cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.905qfttj6
title: Reduction in the metabolic levels due to phenotypic plasticity in the Pyrenean newt, Calotriton asper, during cave colonization

description: According to theories on cave adaptation, cave organisms are expected to
 develop a lower metabolic rate compared to surface organisms as an
 adaptation to food scarcity in the subterranean environments. To test this
 hypothesis, we compared the oxygen consumption rates of the surface and
 subterranean populations of a surface-dwelling species, the newt
 Calotriton asper, occasionally found in caves. In this study, we designed
 a new experimental setup in which animals with free movement were
 monitored for several days in a respirometer. First, we measured the
 metabolic rates of individuals from the surface and subterranean
 populations, both maintained for eight years in captivity in a natural
 cave. We then tested individuals from these populations immediately after
 they were caught and one year later while being maintained in the cave. We
 found that the surface individuals that acclimated to the cave
 significantly reduced their oxygen consumption, whereas individuals from
 the subterranean population maintained in the cave under a light/dark
 cycle did not significantly modify their metabolic rates. Second, we
 compared these metabolic rates to those of an obligate subterranean
 salamander (Proteus anguinus), a surface aquatic Urodel (Ambystoma
 mexicanum), and a fish species (Gobio occitaniae) as references for
 surface organisms from different phyla. As predicted, we found differences
 between the subterranean and surface species, and the metabolic rates of
 surface and subterranean C. asper populations were between those of the
 obligate subterranean and surface species. These results suggest that the
 plasticity of the metabolism observed in surface C. asper was neither
 directly due to food availability in our experiments nor the light/dark
 conditions, but due to static temperatures. Moreover, we suggest that this
 adjustment of the metabolic level at a temperature close to the thermal
 optimum may further allow individual species to cope with the food
 limitations of the subterranean environment.
DOI: 10.5061/dryad.mkkwh70xm
title: Targeted and passive environmental DNA approaches outperform established methods for detection of quagga mussels, Dreissena rostriformis bugensis in flowing water

description: The early detection of invasive non-native species (INNS) is
 important for informing management actions. Established monitoring methods
 require the collection or observation of specimens, which is unlikely at
 the beginning of an invasion when densities are likely to be low.
 Environmental DNA (eDNA) analysis is a highly promising technique for the
 detection of INNS – particularly during the early stages of an
 invasion.  Here, we compared the use of traditional kick-net
 sampling with two eDNA approaches (targeted detection using both
 conventional and quantitative PCR, and passive detection via metabarcoding
 with conserved primers) for detection of quagga mussel, Dreissena
 rostriformis bugensis; a high priority INNS, along a density
 gradient on the River Wraysbury, UK.  All three molecular tools
 outperformed traditional sampling in terms of detection. Conventional PCR
 and qPCR both had 100% detection rate in all samples, and outperformed
 metabarcoding when the target species was at low densities. Additionally,
 quagga mussel DNA copy number (qPCR) and relative read count
 (metabarcoding) were significantly influenced by both mussel density and
 distance from source population, with distance being the most significant
 predictor.  Synthesis and application. All three
 molecular approaches were more sensitive than traditional kick-net
 sampling for the detection of the quagga mussel in flowing water, and both
 qPCR and metabarcoding enabled estimates of relative abundance. Targeted
 approaches were more sensitive than metabarcoding, but metabarcoding has
 the advantage of providing information on the wider community, and
 consequently impacts of INNS. 
description: The following files have been produced as part of the manuscript:
 Targeted and passive environmental DNA approaches outperform established
 methods for detection of quagga mussels, Dreissena rostriformis bugensis
 in flowing water qPCR data from mesocosm
 experiments for the detection of quagga mussel (D. r. bugensis)
 qPCR data from field experiments for the detection of quagga
 mussel (D. r. bugensis) Metabarcoding data generated
 using the COI primer pairs (Leray+Geller) (Leray et al 2013) for the 54
 field samples and 3 positive samples, including OTU ID and taxonomy
 generated from the MetaBEAT pipeline. Sub-sample of
 those sites metabarcoding and qPCR for the detection of quagga mussel (D.
 r. bugensis) Data Descriptions of the columns found
 in each dataset and the contents.
DOI: 10.5061/dryad.s4mw6m953
title: Unstandardized breeding choice grouped by maternal litter

