cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4j0zpc8cz
title: Extant species fail to estimate ancestral geographical ranges at older nodes in primate phylogeny

description: A clade’s evolutionary history is shaped, in part, by geographical range
 expansion, sweepstakes dispersal and local extinction. A rigorous
 understanding of historical biogeography may therefore yield insights into
 macroevolutionary dynamics such as adaptive radiation. Modern historical
 biogeographic analyses typically fit statistical models to molecular
 phylogenies, but it remains unclear whether extant species provide
 sufficient signal or if well-sampled phylogenies of extinct and extant
 taxa are necessary to produce meaningful estimates of past ranges. We
 investigated the historical biogeography of Primates and their euarchontan
 relatives using a novel meta-analytical phylogeny of over 900 extant ( n =
 419) and extinct ( n = 483) species spanning their entire evolutionary
 history. Ancestral range estimates for young nodes were largely congruent
 with those derived from molecular phylogeny. However, node age exerts a
 significant effect on ancestral range estimate congruence, and the
 probability of congruent inference dropped below 0.5 for nodes older than
 the late Eocene, corresponding to the origins of higher-level clades.
 Discordance was not observed in analyses of extinct taxa alone. Fossils
 are essential for robust ancestral range inference and biogeographic
 analyses of extant clades originating in the deep past should be viewed
 with scepticism without them.
DOI: 10.5061/dryad.j9kd51cdq
title: Anchored phylogenomics and a revised classification of the Planidial Larva Clade of Jewel Wasps (Hymenoptera: Chalcidoidea)

description: Planidia are free-living, mobile first-instar larvae that are notable in
 their ability to transition on a single host between different larval
 stadia, and for completing their development on the host prepupa as
 ectoparasitoids, effectively acting as larval-pupal external koinobionts.
 Within Chalcidoidea, a mega-diverse superfamily of parasitoid wasps, taxa
 with a planidium form a monophyletic group, the Planidial-Larva-Clade
 (PLC), which has been comprised of three recognized groups:
 Eutrichosomatinae (Pteromalidae), Perilampidae (Chrysolampinae,
 Perilampinae, Philomidinae and the unplaced genus Jambiya), and
 Eucharitidae (Akapalinae, Eucharitinae, Gollumiellinae and Oraseminae). To
 clarify the classification and better understand the evolution of this
 clade, we conducted a phylogenomic study of the PLC using anchored hybrid
 enrichment data. The phylogenetic analyses support the backbone
 relationship of PLC as: (Eutrichosomatinae, ((Philomidinae,
 Chrysolampinae), (Perilampinae, Eucharitidae))). Although excluded from
 the main analyses, the genus Jambiya, based on only 11 loci recovered, was
 placed as the sister of Chrysolampinae + Philomidinae or Perilampinae +
 Eucharitidae. Our results support the placement of Eutrichosomatinae at
 the base of the PLC phylogeny and demonstrate that Perilampidae
 (Philomidinae, Chrysolampinae and Perilampinae) are paraphyletic. In
 contrast to other studies, anchored enrichment data fail to recover the
 Ponerinae- Ectatomminae-Myrmeciinae (PEM) parasitoid clade within
 Eucharitinae, which may indicate a more complicated evolutionary history
 of ant-host shifts. Traits explored using Likelihood Ancestral State
 Reconstruction include the evolution of host associations, direct versus
 indirect hyperparasitism, ability to attack a host within a cocoon, soft
 versus hard planidial forms, and mobility of the planidium. Divergence
 dating based on four calibration fossils suggests that the planidial clade
 arose approximately 111 Ma and the evolution of ant parasitism at least 64
 Ma. A revised higher-level classification of the planidial larva clade is
 proposed with Eutrichosomatinae elevated to Eutrichosomatidae (Rev.
 Stat.), Chrysolampinae and Philomidinae placed in Chrysolampidae (Rev.
 Stat.), Perilampidae (Rev. Stat.) restricted to what was referred to as
 Perilampinae, and Eucharitidae maintained with four subfamilies, with
 Akapalinae (unknown biology) as sister group to the core Eucharitidae, all
 of which are ant parasitoids. Jambiya is treated as an incertae sedis
 taxon within the planidial clade.
DOI: 10.5061/dryad.8gtht76qm
title: An efficient method for higher heating value estimation of municipal solid wastes electronic supplementary material

