cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.79cnp5hw1
title: Effects of large herbivores on fire regimes and wildfire mitigation

description: 1. Abandonment of agricultural land is widespread in many parts of the
 world, leading to shrub and tree encroachment. The increase of flammable
 plant biomass, i.e. fuel load, increases the risk and intensity of
 wildfires. Fuel reduction by herbivores is a promising management strategy
 to avoid fuel build-up and mitigate wildfires. However, their
 effectiveness in mitigating wildfire damage may depend on a range of
 factors, including herbivore type, population density and feeding
 patterns. 2. Here we review the evidence on whether management with
 herbivores can reduce fuel load and mitigate wildfires, and if so, how to
 identify suitable management that can achieve fire mitigation objectives
 while providing other ecosystem services. We systematically reviewed
 studies that investigated links between herbivores, fire hazard, fire
 frequency and fire damage. 3. We found that in general, herbivores reduce
 fuel load most effectively when they are mixed-feeders, when grazing and
 browsing herbivores are combined, and when herbivore food preferences
 match the local vegetation. In some cases, the combination of herbivory
 with other management strategies, such as mechanical clearing, is
 necessary to reduce wildfire damage. 4. We conclude that herbivores have
 the capacity to mitigate wildfire damage, and we provide guidance for
 grazing management for wildfire mitigation strategies. As areas undergoing
 land abandonment are particularly prone to wildfires, the maintenance or
 promotion of grazing by domestic or wild herbivores is a promising tool to
 reduce wildfire risk in a cost-effective way, while also providing other
 ecosystem services. Relevant land-use policies, including fire-suppression
 policies, agricultural and forest(ry) policies could incentivise the use
 of herbivores for better wildfire prevention.
DOI: 10.5061/dryad.5x69p8d3g
title: Asimina triloba genetic data

description: Dispersal and colonization are among the most important ecological
 processes for species persistence as they allow species to track changing
 environmental conditions. During the last glacial maximum (LGM), many
 cold-intolerant Northern Hemisphere plants retreated to southern glacial
 refugia. During subsequent warming periods, these species expanded their
 ranges northward. Interestingly, some tree species with limited seed
 dispersal migrated considerable distances after the LGM ~19,000 year
 before present (YBP). It has been hypothesized that indigenous peoples may
 have dispersed valued species, in some cases beyond the southern limits of
 the Laurentide Ice Sheet. To investigate this question we employed a
 molecular genetics approach on a widespread North American understory tree
 species whose fruit was valued by indigenous peoples. Twenty putative
 anthropogenic (near pre-Columbian habitations) and 62 wild populations of
 Asimina triloba (pawpaw), which produces the largest edible fruit of any
 North American tree, were genetically assayed with nine microsatellite
 loci. Putative anthropogenic populations were characterized by reduced
 genetic diversity and greater excess heterozygosity relative to wild
 populations. Anthropogenic populations in regions that were glaciated
 during the LGM had profiles consistent with founder effects and reduced
 gene flow, and shared rare alleles with wild populations hundreds of
 kilometers away (mean = 723.1 km). Some of the most compelling evidence
 for human-mediated dispersal is that putative anthropogenic and wild
 populations sharing rare alleles were separated by significantly greater
 distances (mean = 695.3 km) than wild populations sharing rare alleles
 (mean = 607.1 km; p = 0.014). Collectively the genetic data suggest that
 long-distance dispersal played an important role in the distribution of
 pawpaw and is consistent with the hypothesized role of indigenous peoples.
description: Genomic DNA was extracted from frozen
 leaf tissue (~ 0.05 g) using a modified CTAB protocol (Doyle &
 Doyle, 1983) and DNA quality and quantity were evaluated using an ND-1000
 Nanodrop® spectrophotometer. Nine nuclear microsatellite loci (Lu et al.,
 2011; Table S2) were PCR amplified in 12.5 µL reaction volumes containing
 3.25 µL molecular grade ddH2O, 2.5 µL 5X One Taq® standard reaction buffer
 (New England Biolabs, Ipswich, MA), 0.35 µL 25 mM MgCl solution
 (Sigma-Aldrich), 1.25 µL 10X (1 mg/mL) bovine serum albumin
 (Thermo-Fisher), 1 µL 2.5 mM dNTP mix (New England Biolabs, Ipswich, MA),
 1 µL primer mix (0.5 µM CAG-labeled primer and 5 µM unlabeled primer),
 0.45 µL 10 µM universal dye-labeled primer, 0.2 µL One Taq® Hot Start DNA
 polymerase (New England Biolabs, Ipswich, MA), and 2.5 µL of diluted
 template DNA (20 ng/µL). A 3-primer PCR protocol was used whereby a
 CAG-tag sequence (Hauswaldt & Glenn, 2003) was added to the 5’ end
 of one primer and a third fluorescently labeled (FAM, HEX, or NED) primer
 identical to the CAG-tag was included.
description: Missing data is indicated by "0"
DOI: 10.5061/dryad.fqz612jsp
title: Morphological consequences of climate change for resident birds in intact Amazonian rainforest

