cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mkkwh712d
title: Data from: Validity, applicability and universality of fractal scaling laws for natural lakes

description: We conducted a systematic investigation on the validity, applicability and
 universality of the fractal scaling relationships for natural lakes within
 China. Hydro-climatic zones from the Hydrological regionalization of China
 were taken as the statistical units for all the analyses. Lake size and
 hydrological parameters used in the analyses are from the HydroLAKES
 database. To test the validity of the fractal scaling relationships
 between lake properties, power law functions were fitted to these
 properties. To examine the effects of topographical relief on the power
 law size distribution, regional degree of topographical relief
  was calculated for each zone based on ASTER GDEM2. To explore
 the potential impacts of human activities on the applicability of power
 law size distribution, Human modification index data was jointly analyzed
 with the power law distribution of lake size.
description: The Hydrological
 regionalization of China as the statistical units for data analyses.
 Natural lakes from
 HydroLAKES were extracted for each zone. The regional topographical
 reliefs of the study sites was calculated based on ASTER GDEM2 and he mean elevated lake sample sets were formed by
 sampling from locations within ±50 m of the mean elevation of each
 hydro-climatic zone. Human influence in each zone was quantified through
 Human modifacation index data. To compare the differences of human impacts
 among hydro-climatic zones, the HMI data of each zone was extracted and
 divided into three categories: “low” (HMI value is less than
 0.4), “median” (HMI value
 is between 0.4 and 0.7) and  “high” (HMI value is  larger than
 0.7). The data used in
 manuscript, including the Hydrological regionalization of
 China,  HydroLAKES,
 ASTER GDEM2
 and Human modification
 index. All these analyses
 were publicly available and all these analyses were performed in ArcGIS
 10.2.
DOI: 10.5061/dryad.k6djh9w88
title: Rational domestication of a plant-based recombinant expression system expands its biosynthetic range

description: Plant molecular farming aims to provide a green, flexible, and rapid
 alternative to conventional recombinant expression systems, capable of
 producing complex biologics such as enzymes, vaccines, and antibodies.
 Historically, the recombinant expression of therapeutic peptides in plants
 has proven difficult, largely due to their small size and instability.
 However, some plant species harbour the capacity for peptide backbone
 cyclization, a feature inherent in stable therapeutic peptides. One
 obstacle to realizing the potential of plant-based therapeutic peptide
 production is the proteolysis of the precursor before it is matured into
 its final stabilized form. Here we demonstrate the rational domestication
 of Nicotiana benthamiana within two generations to endow this plant
 molecular farming host with an expanded repertoire of peptide sequence
 space. The in planta production of molecules including an insecticidal
 peptide, a prostate cancer therapeutic lead and an orally active analgesic
 are demonstrated.
description: Data were collected using MALDI-TOF -TOF methods described in the
 manuscript. Chromatogram data was produced as a service by the Australian
 Genome Research Foundation in Brisbane, QLD, Australia.
description: Data are presented as MALDI-TOF-TOF trace values exported from AB
 Sciex software as unitless values with internal and relative controls for
 relative representation and quantification. Chromatograms are included
 which were used to produce supplementary figure alignments. RNA-seq data
 relevant to this manuscript are not stored in Dryad but have been uploaded
 to NCBI-SRA (PRJNA784697).
DOI: 10.5061/dryad.0rxwdbs2s
title: Trends in functional composition of small mammal communities across millennial time scales

