cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qjq2bvqgv
title: Data for: Telomere dynamics in relation to experimentally increased locomotion costs and fitness in great tits

description: Evidence that telomere length (TL) and dynamics can be interpreted as
 proxy for ‘life stress’ experienced by individuals stems largely from
 correlational studies. We tested for effects of an experimental increase
 of workload on telomere dynamics by equipping male great tits (Parus
 major) with a 0.9 gram backpack for a full year. In addition, we analysed
 associations between natural life-history variation, TL and TL dynamics.
 Carrying 5% extra weight for a year did not significantly accelerate
 telomere attrition. This agrees with our earlier finding that this
 experiment did not affect survival or future reproduction. Apparently,
 great tit males were able to compensate behaviourally or physiologically
 for the increase in locomotion costs we imposed. We found no
 cross-sectional association between reproductive success and TL, but
 individuals with higher reproductive success (number of recruits) lost
 fewer telomere base pairs in the subsequent year. We used the TRF method
 to measure TL, which method yields a TL distribution for each sample, and
 the association between reproductive success and telomere loss was more
 pronounced in the higher percentiles of the telomere distribution, in
 agreement with the higher impact of ageing on longer telomeres within
 individuals. Individuals with longer telomeres and less telomere
 shortening were more likely to survive to the next breeding season, but
 these patterns did not reach statistical significance. Whether successful
 individuals are characterized by losing fewer or more base pairs from
 their telomeres varies between species, and we discuss aspects of ecology
 and social organisation that may explain this variation.
description: See accompanying paper for details.
description: There are <b>four data files</b>, and their names
 correspond with sections in the results:
 experiment.csv
 reproduction_cross-sectional.csv
 reproduction_longitudinal.csv
 survival.csv <b>Data-dictionary (see
 paper for details):</b> telomere_length
 start_age: age at the start of the experimental
 treatment Time_elapsed: time elapsed between current
 record and start_age addMass_lag: zero for first
 capture always, but added mass as treated at later captures
 ID: individual identity gel: identity of the
 gel age N_Fledglings: number of
 fledglings N_Recruits: number of recruits
 N_Fledglings_lag: zero in spring 1, but N_Fledgings in preceding
 season at later captures N_Recruits_lag: as for
 N_Fledglings_lag perc10 – perc90: telomere length at
 the 10<sup>th</sup> to 90<sup>th</sup> percentile
 within each sample deltaTL: change in telomere length
 from spring 1 to year 2 in bp survived: whether or not
 a bird survived to a later year
DOI: 10.5061/dryad.sj3tx965m
title: Data From - TE Density: a tool to investigate the biology of transposable elements

description: Background: Transposable elements (TEs) are powerful creators of genotypic
 and phenotypic diversity due to theirinherent mutagenic capabilities and
 in this way they serve as a deep reservoir of sequences for genomic
 variation. As agents of genetic disruption, a TE’s potential to impact
 phenotype is partially a factor of its location in the genome. Previous
 research has shown TEs’ ability to impact the expression of neighboring
 genes, however our understanding of this trend is hampered by the
 exceptional amount of diversity in the TE world, and a lack of publicly
 availablecomputational methods that quantify the presence of TEs relative
 to genes. Results: Here, we have developed a tool to more easily
 quantify TE presence relative to genes through the useof only a gene and
 TE annotation, yielding a new metric we call TE density. Briefly defined
 as the proportion of TE-occupied base-pairs relative to a window-size of
 the genome. This new pipeline reports TE density for each gene in the
 genome, for each type descriptor of TE (order and superfamily), and for
 multiple positions and distances relative to the gene (upstream,
 intragenic, and downstream) over sliding, user-defined windows. In this
 way, we overcome previous limitations to the study of TE-gene
 relationships by focusing on all TE types present in the genome, utilizing
 flexible genomic distances for measurement, and reporting a TE presence
 metric for every gene in the genome. Conclusions: Together, this
 new tool opens up new avenues for studying TE-gene relationships, genome
 architecture,comparative genomics, along with the tremendous diversity
 present in the TE world. Data Availability: TE Density is open-source and
 freely available at: https://github.com/sjteresi/TE_Density.
description: Please refer to the README available with this Dryad submission,
 the Implementation section of the publication, and the README of the
 project GitHub repository https://github.com/sjteresi/TE_Density
DOI: 10.57841/casdc.0007115
title: 百米级热等静压系统的优化数据
DOI: 10.5061/dryad.mkkwh7118
title: Amphibian fauna of Pakistan with notes on future prospects of research and conservation

