cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5d6p6
title: Data from: Multigene phylogenetic analyses of the Thelonectria coronata and T. veuillotiana species complexes

description: Thelonectria is a recently established genus of common and ubiquitous
 fungi on woody hosts, previously placed in the genus Neonectria.
 Thelonectria coronata and T. veuillotiana occur sympatrically in several
 geographical areas in tropical, subtropical, and temperate regions.
 Previous taxonomic studies including T. coronata and T. veuillotiana
 suggested these fungi could represent species complexes; however, the
 morphological features used to define species exhibited few differences
 useful for testing this hypothesis. In order to assess the status of T.
 coronata and T. veuillotiana, phylogenetic analyses of six genomic regions
 were combined with a morphological examination of specimens. A multigene
 phylogeny reconstructed using Maximum Parsimony, Maximum Likelihood, and
 Bayesian approaches identified five phylogenetic groups in T. coronata and
 six in T. veuillotiana. As is common for cryptic species, unequivocal
 diagnostic morphological characters could not be identified; however,
 average values of morphological traits correspond to the phylogenetic
 groups. An increased level of non-synonymous/synonymous substitutions in
 the β-tubulin gene and a decreased or absent production of conidia was
 detected within the T. coronata complex, possibly indicating the
 homothallic nature of these isolates. Here, T. coronata and T.
 veuillotiana and related species are described and illustrated; a
 dichotomous key to all species is provided.
description: Actin
 SalgadoAlpha actin gene
 sequence alignment.Btub
 SalgadoB-tubulin gene sequence
 alignmentEF
 Salgadotranslation elongation
 factor 1α gene sequence alignmentITS
 SalgadoComplete internal
 transcribed spacers 1 and 2 (ITS, including 5.8S of the nuclear ribosomal
 DNA) sequence alignmentLSU
 SalgadoPartial large nuclear
 ribosomal subunit sequence alignmentRPB1
 SalgadoRNA polymerase II
 subunit 1 gene sequence alignment
DOI: 10.5061/dryad.00317
title: Data from: Oceanic barriers promote language diversification in the Japanese Islands

description: Good barriers make good languages. Scholars have long speculated that
 geographical barriers impede linguistic contact between speech
 communities, and promote language diversification in a manner similar to
 the process of allopatric speciation. This hypothesis, however, has seldom
 been tested systematically and quantitatively. Here we adopt methods from
 evolutionary biology and attempt to quantify the influence of oceanic
 barriers on the degree of lexical diversity in the Japanese Islands.
 Measuring the degree of beta diversity from basic vocabularies, we find
 that geographical proximity and, more importantly, isolation by
 surrounding ocean, independently explains a significant proportion of
 lexical variation across Japonic languages. Further analyses indicate that
 our results are neither a byproduct of using a distance matrix derived
 from a Bayesian language phylogeny nor an epiphenomenon of accelerated
 evolutionary rates in languages spoken by small communities. Moreover, we
 find that the effect of oceanic barriers is reproducible with the Ainu
 languages, indicating that our analytic approach as well as the results
 can be generalized beyond Japonic language family. The findings we report
 here are the first quantitative evidence that physical barriers formed by
 ocean can influence language diversification, and points to an intriguing
 common mechanism between linguistic and biological evolution.
description: Distance
 matricesThe file contains all
 data matrices used in the study.SI.xlsx
DOI: 10.5061/dryad.6j19m
title: Data from: Sustainable harvesting of non-timber forest products based on ecological and economic criteria