description: Rich fossil deposits of the late Quaternary help us understand responses
 of biodiversity to global change and thus predict the future of
 ecosystems. Studies from the late Quaternary, however, are often limited
 taxonomically, geographically (often one site), and by their use of
 largely taxon-based metrics that do not inform about ecosystem-level
 consequences of biodiversity change. Here, we compare change in functional
 composition of small mammal communities at El Mirón Cave (Spain) and
 Samwell Cave (California, USA) across the last 22,000 years, and examine
 their relationships with climate and vegetation. We find opposing temporal
 trends between the two locations. European small mammal communities
 occupied increasingly greater trait space, driven by increases in arboreal
 granivory and frugivory as ground-dwelling herbivory declined toward the
 late Holocene. North American communities occupied smaller trait space as
 ground-level foraging and insectivory increased and arboreal herbivory and
 mean body mass declined. Our results point to the importance of the
 interaction between climate change and vegetation shifts for explaining
 changes in small mammal functional diversity, through their synergistic
 impacts on individual traits. Specifically, increasing temperature across
 both continents likely led to increases in nocturnal activity and declines
 in assemblage mean body mass, while transition to mixed forest (El Mirón)
 or open woodland (Samwell) resulted in increasing structural complexity of
 vegetation that potentially supported more diverse community-level dietary
 characteristics. These results demonstrate the ability of a trait-based
 approach to identify how environmental variables correlate with changes in
 community functional composition through time and gain insight into the
 potential consequences of environmental change for ecosystem functioning.
description: We submit data used to quantify and compare changes in functional
 composition of small mammal communities at El Miron Cave in Spain and
 Samwell Cave in California across the last 22,000 years. The data used in
 this study include: (1) cleaned-up species count data for El Miron Cave
 (based on Cuenca-Bescos et al. 2009), (2) cleaned-up species count data
 for Samwell Cave (based on Blois et al. 2010), (3) revised traits database
 based on Wilman et al. (2014), (4) environmental data derived from Beyer
 et al. 2020. Please refer to the manuscript for details
 about data collection and processing (VanBuren and Jarzyna 2022,
 Ecography).
description:  All data used in this paper have been previously published, and
 are publically available. Associated code is available on GitHub and
 archived with Zenodo.
DOI: 10.7291/d1f38q
title: Phylogenomic analysis does not support a classic but controversial hypothesis of progenitor-derivative origins for the serpentine endemic Clarkia franciscana

description: Budding speciation involves isolation of marginal populations at the
 periphery of a species range and is thought to be a prominent mode of
 speciation in organisms with low dispersal and/or strong local adaptation
 among populations. Budding speciation is typically evidenced by abutting,
 asymmetric ranges of ecologically-divergent sister species and low genetic
 diversity in putative budded species. Yet these indirect patterns may be
 unreliable, instead caused by post-speciation processes such as range or
 demographic shifts. Nested phylogenetic relationships provide the most
 conclusive evidence of budding speciation. A putative case of budding
 speciation in the serpentine endemic Clarkia
 franciscana and two closely related widespread congeners was
 studied by Harlan Lewis, Peter Raven, Leslie Gottlieb and others over a
 20-year period, yet the origin of C. franciscana remains
 controversial. Here, we reinvestigate this system with phylogenomic
 analyses to determine whether C. franciscana is a
 recently derived budded species, phylogenetically nested within one of the
 other two putative progenitor species. In contrast to the hypothesized
 pattern of relatedness among the three Clarkia species,
 we find no evidence for recent budding speciation. Instead, the data
 suggest the three species diverged simultaneously. We urge caution in
 using contemporary range patterns to infer geographic modes of speciation.
description: This is a phylogenomic dataset, composed of 24 taxa and
 ultimately 233 loci. An enriched genomic sequencing approach was used; a
 bait set was designed from single-copy genes in a related
 species.  In this paper, we processed raw reads
 (sorting reads into gene directories and aligning within directories),
 aligned and trimmed gene sequences, built a variety of gene trees and
 species trees, and analyzed discordance among methods of species trees
 interest, and among gene trees and species trees. 
description: All .R and .Rmd files are to be opened in R
 (https://www.r-project.org) or Rstudio
 (https://posit.co/downloads/).  To view phylogenetic
 tree files (.tree), I use the free program FigTree (v1.4.4)
 (http://tree.bio.ed.ac.uk/software/figtree/) The .svg
 output files from the PhyParts analysis can be viewed in any major browser
 (Chrome, Safari, Firefox, etc.). All other files (e.g.,
 .txt, .fa, .fasta, .py, .sh, .pl, .raxml, .err, .out, .SSLL, .no_outliers,
 .concord.node*, .conflict.node*, .hist, .hist.alts, .node.key) can be
 viewed in your favorite text editor. I use BBedit
 (https://www.barebones.com/products/bbedit/). Please refer to the detailed
 "Code_workflow.txt", and "Code_by_steps" and
 "Data_Outputs" directories to see how these files are used in
 analyses.
DOI: 10.5061/dryad.h18931zns
title: Systematic characterization of wing mechanosensors that monitor airflow and wing deformations