description: First, this dataset contains morphological measurements (body mass, wing
 length) of birds from the Biological Dynamics of Forest Fragments Project
 (BDFFP), located in central Amazonia. Birds were captured using
 mist-nets between 1979 and 2019 in the understory of primary
 forest spanning ~40 km. Second, we have included climate data
 (precipitation, temperature) associated with this study area derived from
 the global EU Copernicus ERA5 climate reanalysis
 (https://cds.climate.copernicus.eu).
description: Birds were captured in understory mist-nets within primary
 forest. Mass was measured either with a Pesola spring scale or an
 electronic balance, whereas mass was measured with an end-stop
 ruler. For methodological details, see
 https://doi.org/10.1093/condor/duaa005. Morphological measurements come in
 large part from bird captures analyzed for abundance trends published
 here: https://doi.org/10.1111/ele.13628.
DOI: 10.5061/dryad.6hdr7sr1f
title: Highly diversified mitochondrial genomes provide new evidence for inter-ordinal relationships in the Arachnida

description: Arachnida is an exceptionally diverse class in the Arthropoda, comprising
 of 20 orders and playing essential roles in the terrestrial ecosystems.
 However, their inter-ordinal relationships have been debated for over a
 century. Rearranged or highly rearranged mitochondrial (mt) genomes were
 consistently found in this class, but their various extent in different
 lineages and efficiency for resolving arachnid phylogenies are unclear.
 Here, we reconstructed phylogenetic trees using mt genome sequences of 290
 arachnid species to decipher inter-ordinal relationships as well as
 diversification through time. Our results recovered monophyly of 10 orders
 (i.e., Amblypygi, Araneae, Ixodida, Mesostigmata, Opiliones,
 Pseudoscorpiones, Ricinulei, Sarcoptiformes, Scorpiones, and Solifugae),
 while rejected monophyly of the Trombidiformes due to unstable position of
 the Eriohyoidea. The monophyly of Acari (subclass) was rejected possibly
 due to long-branch attraction of the Pseudoscorpiones. Basal inter-ordinal
 relationships were partially resolved by sharing conserved mt gene
 arrangements. Highly rearranged mt genomes in mites while less rearranged
 or conserved in the remaining lineages point to their exceptionally
 diversification in mite orders; however, shared derived mt gene clusters
 were found within superfamilies rather than inter-orders, confusing
 phylogenetic signals in arachnid inter-ordinal relationships. Molecular
 dating results show that arachnid orders have ancient origins ranged from
 the Silurian to the Carboniferous, followed by a huge gap, crossing the
 Permian, Triassic, and Jurassic, then especially diversified after the
 Cretaceous in orders Araneae, Mesostigmata, Sarcoptiformes, and
 Trombidiformes. By summarizing previously resolved key positions of some
 orders, we propose a plausible inter-ordinal phylogeny: ((Solifugae,
 Palpigradi) (Phalangiotarbida (Trigonotarbida ((Uraraneida, Araneae)
 (Haptopoda (Amblypygi (Thelyphonida, Schizomida)))) (Opiliones (Ricinulei
 ((Opilioacarida (Mesostigmata (Holothyrida, Ixodida))) (Trombidiformes,
 Sarcoptiformes)))))) (Scorpiones, Pseudoscorpiones))). Our results
 underline a more precise framework for inter-ordinal phylogeny in the
 Arachnida and provide insights into their ancient evolution.
DOI: 10.5061/dryad.4tmpg4f9z
title: Data for: Variation in reproductive isolation across a species range