description: Harvesting of highly valuable non-timber forest products (NTFPs) has been
 considered a win-win strategy where local people profit while conserving
 forest biodiversity and ecosystem services. Nevertheless the
 sustainability of NTFP harvesting has been debated as the nature of NTFPs,
 harvesting regimes, and scale of commercialization are highly
 heterogeneous and few studies have evaluated the cumulative ecological and
 economic effects of such regimes. Here, we assessed the medium-term (10
 years) sustainability of NTFP harvesting, using Chameadorea palm leaves, a
 major NTFP from Mesoamerica that is highly valued in the international
 floral industry, as a case study. We used an experimental ecological study
 and an economic assessment to analyse the sustainability of leaf
 harvesting in C. ernesti-augustii. A four-year leaf removal experiment was
 conducted to assess effects of increasing levels of defoliation (0%, 25%,
 50%, 75%, 100% leaf removal, biannually) on palm survivorship, leaf
 production and leaf quality. Results of this experiment were combined with
 estimations of harvest economic value to make projections of the
 availability of leaves and profit per unit area. Finally, we determined
 harvesting regimes that maximize profit while maintaining medium-term
 viability of exploited populations. Palms tolerated up to 50% chronic
 defoliation, but higher defoliation levels reduced survivorship, leaf
 production, and leaf quality. In the long-term, this 50% defoliation level
 maximized harvest volume and profit without significantly affecting palm
 survival and leaf quality. Our results show that harvesters face the
 dilemma of either maximizing short-term income leading to rapid exhaustion
 of stocks, or maintaining exploited populations but maximizing income in
 the long-term. Synthesis and applications. Our study shows that
 intermediate harvesting levels (≤ 50% leaf removal) are needed to achieve
 long-term sustainability of Chameadorea palm leaves. Results of this study
 have an immediate application for the amendment of the official Mexican
 law, which enables higher harvesting intensities of Chamaedorea leaves,
 and for the design of sustainable management strategies. Applications of
 such strategies should consider community-based management, fair markets,
 regulating norms, as well as a thorough communication among stakeholders.
description: DataHernandezBarriosData from all censuses on experimental leaf harvesting of Chamaedorea ernesti-augustii
DOI: 10.5061/dryad.6nm40
title: Data from: Inbreeding within human Schistosoma mansoni: do host- specific factors shape the genetic composition of parasite populations?

description: The size, structure and distribution of host populations are key
 determinants of the genetic composition of parasite populations. Despite
 the evolutionary and epidemiological merits, there has been little
 consideration of how host heterogeneities affect the evolutionary
 trajectories of parasite populations. We assessed the genetic composition
 of natural populations of the parasite Schistosoma mansoni in northern
 Senegal. A total of 1346 parasites were collected from 14 snail and 57
 human hosts within three villages and individually genotyped using nine
 microsatellite markers. Human host demographic parameters (age, gender and
 village of residence) and co-infection with Schistosoma haematobium were
 documented, and S. mansoni infection intensities were quantified.
 F-statistics and clustering analyses revealed a random distribution
 (panmixia) of parasite genetic variation among villages and hosts,
 confirming the concept of human hosts as ‘genetic mixing bowls’ for
 schistosomes. Host gender and village of residence did not show any
 association with parasite genetics. Host age, however, was significantly
 correlated with parasite inbreeding and heterozygosity, with children
 being more infected by related parasites than adults. The patterns may be
 explained by (1) genotype-dependent ‘concomitant immunity’ that leads to
 selective recruitment of genetically unrelated worms with host age, and/or
 (2) the ‘genetic mixing bowl’ hypothesis, where older hosts have been
 exposed to a wider variety of parasite strains than children. The present
 study suggests that host-specific factors may shape the genetic
 composition of schistosome populations, revealing important insights into
 host–parasite interactions within a natural system.
description: Microsatellite data from
 parasitesThis data consists
 genotypes obtained from Schistosoma mansoni parasites that were type at
 nine microsatellite markers. Each locus (e.g. L46951) is coded by 6 digits
 (e.g. 169175). Each allele is coded by 3 digits (e.g.
 169).1_GenotypeData.txtHuman host dataVillage: location where human host lived. Host: population number that was assigned to the human host. HostIdentifier: code that is linked with that host. SamplingTime: time when parasites were sampled (e.g. Aug-09 or 09-Aug means that parasites were sampled from this host in August 2009. Age: age of the human host. EPG: eggs per gram of feces, i.e. a measure of infection intensity. CoInfectionWithShaematobium: 1 = when human host was coinfected with Schistosoma haematobium, 0 = when human host was NOT coinfected.2_HumanHostData.txtR script written for some of the analysesThis is an R script that was written for some of the analysis, namely: 1) hierarchical f-statistics 2) tests for inbreeding with multilocus heterozygosity and 3) tests for family structure with relatedness estimates3_InbreedingRscript.R
DOI: 10.3535/3w0-19l-c6d
title: Alcedo meninting

description: Digital Specimen for the physical specimen hosted at Natural History Museum of Denmark.
DOI: 10.3535/7lh-359-3h5
title: Corythornis cristatus