description: Animal wings deform during flight in ways that can enhance lift,
 facilitate flight control, and mitigate damage. Monitoring the structural
 and aerodynamic state of the wing is challenging because deformations are
 passive, and the flow fields are unsteady; it requires distributed
 mechanosensors that respond to local airflow and strain on the wing.
 Without a complete map of the sensor arrays, it is impossible to model
 control strategies underpinned by them. Here, we present the first
 systematic characterization of mechanosensors on the dragonfly’s wings:
 morphology, distribution, and wiring. By combining a cross-species survey
 of sensor distribution with quantitative neuroanatomy and a high-fidelity
 finite element analysis, we show that the mechanosensors are well-placed
 to perceive features of the wing dynamics relevant to flight. This work
 describes the wing sensory apparatus in its entirety and advances our
 understanding of the sensorimotor loop that facilitates exquisite flight
 control in animals with highly deformable wings.  
description: Data includes raw measurements of dragonfly wing mechanosensors.
 Values were measured from confocal microscope images using fiji.
DOI: 10.5061/dryad.1ns1rn8wc
title: Experimentally measuring weak fracture toughness anisotropy in graphene

description: Extended finite element analysis (XFEM) modeling the fracture process of
 2D materials with anisotropic fracture toughness. Modification from the
 classic XFEM, this updated script is based on the maximum energy release
 rate criterion, and anisotropic fracture toughness in sine form
 and hexagonal symmetry is included. By modifying the ratio of
 maximum and minimum fracture toughness, model geometry, boundary
 conditions, and pre-crack location and direction, the fracture patterns,
 as well as the local fracture parameters including stress intensity
 factors and energy release rate at the crack tip can be calculated.
 Moreover, in this script, the distance of the crack extension at every
 step is irrelevant to the mesh size of the geometry, thus accuracy and
 computation efficiency is enhanced.
description: This dataset is collected as an example to simulate the fracture
 process of 2D materials with anisotropic fracture toughness. The
 subroutine UEL is created and modified from classic XFEM scripts as
 implemented in ABAQUS, for the fracture theories and control equations,
 please see the publication for detailed information. 
description: This script should be used with the subroutine UEL in ABAQUS. The
 subroutine UEL is not provided here, please contact the authors if you are
 interested.
DOI: 10.5061/dryad.2v6wwpzqg
title: Reproductive ecology of Drosophila obscura: A cold adapted species

description: The study of insect reproductive ecology is essential to determine species
 distributions and fate under changing environments. Species adapted to
 harsh environments are good examples to investigate the reproductive
 mechanisms that allow them to cope with the challenging
 conditions.  We here focus on studying for the first time the
 reproductive ecology of a cold-adapted D. obscura strain collected in
 Finland (subarctic climate region). We tested several reproductive traits
 such as fertility and fecundity to observe the onset of reproduction and
 gauge when sexual maturity is reached in both males and females. We
 combined these measures with an analysis of changes of their reproductive
 organs shortly after eclosion. We found that males matured several days
 before females and that this process was underpinned by female egg
 maturation and male accessory gland growth, while sperm was already
 present in two-day old males. This delayed maturation is not observed to
 the same extent in other closely related species and might be a signature
 of exposure to harsh environments. Whether this delay is an adaptation to
 cope with variation in resource availability or prolonged unfavorable
 temperatures is though not clear. Finally, our study adds to the set of
 reproductive mechanisms used by cold adapted species and the information
 presented here contributes to understanding the breadth of Drosophila
 reproductive ecology.
description: We
 conducted a series of experiments to determine sexual maturity in males
 and females. For that, we paired Drosophila obscura males and females and
 manipulated the interaction time and the oviposition period after a
 mating. We measured both fertility and fecundity by counting the number of
 eggs and the offspring number. We further measured accessory
 gland size and checked for presence of mature sperm in the testes in males
 and we counted the number of mature and immature eggs inside the female
 reproductive tract. All measurements were taken at different time points
 after eclosion of adult flies to get an extended overview of the sexual
 maturation process.
description: The data sets concerning egg number and
 offspring counts contain missing values represented as NA when one of the
 individuals escaped or died during the experiment. Data sets regarding the
 analysis of the male reproductive system contain missing values (also
 represented as NA), when the picture was not good enough to measure the
 organ area or the wing length (e.g., broken tissue).
DOI: 10.5061/dryad.r7sqv9sdw
title: Enhanced durability of round bamboo treated with copper naphthenate under heat-cold impregnation

