cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.00000003f
title: Cumulative germination of seeds ingested by black howler monkeys

description: Premise of the Study: Primates are important seed dispersers, especially
 for large-seeded (&gt; 1 cm length) tropical species in continuous and
 fragmented rainforests. Methods: In three forest fragments within the
 Montes Azules Biosphere Reserve, southern Mexico, we investigated the
 effect of howler monkeys´ (Alouatta pigra) gut passage on the germination
 rate and maximum germination (%) of native large-seeded species. One group
 of howler monkeys, per fragment, was followed and fresh feces collected.
 Large seeds were removed to compare their germination success with
 non-ingested seeds of the same species collected underneath parent plants.
 Results: Feces contained large seeds from seven tree species and one liana
 species: Ampelocera hottlei, Castilla elastica, Dialium guianense,
 Garcinia intermedia, Pourouma bicolor, Spondias mombin, Trophis racemosa
 and the liana Abuta panamensis. Except for G. intermedia, ingested seeds
 showed significantly greater germination rates than non-ingested seeds.
 Non-ingested seeds of D. guianense showed negligible germination.
 Regarding maximum germination, ingested seeds of D. guianense, P. bicolor,
 S. mombin, T. racemosa and A. panamensis showed significantly greater
 germination percentage; while G. intermedia showed significantly lower
 germination percentage and no effect of seed ingestion was observed on A.
 hottlei and C. elastica. Conclusions: In general, seed ingestion by howler
 monkeys confers greater germination rates than non-ingested seeds. Greater
 germination rates reduce predation probabilities and increases seedling
 establishment in forest fragments. Primate dispersal services contribute
 to germination heterogeneity within plant populations of old-growth forest
 species and to their persistence in forest fragments.
description: In three forest fragments within the Montes Azules Biosphere
 Reserve, southern Mexico, we investigated the effect of howler monkeys´
 (<i>Alouatta pigra</i>) gut passage on the germination rate
 and maximum germination (%) of native large-seeded
 species: <i>Ampelocera hottlei</i>, <i>Castilla
 elastica</i>, <i>Dialium guianense</i>,
 <i>Garcinia intermedia</i>, <i>Pourouma
 bicolor</i>, <i>Spondias mombin</i>, <i>Trophis
 racemosa</i> and the liana <i>Abuta panamensis.</i> One
 group of howler monkeys, per fragment, was followed and fresh feces
 collected. Large seeds were removed to compare their germination success
 with non-ingested seeds of the same species collected underneath parent
 plants.
DOI: 10.5061/dryad.sf7m0cg65
title: Differential speciation rates, colonization time, and niche conservatism affect community assembly across adjacent biogeographical regions

description: Aim: To test the importance of evolutionary and biogeographic processes in
 shaping the assembly of local frog communities in two adjacent regions
 (hereafter, coastal and inland regions) with different historical
 signatures. We asked two main questions: i) why does the coastal region
 harbor more frog species than the inland region? and ii) how do these
 processes affect the relationship between the spatial variation of
 taxonomic, phylogenetic, and functional diversities within and across
 these regions?  Location: southeastern Brazil Taxon: Anurans
 Methods: We generated time-calibrated phylogenies to estimate the relative
 timing of colonization, rates of speciation, extinction, and dispersal
 between regions. We tested the phylogenetic signal in reproductive modes.
 These traits were also used to examine variation in functional composition
 across sites. We calculated metrics of phylogenetic community structure
 that capture the relationships near the root and tips of the tree.
 Finally, we tested the relationships between the spatial variation of
 multiple diversity dimensions and topographic complexity, Pleistocene and
 contemporary climate gradients for three spatial extents: (i) only coastal
 sites; (ii) only inland sites; and (iii) the two regions combined.
 Results: The structure of communities was related to the region in which
 they are located, with regional pool size being two times greater for the
 coastal than inland region. This pattern seems to reflect both a higher
 speciation rate and earlier colonization time in the coastal than in the
 inland region. Reproductive modes within frog genera were less variable
 than among families, indicating phylogenetic signal. This pattern
 influenced local community assembly within the inland region due to the
 absence of species with direct development, tadpoles in bromeliads, or
 eggs and tadpoles in streams in this region. Main Conclusions:
 Macroevolutionary dynamics, such as colonization time, differences in
 speciation rates, and niche conservatism generate the disparity in species
 richness and assembly patterns of local communities between regions, but
 not within regions, in which local communities were more similar to each
 other.
description: We collected frog species presence-absence data in 14 protected
 areas, spanning 4° of latitude and 6° of longitude and encompassing a
 spatial extent of 98,000 km<sup>2</sup> in southeastern
 Brazil. Seven of these protected areas are within the inland region
 encompassing a spatial extent of ~19,400 km<sup>2</sup>, with
 an average linear geographic distance of 152.5 ± 86.5 km between areas.
 Data on reproductive modes of frogs were obtained from Haddad, Toledo,
 Prado, Loebmann, & Gasparini (2013). We downloaded climatic
 variables from WorldClim v. 2.0 (Fick & Hijmans, 2017; http://www.worldclim.org).
DOI: 10.5061/dryad.dbrv15f18
title: Data from: A maximalist approach to the systematics of a biological control agent: Gryon aetherium Talamas, sp. nov. (Hymenoptera, Scelionidae)