description: The research on amphibians and their conservation efforts have gained
 worldwide attention, since the group includes the highest number of
 threatened and data deficient species when compared with other
 vertebrates. However, amphibians have long been neglected in wildlife
 conservation, management decisions, policy making and research agendas in
 Pakistan.  In this paper, the annotated checklist of the 21
 amphibian species of Pakistan, the key to their identification, and
 detailed discussions on the occurrence of variation in species including
 the genera Minervarya, and Sphaerotheca are provided. We found
 statistically significant difference in the morphometric measurements of
 males but non-significant difference in the females of the two forms
 (rusty dorsum and dotted dorsum) of S. maskeyi. Some genera, such as
 Microhyla, Uperodon, Minervarya, Allopaa, Chrysopaa, Euphlyctis, Nanorana
 and Sphaerotheca that are found in Pakistan need additional data to
 compare molecular taxonomy and detailed comparisons with those found in
 other South Asian countries. Predicaments in amphibian research in
 Pakistan are discussed, gaps identified, and suggestions have been made.
 Although the likelihood of occurrence of chytrid fungus in Pakistan is
 predicted to be low, the data deficiency merits studying the prevalence of
 the fungus, particularly in the northern regions of the country which
 exhibit complex and dynamic ecosystems. It is recommended to conduct
 systematic and coordinated surveys throughout the country to build a data
 base on species occurrence and distribution. Additionally, monitoring of
 wild populations, threat mitigation, and appropriate legislation are
 suggested as long term measures. By adopting an inclusive wildlife
 conservation approach in Pakistan, amphibians could be integrated into
 wildlife conservation and management efforts.
DOI: 10.5061/dryad.xgxd254hb
title: Taxonomic revision of Ediacaran tubular fossils: Cloudina, Sinotubulites and Conotubus

description: The Ediacaran tubular fossils, Cloudina, Sinotubulites, and Conotubus, are
 taxonomically revised with type materials. It is proposed that Aulophycus
 lucianoi Beurlen and Sommer, 1957 is not a senior synonym of Cloudina
 hartmannae Germs, 1972. Instead, most of its syntypes may be assigned to
 Sinotubulites or other taxa. Lectotypes of Sinotubulites baimatuoensis
 Chen et al., 1981 and Conotubus hemiannulatus Zhang and Lin, 1986 are
 designated from rediscovered syntypes. Sinotubulites baimatuoensis Chen et
 al., 1981 is reported from the Mooifontein Member of Nama Group at Aar
 Farm, Namibia. Cloudina waldei Hahn and Pflug, 1985 is assigned to
 Sinotubulites baimatuoensis and thus its occurrence range is extended to
 Brazil. The lectotype of Conotubus hemiannulatus shows corrugations and
 annulations on the surface distinguishing it from Cloudina and other
 collared Ediacaran tubular fossils. Based on the taxonomic revision, we
 propose a Cloudina hartmannae Interval Zone for the terminal Ediacaran
 with the upper boundary defined by the first appearance datum of
 Protohertzina anabarica, i.e. the index fossil of the early Cambrian
 Anabarites trisulcatus–Protohertzina anabarica Assemblage Zone.
DOI: 10.5061/dryad.6q573n603
title: Using species distribution models and decision tools to direct surveys and identify potential translocation sites for a critically endangered species