description: Digital Specimen for the physical specimen hosted at Natural History Museum of Denmark.
DOI: 10.3535/6es-nv0-vlc
title: Alcedo leucogaster

description: Digital Specimen for the physical specimen hosted at Natural History Museum of Denmark.
DOI: 10.3535/9mq-p76-3v3
title: Specimen from Natural History Museum of Denmark

description: Digital Specimen for the physical specimen hosted at Natural History Museum of Denmark.
DOI: 10.5061/dryad.93p4q
title: Data from: Genetic basis of local adaptation and flowering time variation in Arabidopsis lyrata

description: Understanding how genetic variation at individual loci contributes to
 adaptation of populations to different local environments is an important
 topic in modern evolutionary biology. To date, most evidence has pointed
 to conditionally neutral quantitative trait loci (QTL) showing fitness
 effects only in some environments, while there has been less evidence for
 single-locus fitness trade-offs. At QTL underlying local adaptation,
 alleles from the local population are expected to show a fitness
 advantage. Cytoplasmic genomes also can have a role in local adaptation,
 but the role of cytonuclear interactions in adaptive differentiation has
 remained largely unknown. We mapped genomic regions underlying adaptive
 differentiation in multiple fitness components and flowering time in
 diverged populations of a perennial plant Arabidopsis lyrata. Experimental
 hybrids for this purpose were grown in natural field conditions of the
 parental populations in Norway and North Carolina (NC), USA and in the
 greenhouse. We found QTL where high fitness and early flowering were
 associated with local alleles, indicating a role of different selection
 pressures in phenotypic differentiation. At two QTL regions, a fitness
 component showing local adaptation between the parental populations also
 showed signs of putative fitness trade-offs. Beneficial dominance effects
 of conditionally neutral QTL for different fitness components resulted in
 hybrid vigor at the Norwegian site in the F2 hybrids. We also found that
 cytoplasmic genomes contributed to local adaptation and hybrid vigor by
 interacting with nuclear QTL, but these interactions did not show evidence
 for cytonuclear coadaptation (high fitness of local alleles combined with
 the local cytoplasm).
description: AlyrataGHSpMaQTLAlyrataNCSpMaQTLAlyrataNorSpMaQTL
DOI: 10.3535/80m-2zp-d2s
title: Alcedo coerulescens

description: Digital Specimen for the physical specimen hosted at Natural History Museum of Denmark.
DOI: 10.3535/n4g-zg1-64g
title: Corythornis cristatus thomensis

description: Digital Specimen for the physical specimen hosted at Natural History Museum of Denmark.
DOI: 10.3535/78v-yv4-9fl
title: Alcedo cristata

description: Digital Specimen for the physical specimen hosted at Natural History Museum of Denmark.
DOI: 10.5061/dryad.p1pt2
title: Data from: Squamate hatchling size and the evolutionary causes of negative offspring size allometry

description: Although fecundity selection is ubiquitous, in an overwhelming majority of
 animal lineages, small species produce smaller number of offspring per
 clutch. In this context, egg, hatchling and neonate sizes are absolutely
 larger, but smaller relative to adult body size in larger species. The
 evolutionary causes of this widespread phenomenon are not fully explored.
 The negative offspring size allometry can result from processes limiting
 maximal egg/offspring size forcing larger species to produce relatively
 smaller offspring (‘upper limit’), or from a limit on minimal
 egg/offspring size forcing smaller species to produce relatively larger
 offspring (‘lower limit’). Several reptile lineages have invariant clutch
 sizes, where females always lay either one or two eggs per clutch. These
 lineages offer an interesting perspective on the general evolutionary
 forces driving negative offspring size allometry, because an important
 selective factor, fecundity selection in a single clutch, is eliminated
 here. Under the upper limit hypotheses, large offspring should be selected
 against in lineages with invariant clutch sizes as well, and these
 lineages should therefore exhibit the same, or shallower, offspring size
 allometry as lineages with variable clutch size. On the other hand, the
 lower limit hypotheses would allow lineages with invariant clutch sizes to
 have steeper offspring size allometries. Using an extensive data set on
 the hatchling and female sizes of &gt; 1800 species of squamates, we
 document that negative offspring size allometry is widespread in lizards
 and snakes with variable clutch sizes and that some lineages with
 invariant clutch sizes have unusually steep offspring size allometries.
 These findings suggest that the negative offspring size allometry is
 driven by a constraint on minimal offspring size, which scales with a
 negative allometry.
description: Appendix
 1Data
 on hatchling/neonate and female masses. For each species, the lineage is
 depicted, as well as an explanation of how it was classified for the
 analyses and whether or not it is represented in the phylogenetic tree,
 and hence in the phylogenetic analyses.
DOI: 10.5061/dryad.696js
title: Data from: Is male rhesus macaque facial coloration under intrasexual selection?