description: A morphological and molecular analysis of Gryon Haliday (Platygastroidea,
 Scelionidae) was conducted to provide a taxonomic and phylogenetic context
 for a species under evaluation as a biological control agent of Bagrada
 hilaris (Burmeister) (Hemiptera, Pentatomidae). Our analysis revealed that
 Gryon is polyphyletic and that the biological control agent is not G.
 gonikopalense, a name that was tentatively applied to this species in
 2019. We here describe this species as new, Gryon aetherium Talamas sp.
 nov., and resurrect the generic name Hadronotus Förster. Morphological
 characters that delimit our concepts of Gryon and Hadronotus are
 presented. Based on morphological characters and multilocus phylogenies,
 we determined that five presently valid scelionid genera belong within
 Gryon. In total, 15 species are transferred into Gryon from these genera,
 215 species are transferred from Gryon to Hadronotus, and 6 species are
 transferred from Gryon to Dyscritobaeus Perkins. Specimens collected
 during field studies in California and reevaluation of specimens
 determined as G. myrmecophilum in Mexico reveal that G. aetherium is
 adventive in North America.
description: Please see the Materials and Methods section of corresponding
 manuscript.
description: Please see the README of the attached dataset.
DOI: 10.5061/dryad.2z34tmpmf
title: Evidence of hippocampal learning in human infants

description: The hippocampus is essential for human memory. The protracted maturation
 of memory capacities from infancy through early childhood is thus often
 attributed to hippocampal immaturity. The hippocampus of human infants has
 been characterized in terms of anatomy, but its function has never been
 tested directly because of technical challenges. Here we use recently
 developed methods for task-based fMRI in awake human infants to test
 whether the infant hippocampus supports statistical learning. Hippocampal
 activity increased with exposure to visual sequences of objects when the
 temporal order contained regularities to be learned, compared to when the
 order was random. Despite the hippocampus doubling in volume across
 infancy, learning-related functional activity bore no relationship to age.
 This suggests recruitment of the hippocampus for statistical learning at
 the youngest ages in our sample, around three months. Within the
 hippocampus, evidence of statistical learning was clearer in anterior than
 posterior divisions. This is consistent with the theory that statistical
 learning occurs in the monosynaptic pathway, which is more strongly
 represented in the anterior hippocampus. The monosynaptic pathway develops
 earlier than the trisynaptic pathway, linked to episodic memory,
 suggesting that the infant hippocampus participates in statistical
 learning before it can form durable memories. Beyond the hippocampus, the
 medial prefrontal cortex showed evidence of statistical learning,
 consistent with the adult role of this region in memory integration and
 generalization. These results suggest that the hippocampus supports the
 vital ability of infants to extract the structure of their environment
 through experience.
description: Please refer to the manuscript for details. Citation: Ellis, C.
 T., Skalaban, L. J., Yates, T. S., Bejjanki, V. R., Córdova, N. I.,
 & Turk-Browne, N. B. (2021) Evidence of hippocampal learning in
 human infants. <em>Current Biology</em>
description: Please refer to the README for guidance on how to use this
 data Note from Aug 19th, 2021: Note that the burn-in
 information for each of the raw runs was not previously provided. This has
 now also been uploaded. The README was edited to include this information
 but otherwise, nothing else was changed.
DOI: 10.5061/dryad.t4b8gtj1z
title: The Hydroperoxyl Radical Scavenging Activity of Sulfuretin: Insights from Theory