description: To facilitate the disposal of municipal solid wastes (MSWs) via
 thermo-chemical approaches, the accurate measurement of MSWs’ higher
 heating value (HHV) plays a key role. This study aims to forecast the HHV
 of MSWs using the optimized multi-variate grey model (OBGM (1, N)) due to
 its high accuracy under the condition of scanty data. Results show that
 POBGM (1, 5) with proximate analysis data is the most accurate model with
 the least error of 5.41% MAPE (mean absolute percentage error). This model
 also illustrates that ash is the most important factor affecting HHV due
 to its significant fraction in MSWs, followed by volatiles, fixed carbon
 and water contents, respectively. With prediction interval (PI) method,
 most of the actual data can be included by using the 95% confidence
 intervals.
DOI: 10.5061/dryad.qrfj6q5hj
title: Beaked whales and state-dependent decision-making: how does body condition affect the trade-off between foraging and predator avoidance?

description: Body condition is central to how animals balance foraging with
 predator-avoidance – a trade-off that fundamentally affects animal
 fitness. Animals in poor condition may accept greater predation risk to
 satisfy current foraging “needs”, whilst those in good condition may be
 more risk averse to protect future “assets”. These state-dependent
 behavioural predictions can help interpret responses to human activities,
 but are little explored in marine animals. This study investigates the
 influence of body condition on how beaked whales trade off foraging and
 predator-avoidance. Body density (indicating lipid-energy stores) was
 estimated for 15 foraging northern bottlenose whales tagged near Jan
 Mayen, Norway. Composite indices of foraging (diving and echolocation
 clicks) and anti-predation (long ascents, non-foraging dives and silent
 periods reducing predator eavesdropping) were negatively related.
 Experimental sonar exposures led to decreased foraging and increased risk
 aversion, confirming a foraging/perceived safety trade-off. However, lower
 lipid stores were not related to a decrease in predator-avoidance versus
 foraging, i.e. worse condition animals did not prioritise foraging.
 Individual differences (‘personalities’) or reproductive context could
 offer alternative explanations for the observed state-behaviour
 relationships. This study provides evidence of foraging/predator-avoidance
 trade-offs in a marine top predator and demonstrates that animals in worse
 condition might not always take more risks.
DOI: 10.5061/dryad.j3tx95xft
title: The predicted haploid gene set of the genome of Nitzschia putrida

description: Secondary loss of photosynthesis is observed across almost all
 plastid-bearing branches of the eukaryotic tree of life. However,
 genome-based insights into the transition from a phototroph into a
 secondary heterotroph have so far only been revealed for parasitic
 species. Free-living organisms can yield unique insights into the
 evolutionary consequence of the loss of photosynthesis, as the parasitic
 lifestyle requires specific adaptations to host environments. Here we
 report on the diploid genome of the free-living diatom Nitzschia putrida
 (35 Mbp), a non-photosynthetic osmotroph whose photosynthetic relatives
 contribute ca. 40% of net oceanic primary production. Comparative analyses
 with photosynthetic diatoms and heterotrophic algae with parasitic
 lifestyle revealed that a combination of gene loss, the accumulation of
 genes involved in organic carbon degradation, a unique secretome and the
 rapid divergence of conserved gene families involved in cell wall and
 extracellular metabolism appear to have facilitated the lifestyle of a
 free-living secondary heterotroph.
description: The dataset was created through processes in the genome analyses
 of Nitzschia putrida, by BRAKER2 gene annotation pipeline (ver
 2.0.3).
description: The readme file contains an explanation of each of the uploaded
 files.
DOI: 10.5061/dryad.fbg79cnw6
title: Data for: Apparent stability masks underlying change in a mule deer herd with unmanaged chronic wasting disease