description: Exaggerated male traits can evolve under intra- or intersexual selection,
 but it remains less clear how often both mechanisms act together on trait
 evolution. While the males of many anthropoid primate species exhibit
 colorful signals that appear to be badges of status under intrasexual
 selection, the red facial coloration of male rhesus macaques (Macaca
 mulatta) appears to have evolved primarily under intersexual selection and
 female mate choice. Nonetheless, experiments show that red color is
 salient to males, raising the question of whether the signal may also be
 under intrasexual selection. Here, we examine whether males express this
 signal more strongly in competitive contexts. Facial images were collected
 on all 15 adult males of a free-ranging social group during the peak of
 the mating season, and coloration was quantified using visual models.
 Results show that males more similar in facial redness were more likely to
 interact aggressively than more dissimilar ones, suggesting that color may
 be involved in the assessment of rivals. Furthermore, males exhibited
 darker coloration on days they were observed copulating, and dominance
 rank predicted facial redness only on copulating days, suggesting that
 coloration may also advertise motivation to defend a mate. Male rhesus
 macaque facial coloration may thus mediate agonistic interactions with
 rivals during competition over reproductive opportunities, such that it is
 under both inter- and intrasexual selection. However, color differences
 were small, raising perceptibility questions. It remains possible that
 color variation reflects differences in male condition, which in turn
 alter investment towards male–male competition and mating effort.
description: agonism.weekly(dryad)Weekly agonism rates and facial coloration measurements for study males (Aim 1)agonism.dyads(dryad)Agonistic interactions between study males with corresponding coloration measurements for both males (Aim 2)mating(dryad)Daily mating behavior and coloration measurements for study males (Aim 3)
DOI: 10.5061/dryad.r99p7
title: Data from: Song evolution, speciation, and vocal learning in passerine birds

description: Phenotypic divergence can promote reproductive isolation and speciation,
 suggesting a possible link between rates of phenotypic evolution and the
 tempo of speciation at multiple evolutionary scales. To date, most
 macroevolutionary studies of diversification have focused on morphological
 traits, whereas behavioral traitsࣧincluding vocal signalsࣧare rarely
 considered. Thus, although behavioral traits often mediate mate choice and
 gene flow, we have a limited understanding of how behavioral evolution
 contributes to diversification. Furthermore, the developmental mode by
 which behavioral traits are acquired may affect the rates of behavioral
 evolution, although this hypothesis is seldom tested in a phylogenetic
 framework. Here, we examine evidence for rate shifts in vocal evolution
 and speciation across two major radiations of codistributed passerines:
 one oscine clade with learned songs (Thraupidae) and one suboscine clade
 with innate songs (Furnariidae). We find that evolutionary bursts in rates
 of speciation and song evolution are coincident in both thraupids and
 furnariids. Further, overall rates of vocal evolution are higher among
 taxa with learned rather than innate songs. Taken together, these findings
 suggest an association between macroevolutionary bursts in speciation and
 vocal evolution, and that the tempo of behavioral evolution can be
 influenced by variation in developmental modes among lineages.
description: Appendix1_ThraupidFurnariid_SongMassAppendix of phenotypic data used in this study. This is referenced by the R Scripts also included in this Dryad submission.Thraupidae and Furnariidae SupertreeThis phylogeny is a supertree that combines the MCC trees presented in Burns et al. (2014) and Derryberry et al. (2011). The Jetz et al. (2012) phylogeny is used to calibrate the age of the node that unites these two families. This phylogeny is referenced in the R scripts also included in this Dryad submission.mcctrim.treExampleBAMMInputfile_NoteCountThis is an example input file for BAMM using the character "Note Count".BAMMsetup_v3This R script generates input files for the BAMM analyses conducted in this study.BAMMOutput_v7This R script analyzes the BAMM output generated by this study and includes code for generating the figures presented here.SongRates_AdamsThis R script includes the code that was used to estimate and compare multivariate rates of trait evolution between Thraupids and Furnariids using the method developed by Adams (2014).
DOI: 10.5061/dryad.m31r8
title: Data from: Plant-soil feedback and the maintenance of diversity in Mediterranean-climate shrublands

