cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.05qfttf04
title: Data from: Division of functional roles for termite gut protists revealed by single-cell transcriptomes

description: The microbiome in the hindgut of wood-feeding termites comprises various
 species of bacteria, archaea, and protists. This gut community is
 indispensable for the termite, which thrives solely on recalcitrant and
 nitrogen-poor wood. However, the difficulty in culturing these
 microorganisms has hindered our understanding of the function of each
 species in the gut. Although protists predominate in the termite gut
 microbiome and play a major role in wood digestion, very few
 culture-independent studies have explored the contribution of each species
 to digestion. Here, we report single-cell transcriptomes of four protists
 species comprising the protist population in worldwide pest Coptotermes
 formosanus. Comparative transcriptomic analysis revealed that the
 expression patterns of the genes involved in wood digestion were different
 among species, reinforcing their division of roles in wood degradation.
 Transcriptomes, together with enzyme assays, also suggested that one of
 the protists, Cononympha leidyi, actively degrades chitin and assimilates
 it into amino acids. We propose that C. leidyi contributes to nitrogen
 recycling and inhibiting infection from entomopathogenic fungi through
 chitin degradation. Two of the genes for chitin degradation were further
 revealed to be acquired via lateral gene transfer (LGT) implying the
 importance of LGT in the evolution of symbiosis. Our single-cell-based
 approach successfully characterized the function of each protist in
 termite hindgut and explained why the gut community includes multiple
 species.
description: The libraries prepared from single-cells of protist inhabiting
 the hindgut of wood-feeding termites <em>Coptotermes formosanus
 </em>following Quarz-seq protocol. Three libraries were prepared for
 the each spieces, i.e., <em>Pseudotrichonympha grassii</em>,
 <em>Holomastigotoides hartmanii</em> (commonly confused with
 <em>Holomastigotoides mirabile</em>),
 <em>Holomastigotoides minor</em>, and<em> Cononympha
 leidyi</em> (previously called <em>Spirotrichonympha
 leidyi</em>).   The generated reads were concatenated by species and
 assembled with Trinity. The apparent contamination in the assemblies were
 removed as described in Manuscript. The gene model was predicted from the
 assembly with Transdecoder. 
description: Although we carefully removed the contamination, the assembly
 files still contain the contaminatin.
DOI: 10.5061/dryad.gqnk98sj1
title: Large herbivores facilitate an insect herbivore by modifying plant community composition in a temperate grassland

description: Large herbivores often co-occur and share plant resources with herbivorous
 insects in grassland ecosystems, yet how they interact with each other
 remains poorly understood. We conducted a series of field experiments to
 investigate whether and how large domestic herbivores (sheep;
 Ovis aries) may affect the abundance of a common herbivorous
 insect (aphid; Hyalopterus pruni) in a temperate grassland of
 northeast China. Our exclosure experiment showed that three years
 (2010-2012) of sheep grazing had led to 86% higher aphid abundance
 compared with ungrazed sites. Mechanistically, this facilitative effect
 was driven by grazing altering the plant community, rather than by changes
 in food availability and predator abundance for
 aphids. Sheep significantly altered plant community by reducing
 the abundance of unpalatable forbs for the aphids. Our
 small-scale forb removal experiment revealed an
 “associational plant defense” by forbs which protect
 the grass Phragmites australis from being
 attacked by the aphids. However, selective grazing on forbs by
 sheep indirectly disrupted such associational plant defense, making
 P. australis more susceptible to aphids, consequentially
 increasing the density of aphids. These findings provide
 a novel mechanistic explanation for the effects of large herbivores on
 herbivorous insects by linking selective grazing to plant community
 composition and the responses of insect populations in grassland
 ecosystems.
DOI: 10.5061/dryad.x0k6djhg1
title: Unravelling species co-occurrence in a steppe bird community of Inner Mongolia: insights for the conservation of the endangered Jankowski’s Bunting

