. Importantly, the spatial pattern of the migration of
 weevils, but not that of camellias, imposed significant effects on the
 geographic configuration of the levels of coevolutionary escalation. This
 result suggests that even if migration is limited in one species
 (camellia), local coevolution with the other species that migrates between
 neighboring localities (weevil) can reduce the inter-population difference
 in the local adaptive optima of the former species. Thus, gene flow of a
 species potentially homogenizes local biological environments provided by
 the species and thereby promotes the evolutionary convergence of its
 coevolving counterparts. Consequently, by focusing on coevolutionary
 interactions in natural communities, “indirect” effects of gene flow on
 the adaptive divergence of organisms could be identified.
description: Morphology_Climate_dataStudy sites, Morphological data and climatic conditions of the study sites.Camellia_SSR_data_GenAlExThe microsatellite data of the Japanese camellia in the GenAlEx format.Weevil_COI_data_ArlequinThe mitochondrial COI data of the camellia weevil in the Arlequin format.Migrate_infile_CamelliaThe camellia microsatellite data for the Migrate-n analysis.Migrate_infile_WeevilThe weevil mt COI data for the Migrate-n analysis.
DOI: 10.5061/dryad.73180
title: Data from: Paternal signature in kin recognition cues of a social insect: concealed in juveniles, revealed in adults

description: Kin recognition is a key mechanism to direct social behaviours towards
 related individuals or avoid inbreeding depression. In insects,
 recognition is generally mediated by cuticular hydrocarbon (CHC)
 compounds, which are partly inherited from parents. However, in social
 insects, potential nepotistic conflicts between group members from
 different patrilines are predicted to select against the expression of
 patriline-specific signatures in CHC profiles. Whereas this key prediction
 in the evolution of insect signalling received empirical support in
 eusocial insects, it remains unclear whether it can be generalized beyond
 eusociality to less-derived forms of social life. Here, we addressed this
 issue by manipulating the number of fathers siring clutches tended by
 females of the European earwig, Forficula auricularia, analysing the CHC
 profiles of the resulting juvenile and adult offspring, and using
 discriminant analysis to estimate the information content of CHC with
 respect to the maternal and paternal origin of individuals. As predicted,
 if paternally inherited cues are concealed during family life, increases
 in mating number had no effect on information content of CHC profiles
 among earwig juveniles, but significantly decreased the one among adult
 offspring. We suggest that age-dependent expression of patriline-specific
 cues evolved to limit the risks of nepotism as family-living juveniles and
 favour sibling-mating avoidance as group-living adults. These results
 highlight the role of parental care and social life in the evolution of
 chemical communication and recognition cues.
description: CHC
 profilesCHC profiles of nymphs
 and adults used in the experimentData for
 DRYAD.xlsx
DOI: 10.5061/dryad.9p1tc81
title: Data from: Mating consequences of contrasting hermaphroditic plant sexual systems

description: For hermaphroditic angiosperms with multiple flowers the sex roles can be
 exclusively combined in bisexual flowers (monocliny), strictly separated
 among different flowers (monoecy), or arrayed in mixtures of bisexual
 flowers with female flowers (gynomonoecy) or male flowers (andromonoecy).
 The hypothesized benefits favoring the evolution of these contrasting
 hermaphroditic sexual systems are typically examined individually, usually
 by assessing success through only one sex role. We tested predictions of
 most hypotheses experimentally with an andromonoecious species, Anticlea
 occidentalis (Melanthiaceae), based on the performance of intact plants
 (andromonoecy) and those with emasculated bisexual flowers (functionally
 monoecious) or emasculated male flowers (functionally monoclinous with
 sterile peripheral flowers). Andromonoecy in this species enables
 efficient, size-dependent resource allocation, emphasizing female function
 in large plants. Emasculation revealed that anthers in male flowers
 promote female mating quality (outcrossing rate and mate diversity),
 whereas anthers in bisexual flowers promote male mating quantity (pollen
 dispersal distance and probability of any siring success). Thus, different
 hermaphroditic sexual systems likely evolve to capitalize on suites of
 benefits, rather than just one, and provide compromises between
 quantitative and qualitative reproductive components. These compromises
 apparently maximize an individual’s combined genetic contributions through
 female and male functions, rather than separate contributions through each
 sex role.
description: Anticlea plant
 dataThis spreadsheet
 presents plant-level data. Two individual worksheets (each accompanied by
 legend worksheets) are included. The "plant" worksheet presents
 variables describing aspects of plant stature, flower and fruit
 production, fates during hail storm, and female and male reproductive
 success for all 163 study plants. The "mating" worksheet
 identifies the parents of genotyped seeds and the intermate distance if
 the identity of both parents was known.Anticlea flower
 dataThe Excel spreadsheet
 includes 4 worksheets (each accompanied by legend worksheets) that present
 flower-level data for different aspects of reproduction. The "floral
 traits" worksheet includes variables identifying flower position,
 type and size and ovule number. The "pollen production"
 worksheet presents pollen counts for a sampled subset of flowers. The
 "pollen receipt" worksheet presents pollen receipt for a sampled
 subset of flowers. The "fruits & seeds" worksheet identifies
 whether individual flowers produced a fruit and, if so, how many seeds it
 contained.
DOI: 10.5061/dryad.7670p
title: Data from: First discovery of the charophycean green alga Lychnothamnus barbatus (Charophyceae) extant in the New World