description: This dataset contains data from the calculations described in the paper:
 “Nguyen Thi Hoa, Do Thi My Hang, Do Phu Hieu, Huynh Van Truong, Loc Phuoc
 Hoang, Adam Mechler and Quan V. Vo*. (2021), The Hydroperoxyl
 Radical Scavenging Activity of Sulfuretin: Insights from Theory. Royal
 Society Open Science. 2021. The thermodynamic and kinetic calculations
 were applied to evaluate the HOO· radical scavenging activity of
 sulfuretin (SFR) in the gas phase and solvents (water and pentyl
 ethanoate) by the M06-2X/6-311++G(d,p) level of theory. SFR is predicted
 to be an excellent HOO• scavenger in water at pH = 7.40 with koverall =
 4.75´107 M-1 s-1, principally due to an increase in the activity of the
 anionic form following the single electron transfer mechanism.
 Consistently the activity of the neutral form is more prominent in the
 nonpolar environment with koverall = 1.79´104 M-1 s-1 following the formal
 hydrogen transfer mechanism. Thus it is predicted that SFR exhibits better
 HOO· antiradical activity than typical antioxidants such as resveratrol,
 ascorbic acid, and Trolox in the lipid medium. The hydroperoxyl radical
 scavenging of SFR in the aqueous solution is ~530 times faster than that
 of Trolox and similar to ascorbic acid or resveratrol. This suggests that
 SFR is a promising radical scavenger in physiological environments.
  
description: The dataset was collected during the Gaussian 09 suite of
 programs at The University of Danang - University of Technology and
 Education, Vietnam, and La Trobe University, Australia.
 M06-2X/6-311++G(d,p) model chemistry was used for all calculations. It was
 demonstrated before that the M06-2X functional is one of the most reliable
 methods to study thermodynamics and kinetics of radical reactions,
 particularly in physiological environments. The solvation model density
 (SMD) method was used for including the effects of water and pentyl
 ethanoate in the computations. The kinetic calculations were performed
 following the quantum mechanics-based test for the overall free radical
 scavenging activity (QM-ORSA) protocol, using the conventional transition
 state theory (TST) and 1M standard state at 298.15 K.
description: The readme file contains the calculation methods (Table S1, SI),
 the Cartesian coordinates of the transition states (Table S2, SI), and the
 Gaussian input files for thermodynamic and kinetic study in all the
 studied environments. Information on how the calculations were done can
 also be found in the associated manuscript referenced above.
DOI: 10.5061/dryad.2ngf1vhnd
title: Tree species richness and soil organic carbon stock

description: Recently, the perspectives for the stronger persistence of soil organic
 carbon (SOC) caused by the higher molecular diversity of organic compounds
 were proposed. Therefore, the effects of tree species richness and
 composition on the diversity of molecular components of SOC need to be
 explored. In this study, we collected data on tree species diversity and
 composition, SOC concentration, chemical composition, litter and fine root
 properties, and examined the relationships between the richness,
 composition and functional diversity of tree species, and the evenness of
 SOC chemical compositions at a molecular level by 13C nuclear magnetic
 resonance, across six natural forest types encompassing a diversity
 gradient, ranging from cold temperate to tropical forests. Across the
 range, tree species richness correlated to the evenness of SOC chemical
 components through tree species composition. The negative correlation of
 evenness of SOC chemical components with tree species composition and the
 positive correlation of evenness of SOC chemical components with tree
 functional diversity were found. The positive correlation of the evenness
 of SOC chemical components with indicator tree species. These findings
 suggest that the indicator tree species conservation might be preferable
 to simply increasing tree species richness, for enhancing the potential
 resistance of SOC to decomposition.
DOI: 10.5061/dryad.0gb5mkm17
title: Neural processing and perception of Schroeder‐phase harmonic tone complexes in the gerbil: Relating single‐unit neurophysiology to behavior