description: The contagious prion disease “chronic wasting disease” (CWD) infects mule
 deer (Odocoileus hemionus) and related species. Unchecked epidemics raise
 ecological, socioeconomic, and public health concerns. Prion infection
 shortens a deer’s lifespan, and when prevalence (proportion of adults
 infected) becomes sufficiently high CWD can affect herd dynamics.
 Understanding population responses over time is key to forecasting
 long-term impacts. Here we describe unexpected stability in prevalence and
 abundance in a mule deer herd where CWD has been left unmanaged. High
 apparent prevalence (~30%) since at least 2005 likely drove observed
 changes in the proportion and age distribution of wild-type native prion
 protein (PRNP) gene homozygotes among deer sampled. Predation by mountain
 lions (Puma concolor) may be helping keep CWD in check. Despite stable
 appearances, prion disease nonetheless impairs adult survival and likely
 resilience in this deer herd, limiting its potential for growth despite
 refuge from hunter harvest and favorable habitat and winter conditions.
description: Please see Methods in accompanying manuscript for details.
DOI: 10.5061/dryad.j9kd51cds
title: Systematics of Lepidothrix manakins (Aves: Passeriformes: Pipridae) using RADcap markers

description: Although recent molecular phylogenetic analyses of Lepidothrix
 manakins (family Pipridae) have helped clarify their evolutionary
 relationships, the placement of several lineages remains in question
 because of low or conflicting branch support. In particular, the
 relationship of L. coronata to other members of the genus and
 relationships within the L. nattereri+L. vilasboasi+L. iris clade have
 been difficult to resolve. We used RADcap to collect restriction
 site-associated DNA sequence data and estimate the first subspecies-level
 phylogeny of the genus Lepidothrix (17 of 18 currently recognized
 subspecies), and we included extensive geographic representation of the
 widespread and phenotypically variable L. coronata. We found strong
 support for the phylogenetic position and monophyly of L. coronata, and we
 resolved two clades separated by the Andes that, along with previous
 divergence time estimates and our assessment of morphological and vocal
 evidence, suggest the presence of two biological species: Velvety Manakin
 (L. velutina) west of the Andes and Blue-capped Manakin (L. coronata) east
 of the Andes. Species-level relationships within the L. nattereri+L.
 vilasboasi+L. iris clade remained poorly resolved in concatenated and
 coalescent-based analyses, with SNAPP analyses suggesting that the lack of
 reciprocal monophyly is due to extensive allele sharing among these taxa.
 Finally, we confirmed a previously documented hybrid between L. coronata
 and L. suavissima as an F1 individual, consistent with the view that
 hybridization between these two species is a rare event and that
 postmating reproductive barriers prevent successful backcrossing.
DOI: 10.5061/dryad.fbg79cnw7
title: Sex roles in birds: influence of climate, life histories and social environment

description: For detailed information concerning data collection please see
 Gonzalez-Voyer et al. Sex roles in birds: phylogenetic analyses of the
 influence of climate, life histories and social environment. Ecology
 Letters. Briefly, data on ecology, life histories and behaviour of birds
 were extracted from published literature. If several data were available
 for a given species, we included the ones that were extracted from
 breeding individuals or had larger sample sizes. The details
 regarding data processing are provided in the Supplementary
 Material of Gonzalez-Voyer et al. (accepted).
description: The dataset and the associated notes should be
 self-explanatory.
description: Missing values are coded as "NA". All code necessary to
 repeat the anlayses will be uploaded with the manuscript as supplementary
 material.
DOI: 10.6084/m9.figshare.31154185
title: Qiang Cao, et al., Nature Chemical Engineering, 2026

description: Source Data for Figures and Supplementary Figures of Qiang Cao, et al., Nature Chemical Engineering, 2026.
DOI: 10.6084/m9.figshare.31154185.v1
title: Qiang Cao, et al., Nature Chemical Engineering, 2026

description: Source Data for Figures and Supplementary Figures of Qiang Cao, et al., Nature Chemical Engineering, 2026.
DOI: 10.6084/m9.figshare.31154185.v2
title: Qiang Cao, et al., Nature Chemical Engineering, 2026