description: Aim: To evaluate the patterns of bird assemblage and distribution in an
 endangered grassland system, taking into accounts both environmental and
 biotic effects. To further focus on an endangered songbird and associated
 steppe birds. Location: Inner Mongolia, China Methods: We investigated the
 relative importance of abiotic and biotic factors driving the abundance
 and co-occurrence of steppe birds in Inner Mongolia by using joint species
 distribution models. We examined the general patterns of species
 assemblage, with a focus on the endangered Jankowski’s Bunting and other
 species potentially sharing the same niche or interacting with it,
 including potential competitors (especially the closely-related Meadow
 Bunting), predators (corvids, raptors) and a parasite (cuckoo). Results:
 The studied steppe species exhibited varied responses to environmental
 variables, including climate, landscape and habitat predictors. We
 observed stronger species correlations due to residual covariates than to
 abiotic covariates. Jankowski’s Bunting displayed strong positive
 co-occurrences with other ground-nesting songbirds, and exhibited
 significant responses to all measured habitat and climate variables,
 indicating that this endangered bird has a high niche specialization and
 wide associations with other sympatric steppe bird species. Main
 conclusion: Our results pointed out that climate, landscape, and steppe
 habitat predictors are not the only factors structuring bird assemblages.
 Our results suggested that Jankowski’s Bunting is an indicator of the
 occurrence of other species, especially open-nesting specialized steppe
 songbirds, so it could act as a surrogate for overall steppe bird
 conservation. These findings are helpful for understanding how abiotic and
 biotic processes interactively alter bird communities and making effective
 management decisions to mitigate multiple threats to the entire community.
DOI: 10.5061/dryad.9w0vt4bbp
title: Habitat light sets the boundaries for the rapid evolution of cichlid fish vision, while sexual selection can tune it within those limits

description: Cichlid fishes’ famous diversity in body coloration is accompanied by a
 highly diverse and complex visual system. Although cichlids possess an
 unusually high number of seven cone opsin genes, they express only a
 subset of these during their ontogeny, accounting for their astonishing
 interspecific variation in visual sensitivities. Much of this diversity is
 thought to have been shaped by natural selection as cichlids inhabit a
 variety of habitats with distinct light environments. Also, sexual
 selection might have contributed to the observed visual diversity, and
 sexual dimorphism in coloration potentially co-evolved with sexual
 dimorphism in opsin expression. We investigated sex-specific opsin
 expression of several cichlids from Africa and the Neotropics and
 collected and integrated datasets on sex-specific body coloration,
 species-specific visual sensitivities, lens transmission and habitat light
 properties for some of them. We comparatively analyzed this wide range of
 molecular and ecological data, illustrating how integrative approaches can
 address specific questions on the factors and mechanisms driving
 diversification, and the evolution of cichlid vision in particular. We
 found that both sexes expressed opsins at the same levels - even in
 sexually dimorphic cichlid species – which argues against coevolution of
 sexual dichromatism and differences in sex-specific visual sensitivity.
 Rather, a combination of environmental light properties and body
 coloration shaped the diversity in spectral sensitivities among cichlids.
 We conclude that although cichlids are particularly colorful and diverse
 and often sexually dimorphic, it would appear that natural rather than
 sexual selection is a more powerful force driving visual diversity in this
 hyper-diverse lineage.
description: expression_data.csv: qRT-PCR values of investigated cichlid
 individuals and standardized expression considering the slightly variable
 efficiency values of used primers.
 lens_transmission_individually.csv: individuals' raw
 relative lens transmission dataset (prior standardization). Measured with
 a Optics USB2000-UV-VIS-ES photospectrometer.
 raw_reflectance.csv: individuals' raw relative reflectance
 values for investigated measurement spots. Measured with a Optics
 USB2000-UV-VIS-ES photospectrometer.  
description: Please contact me if you have any questions: r.f.schneider@gmx.de
 or https://orcid.org/0000-0001-6015-7219
DOI: 10.15468/dl.jdzkm8
title: Occurrence Download

description: A dataset containing 7261 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Geositta peruviana"
 ]
}