description: Schroeder-phase harmonic tone complexes have been used in physiological
 and psychophysical studies in several species to gain insight into
 cochlear function. Each pitch period of the Schroeder stimulus contains a
 linear frequency sweep; the duty cycle, sweep velocity, and direction are
 controlled by parameters of the phase spectrum. Here, responses to a range
 of Schroeder-phase harmonic tone complexes were studied both behaviorally
 and in neural recordings from the auditory nerve and inferior colliculus
 of Mongolian gerbils. Gerbils were able to discriminate Schroeder-phase
 harmonic tone complexes based on sweep direction, duty cycle, and/or
 velocity for fundamental frequencies up to 200 Hz. Temporal representation
 in neural responses based on the van Rossum spike-distance metric, with
 time constants of either 1 ms or related to the stimulus’ period, was
 compared to average discharge rates. Neural responses and behavioral
 performance were both expressed in terms of sensitivity, d’, to allow
 direct comparisons. Our results suggest that in the auditory nerve,
 stimulus fine structure is represented by spike timing while envelope is
 represented by rate. In the inferior colliculus, both temporal fine
 structure and envelope appear to be represented best by rate. However,
 correlations between neural d’ values and behavioral sensitivity for sweep
 direction were strongest for both temporal metrics, for both auditory
 nerve and inferior colliculus. Furthermore, the high sensitivity observed
 in the inferior colliculus neural rate-based discrimination suggests that
 these neurons integrate across multiple inputs arising from the auditory
 periphery.
DOI: 10.5061/dryad.fbg79cntw
title: ITS and nrLSU DNA sequence data from four species of Coreomyces (Laboulbeniomycetes)

description: The genus Coreomyces (Laboulbeniaceae, Laboulbeniomycetes, Ascomycota)
 includes minute parasites on water boatmen (Corixidae, Hemiptera,
 Insecta). This taxonomic study is primarily based on freshly sampled
 corixids infected by Coreomyces from Sweden, although a few samples from
 Denmark and Turkey were also included. All records were verified using DNA
 sequence data from the internal transcribed spacer region and large
 subunit of the nuclear ribosomal DNA repeat region. We recognise four
 species, two of which are new to science: Coreomyces confusus H. Sundb. et
 al. sp. nov., C. dextrorsus H. Sundb. et al. sp. nov., C. macropus Thaxt.,
 and C. corixae Thaxt. C. corixae is a new record for Denmark, Sweden, and
 Turkey, while C. macropus is a new record for Denmark and
 Sweden. All four species can inhabit two different yet distinct
 positions on the host. We observe that morphology is affected by the
 position on the host and that different species sharing the same position
 on the host tend to be difficult or impossible to separate on morphology
 only. We conclude that species circumscriptions in Coreomyces must be
 based on the integration of molecular and morphological data.
description: Corixids were collected from 15 localities in southern Sweden and
 one in Turkey. They were scanned for <i>Coreomyces</i> thalli
 under a dissecting microscope. In total, 88 mature thalli were sampled
 from 48 corixids of the genera <i>Arctocorisa,
 Callicorixa</i>, <i>Cymatia</i>, and
 <i>Sigara</i>. DNA sequences were generated following the
 methods of Sundberg et al. in Methods Ecol. Evol. 9: 148–158 (2018). We
 generated new sequences primarily from the internal transcribed spacer
 (ITS) region or, in some cases, from the large subunit of the nuclear
 ribosomal DNA (nrLSU) in case the ITS sequencing failed. New sequences
 were added to the alignments of Sundberg et al. in Fung. Syst. Evol. 1:
 217–228 (2018) using the “--add” option of MAFFT version 7.475 with
 L-INS-i iterative refinement. Maximum likelihood trees were estimated
 using IQ-TREE version 2.1.2. A standard model selection (among models with
 1, 2 or 6 rates) was performed and followed by a search for the best tree
 using default settings except that all nearest neighbour interchange (NNI)
 branch swaps were explored.
description: The data consist of two text files in NEXUS format, one
 containing the ITS data (Coreomyces_ITS.nex) and the other the nrLSU data
 (Coreomyces_LSU.nex). Each file contains the alignment in a characters
 block as well as the inferred maximum likelihood tree in a trees
 block.
DOI: 10.5061/dryad.q83bk3jhp
title: Data from: The evolution of the traplining pollinator role in hummingbirds, specialization is not an evolutionary dead end