description: Aim: Occurrence records for cryptic species are typically limited or
 highly uncertain, leaving their distributions poorly resolved and
 hampering conservation. This can apply to well‐studied species, and
 increased survey effort and/or novel methods are required to improve
 distribution data. Here, we paired species distribution modelling (SDM)
 with decision tools to direct surveys for the critically endangered
 Leadbeater's possum (Gymnobelideus leadbeateri) outside its current
 restricted range. We also assessed survey areas for their suitability to
 host translocations. Location: Victoria, Australia. Method: We used both
 recent and historic records (now out of range and spatially uncertain) of
 Leadbeater's possum to build SDMs using MaxEnt. The SDMs informed an
 initial multi‐criteria decision analysis (MCDA) that enabled
 prioritization of 80 survey sites across seven forest patches
 (13–145 km outside the known range), which we surveyed using
 camera traps. Site and vegetation data were used in a post‐survey MCDA to
 rank their potential translocation suitability. Results: The SDM
 predictions were consistent with the species’ ecology, identifying cold
 areas with high rainfall that had not recently burnt as suitable. The
 spatial uncertainty of records did not exert a strong influence on either
 model predictions or the ranking of patches for surveys. Camera trap
 surveys yielded records of 19 native species, with Leadbeater's
 possum detected in only one survey patch, 13 km outside of its
 previously known range. The post‐survey MCDA identified three forest
 patches as potentially suitable for conservation translocations, and these
 priorities were not sensitive to the decision criteria used. Main
 conclusions: The approach outlined here prioritized survey effort over a
 large area, resulting in detection of Leadbeater's possum in one new
 patch. The potential translocation sites identified could present an
 important risk‐spreading measure for the species given the threat posed by
 bushfire. Combining SDMs and decision tools can help target surveys and
 guide subsequent conservation strategies.
description: We used both recent and historic records (now out of range and
 spatially uncertain) of Leadbeater's possum to build SDMs using
 MaxEnt. The SDMs informed an initial multi‐criteria decision analysis
 (MCDA) that enabled prioritization of 80 survey sites across seven forest
 patches (13–145 km outside the known range), which we surveyed using
 camera traps. Site and vegetation data were used in a post‐survey MCDA to
 rank their potential translocation suitability.
DOI: 10.5061/dryad.7d7wm37vz
title: Data from: Frictional stability of metamorphic epidote in granitoid faults under hydrothermal conditions and implications for injection-induced seismicity

description: The effect of low-grade metamorphic epidote on fault stability in
 granitoids at shallow depth is not well understood. We present structured
 laboratory observations of epidote and simulated Pohang granodiorite (an
 EGS site) gouges and mixtures to evaluate their frictional responses. The
 experiments were performed on powdered rock gouges at a constant confining
 pressure of 110 MPa, pore fluid pressures of 42 and 63 MPa, temperatures
 of 100-250℃ and epidote percentages in the range of 0-100 vol.%. Results
 show that the simulated Pohang granodiorite gouge is frictionally strong
 (friction coefficient of ~0.71) but exhibits a transition from
 velocity-strengthening to velocity-weakening behavior at in-situ
 temperatures &gt;150℃. Epidote gouge displays similar frictional
 strength to the simulated granodiorite gouge but a stronger
 velocity-weakening response at 150℃.  Increasing the epidote
 content in the homogeneously mixed gouges maintains the high frictional
 strength but increases velocity-weakening response approximately
 proportionately with epidote content. Modes of epidote precipitation
 likely control patch dimension and this in turn potentially changes the
 response of the 50:50 epidote-granodiorite mixed gouges in different
 geometric configurations. However, 50:50 mixtures that are variously
 homogeneously mixed, encapsulated and checkerboarded in their
 architectures are insensitive to their various geometries – all reflect
 the high frictional strength and strong velocity-weakening response of
 100:0 pure epidote. This suggests that small volume percentages of epidote
 present as thin coatings on fractures and faults can impart
 velocity-weakening behavior, independent of individual patch size and can
 thereby support the potential seismic reactivation of faults. Considering
 the frictional and stability properties of epidote at conditions typical
 of shallow depths, the presence of low-grade metamorphism exerts a
 potentially important control on fault stability in granitoids with
 relevance as a marker mineral for susceptibility to injection-induced
 seismicity.
description: Refer to the README file for more information.
 The column headings for each file: <br> Column 1 = The
 shear displacement<br> Column 2 = Coefficient of friction
DOI: 10.5061/dryad.bvq83bk95
title: Variation in parasite resistance of Arctic charr, Salvelinus alpinus, between and within sympatric morphs