description: Reproductive isolation is often variable within species, a phenomenon that
 while largely ignored by speciation studies, can be leveraged to gain
 insight into the potential mechanisms driving the evolution of genetic
 incompatibilities. We used experimental greenhouse crosses to characterize
 patterns of reproductive isolation among three divergent genetic lineages
 of Campanulastrum americanum that occur in close geographic proximity in
 the Appalachian Mountains. Substantial, asymmetrical reproductive
 isolation for survival due to cytonuclear incompatibility was found among
 the lineages (up to 94% reduction). Moderate reductions in pollen
 viability, as well as cytoplasmic male sterility, were also found between
 some Mountain populations. We then compared these results to previously
 established patterns of reproductive isolation between these Mountain
 lineages and a fourth, widespread Western lineage to fully characterize
 reproductive isolation across the complete geographic and genetic range of
 C. americanum. Reproductive isolation for survival and pollen viability
 was consistent across studies, indicating the evolution of the underlying
 genetic incompatibilities is primarily determined by intrinsic factors. In
 contrast, reproductive isolation for germination was only found when
 crossing Mountain populations with the Western lineage, suggesting the
 underlying genetic incompatibility is likely influenced by environmental
 or demographic differences between the two lineages. Cytoplasmic male
 sterility was also limited in occurrence, being restricted to a handful of
 Mountain populations in a narrow geographic range. These findings
 illustrate the complexity of speciation by demonstrating multiple,
 independent genetic incompatibilities that lead to a mosaic of genetic
 divergence and reproductive isolation across a species range.
DOI: 10.5061/dryad.3r2280ggk
title: Scaling of locomotor muscle oxidative and glycolytic metabolic enzymes during the ontogeny of regional endothermy in Pacific bluefin tuna (Thunnus orientalis)

description: In this study, the scaling of the oxidative metabolic enzymes citrate
 synthase (CS) and cytochrome c oxidase (COX) and the glycolytic enzyme
 pyruvate kinase (PK) in the red (‘slow-twitch’, oxidative) and the white
 (‘fast-twitch’, glycolytic) locomotor muscle of young (~2 to ~16 months of
 age) Pacific bluefin tuna (Thunnus orientalis) during the ontogeny of red
 muscle endothermy was investigated. On a mass-specific basis (units g-1
 muscle tissue), CS activity scaled negatively with body mass with scaling
 coefficients of -0.12 for red muscle and -0.21 for white muscle, whereas
 COX activity did not scale in either muscle type and PK activity scaled
 positively in white muscle, with a scaling coefficient of 0.09, but did
 not scale in red muscle. Thus mass-specific metabolic heat production
 potential either decreased or remained constant in the red muscle during
 the ontogeny of red muscle endothermy. In contrast, total red muscle mass,
 total red muscle CS activity and total red muscle COX activity all scaled
 positively with body mass with scaling coefficients of 0.90, 0.78 and
 0.92, respectively, and each of these correlated positively with the
 magnitude of the red muscle thermal excess. Thus, increasing total, but
 not mass-specific, metabolic heat production capacity contributed to the
 increasing red muscle thermal excess with increasing body size in juvenile
 T. orientalis. Additionally, for CS and COX, transcript abundance was a
 poor predictor of enzyme activity. Thus, transcriptional regulation played
 a limited role in determining the differences between the two muscle types
 and the scaling relationships for these enzymes.
DOI: 10.5061/dryad.1ns1rn8tn
title: Original data of compression test for cracked specimen

description: To explore the crack propagation and failure process of surrounding rock
 with deep cracks under external stress adjustment, the failure of cracked
 specimens under external load was studied. The required test pieces were
 prepared by using a self-developed mold and using cement mortar as a
 similar material. Through the uniaxial compression test, the basic
 mechanical properties of the material and the specimen were obtained, and
 the crack propagation process and the failure evolution mechanism of the
 specimen under different crack inclination angles and loading rates were
 revealed. The test results show that the presence of cracks can
 significantly affect the overall strength of the specimen, and the
 strength and failure mechanism of the specimen vary with the change in the
 crack angle and rate of loading. The larger the crack inclination angle,
 the lower the strength of the specimen, and the two are linearly related.
 With the increase in the loading rate, the failure mode of the specimen
 gradually changes, the dynamic effect is enhanced, and typical
 characteristics of a rockburst appear. Furthermore, the reasons for the
 modes of failure and changes in strength of the specimens were analyzed
 from the energy point of view, and the non-contact full-field strain
 measurement system (DIC) was used to explain the macroscopic failure modes
 of the specimens from a meso-level perspective. Combining this with the
 failure behavior of the specimen, reasonable suggestions are proposed for
 the smooth construction of the actual project in the later stage.
description: In this experimental study, a Servo-hydraulic Universal rock
 mechanics testing machine (Serial Number: 1606008) was used to maintain
 the consistency of the loading method and reduce error. According to the
 measured data, the failure law of the cracked specimen was analyzed by
 Origin 2018 drawing.
DOI: 10.5061/dryad.3j9kd51jb
title: Muscle mass of the long head of the biceps following single and double nerve transfer

