cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.44j0zpcd8
title: Seeing through the hedge: Phylogenomics of Thuja (Cupressaceae) reveals prominent incomplete lineage sorting and ancient introgression for Tertiary relict flora

description: The eastern Asia (EA) – eastern North America (ENA) disjunction is a
 typical and well known biogeographic. Although its origin has been the
 topic of many studies, some new insights will arise when more complex
 evolutionary histories are revealed using phylogenomic methods. Here, we
 used targeted exon capture and sequenced &gt;1,000 single copy
 nuclear, plus 73 chloroplast genes, to resolve interspecific relationships
 and the biogeographic history of an intercontinental disjunct genus Thuja.
 Two separate clades were detected: the “EA clade” comprised two species
 (T. standishii and T. sutchuenensis) from EA, and the “disjunct clade”
 comprising T. koraiensis, T. occidentalis, and T. plicata, with the first
 two comprising an EA–ENA disjunct pattern and T. plicata in western North
 America. The disjunct clade experienced a rapid radiation in the
 Mid–Miocene, and furthermore multispecies coalescent analysis revealed
 that ancient lineages of Thuja had large population sizes. These two
 factors might have contributed to the significant levels of incomplete
 lineage sorting (ILS) we detected within Thuja, and especially the
 disjunct clade. Because of this, EA–ENA disjunct pattern of T. koraiensis
 and T. occidentalis is exhibited by only 13.98% of genes examined. In
 addition, we found that ~20% of the T. sutchuenensis nuclear genome is
 derived from an as–yet–unrecognized ancestral lineage of Thuja, which
 might explain the close resemblance of cone morphology between T.
 sutchuenensis and the Paleocene fossil species T. ehrenswaerdii. Overall,
 our study demonstrates that single genes may produce incomplete or
 inaccurate phylogenies for disjunct taxa, and that more accurate results
 will come from using genomic data, revealing a more complex evolutionary
 history. This will steadily improve our understanding of their origin and
 evolution.
DOI: 10.6084/m9.figshare.31055431
title: <b>Constrained projection of future decline in the stability of terrestrial carbon sinks</b>

description: A temporally stable terrestrial carbon sink (TCS) is central for climate change mitigation, but how the stability in TCS will evolve remains elusive. Here we explored spatial variations of historical TCS stability using atmospheric inversions and dynamic global vegetation models, and its future changes by the end of this century through constraining Earth system models projections.<br>The datasets include: (1) Spatial pattern of stability in TCS during the past four decades; (2) Constrained changes in stability of TCS in future scenarios; (3) Future changes in interannual variability of TCS; (4) Future changes in climate fluctuations and sensitivities of TCS to climate variability in future scenarios. Results of each model have been included. The main figures can be directly produced by using the codes and datasets here.<br>CMIP6 model outputs are available at https://pcmdi.llnl.gov/CMIP6/. The climate data from CRUJRAv2 is available at https://catalogue.ceda.ac.uk/uuid/863a47a6d8414b6982e1396c69a9efe8. The simulations from TRENDY DGVMs can be accessed at https://sites.exeter.ac.uk/trendy. The gridded carbon fluxes from atmospheric inversions can be accessed at https://meta.icos-cp.eu/objects/FHbD8OTgCb7Tlvs99lUDApO0.<br>Please note that all the original data files and codes should be put in the same folder and the users need to set the workspace in the data folder first before running the codes.
DOI: 10.6084/m9.figshare.31055431.v2
title: <b>Constrained projection of future decline in the stability of terrestrial carbon sinks</b>