description: Banded mongooses play a delicate balancing act between incest and warfare.
 Some females have to choose between mating with a relative within their
 own social group or trying to sneakily mate with a male from a rival group
 during fights between groups. We show that females are more likely to mate
 with extra-group males when the risk of inbreeding within their group is
 high, but not all females get this opportunity for extra-group mating.
description: Full details of data collection are provided in the methods
 section of "Extra-group paternity varies with proxies of relatedness
 in a social mammal with high inbreeding risk" in Behavioural
 Ecology.
description: See the methods section for details of how data was collected and
 analysed. This data is NOT standardised. Before fitting models, these data
 were standardised by subtracting the mean and dividing by the standard
 deviation. Data is a .csv (comma separated value) file,
 each row is a single maternal litter of banded mongooses describing the
 conditions of the litter's dam at conception. This dataset was used
 to investigate extra-group breeding behaviour in female banded mongooses.
 The analyses were performed on this dataset using R. Note that this data
 is NOT standardised. Before fitting models, these data were standardised
 by subtracting the mean and dividing by the standard deviation.
 Description of columns: clutch: aka maternal
 litter, id code for a litter of a single dam
 groupsize: The number of individuals over six months old in the
 breeding female’s group at conception. pack_year: aka
 group age, Time between the first time the social group was observed
 (usually the point at which the group formed) and the time the maternal
 litter was conceived. dam_in_np: Was the dam in her
 natal group at conception? Females still in the group they were born in
 when they conceived were said to be in their natal group.
 r_tr_na_mates: relatedness to top ranked males, The average
 pedigree relatedness of a focal female to males of the top three age ranks
 (assuming they are over 6 months old) and immigrants to the
 population. age: age of breeding female at
 conception bexp: Were any pups in the maternal litter
 (clutch) fathered by a male which was not in the breeding female’s social
 group at the time of conception (in either the second or third month
 before birth). clutchf: The average inbreeding
 coefficient of a maternal litter measured by pedigree.
 clutchsmlh: The average inbreeding coefficient of a maternal
 litter measured by microsatellite standardised multilocus
 heterozygosity. dam_conception_pack: The social group
 the dam was in at conception dam: The identity of the
 dam litter: The identitiy of the "Communal
 litter" (Collective term for all pups in a group born during a single
 breeding event.) NOTE, microsoft excel interprets some of these codes as
 dates and automatically converts them.
DOI: 10.5061/dryad.gb5mkkwn8
title: Robustness of consensus is independent from preference diversity among group members in the American cockroach (Periplaneta american)

description: Collective choices and consensus resulting from the competition of
 positive feedbacks, are the subject of numerous studies. However, how the
 interindividual diversity of preferences among the group members affects
 these dynamics is usually overlooked apart from vertebrates based studies.
 Gregarism is a useful model for studying how the interindividual diversity
 of preferences affects the collective choices and consensus. The
 decision-making of three types of groups of the cockroach Periplaneta
 americana is tested in a choice between an odorous shelter and an
 odourless one: naïves (individuals showing an inherent preference towards
 the odorous shelter); conditioned (individuals with the preference for the
 odorous shelter inhibited); and mixed (a combination of conditioned
 individuals and a minority of naïve ones). We show that while the
 consensus is robust for all groups (&gt;90% of the total population is
 in the same shelter), the group composition determines the rate to achieve
 a consensus and the frequency of selection of the odorous shelter. Indeed,
 increasing the proportion of naïves in the group leads to an increasing
 number of consensuses towards the odorous shelter and to an increasing
 rate to reach them. We also show that the minority of naïve individuals in
 mixed groups act as leaders or influencers.
DOI: 10.5061/dryad.cjsxksn4d
title: A regional assessment of changes in plant-plant interactions along topography gradients in Tunisian sebkhas