description: The aim of this dataset was to compare the effects of single nerve
 transfer and double nerve transfer on muscle mass. We developed a novel
 rat model to investigate the neurophysiological effects of peripheral
 double nerve transfers to a single target muscle. In 62 male
 Sprague-Dawley rats the ulnar nerve of the antebrachium alone (n=30) or
 together with the anterior interosseus nerve (n=32) was transferred to
 reinnervate the long head of the biceps brachii. To further assess
 reinnervation, muscle mass was analyzed. Twelve weeks following surgery,
 after successful reinnervation was confirmed by muscle response to nerve
 crush and neurotomy, the long head of the biceps muscles were harvested
 and weighed. To provide internal control, the untreated contralateral
 muscle heads were also harvested and weighed.
description: The entire long head of the biceps was removed and weighed using
 a precision scale.
DOI: 10.5061/dryad.ghx3ffbp9
title: Collaboration for conservation: assessing country-wide carnivore occupancy dynamics from sparse data

description: Aim: Assessing the distribution and persistence of species across their
 range is a crucial component of wildlife conservation. It demands data at
 adequate spatial scales and over extended periods of time, which may only
 be obtained through collaborative efforts, and the development of methods
 that integrate heterogeneous datasets. We aimed to combine existing data
 on large carnivores to evaluate population dynamics and improve knowledge
 on their distribution nationwide. Location: Botswana Methods: Between 2010
 – 2016, we collated data on African wild dog, cheetah, leopard, brown and
 spotted hyaena, and lion gathered with different survey methods by
 independent researchers across Botswana. We used a multi-species,
 multi-method dynamic occupancy model to analyse factors influencing
 occupancy, persistence, and colonisation, while accounting for imperfect
 detection. Lastly, we used the gained knowledge to predict the probability
 of occurrence of each species countrywide. Results: Wildlife areas and
 communal rangelands had similar occupancy probabilities for most species.
 Large carnivore occupancy was low in commercial farming areas and where
 livestock density was high, except for brown hyaena. Lion occupancy was
 negatively associated with human density; lion and spotted hyena occupancy
 was high where rainfall was high, while the opposite applied to brown
 hyaena. Lion and leopard occupancy remained constant countrywide over the
 study period. African wild dog and cheetah occupancy declined over time in
 the south and north, respectively, whereas both hyaena species expanded
 their ranges. Countrywide predictions identified the highest occupancy for
 leopards and lowest for the two hyaena species. Main Conclusions: We
 highlight the necessity of data sharing and propose a generalisable
 analytical method that addresses the challenges of heterogeneous data
 common in ecology. Our approach, which enables a comprehensive
 multi-species assessment at large spatial and temporal scales, supports
 the development of data-driven conservation guidelines and the
 implementation of evidence-based management strategies nationally and
 internationally.
DOI: 10.5061/dryad.cnp5hqc53
title: Data from: Motherly love curbs harm: maternal effects modulate sexual conflict

description: Strong sexual selection frequently favours males that increase their
 reproductive success by harming females, with potentially negative
 consequences for population growth. Understanding what factors modulate
 conflict between the sexes is hence critical to understand both the
 evolution male and female phenotypes and the viability of populations in
 the wild. Studies addressing the evolution of sexual
 conflict have so far considered direct effects on
 male and female reproductive success along
 with indirect genetic benefits (e.g. good
 genes) to females. Here, we model the evolution
 of male harm while incorporating
 male-induced maternal effects on offspring quality. We show that, because
 male harm can induce maternal effects that reduce the
 quality of a harming male’s own offspring, maternal effects can
 partially align male and female evolutionary interests and
 significantly curb the evolution of male harm. These effects are
 independent of population structure and whether male harm comes before
 (i.e. harassment) or during/after (i.e. traumatic inseminations or toxic
 ejaculates) mating, and are particularly salient when maternal effects
 influence offspring ability to inflict (sons) or resist (daughters) harm.
 Our results fit broadly with available evidence across the tree of life,
 opening a novel avenue to unravel the evolution of sexual conflict.
description: Systematic literature search (details provided in the
 manuscript).
DOI: 10.5061/dryad.7wm37pvt2
title: TNT file for phylogenetic analysis of the moss class Polytrichopsida composed of morphological and sequence level characters