description: A temporally stable terrestrial carbon sink (TCS) is central for climate change mitigation, but how the stability in TCS will evolve remains elusive. Here we explored spatial variations of historical TCS stability using atmospheric inversions and dynamic global vegetation models, and its future changes by the end of this century through constraining Earth system models projections.<br>The datasets include: (1) Spatial pattern of stability in TCS during the past four decades; (2) Constrained changes in stability of TCS in future scenarios; (3) Future changes in interannual variability of TCS; (4) Future changes in climate fluctuations and sensitivities of TCS to climate variability in future scenarios. Results of each model have been included. The main figures can be directly produced by using the codes and datasets here.<br>CMIP6 model outputs are available at https://pcmdi.llnl.gov/CMIP6/. The climate data from CRUJRAv2 is available at https://catalogue.ceda.ac.uk/uuid/863a47a6d8414b6982e1396c69a9efe8. The simulations from TRENDY DGVMs can be accessed at https://sites.exeter.ac.uk/trendy. The gridded carbon fluxes from atmospheric inversions can be accessed at https://meta.icos-cp.eu/objects/FHbD8OTgCb7Tlvs99lUDApO0.<br>Please note that all the original data files and codes should be put in the same folder and the users need to set the workspace in the data folder first before running the codes.
DOI: 10.6084/m9.figshare.31055431.v1
title: <b>Constrained projection of future decline in the stability of terrestrial carbon sinks</b>

description: A temporally stable terrestrial carbon sink (TCS) is central for climate change mitigation, but how the stability in TCS will evolve remains elusive. Here we explored spatial variations of historical TCS stability using atmospheric inversions and dynamic global vegetation models, and its future changes by the end of this century through constraining Earth system models projections.<br>The datasets include: (1) Spatial pattern of stability in TCS during the past four decades; (2) Constrained changes in stability of TCS in future scenarios; (3) Future changes in interannual variability of TCS; (4) Future changes in climate fluctuations and sensitivities of TCS to climate variability in future scenarios. Results of each model have been included. The main figures can be directly produced by using the codes and datasets here.<br>CMIP6 model outputs are available at https://pcmdi.llnl.gov/CMIP6/. The climate data from CRUJRAv2 is available at https://catalogue.ceda.ac.uk/uuid/863a47a6d8414b6982e1396c69a9efe8. The simulations from TRENDY DGVMs can be accessed at https://sites.exeter.ac.uk/trendy. The gridded carbon fluxes from atmospheric inversions can be accessed at https://meta.icos-cp.eu/objects/FHbD8OTgCb7Tlvs99lUDApO0.<br>Please note that all the original data files and codes should be put in the same folder and the users need to set the workspace in the data folder first before running the codes.
DOI: 10.15468/dl.4ap55d
title: Occurrence Download

description: A dataset containing 7321 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Olyra latifolia"
 ]
}

 The dataset includes 7321 records from 332 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002802-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.ffbg79ctp
title: Limitations of acoustic monitoring at wind turbines to evaluate fatality risk of bats

description: Wind turbines (WTs) frequently kill bats worldwide. During environmental
 impact assessments, consultant ecologists often use automated ultrasonic
 detectors (AUDs) to estimate the activity and identity of bats in the zone
 of highest mortality risk at WTs in order to formulate mitigation schemes,
 such as increased curtailment speeds to prevent casualties. While
 acknowledging the potential of acoustic monitoring, we evaluate the
 limitations of AUDs for monitoring bats at WTs and highlight directions
 for future research. We show that geometric and atmospheric attenuation of
 ultrasonic echolocation calls, in conjunction with limited sensitivity of
 ultrasonic microphones, severely constrain detection distances of bats at
 WTs. Taking into account the acoustic shadow produced by the nacelle, AUDs
 cover only approximately 23% of the risk zone for a bat calling at 20 kHz
 and 4% for a bat calling at 40 kHz, assuming a 60 m blade length. This
 percentage will further decrease with increasing blade lengths in modern
 WTs. Additionally, the directionality of echolocation calls and the
 dynamic flight behaviour of bats constrain the detectability of bats. If a
 call can be detected, the low interspecific and high intraspecific
 variation of echolocation call characteristics may impair species
 identification, limiting the power to predict population-level effects of
 fatalities. We conclude that technical, physical, and biological factors
 severely constrain acoustic monitoring in its current form. We suggest the
 use of several AUDs, installed at complementary sites at WTs, and the
 testing of other techniques, such as radar, cameras, and thermal imaging,
 to inform stakeholders on the mortality risk of bats at WTs.
description: Attenuation of sound pressure level
 (SPL) of echolocation calls as they propagate through air. Estimates were
 developed for two bats calling at 20 kHz and 110 dB peSPL and 40 kHz and
 104 dB peSPL (source SPLs are referenced to 20 µPa at 1 m in front of the
 bat). The received SPLs were calculated from source SPL by subtracting
 geometric attenuation (-6 dB per doubling of distance) and frequency- and
 weather-dependent atmospheric attenuation (see insets on the right).  The
 received SPLs are calculated for the full range of atmospheric
 attenuation,  Percentage
 of the rotor-swept area of wind turbines covered by automated
 ultrasonic detectors (AUDs) with increasing blade length, for bats calling
 at 20 kHz  and 40 kHz. For this estimate, we assumed the risk zone to
 equal the circular rotor-swept area with the blade length as radius. AUDs
 usually do not cover the upper half of this zone, because AUDs are
 installed at the nacelle bottom (between tower and blades) with the
 microphone pointing downwards. We further used the maximum distance at
 which bats can be detected by AUDs (trigger threshold: 60 dB SPL), which
 only applies for bat calls that are directed towards the
 AUD.
DOI: 10.5061/dryad.p8cz8w9px
title: Data and code for analysis of effects of climate change on kangaskhan and summary of simulations from Warren et al. 2020