 The dataset includes 7261 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002236-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.rr4xgxd5v
title: Temperature-related body size change of marine benthic macroinvertebrates across the early Toarcian Anoxic Event

description: The Toarcian Oceanic Anoxic Event (TOAE, Early Jurassic, ~182 Ma ago) was
 characterised by severe environmental perturbations which led to habitat
 degradation and extinction of marine species. Warming-induced anoxia is
 usually identified as main driver, but because marine life was also
 affected in oxygenated environments the role of raised temperature and its
 effects on marine life need to be addressed. Body size is a fundamental
 characteristic of organisms and is expected to decrease as a response to
 heat stress. We present quantitative size data of bivalves and brachiopods
 across the TOAE from oxygenated habitats in the Iberian Basin, integrated
 with geochemical proxy data (δ13C and δ18O), to investigate the
 relationship between changes in temperature and body size. We find a
 strong negative correlation between the mean shell size of bivalve
 communities and isotope-derived temperature estimates, suggesting heat
 stress as a main cause of body size reduction. While within-species size
 changes were minor, we identify changes in the abundance of differently
 sized species as the dominant mechanism of reduced community shell size
 during the TOAE. Brachiopods experienced a wholesale turnover across the
 early warming phase and were replaced by a virtually monotypic assemblage
 of a smaller-sized, opportunistic species.
description: Quantitative bed-by-bed sampling performed by consistently
 collecting the same amount of bulk rock for each sample. Fossils of
 benthic macroinvertebrates (brachiopods and bivalves) were identified
 preferentially at species level. Shell size measurements (length and
 heigth) obtained in the field and/or after preparation.
DOI: 10.5061/dryad.t76hdr7xn
title: Geographic variation in the duets of the Rufous-naped Wren (Campylorhynchus rufinucha) complex

description: Acoustic signals used in animal communication play a key role in mate
 attraction, species recognition and territory defense. Variation in
 acoustic signals may reflect population structure, lack of gene flow, and
 phylogenetic relationships. In birds, the study of geographic variation in
 acoustic signals has been useful for elucidating potential factors
 involved in phenotypic divergence and for establishing species limits.
 However, most of the studies on geographic variation have focused on calls
 and solo songs, with few studies focusing on complex behaviors such as
 duets. In this study, we investigated the variation in the duets of the
 Rufous-naped Wrens (Campylorhynchus rufinucha). Our results suggest that
 duets vary across the distribution range of the species complex, matching
 the three taxonomic groups previously suggested (rufinucha, humilis and
 capistratus). We also found a marked song sexual dimorphism in two groups,
 rufinucha and humilis, that is lacking in capistratus. At the local level,
 we found that duets also vary among sites within groups, but less than
 between groups. Our results suggest that groups rufinucha and humilis sing
 the most similar duets, while capistratus performs the most divergent
 duets of the three groups. Further, when comparing duet variation across
 geography, we found that birds living closer to each other sing more
 similar duets. We suggest that the existence of three vocal lineages is
 probably the result of historical geographic isolation followed by other
 selective (i.e. sexual selection, social selection, habitat structure)
 and/or non-selective factors (i.e. drift, isolation by distance), and that
 variation found within groups may be the result of cultural drift or
 social selection.
DOI: 10.5061/dryad.905qfttgw
title: Acoustic data in four species of macaques