description: Trapliners are pollinators that visit widely dispersed flowers along
 circuitous foraging routes. Through coevolution with the flowers they
 pollinate, trapliners are hypothesised to become more morphologically and
 ecologically specialised than their non-traplining counterparts. We
 hypothesised that independent transitions to traplining in hummingbirds
 should entail convergent morphological specialisation, and we tested
 whether such transitions are irreversible and lead to lower rates of
 diversification as predicted by the hypothesis that specialisation is an
 ‘evolutionary dead end’. We find that there have been multiple independent
 transitions to traplining across the hummingbird phylogeny, but reversals
 have been rare or incomplete at best. Multiple independent lineages of
 trapliners have become morphologically specialised, convergently evolving
 relatively large bills for their body size. Traplining is not an
 evolutionary dead end however, since trapliners continue to give rise to
 new traplining species at a rate comparable to non-trapliners.
description: # Data from: The evolution of the traplining pollinator role in
 hummingbirds, specialization is not an evolutionary dead end
 These are the code and
 data necessary to reproduce the analyses in this paper. They contain
 morphological, ecological and phylogenetic data on hummingbirds. Details
 on how these were obtained and references to the primary sources can be
 found in the accompanying paper. ## Description of the data and file
 structure The file morpho.csv contains morphological measurements of
 hummingbird species used in this study. The units for each measurement are
 in the column names, for example Bill_dep_mm has the bill depth in mm. PC
 columns 1-3 contain the first three principal component scores of beak
 shape variation of museum specimens computed with geometric morphometrics.
 Csize_mm is the centroid size of the beak, a measure of size used in
 geometric morphometrics. The file foraging.csv contains data on the
 foraging ecology of hummingbird species obtained from the literature-
 divided into the traplining, opportunist and territorial category
 classifications. A subjective index of classification certainty is
 provided based on the amount and quality of evidence in the literature and
 the congruence between sources. The files jetz_hum_mcc.tree and
 mcguire_hum_mcc.tree are the two phylogenies used in this study in nexus
 format.
DOI: 10.5061/dryad.59zw3r271
title: The geography of parasite local adaptation to host communities

description: Fitness responses to environment can shape species distributions, though
 opposing eco-evolutionary processes can obscure environmental effects. For
 example, host specificity influences parasite dynamics, but is unclear how
 adaptation of parasites to local host communities may scale up to
 continental distributions. Here, we develop a macroecological framework to
 determine how host community structure affects the distribution of
 specialist and generalist populations of Striga hermonthica, an African
 parasitic plant of cereal crops. Combining data from global crop
 production and parasite experimental trials, we find that parasites
 perform best on the host species that is most common in their location of
 origin. Moreover, niche model contrasts predict parasite specialization on
 two hosts that evolved alongside Striga during domestication (pearl millet
 and sorghum), indicating that specialist parasites may be most likely to
 occur where host niches differ most in multivariate environmental space.
 Our study demonstrates that patterns of parasite local adaptation to host
 communities can emerge at continental scales and that differential
 environmental tolerances of hosts indirectly shape the distribution of
 specialist and generalist parasites. By predicting spatial dynamics of
 parasite specialization versus generalization directly from environmental
 data, our approach may help inform current and future management of pests
 and disease.
description: Analyses in this manuscript are based on previously published
 data. This data publication includes code used for data analysis at the
 time of publication. For the most up-to-date version of the code, see
 https://github.com/em-bellis/StrigaMacroecologyMS.
DOI: 10.5061/dryad.dr7sqv9z2
title: Cytoplasmic incompatibility between Old and New World populations of a tramp ant

description: Reproductive manipulation by endosymbiotic Wolbachia can
 cause unequal inheritance, allowing the manipulator to spread and
 potentially impacting evolutionary dynamics in infected hosts. Tramp and
 invasive species are excellent models to study the dynamics of
 host-Wolbachia associations because introduced populations often
 diverge in their microbiomes after colonizing new habitats, resulting in
 infection polymorphisms between native and introduced
 populations. Ants are the most abundant group of insects on
 earth, and numerous ant species are classified as highly invasive.
 However, little is known about the role of Wolbachia in
 these ecologically dominant insects. Here, we provide the first
 description of reproductive manipulation by Wolbachia in
 an ant. We show that Old and New World populations of the cosmotropic
 tramp ant Cardiocondyla obscurior harbor
 distinct Wolbachia strains, and that only the Old World
 strain manipulates host reproduction by causing cytoplasmic
 incompatibility in hybrid crosses. By uncovering a symbiont-induced
 mechanism of reproductive isolation in a social insect, our
 study provides a novel perspective on the biology of tramp ants
 and introduces a new system for studying the evolutionary
 consequences of cytoplasmic incompatibility.