description: Species distribution models (SDMs) are frequently used to predict the
 effects of climate change on species of conservation
 concern. Biases inherent in the process of constructing SDMs and
 transferring them to new climate scenarios may result in undesirable
 conservation outcomes. We explore these issues and demonstrate
 new methods to estimate biases induced by the design of SDM
 studies. We present these methods in the context of estimating
 the effects of climate change on Australia’s only endemic
 Pokémon. Using a citizen science data set, we build species
 distribution models for G. kangaskhani to predict the effects of climate
 change on the suitability of habitat for the species. We
 demonstrate a novel Monte Carlo procedure for estimating the biases
 implicit in a given study design, and compare the results seen for Pokémon
 to those seen from our Monte Carlo tests as well as previous studies in
 the same region using both simulated and real data. Our models
 suggest that climate change will impact the suitability of habitat for G.
 kangaskhani, which may compound the effects of threats such as habitat
 loss and their use in blood sport. However, we also find that
 using SDMs to estimate the effects of climate change can be accompanied by
 biases so strong that the data itself has minimal impact on modeling
 outcomes.  We show that the direction and magnitude of bias in
 estimates of climate change impacts are affected by every aspect of the
 modeling process, and suggest that bias estimates should be included in
 future studies of this type. Given the widespread use of SDMs,
 systemic biases could have substantial financial and opportunity
 costs. By demonstrating these biases and presenting a novel
 statistical tool to estimate them, we hope to provide a more secure future
 for G. kangaskhani and the rest of the world’s biodiversity.
description: Data was collected from websites for the video game Pokemon Go,
 as well as reanalysis of simulations and models from Warren et al.
 2020. Warren, D.L, N. Matzke, and T.L. Iglesias.
 2020.<i> </i>Evaluating presence-only species distribution
 models with discrimination accuracy is uninformative for many
 applications. <i>Journal of Biogeography
 </i>47:167-180<i>.</i>
description: Data in "kangaskhan points.csv" was collected from
 online websites dedicated to the Pokémon Go video game. Duplicate
 occurrences were removed. Appendix S2 contains code for summarizing
 results of the simulations from Warren et al. 2020 when projected to
 future climate scenarios, and "regback.aggregated
 projections.csv" contains the data being summarized. Appendix S3
 contains results from Monte Carlo simulations. Files
 ending in "mc.csv" are the summary statistics from the Monte
 Carlo models, while "prediction_summary.csv" contains summary
 statistics from the projections of the empirical models for
 kangaskhan.
DOI: 10.5061/dryad.w3r2280qc
title: Grow fast but don’t die young: maternal effects mediate life-history tradeoffs of lizards under climate warming