description: Facilitation among plants in dry ecosystems is crucial for diversity and
 ecosystem functioning and stability. However, the importance of
 facilitation in extremely stressful conditions is highly
 debated.  We attempt to separate the effects of direct
 non-resource and resource stress factors on plant-plant interactions by
 assessing changes in facilitation and competition along salinity gradients
 at two contrasting levels of aridity. We selected eight saline depressions
 (hereafter sebkhas) in the wet and dry Mediterranean arid climate of
 North-Africa, from central Tunisia to the Libyan border 500 km
 south-eastward. In each sebkha, we transplanted at four positions along
 the salinity gradient induced by topography, both in open areas and below
 dominant shrubs, three target species with contrasting tolerances to
 salinity stress. Target plant survival, soil electrical conductivity and
 moisture were recorded before and after the dry summer season in all
 treatments. Shrubs decreased salinity and drought stresses in all
 treatments and facilitation was the dominant interaction. However, we
 found a strong collapse of facilitation along the salinity gradient, due
 to a dramatic mortality of the three target species both with and without
 neighbours above their threshold of salinity tolerance. Increasing aridity
 induced an earlier collapse of facilitation along the gradient. The three
 target species had contrasting responses to neighbours, with the least
 stress-tolerant species being facilitated and the two most stress-tolerant
 ones negatively affected by neighbours. Our study shows that disentangling
 resource and non-resource stresses along gradients and controlling for
 target species effects help understanding variation in plant-plant
 interactions under highly stressful conditions.
DOI: 10.5061/dryad.18931zcvk
title: The interacting effect of habitat amount, habitat diversity and fragmentation on insect diversity along elevational gradients.

description: Aim: Elevational gradients are a useful approach to evaluate how
 environmental factors affect animal diversity. Decades of studies on the
 elevation-diversity gradient have revealed that this gradient varies
 greatly with taxa and geographic regions. One potential explanation for
 this may be the dependence of the relationship on landscape features. We
 explore the impact of fragmentation, habitat diversity and habitat amount
 on insect diversity (alpha and beta) and abundance along elevational
 gradients. We hypothesize that insect diversity and abundance will relate
 negatively with elevation, but positively with these landscape features.
 We also hypothesize that landscape features will interact in a way that
 the positive effect of a given variable on insect diversity may be offset
 by the others. Location: Reunion Island (Indian Ocean) Taxon: The insect
 order thrips (Thysanoptera) Methods: Insects were sampled along replicated
 elevational gradients, and at each sampling plot landscape features and
 abiotic variables were estimated within buffers surrounding the site.
 Insect alpha diversity was estimated using abundance-based rarefaction
 methods, whereas beta diversity was estimated calculating the "local
 contributions to beta diversity" metric. The effect of elevation,
 rainfall, landscape features and their interactions was assessed on insect
 alpha and beta diversity and abundance during two consecutive seasons
 using linear mixed effects models. Results: We found that thrips alpha and
 beta diversity was negatively related with elevation, but the relationship
 varied between seasons and rainfall regimes. Among the different landscape
 features considered, we found that habitat amount had the strongest effect
 on diversity. The effect of habitat amount on diversity, however, was
 offset in areas of low habitat (or land cover) diversity. Main
 conclusions: Generalizing the factors that underlie the elevation
 diversity gradient has become a cornerstone in ecological theory because
 it can help to understand the impact of human activities on diversity.
 Here we show that taking landscape information into account may help to
 fulfil this objective because landscape effects co-vary with elevation
 with often intricate consequences for diversity.
description: For details see the manuscript published at the Journal of
 Biogeography entitled "The interacting effect of habitat amount,
 habitat diversity and fragmentation on insect diversity along elevational
 gradients" and authored by Niry T. Dianzinga, Marie-Ludders
 Moutoussamy, Joëlle Sadeyen, Lala H. R. Ravaomanarivo & Enric
 Frago
description: For details and abreviations see the manuscript published at the
 Journal of Biogeography entitled "The interacting effect of habitat
 amount, habitat diversity and fragmentation on insect diversity along
 elevational gradients" and authored by Niry T. Dianzinga,
 Marie-Ludders Moutoussamy, Joëlle Sadeyen, Lala H. R. Ravaomanarivo
 & Enric Frago
DOI: 10.5061/dryad.2rbnzs7m3
title: Data from: Seed quality and seed quantity in red maple depends on weather and individual tree characteristics