description: We provide comparative data on vocal signals in adult females of four
 species of macaque : Tonkean macaques (Macaca tonkeana), crested macaques
 (M. nigra), Japanese macaques (M. fuscata), and rhesus macaques (M.
 mulatta). We distinguished three social contexts: agonistic, affiliative
 and neutral. The agonistic context included aggression (supplantation,
 lunge, chase, slap, grab, bite, facial threat display) and response to
 aggression (aggression, avoidance, flight, crouch, submissive facial
 displays). The affiliative context included affiliative behaviours
 (approach, sitting in contact, social grooming, social play, grasp,
 embrace, mount, affiliative facial display). In the neutral context, the
 caller was not involved in a social interaction. We drew spectrograms
 using the sofware Raven Pro v1.4’ (Cornell Lab of
 Ornithology, www.birds.cornell.edu/raven) with a
 256 fast Fourier transform length and a Hanning window.
 With the same software, we measured the following variables: Duration:
 duration from the beginning to the end of a call, in seconds; Q2 ratio:
 ratio between duration that divides a call into two intervals of equal
 energy and duration in percentage; Q1 frequency: value of the frequency
 that divides a call into two intervals containing 25% and 75% of the
 energy, in Herz; Q2 frequency: value of the frequency that divides a call
 into two intervals of equal energy, in Herz; Q3 frequency: value of the
 frequency that divides a call into two intervals containing 75% and 25% of
 the energy, in Herz; Wiener’s aggregate entropy: degree of disorder (i.e.
 noisiness) of the call, which uses the total energy in a
 frequency bin over the entire call; Wiener’s average entropy:
 mean of the mean entropies of the different time slices of a call. Our
 objective was to compare the four species on tonal and atonal calls, so we
 did not take into account the variables associated with fundamental
 frequencies since they are absent in atonal calls.
description: We made behavioural acoustic recordings in 14 adult females from two groups of Japanese macaques, 16 adult females from two groups of rhesus macaques, 11 adult females from four groups of Tonkean macaques, and 18 adult females from two groups of crested macaques.
description: There are no missing values.
DOI: 10.5061/dryad.0zpc866v2
title: Data from: Rediscovery of a presumed extinct species, Salvelinus profundus, after re-oligotrophication

description: Lake Constance (47° 38’ N, 9° 22’ E) is a deep (max. depth 251m) and large
 (surface area 536 km2) postglacial lake in Central Europe. Originally, it
 harboured two charr species – Salvelinus umbla and S. profundus. The first
 is a medium-sized, colorful, winter spawning charr, which is widespread
 across Central European lakes, the second a small, pale, summer spawning,
 deepwater charr, which is endemic to Lake Constance (Schillinger 1901,
 Kottelat and Freyhof 2007). S. profundus has exceptionally large eyes and
 the upper jaw strongly overlaps the lower jaw. These traits are both
 considered adaptations to its life in the deep where it mostly feeds on
 profundal benthos (Schillinger 1901). During the second half of the last
 century, Lake Constance became eutrophic, resulting in oxygen-depletion in
 deep waters (IGKB 2004). The anoxic conditions harmed the development of
 eggs by profundal spawning fish (Baer et al. 2017). Thanks to strict
 management interventions, the lake has returned to an oligotrophic state,
 and oxygen is again available in the water column down to the greatest
 depth (IGKB 2004).
description: Individual measures of morphological distances, gill raker
 numbers, age, capture depth as well as microsatellite genotypes. Linear
 morphometric distances (TL-jaw_overlap) were measured on the preserved
 fish using a digital caliper, are given in mm, and are described in Figure
 S1 in the Appendix. Alleles of the 9 microsatellite markers are coded as
 retention time, missing data is indicated with 999.
DOI: 10.5061/dryad.k0p2ngf50
title: Data from: The role of nocturnal omnivorous lemurs as seed dispersers in Malagasy rain forests

description: Fruit-eating animals play important roles as seed dispersal agents in
 terrestrial systems. Yet, the extent to which seed dispersal by nocturnal
 omnivores may facilitate germination and the recruitment of plant
 communities has rarely been investigated. Characterizing their roles in
 seed dispersal is necessary to provide a more complete picture of how seed
 dispersal processes affect ecosystem functioning. We investigated the
 roles and impacts of two species of nocturnal omnivorous lemur species,
 Microcebus jollyae and M. rufus, on seed dispersal in Madagascar’s rain
 forests, through analysis of fecal samples and germination experiments.
 Data show that these lemur species, which are among the world’s smallest
 primates, dispersed 22 plant species from various forest strata and that
 the defecated seeds germinated faster and at higher rates than control
 seeds for the eight plant species we tested. Even though mouse lemurs
 dispersed both native and non-native plant species, non-native plant
 species represented a relatively small proportion (17%). These results
 demonstrate that overlooked nocturnal omnivores can act as important seed
 dispersers, which may have critical implications for forest regeneration
 and the maintenance of plant diversity in fragmented/degraded forests.
 Finally, we provide critical insights into the previously unobserved
 behavior and diet of endangered nocturnal lemurs for their effective
 conservation.
description: Missing values are already replaced by "n/a".
 There are two sheets in this dataset. There is
 a README.docx, which contains the explanation of the variables in the
 datasets.
DOI: 10.5061/dryad.pc866t1k5
title: Climate associated genetic variation in Fagus sylvatica and potential responses to climate change in the French Alps