description: Genetic variation in resistance against parasite infections is a
 predominant feature in host-parasite systems. However, mechanisms
 maintaining genetic polymorphism in resistance in natural host populations
 are generally poorly known. We explored if differences in natural
 infection pressure between resource-based morphs of Arctic charr
 (Salvelinus alpinus) has resulted in differentiation in resistance
 profiles. We experimentally exposed offspring of two morphs from Lake
 Þingvallavatn (Iceland), the pelagic planktivorous charr (‘murta’) and the
 large benthivorous charr (‘kuðungableikja’), to their common parasite, eye
 fluke Diplostomum baeri, infecting the eye humour. We found that there
 were no differences in resistance between the morphs, but clear
 differences among families within each morph. Moreover, we found
 suggestive evidence of resistance of offspring within families being
 positively correlated with the parasite load of the father, but not with
 that of the mother. Our results suggest that the inherited basis of
 parasite resistance in this system is likely to be related to variation
 among host individuals within each morph rather than ecological factors
 driving divergent resistance profiles at morph level. Overall, this may
 have implications for evolution of resistance through processes such as
 sexual selection.
description: The dataset presents data from experimental infection of
 lab-raised offspring of Arctic charr (<i>Salvelinus
 alpinus</i>) and the wild-caught parent fish from Lake
 Þingvallavatn.
description: The dataset has two sheets.
 The fist sheet contains infection data for lab-raised offspring of Arctic
 charr (<i>Salvelinus alpinus</i>) with variables indicating
 the fish morph (planktivorous and benthivorous), fish family, adult
 wild-caught females and males used to produce the families, and total
 length and parasite numbers of the offspring. The second sheet contains
 the corresponding information for the parent female and male
 fish.
DOI: 10.5061/dryad.79cnp5hw6
title: Database of the list for associations between host plants and fruit flies

description: Insects tend to feed on related hosts. Coevolution tends to be
 dominated by interactions resulting from plant chemistry in defense
 strategies, and evolution of secondary metabolisms being in response to
 insect herbivory remains a classic explanation of
 coevolution. The present study examines whether evolutionary constraints
 existing in host associations of economically important fruit flies in the
 species-rich tribe Dacini (Diptera: Tephritidae) and to
 what extent these species have evolved specialized dietary patterns. We
 found a strong effect of host phylogeny on associations on the 37 fruit
 flies tested, although the fruit fly species feeding on
 ripe commercially grown fruits that lost the toxic
 compounds after long domestication are mostly
 polyphagous. We assessed the phylogenetic signal of host breadth across
 the fruit fly species, showing that the results were substantially
 different depending on partition levels. Further, we
 mapped main host family associations onto the fruit fly phylogeny
 and Cucurbitaceae has been inferred as the most likely
 ancestral host family for Dacini based on ancestral state reconstruction.
DOI: 10.5061/dryad.5hqbzkh6h
title: Data from: Effectiveness of signs of activity as relative abundance indices for wild boar

description: Population growth in wild boars and feral pigs (Sus scrofa) has negative
 environmental and economic implications worldwide. Accordingly, it is
 necessary to monitor population trends for appropriate management. Despite
 the potential for bias, relative abundance indices based on signs of
 activity have the potential to be practical, low-cost monitoring tools for
 data collection at a local scale and over large areas. However, few
 studies have examined the effectiveness of specific signs as measures of
 relative wild boar abundance in comparison with reliable density
 estimates. In this study, we examined whether three activity signs
 (digging marks, rubbing marks, and fecal pellet groups) could be used as
 relative abundance indices for wild boar. In particular, we conducted
 transect surveys for signs of activity as well as camera trap surveys from
 September 2017 to January 2018 at six sites in Hyogo Prefecture and eight
 sites in Chiba Prefecture, Japan. We modeled the relations between the
 number of activity signs and wild boar densities or abundances estimated
 from camera trap data in a hierarchical framework. Fecal pellet counts are
 a well-established method for estimating the abundance of herbivores,
 including wild boar; however, we found few fecal pellet groups in our
 study area, and the counts were not related to wild boar densities.
 Instead, we found that digging marks were strongly associated with
 estimates of wild boar density. Although fluctuations in the number of
 digging marks may be affected by factors other than boar density,
 including environmental conditions and seasonality, our results suggest
 that digging marks are an effective relative abundance index for
 evaluations of the spatial patterns of wild boar in Japan.
DOI: 10.5061/dryad.dbrv15f21
title: Re-allocation of nitrogen and phosphorus from roots drives regrowth of grasses and sedges after defoliation under deficit irrigation and nitrogen enrichment