description: 1. As postulated by life-history theory, not all life-history traits can
 be maximized simultaneously. In ectothermic animals, climate warming is
 predicted to increase growth rates, but at a cost to overall lifespan.
 Maternal effects are expected to mediate this life-history tradeoff, but
 such effects have not yet been explicitly elucidated. 2. To understand
 maternal effects on the life-history responses to climate warming in
 lizard offspring, we conducted a manipulative field experiment on a
 desert-dwelling viviparous lacertid lizard (Eremias multiocellata), using
 open-top chambers in a factorial design (maternal warm climate and
 maternal present climate treatments × offspring warm climate and offspring
 present climate treatments). 3. We found that the maternal warm climate
 treatment had little impact on the physiological and life-history traits
 of adult females (i.e., metabolic rate, reproductive output, growth, and
 survival). However, the offspring warm climate treatment significantly
 affected offspring growth, and both maternal and offspring warm climate
 treatments interacted to affect offspring survival. 4. Offspring from the
 warm climate treatment grew faster than those from the present climate
 treatment. However, the offspring warm climate treatment significantly
 decreased the survival rate of offspring from maternal present climate
 treatment, but not for those from the maternal warm climate treatment. 5.
 Our study demonstrates that maternal effects mediate the tradeoff between
 growth and survival of offspring lizards, allowing them to grow fast
 without a concurrent cost of low survival rate (short lifespan). These
 findings stress the importance of adaptive maternal effects in buffering
 the impact of climate warming on organisms, which may help us to
 accurately predict the vulnerability of populations and species to future
 warming climates.
DOI: 10.5061/dryad.vx0k6djr1
title: How biases in sperm storage relate to sperm use during oviposition in female yellow dung flies

description: Precise mechanisms underlying sperm storage and utilization are largely
 unknown, and data directly linking stored sperm to paternity remain
 scarce. We used competitive microsatellite PCR to study the effects of
 female morphology, copula duration and oviposition on the proportion of
 stored sperm provided by the second of two copulating males (S2) in
 Scathophaga stercoraria (Diptera: Scathophagidae), the classic model for
 sperm competition studies. We genotyped all offspring from potentially
 mixed-paternity clutches to establish the relationship between a second
 male’s stored sperm (S2) and paternity success (P2). We found consistent
 skew in sperm storage across the three female spermathecae, with
 relatively more second-male sperm stored in the singlet spermatheca than
 in the doublet spermathecae. S2 generally decreased with increasing
 spermathecal size, consistent with either heightened first-male storage in
 larger spermathecae, or less efficient sperm displacement in them.
 Additionally, copula duration and several two-way interactions influenced
 S2, highlighting the complexity of postcopulatory processes and sperm
 storage. Importantly, S2 and P2 were strongly correlated. Manipulation of
 the timing of oviposition strongly influenced observed sperm-storage
 patterns, with higher S2 when females laid no eggs before being sacrificed
 than when they oviposited between copulations, an observation consistent
 with adaptive plasticity in insemination. Our results identified multiple
 factors influencing sperm storage, nevertheless suggesting that the
 proportion of stored sperm is strongly linked to paternity (i.e. a fair
 raffle). Even more detailed data in this vein are needed to evaluate the
 general importance of sperm competition relative to cryptic female choice
 in postcopulatory sexual selection.
description: These data were collected in the course of a lab experiment that
 manipulated the possibility and timing of oviposition relative to the
 occurrence of two consecutive mating events for female yellow dung flies.
 Following this manipulation, females were sacrificed, their reproductive
 tracts dissected, and the sperm stored within analysed using molecular
 markers to quantify the relative contributions of two males to stored
 sperm. Further details of data processing are described
 in the associated paper, and an R script is also included to allow the
 reproduction of results and figures.
description: Metadata including keys to column names are in the associated
 ReadMe file.
DOI: 10.5061/dryad.qfttdz0gb
title: Trajectories of groups of Rana latastei tadpoles