description: Soil biota influence plant performance through plant-soil feedback, but it
 is unclear whether the strength of such feedback depends on plant traits
 and whether plant-soil feedback drives local plant diversity. We grew 16
 co-occurring plant species with contrasting nutrient-acquisition
 strategies from hyperdiverse Australian shrublands and exposed them to
 soil biota from under their own or other plant species. Plant responses to
 soil biota varied according to their nutrient-acquisition strategy,
 including positive feedback for ectomycorrhizal plants and negative
 feedback for nitrogen-fixing and nonmycorrhizal plants. Simulations
 revealed that such strategy-dependent feedback is sufficient to maintain
 the high taxonomic and functional diversity characterizing these
 Mediterranean-climate shrublands. Our study identifies
 nutrient-acquisition strategy as a key trait explaining how different
 plant responses to soil biota promote local plant diversity.
description: Teste et al. Science
 PSF-Survival-BiomassPlant survival and
 biomass data.TestePSF-Survival-Biomass.xlsxTeste et al. Science PSF-RootStrategyOccupancyRoot strategy occupancy (nodule, cluster roots, ectomycorrhizal and arbuscular mycorrhizal colonization levels) dataTestePSF-RootStrategyOccupancy.xlsx
DOI: 10.5061/dryad.3j80h8d4
title: Data from: Hybridization and barriers to gene flow in an island bird radiation

description: While reinforcement may play a role in all major modes of speciation,
 relatively little is known about the timescale over which species
 hybridize without evolving complete reproductive isolation. Birds have
 high potential for hybridization, and islands provide simple settings for
 uncovering speciation and hybridization patterns. Here we develop a
 phylogenetic hypothesis for a phenotypically-diverse radiation of
 finch-like weaver-birds (Foudia) endemic to the western Indian Ocean
 islands. We find that unlike Darwin’s finches, each island-endemic Foudia
 population is a monophyletic entity for which speciation can be considered
 complete. In explaining the only exceptions – mismatches between taxonomy,
 mitochondrial and nuclear data – phylogenetic and coalescent methods
 support introgressive hybridization rather than incomplete lineage
 sorting. Human introductions of known timing of one island-endemic
 species, to all surrounding archipelagos provide two fortuitous
 experiments; (1) population sampling at known times in recent evolutionary
 history, (2) bringing allopatric lineages of an island radiation into
 secondary contact. Our results put a minimum time bound on introgression
 (235 years), and support hybridization between species in natural close
 contact (parapatry), but not between those in natural allopatry brought
 into contact by human introduction. Time in allopatry, rather than in
 sympatry, appears key in the reproductive isolation of Foudia species.
description: Concatenated mtDNA
 sequence alignmentConcatenated mtDNA
 sequence alignment. ATPase 8: bases 1-168. ATPase 6: bases 169-852. ND3:
 bases 853-1203. Sequences are labelled with specimen numbers as in the
 publication graphics. See ReadMe file for the corresponding GenBank
 accessions.Foudia_mtDNA.nexCHD1Z sequence alignmentSee ReadMe file for the corresponding GenBank accessions.Foudia_CHD1Z_.nexFoudia mtDNA Bayesian tree topologyBayesian analysis of Foudia mitochondrial ATPase6, ATPase8 and ND3 data. Consensus of the last 35,000 trees after 4 million generations based on the GTR+I model. Bayesian branch support values are indicated below bootstrap values (heuristic search, 1000 replicates) from a ML tree constructed using the TrN+I model.Foudia_mtDNA_Bayesian.treFoudia CHD1Z Maximim Likelihood tree topologyMaximum likelihood tree based on the K81uf + I model for Foudia CHD1Z data.Foudia_CHD1Z_ML.treFoudia data used in file S3Foudia morphological data from collections of the Natural History Museum (BMNH), Tring, the University Museum of Zoology, Cambridge, the Muséum national d'Histoire naturelle, Paris, and the Royal Museum for Central Africa, Tervuren. All measurements are from male birds in breeding plumage and are in mm.Foudia_fileS3_data.xls