description: Source Data for Figures and Supplementary Figures of Qiang Cao, et al., Nature Chemical Engineering, 2026.
DOI: 10.5061/dryad.gqnk98sph
title: Repeated measure plant community data after fire in boreal forest, Taiga Shield, Northwest Territories, Canada, 1998-2018

description: 10 transects were established in the years following fire in boreal forest
 stands on the Taiga Shield, Northwest Territories, Canada in 1998-1999.
 These were remeasured annually. Six transects were returned to on 2018 for
 another measurement. At each measurement, we recorded ground covers,
 species identities, and counted tree stems (seedlings).
DOI: 10.6084/m9.figshare.30616094
title: Dataset for typical living spaces

description: bedroom, living room, kitchen, bathroom
DOI: 10.6084/m9.figshare.30616094.v1
title: Dataset for typical living spaces

description: bedroom, living room, kitchen, bathroom
DOI: 10.5061/dryad.v15dv41x1
title: Data from: Habitat change and its consequences on reef fish specialization in biogeographic transition zones

description: Aim Reef fishes are commonly recognized as sentinels of the
 ongoing tropicalization in biogeographic transition zones between
 temperate and tropical areas. Despite the reliance of these marine
 ectotherms on the benthos, the importance of benthic habitat has rarely
 been considered as a factor constraining fish distribution. Therefore, our
 study aims at examining the consequences of both temperature and benthic
 variations on the fish fauna and diagnosing potential sentinels of these
 environmental changes.  Location Taiwan, West Pacific.
 Taxon Teleostei (184 species). Methods We examined how the
 partitioning of habitats can influence the specialization of fish fauna
 along a latitudinal gradient. We diagnosed ‘specialist’ and ‘generalist’
 fishes in this partitioning. For each specialist, we further evaluated
 whether its distribution is constrained by temperature, benthic habitat,
 or both factors combined. The change in sea surface temperature over the
 last three decades was also monitored. Results Fish fauna showed
 the highest specialization when tropical and subtropical partitions of
 habitat were considered. Fifty-one tropical specialists, seven subtropical
 specialists, and 21 possible generalists were identified. Among
 specialists, 13 species were associated with temperature, 19 with habitat,
 and 26 with both factors. Steady warming occurred across latitudes but was
 accentuated in the winter of subtropical habitat.  Main
 conclusions Our results suggested that the distribution of some
 specialist fishes was constrained only by temperature while the
 distribution of some others also depended on the availability of benthic
 habitats. Consequently, under global warming, the distribution of some
 specialists might shift in a manner that follows the movement of
 isotherms, while the distribution of others might also be conditioned by
 the poleward shifts of benthos. A temporal mismatch between the emergence
 of suitable thermal environments and the arrival of some specialists may
 exist. Therefore, the tropicalization of high-latitude areas may be
 characterized by different waves of colonization. 
description: Full details on sample collection and analyses are available in
 the published manuscript.
description: See README file.
DOI: 10.5061/dryad.nzs7h44sz
title: High variation in hydraulic efficiency but not xylem safety between roots and branches in four temperate broad-leaved tree species

description: Xylem hydraulic safety and efficiency are key traits determining tree
 fitness in a warmer and drier world. While numerous plant hydraulic
 studies have focused on branches, our understanding of root hydraulic
 functioning remains limited, although roots control water uptake,
 influence stomatal regulation and have commonly been considered as the
 most vulnerable organ along the hydraulic pathway. We investigated 11
 traits related to xylem safety and efficiency along the hydraulic pathway
 in four temperate broad-leaved tree species. Continuous vessel tapering
 from coarse roots to stems and branches caused considerable reduction in
 hydraulic efficiency. Wood density was always lowest in roots, but did not
 decline linearly along the flow path. In contrast, xylem embolism
 resistance (P50) did not differ significantly between roots and branches,
 except for one species. The limited variation in xylem safety between
 organs did not adequately reflect the corresponding reductions in vessel
 diameter (by ~70%) and hydraulic efficiency (by ~85%). Although we did not
 observe any trade-off between xylem safety and specific conductivity,
 vessel diameter, vessel lumen fraction and wood density were related to
 embolism resistance, both across and partly within organs. We conclude
 that coarse roots are not highly vulnerable to xylem embolism as commonly
 believed, indicating that hydraulic failure during soil drying might be
 restricted to fine roots.
description: For methodological details, please refer to the material and
 methods chpater of the following publication: Journal:
 Functional Ecology Title: High
 variation in hydraulic efficiency but not xylem safety between roots and
 branches in four temperate broad-leaved tree
 species Acceptance date:
 13.11.2021
DOI: 10.5061/dryad.6q573n60k
title: Searching for the causes of decline in the Dutch population of turtle doves Streptopelia turtur