description: Round bamboo has aroused much interest in construction for its mechanical
 properties, but poor biological durability seriously restricts its
 application. In order to develop a suitable and effective preservative
 treatment method for round bamboo, copper naphthenate (CuN) was adopted
 and impregnated into round bamboo using heat-cold procedure. The
 distribution and retention of copper naphthenate in round bamboo were
 studied, and the biological durability represented by the mold and decay
 resistance were investigated. The results showed that the retention and
 fixation of copper reached 0.39 kg/m3 and 85.3%, respectively. Scanning
 electron microscopy-energy dispersive x-ray spectrometry further disclosed
 an increasing trend in the composition of CuN from the end inward. X-ray
 photoelectron spectroscopy and Fourier transform infrared spectroscopy
 analyses later revealed that CuN could be fixed on bamboo in the form of a
 hydrogen bond or a complex reaction. Statistical analysis showed that the
 increasing concentration of CuN from 0.3% to 0.5% and 0.8% (calculated as
 Cu2+ content) has a significant contribution against Trametes versicolor
 and Gloeophyllum trabeum in comparison with the untreated bamboo.
 Meanwhile, when the concentration of treating solution increased to 0.8
 wt.%, the resisting efficacy for Aspergillus niger, Penicillium citrinum,
 and Trichoderma viride soared as high as 85.9%, 94.8%, and 70.3%,
 respectively.
DOI: 10.5061/dryad.m63xsj43s
title: Selectivity improvement of polysulfone-zeolite templated carbon membrane by annealing and coating treatment for CO2/CH4 and H2/CH4 separation

description: Natural gas, which majorly consists of methane (CH4), is a renewable
 energy source widely used as fuel, as well as hydrogen (H2). However, in
 its production process of each gas containing other impurity gasses.
 Therefore, membrane technology is needed to separate the gasses from the
 impurities. Mixed Matrix Membrane (MMM) is a more promising membrane
 compared to the others. Zeolite Templated Carbon-based MMM offers a good
 separation performance because of ZTC’s large surface area and
 well-defined pore structure. However, the interfacial void in MMM is
 challenging to be prevented, which contributes to the reduced separation
 performance. This study aims to enhance separation performance by
 modifying membrane surfaces using various methods. MMM PSF/ZTC modified by
 annealing at 120, 150, and 190 °C; coating using 0.01, 0.03, and 0.05 mol
 tetramethylorthosilicate (TMOS); and both combinations annealing at 190 °C
 and coating using 0.03 mol TMOS. MMM PSF/ZTC was successfully
 significantly improved CO2/CH4 selectivity by both combinations of
 annealed at 190 °C and coated 0.03 mol TMOS from 1.37 to 5.90 (331%) and
 H2/CH4 selectivity by coating with 0.03 mol TMOS from 4.58 to 65.76
 (1378%). The enhancement of selectivity was due to structural changes of
 the membrane that was denser and smoother, which SEM and AFM observed. In
 this study, annealing and coating treatment are the methods that can use
 for improving the polymer matrix and filler particle adhesion.
description: The data set was obtained from literature, we also have our own
 dataset in this file which was obtained through the experiments.
DOI: 10.5281/zenodo.17542391
title: A Global Atlas of the Pan-Urban Virome Reveals Extensive Viral Diversity and Its Links to Ecology and Public Health
DOI: 10.5061/dryad.stqjq2c50
title: Data from: The origins of global biodiversity on land, sea, and freshwater