description: Under future climate change, plant species are expected to shift their
 ranges in response to increasing temperatures and altered precipitation
 patterns. As seeds represent the single opportunity for plants to move, it
 is critical to quantify the factors that influence reproduction. While
 total seed production is clearly important, seed quality is equally as
 critical and often overlooked. Thus, to quantify how environmental and
 tree-level characteristics affect seed quality and quantity, the
 reproductive output of red maple (Acer rubrum) was measured along an
 elevation gradient in the Monongahela National Forest, WV. A variety of
 individual-level characteristics were measured (i.e., DBH, canopy area,
 tree cores), and seed traps were placed under seed-bearing trees to
 collect samaras and quantify total seed production. A random subsample of
 collected seeds from each tree were micro-CT scanned to determine embryo
 volume, photographed for morphology measurements, and used for germination
 trials. The number of seeds produced was negatively affected by frost
 events during flowering, and stand density. The trees with the most seeds
 also showed reduced growth in recent years. Only 63% of scanned seeds
 showed embryo development, and of those seeds – only 23% germinated. The
 likelihood of embryo presence increased as growth rate decreased, while
 embryo size increased with tree height, smaller DBH, and in areas
 dominated by hemlock. Both larger embryo volume and larger overall seed
 size increased the likelihood of germination. The results highlight the
 importance of including seed quality in addition to seed quantity for a
 more complete representation of reproductive output.
DOI: 10.5061/dryad.bcc2fqz9q
title: Data from: A test of the niche variation hypothesis in a ruminant herbivore

description: 1. Despite the shared prediction that the width of a population’s dietary
 niche expands as food becomes limiting, the Niche Variation Hypothesis
 (NVH) and Optimal Foraging Theory (OFT) offer contrasting views about how
 individuals alter diet selection when food is limited.
 2. Classical OFT predicts that dietary preferences do not change
 as food becomes limiting, so individuals expand their diets as they
 compensate for a lack of preferred foods. In contrast, the NVH predicts
 that among-individual variation in cognition, physiology, or morphology
 create functional trade-offs in foraging efficiency, thereby causing
 individuals to specialize on different subsets of food. 3. To evaluate (a)
 the predictions of the NVH and OFT and (b) evidence for physiological and
 cognitive-based functional trade-offs, we used DNA microsatellites and
 metabarcoding to quantify the diet, microbiome, and genetic relatedness (a
 proxy for social learning) of 218 moose (Alces alces) across six
 populations that varied in their degree of food limitation.
 4. Consistent with both the NVH and OFT, dietary niche breadth
 increased with food limitation. Increased diet breadth of
 individuals—rather than increased diet specialization—was strongly
 correlated with both food limitation and dietary niche breadth of
 populations, indicating that moose foraged in accordance with OFT. Diets
 were not constrained by inheritance of the microbiome or inheritance of
 diet selection, offering support for the little-tested hypothesis that
 functional trade-offs in food use (or lack thereof) determine whether
 populations adhere to the predictions of the NVH or OFT. 5. Our
 results indicate that both the absence of strong functional trade-offs and
 the digestive physiology of ruminants provide contexts under which
 populations should forage in accordance with OFT rather than the NVH.
 Also, because dietary niche width increased with increased food
 limitation, OFT and the NVH provide theoretical support for the notion
 that plant-herbivore interaction networks are plastic rather than static,
 which has important implications for understanding interspecific niche
 partitioning. Lastly, because population-level dietary niche breadth and
 calf recruitment are correlated, and because calf recruitment is a proxy
 for food limitation, our work demonstrates how diet data can be employed
 to understand a populations’ proximity to carrying capacity.
DOI: 10.5061/dryad.z08kprr9v
title: Phylogenomics resolves the invasion history of Acacia auriculiformis in Florida