description: 1. Re-allocation of nutrients from roots to shoots is essential
 for plant regrowth in grasslands, particularly in nutrient-poor
 conditions. However, the response of root nutrient re-allocation to
 changes in nitrogen (N) and water availability remains largely unknown. 2.
 Using a novel 15N and 32P labelling technique, we quantified the
 contribution of N and phosphorus (P) to shoot regrowth from either root
 re-allocation or direct soil uptake for perennial grasses exposed to
 high-frequency deficit irrigation (HFDI) and N addition. 3. Without N
 addition, HFDI showed no impact on uptake and re-allocation of N and P,
 likely due to unaffected soil N availability and a greater diffusion
 barrier offsetting increased accumulation in plant-available soil P. With
 N addition, HFDI increased plant N rather than P uptake, because of
 increasing soil N availability instead of P under combined HFDI and N
 addition. The HFDI decreased both N and P re-allocation with N addition,
 possibly due to exhaustion of nutrient reserves in roots that were
 re-allocated aboveground. Re-allocation contributed 48-97% of N and 58-79%
 of P required during the first two weeks of shoot regrowth. 4. Synthesis.
 Our results highlight the importance of N and P re-allocation from roots
 to buffer against changes in soil N and P availability and to maintain N:P
 ratio in shoot regrowth.
DOI: 10.5061/dryad.0gb5mkm1z
title: Green fluorescent protein-like pigments optimize the internal light environment in symbiotic reef building corals

description: Pigments homologous to the Green Fluorescent Protein (GFP) have been
 proposed to fine-tune the internal light microclimate of corals,
 facilitating photoacclimation of photosynthetic coral symbionts
 (Symbiodiniaceae) to life in different reef habitats and environmental
 conditions. However, direct measurements of the in vivo light conditions
 inside the coral tissue supporting this conclusion are lacking. Here, we
 quantified the intra-tissue spectral light environment of corals
 expressing GFP-like proteins from widely different light regimes. We focus
 on (1) photoconvertible red fluorescent proteins (pcRFPs), thought to
 enhance photosynthesis in mesophotic habitats via wavelength conversion,
 and (2) chromoproteins (CPs), which provide photoprotection to the
 symbionts in shallow water via light absorption. Optical microsensor
 measurements indicated that both pigment groups strongly alter the coral
 tissue light environment. Estimates derived from light spectra measured in
 pcRFP-containing corals showed that fluorescence emission can contribute
 to &gt;50% of orange-red light available to the photosynthetic
 symbionts at mesophotic depths. We further show that upregulation of pink
 CPs in shallow-water corals during bleaching leads to a reduction of
 orange light by 10-20% compared to low-CP tissue. Thus, screening by CPs
 has an important role in mitigating the light-enhancing effect of coral
 tissue scattering during bleaching. Our results provide the first
 experimental quantification of the importance of GFP-like proteins in
 fine-tuning the light microclimate of corals during photoacclimation.
DOI: 10.5061/dryad.cvdncjt50
title: Seascape genetics of the Atlantic spotted dolphin (Stenella frontalis) based on mitochondrial DNA

description: The Atlantic spotted dolphin (Stenella frontalis) is endemic to tropical,
 subtropical, and warm temperate waters of the Atlantic Ocean. Throughout
 its distribution, both geographic distance and environmental variation may
 contribute to population structure of the species. In this study we follow
 a seascape genetics approach to investigate population differentiation of
 Atlantic spotted dolphins based on a large worldwide dataset and the
 relationship with marine environmental variables. The results revealed
 that the Atlantic spotted dolphin exhibits population genetic structure
 across its distribution based on mitochondrial DNA control region
 (mtDNA-CR) data. Analyses based on the contemporary landscape suggested,
 at both the individual and population-level, that the population genetic
 structure is consistent with the isolation-by-distance model. However,
 because geography and environmental matrices were correlated, and because
 in some, but not all analyses, we found a significant effect for the
 environment, we cannot rule out the addition contribution of environmental
 factors in structuring genetic variation. Future analyses based on nuclear
 data are needed to evaluate whether local processes, such as social
 structure and some level of philopatry within populations, may be
 contributing to the associations among genetic structure, geographic, and
 environmental distance.