description: Predation is a strong driver for the evolution of prey behaviour. To
 properly assess the actual risk of predation, anuran tadpoles mostly rely
 on water-borne chemical cues, and their ability to evaluate environmental
 information is even more crucial when potential predators consist of
 unknown alien species. Behavioural plasticity, that is the capacity to
 express changes in behaviour in response to different environmental
 stimuli, is crucial to cope with predation risk. We explored the defensive
 behaviour of Italian agile frog (Rana latastei) tadpoles when exposed to
 the chemical cues of two predators’ species, one native (dragonfly larvae)
 and one alien (red swamp crayfish). Firstly, we observed if a sensible
 life history trait (i.e. hatching time) might be affected by native
 predatory cues. Secondly, we recorded a suite of behavioural responses
 (activity level, lateralization and sinuosity) to each cue. For assessing
 lateralization and sinuosity, we developed a C++ code for the automatic
 analysis of digitally recorded tadpole tracks. Hatching time seemed not to
 be affected by the potential risk of predation, while both predator
 species and diet affected tadpoles’ defensive behaviour. Tadpoles
 responded to predator threat by two main defensive strategies: freezing
 and “zig-zagging”. While the first behaviour had been previously reported,
 the analysis of individual trajectories pointed out that tadpoles can also
 increase path complexity, probably to prevent predators from anticipating
 their location. We also recorded a decrease in lateralization intensity,
 which suggested that under predation risk tadpoles tend to scrutinize the
 surrounding environment equally on both sides.
description: Two lateralization indices were calculated for tadpoles: LR =
 [(clockwise swimming time – anticlockwise swimming time) / (clockwise
 swimming time + anticlockwise swimming time)] × 100, and LA = |LR|, which
 assesses the intensity of lateralization. These procedures were applied to
 all 375 tadpoles, each recorded for 300 s before and after the stimulus
 for a total amount of about 15000 locations for each tadpole. See
 "Contextual behavioural plasticity in Italian agile frog
 (<i>Rana latastei</i>) tadpoles exposed to native and alien
 predator cues" (Gazzola et al.) for further details.
DOI: 10.5281/zenodo.18389834
title: REVISE-reconstructed sp-SVC
DOI: 10.5281/zenodo.18389835
title: REVISE-reconstructed sp-SVC
DOI: 10.5061/dryad.p8cz8w9pz
title: Rhagoletis cingulata and Rhagoletis cerasi genome comparison

description: Wolbachia is a maternally inherited obligate endosymbiont that can induce
 a wide spectrum of effects in its host, ranging from mutualism to
 reproductive parasitism. At the genomic level, recombination within and
 between strains, transposable elements, and horizontal transfer of strains
 between host species make Wolbachia an evolutionarily dynamic bacterial
 system. The invasive cherry fruit fly Rhagoletis cingulata arrived in
 Europe from North America ~40 years ago, where it now co-occurs with the
 native cherry pest R. cerasi. This shared distribution has been proposed
 to have led to the horizontal transfer of different Wolbachia strains
 between the two species. To better understand transmission dynamics, we
 performed a comparative genome study of the strain wCin2 in native United
 States and invasive European populations of R. cingulata with wCer2 in
 European R. cerasi. Previous multilocus sequence genotyping (MLST) of six
 genes implied that the source of wCer2 in R. cerasi was wCin2 from R.
 cingulata. However, we report genomic evidence discounting the recent
 horizontal transfer hypothesis for the origin of wCer2. Despite near
 identical sequences for the MLST markers, substantial sequence differences
 for other loci were found between wCer2 and wCin2, as well as structural
 rearrangements, and differences in prophage, repetitive element, gene
 content, and cytoplasmic incompatibility inducing genes. Our study
 highlights the need for whole-genome sequencing rather than relying on
 MLST markers for resolving Wolbachia strains and assessing their
 evolutionary dynamics, and calls for additional studies of wCer2 to
 determine its origin and history in R. cerasi.
description: The dataset represents analyses performed on Rhagoletis cerasi
 and Rhagoletis cingulata flies, using Nanopore, PaBio, and Illumina
 sequencing. The main plots were performed with circos.
DOI: 10.82294/dvnjigmpi
title: Datos consolidados de COPUS. Territorio: Guainía. Sector: Cultura, Educación, Total. Año: 2025

description: En este apartado se presentan los datos consolidados del territorio de Guainía a partir de las observaciones semiestructuradas realizadas en 2025, esta vez analizadas bajo los criterios del protocolo de observación estructurada COPUS. Este dataset contiene la sumatoria de todas las observaciones COPUS por territorio, por sector, cultura y educación, una sumatoria de estos dos para definir la tendencia en el territorio y una sumatoria de todos los territorios.