description: Aim: Understanding the genetic structure of plants in their native range
 is crucial when reconstructing the invasion history of weeds. This
 information allows researchers to pin-point the provenance of invasive
 plants, and to test the importance of genetic admixture in facilitating
 invasion success. We assessed genetic structuring across the native range
 of A. auriculiformis, to determine whether genetic admixture contributes
 to the success of this weed in its introduced range, and test for rapid
 adaptation to environmental conditions in the invasive lineage. Location:
 Australia, Papua New Guinea, Florida Taxon: Acacia auriculiformis Methods:
 We sampled A. auriculiformis from across its entire native distribution
 (northern Australia, Papua New Guinea) and its invasive range in Florida,
 and used Genotyping-by-sequencing (GBS) to assess population structuring.
 Results: Principal component analysis, based on 9,591 SNPs, indicated
 significant differentiation among samples from Papua New Guinea, the
 Northern Territory (Australia), and north Queensland (Australia). Florida
 samples also formed a distinct cluster, with these samples most closely
 related to samples from the Northern Territory. These results indicate
 that the Florida A. auriculiformis lineage most likely originates from the
 Northern Territory, with no evidence that plants were introduced from
 different parts of the native range. We found evidence of allelic shifts
 in the Florida population, suggesting rapid adaptation to environmental
 conditions may contribute the success of the invasive lineage. Main
 conclusions: Two well-known biogeographic barriers – the Carpentaria Gap
 and Torres Strait – have caused genome-wide divergence among A.
 auriculiformis plants from north Queensland, Northern Territory, and Papua
 New Guinea. The taxonomic status of these allopatric populations should be
 further assessed. As the Florida lineage originated in the Northern
 Territory the search for potential biological control agents should be
 focused in this region. Our results also demonstrate how artificial
 selection and strong genetic drift may cause introduced plants to have a
 unique genetic make-up not found in the native range.
DOI: 10.5061/dryad.1rn8pk0rp
title: Amblyanthus chenii, a new species and generic record from Xizang, China

description: Amblyanthus chenii (Primulaceae; Myrsinoideae), a new species discovered
 growing in the understory of primeval forests in Medog County, southeast
 Xizang, China, is described based on morphological evidence. This is also
 the first generic record of Amblyanthus in China. The new species is most
 similar morphologically to A. multiflorus based on its axillary
 inflorescence and connate filament, but it differs in its 2-4 cm long
 condensed panicle and up to half adnation of its sepals and petals.
 Amblyanthus chenii can also be easily distinguished from other congeneric
 species by various morphological differences. Phylogenetic analysis based
 on nuclear ribosomal ITS and six plastid markers indicates that
 Amblyanthus chenii and Amblyanthopsis burmanica form a clade that is
 nested within the large pantropical genus Ardisia and is sister to the
 Ardisia subgenus Crispardisia. The close relationships among Amblyanthus,
 Amblyanthopsis, and Ardisia subg. Crispardisia are strongly supported by
 their shared synapomorphy of crenulate leaves with marginal glands.
description: Appendix S1<br> Data matrix of ITS sequences
 Appendix S2<br> Data matrix of combined atpB, matk, ndhF,
 psbA-trnH, rbcL and trnL-trnF sequences. Appendix
 S3<br> Data matrix of combined bases sequences and
 coded-gaps. Fig. S1<br> Bayesian majority-rule
 consensus tree based on ITS datasets. Posterior probabilities are noted
 above branches, and the bootstrap values in the maximum likelihood
 analysis are noted under branches. The asterisk indicates that the value
 is less than 30 or clade collapsed. Fig. S2<br>
 Bayesian majority-rule consensus tree based on combined six plastid
 datasets. Posterior probabilities are noted above branches, and the
 bootstrap values in the maximum likelihood analysis are noted under
 branches. The asterisk indicates that the value is less than 30 or clade
 collapsed. Fig. S3<br> Bayesian majority-rule
 consensus tree based on combined bases-gaps datasets. Posterior
 probabilities are noted above branches, and the bootstrap values in the
 maximum likelihood analysis are noted under branches. The asterisk
 indicates that the value is less than 30 or clade collapsed.