description: Premise of the study: Although some species of Characeae, known as
 stoneworts, can be found on every continent except Antarctica, many
 species and some genera have limited geographic distributions. The genus
 Lychnothamnus, represented by a single extant species L. barbatus, was
 known only from scattered localities in Europe and Australasia until it
 was recently discovered in North America. Methods: Morphological
 identifications were made from specimens collected in Minnesota and
 Wisconsin, U.S.A. DNA sequences were obtained for three plastid-encoded
 genes (atpB, psbC, rbcL) from seven putative Lychnothamnus samples from
 two states in the U.S.A. Distribution and abundance were estimated in each
 lake using point intercept surveys where surveyors sampled aquatic
 vegetation. Key results: Fourteen lakes in Wisconsin and two lakes in
 Minnesota, U.S.A., were found to harbor Lychnothamnus barbatus. These
 represent the first report of this rare charophycean extant in the New
 World. The North American specimens matched the morphological description
 for L. barbatus and were compared directly with the neotype. Phylogenetic
 results using three plastid-encoded genes confirmed the identification
 placing New World samples with those from Europe and Australasia. Our
 phylogenetic analyses also confirmed the sister relationship between L.
 barbatus and Nitellopsis obtusa. Conclusions: Because this taxon is not
 known for aggressive invasiveness in its native range, it may have existed
 in heretofore-undiscovered native populations, although the possibility
 that it is a recent introduction cannot be eliminated. The potential for
 discovery of novel lineages of green algae in even well studied regions is
 apparently far from exhausted.
description: Karol_etal_threegene_alignment.nexThree plastid gene alignment for the Characeae including Lychnothamnus barbatus from the New World.Karol_etal_3gene.nexKarol_etal_threegene_phylogeny.pdfBayesian inference three gene phylogeny for the Characeae including Lychnothamnus barbatus from the New World.Karol_etal_3gene_phylogeny.pdf
DOI: 10.5061/dryad.g9089
title: Data from: Practical performance of tree comparison metrics

description: The phylogenetic literature contains numerous measures for assessing
 differences between two phylogenetic trees. Individual measures have been
 criticized on various grounds, but little is known about their comparative
 performance in typical applications. We evaluate the performance of nine
 tree distance measures on two tasks: (1) distinguishing trees separated by
 lesser versus greater numbers of recombinations, and (2) distinguishing
 trees inferred with lower versus higher quality data. We find that when
 the trees being compared are similar, measures which make use of branch
 lengths are superior, with the branch-length version of the
 Robinson-Foulds metric (Robinson & Foulds, 1979) performing best.
 In contrast, for dissimilar trees topology-only measures are superior,
 with the Alignment metric of Nye et al. (2006) performing best. We also
 apply the measures to a mammalian data set and observe that the best
 metric depends on whether branch-length information is of interest. We
 give practical recommendations for choosing a tree distance metric in
 different applications.
description: Python tree-comparison
 programsTar gzip archive of
 Python programs for calculating and plotting tree comparison
 metrics.kuhner_pyprogs.tgzC programs for simulating trees and DNAC programs used to simulate evolutionary trees and simulate DNA data on those trees. Also includes all needed parameter files and a script for a simple case.kuhner_cprogs.tgzSupplementary FiguresSupplementary figures for coalescent trees and for variations of the distance metrics in the main paper.metrics2_suppl.pdf
DOI: 10.5061/dryad.f3p75
title: Data from: Arthropod diversity in a tropical forest

description: Most eukaryotic organisms are arthropods. Yet, their diversity in rich
 terrestrial ecosystems is still unknown. Here we produce tangible
 estimates of the total species richness of arthropods in a tropical
 rainforest. Using a comprehensive range of structured protocols, we
 sampled the phylogenetic breadth of arthropod taxa from the soil to the
 forest canopy in the San Lorenzo forest, Panama. We collected 6,144
 arthropod species from 0.48 ha and extrapolated total species richness to
 larger areas based on competing models. The whole 6,000 ha forest reserve
 most likely sustains 25,000 arthropod species. Remarkably, just 1 ha of
 rainforest yields &gt; 60% of the arthropod biodiversity held in the
 wider landscape. Models based on plant diversity fitted the accumulated
 species richness of both herbivore and non-herbivore taxa exceptionally
 well. This lends credence to global estimates of arthropod biodiversity
 developed from plant models.
description: DRYADBassetLeponceArthropod distribution in 12 sites within San Lorenzo Protected Area in Panama (9°16’N, 79°58’W, elevation ca 130 m). Version: 10 May 2012.
DOI: 10.5061/dryad.17b01
title: Data from: Investigation of nitrogen and phosphorus contents in water in the tributaries of Danjiangkou Reservoir

description: .As part of the efforts to ensure adequate supply of quality water from
 Danjiangkou Reservoir to Beijing, surface water were sampled from the
 tributaries of Danjiangkou Reservoir in normal (May), flood (August) and
 dry (December) seasons of 2014, and characterized for nitrogen and
 phosphorus contents as specified in the applicable standards. Test results
 indicated that 1)the organic pollutions in Sihe and Shendinghe rivers were
 more serious than those in other tributaries, and the concentrations of
 nitrogen and phosphorus favoured the growth of most algae; 2) total
 phosphorus (TP), total nitrogen (TN) and dissolved inorganic nitrogen
 (DIN) were in the forms of dissolved phosphorus (DTP), dissolved nitrogen
 (DTN) and nitrate nitrogen (NO3-N) in these seasons, respectively; 3)
 compared with nitrogen, phosphorus was more likely to block phytoplankton
 overrunning; 4)TN, TP, permanganate index (CODMn) and other ions were
 positively correlated. These findings provided an important basis for the
 effective measures taken later on as appropriate to ensure adequate supply
 of quality water from Danjiangkou Reservoir to Beijing.
description: Supporting
 dataThere are two files in
 the data package. One file gives the geographic information about the
 research area and sampling points, the other supplies all the experimental
 data used in the manuscript.supporting_data.zip