description: European Turtle Doves Streptopelia turtur have
 experienced a sharp decline in population numbers over past decades. Much
 uncertainty exists about the main cause or causes. Several pressures have
 been suggested, but because they affect different stages of the life cycle
 of the Turtle Dove, it is difficult to compare their contributions to
 population decline. Here we applied a full life cycle approach to study
 how different pressures may have resulted in the decline. This was
 achieved by combining a review of existing literature on possible threats,
 pressures, and the vital rates they concerned, with the analysis of an
 age-structured matrix model. The population model was parameterized using
 estimates from a mark-recapture analysis and supplemented with vital rate
 estimates from the literature. Comparison with a Life Table Response
 Experiment (LTRE) was used to determine whether the Turtle Dove literature
 focusses on those vital rates in which the most important changes have
 taken place over time. The population model projected a similar decline to
 that observed in population counts. The LTRE analysis showed that declines
 in the number of clutches (halved since the 1960s) and in juvenile
 survival (relative annual rate of change of -1.33% since the 1950s)
 contributed most to the decline in the projected population growth rate.
 Although these vital rates are often reported as possible causes of
 population decline, the reviewed studies often focused on specific
 reproductive stages, such as egg survival or nestling survival, which did
 not show a large temporal change. Thus, there is a partial mismatch
 between our modelling results and the focus in the literature. Juvenile
 survival is thought to be affected by hunting, degradation of wintering
 habitat and infection with Trichomonas gallinae, while loss of
 foraging habitat seems to affect the number of clutches. The focus of
 conservation measures should therefore be on these threats and pressures.
 The first steps have already been taken with completion of the
 international single species action plan for the conservation of the
 Turtle Dove and the implementation of the first conservation measures on
 the breeding grounds.
description: Adult survival was therefore estimated from ringing and
 dead-recovery data of Turtle Dove (Streptopelia turtur) collected between
 1930 and 2017 in the Netherlands. The data is divided into birds ringed as
 adults, and birds ringed juveniles (i.e. either as nestlings or fledged
 first calendar-year birds). Survival was estimated using a Seber
 dead-recovery model with S and r parameterisation in RMark.
description: The .inp file contains encounter histories of Turtle Doves ringed
 in the Netherlands since 1930 and was used in a Seber dead-recovery model
 Rmark. For more information on the data collection, see the accompanying
 paper.
DOI: 10.5061/dryad.xsj3tx9gp
title: Dataset for quantifying avian inertial properties using calibrated computed tomography

description: Estimating centre of mass and mass moments of inertia is an important
 aspect of many studies in biomechanics. Characterising these parameters
 accurately in three dimensions is challenging with traditional methods
 requiring dissection or suspension of cadavers. Here, we present a method
 to quantify the three-dimensional centre of mass and inertia tensor of
 birds of prey using calibrated computed-tomography (CT) scans. The
 technique was validated using several independent methods, providing body
 segment mass estimates within approximately 1% of physical dissection
 measurements and moment of inertia measurements with a 0.993 R2
 correlation with conventional trifilar pendulum measurements. Calibrated
 CT offers a relatively straightforward, non-destructive approach that
 yields highly detailed mass distribution data that can be used for
 three-dimensional dynamics modelling in biomechanics. Although
 demonstrated here with birds, this approach should work equally well with
 any animal or appendage capable of being CT scanned.
DOI: 10.15468/dl.7j3qp2
title: Occurrence Download

description: A dataset containing 3037 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Appias albina"
 ]
}

 The dataset includes 3037 records from 73 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003002-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.