description: PREMISE OF THE STUDY:  When fossils are sparse in
 morphologically divergent lineages, phylogenetic analyses based on
 morphology may support hypotheses of relationships incongruent with those
 supported by gene sequence data. Integration of morphological and sequence
 data from conservative gene regions may reconcile such situations by
 circumscribing the search space of combined analyses.
 METHODS:  We revisited the phylogeny of Polytrichopsida,
 a highly divergent group of mosses, in parsimony analyses. We supplemented
 the existing morphological matrix with sequence data of four genes (nt
 18S, cp rbcL & rps4, mt nad5) commonly
 used in mosses; we included both fossils and extant terminals that lack
 sequence data. KEY RESULTS:  We recovered patterns of
 relationships largely congruent with those supported by analyses of
 sequence data from a higher number of terminals. Analyses including all
 terminals recovered one optimal tree with Alophosia and
 the fossil Meantoinea forming a clade sister to the rest
 of the ingroup. Outgroup sampling experiments produced congruent
 topologies for most ingroup relationships.
 CONCLUSIONS:  The potential of total-evidence analyses
 sampling conservative genes to alleviate conflict with morphology-based
 hypotheses should be tested in groups with denser fossil
 record. Although bryophyte fossils have been deemed fragmentary,
 it was recently shown that integrating fossils in total-evidence analyses
 may not reduce phylogenetic resolution. Therefore, total-evidence analyses
 incorporating fossils bear promise for clarifying bryophyte phylogenetic
 relationships. In Polytrichopsida, a group with a long evolutionary
 history, we cannot assume, a priori, that currently known
 fossils, which date back to only c. 140 Ma ago, represent the oldest
 lineages.
description: TNT-file with 11 continuos additive characters, followed by a
 combined matrix of 89 non-additive chars. of morphology; 83 of 18S, 254
 rbcL, 158 rps4 & 40 of nad5
DOI: 10.5061/dryad.ksn02v74n
title: Concordance between PCR-based extraction-free saliva and nasopharyngeal swabs for SARS-CoV-2 testing

description: Introduction: Saliva represents a less invasive alternative to
 nasopharyngeal swab (NPS) for severe acute respiratory syndrome
 coronavirus 2 (SARS-CoV-2) detection. SalivaDirect is a nucleic acid
 extraction-free method for detecting SARS-CoV2 in saliva specimens.
 Studies evaluating the concordance of gold standard NPS and newly
 developed SalivaDirect protocols are limited. The aim of our study was to
 assess SalivaDirect as an alternative method for COVID-19 testing.
 Methods: Matching NPS and saliva samples were analysed from a cohort of
 symptomatic (n=127) and asymptomatic (n=181) participants recruited from
 hospital and university settings respectively. RNA was extracted from NPS
 while saliva samples were subjected to the SalivaDirect protocol before
 RT-qPCR analysis. The presence of SARS-Cov-2 was assessed using RdRP and
 N1 gene targets in NPS and saliva respectively. Results: Overall we
 observed 94.3% sensitivity (95% CI 87.2-97.5%), and 95.9% specificity (95%
 CI 92.4-97.8%) in saliva when compared to matching NPS samples. Analysis
 of concordance demonstrated 95.5% accuracy overall for the saliva test
 relative to NPS, and a very high level of agreement (κ coefficient =
 0.889, 95% CI 0.833–0.946) between the two sets of specimens. Fourteen of
 308 samples were discordant, all from symptomatic patients. Ct values were
 &gt;30 in 13/14 and &gt;35 in 6/14 samples. No significant
 difference was found in the Ct values of matching NPS and saliva sample
 (p=0.860). A highly significant correlation (r = 0.475, p&lt;0.0001)
 was also found between the Ct values of the concordant positive saliva and
 NPS specimens. Conclusions: Use of saliva processed according to the
 SalivaDirect protocol represents a valid method to detect SARS-CoV-2. Less
 invasive and accurate saliva screening is an attractive alternative to
 current testing methods based on NPS and would afford greater capacity to
 test asymptomatic populations especially in the context of frequent
 testing.