description: Local adaptation patterns have been found in many plants and animals,
 highlighting the genetic heterogeneity of species along their range of
 distribution. In the next decades, global warming is predicted to induce a
 change in the selective pressures that drive this adaptive variation,
 forcing a reshuffling of the underlying adaptive allele distributions. For
 species with low dispersion capacity and long generation time such as
 trees, the rapidity of the change could imped the migration of beneficial
 alleles and lower their capacity to track the changing environment.
 Identifying the main selective pressures driving the adaptive genetic
 variation is thus necessary when investigating species capacity to respond
 to global warming. In this study, we investigate the adaptive landscape
 of Fagus sylvatica along a gradient of populations in
 the French Alps. Using a double digest restriction-site associated DNA
 (ddRAD) sequencing approach, we identified 7,000 SNPs from 570 individuals
 across 36 different sites. A redundancy analysis (RDA)-derived method
 allowed us to identify several SNPs that were strongly associated with
 climatic gradients; moreover, we defined the primary selective gradients
 along the natural populations of F. sylvatica in the
 Alps. Strong effects of elevation and humidity, which contrast
 north-western and south-eastern site, were found and were believed to be
 important drivers of genetic adaptation. Finally, simulations of future
 genetic landscapes that used these findings allowed identifying
 populations at risk for F. sylvatica in the Alps, which
 could be helpful for future management plans.
DOI: 10.5061/dryad.wstqjq2h6
title: Seasonal variation in the strength of interference competition among headwater stream predators

description: 1. Vertebrate communities in headwater streams are assumed to be regulated
 through competitive and predatory interactions. Although documented
 predation is rare, studies regularly report competitive dominance by fish
 that, as larger competitors reliant on aquatic habitat, exclude
 semi-aquatic salamanders to marginal stream habitat. However, it is
 unclear whether fish interact with stream-breeding salamanders through
 indirect effects such as, competition for resources (e.g., food or cover)
 or fear (i.e., threat of predation) nor is it known whether these
 interactions are consistent through time. 2. This study used a novel
 caging approach to determine if competitive outcomes between a headwater
 fish and salamanders were regulated primarily through resource depletion
 (exploitative competition) or behavioural avoidance (interference
 competition). 3. We paired banded sculpin (Cottus carolinae) and larval
 red salamanders (Pseudotriton ruber) of similar body size in independent
 flow through mesocosms with intra- and inter-specific pairs allowed to
 interact physically or non-physically. The experiment was repeated in the
 fall and in the spring when stream salamander larvae begin to transform
 into terrestrial juveniles. 4. Banded sculpin negatively influenced growth
 of red salamanders regardless of whether they were allowed to physically
 interact, suggesting interference competition and behavioural avoidance.
 This asymmetrical effect was strongest in the spring when salamanders
 underwent metamorphosis at higher rates in the presence of fish. However,
 in the fall, the effects were more balanced between the two species with
 salamanders impacting fish through exploitative competition. 5. By
 studying the temporal relationships between two competitors and using a
 caging method novel to competition studies, we established that the
 outcomes of competition are dependent on season and may vary in type
 relative to the timing of life history events. For this community, these
 results suggest that outcomes of competition are highly dependent on
 season and could indicate a biotic mechanism maintaining headwater
 salamander distributions through source-sink dynamics. Our results also
 suggest that, in this species interaction, it may be unwarranted to assume
 that the outcomes of competition at one time represent the complex
 relationships regulating community interactions.