description: Many biodiversity studies focus on explaining high tropical species
 richness, but an equally dramatic yet understudied pattern involves the
 divergent richness of land, sea, and freshwater. Here, we reveal the
 origins of these richness differences among habitats across animals and
 plants. Most plant and animal species are terrestrial, although these
 habitats cover only ~28% of Earth’s surface. Marine habitats have fewer
 species over a larger area (~70%). Freshwater habitats have relatively
 high richness and exceptional phylogenetic diversity given their tiny area
 (2%). The relative richness of habitats is related to variation in
 diversification rates. Based on ancestral reconstructions of habitat, we
 find that most marine species are descended from marine ancestors and most
 terrestrial species from freshwater ancestors. Yet, most extant animal
 richness in freshwater is derived from terrestrial ancestors. Overall, our
 results reveal the origins of fundamental but neglected biodiversity
 patterns and highlight the conservation importance of freshwater habitats.
DOI: 10.5061/dryad.9ghx3ffk7
title: A community and functional comparison of coral and reef fish assemblages between four decades of coastal urbanisation and thermal stress.

description: Urbanised coral reefs experience anthropogenic disturbances caused by
 coastal development, pollution and nutrient runoff, resulting in turbid,
 marginal conditions in which only certain species can persist. Mortality
 effects are exacerbated by increasingly regular thermal stress events,
 leading to shifts towards novel communities dominated by habitat
 generalists and species with low structural complexity. There is limited
 data on the turnover processes that occur due to this convergence of
 anthropogenic stressors, and how novel urban ecosystems are structured
 both at the community and functional level. As such, it is unclear how
 they will respond to future disturbance events. Here, we examine the
 patterns of coral reef community change, and determine whether ecosystem
 functions provided by specialist species are lost post-disturbance. We
 present a comparison of community and functional trait-based changes for
 scleractinian coral genera and reef fish species assemblages subject to
 coastal development, coastal modification, and mass bleaching between two
 time periods, 1975-6 and 2018, in Nakagusuku Bay, Okinawa, Japan. We
 observed an increase in fish habitat generalists, a dominance shift from
 branching to massive/ sub-massive corals and increasing site-based coral
 genera richness between years. Fish and coral communities significantly
 reassembled, but functional trait-based multivariate space remained
 constant, indicating a turnover of species with similar traits. A
 compression of coral habitat occurred, with shallow (&lt;5m) and deep
 (&gt;8m) coral genera shifting towards the mid-depths (5-8m). We show
 that although reef species assemblages altered post disturbance, new
 communities retained similar ecosystem functions. This result could be
 linked to the stressors experienced by urban reefs, which reflect those
 that will occur at an increasing frequency globally in the near future.
 Yet, even after shifts to disturbed communities, these fully functioning
 reef systems may maintain high conservation value.
DOI: 10.5061/dryad.dncjsxm1z
title: Lichen holobionts show compositional structure along elevation

description: Holobionts are dynamic ecosystems that may respond to abiotic drivers with
 compositional changes. Uncovering elevational diversity patterns within
 these microecosystems can further our understanding of
 community-environment interactions. Here we assess how the major
 components of lichen holobionts – fungal hosts, green algal symbionts, and
 the bacterial community – collectively respond to an elevational gradient.
 We analyze populations of two lichen symbioses, Umbilicaria pustulata and
 U. hispanica, along an elevational gradient spanning 2100 altitudinal
 meters and covering three major biomes. Our study shows (i) discontinuous
 genomic variation in fungal hosts with one abrupt genomic differentiation
 within each of the two host species, (ii) altitudinally structured
 bacterial communities with pronounced turnover within and between hosts,
 and (iii) altitude-specific presence of algal symbionts. Alpha diversity
 of bacterial communities decreased with increasing elevation. A marked
 turnover in holobiont diversity occurred across two altitudinal belts: at
 11-13°C average annual temperature (here: 800-1200m a.s.l.), and at 7-9°C
 average annual temperature (here: 1500-1800m a.s.l.). The two observed
 zones mark a clustering of distribution limits and community shifts. The
 three ensuing altitudinal classes, i.e. the most frequent combinations of
 species in holobionts, approximately correspond to the Mediterranean,
 cool-temperate, and alpine climate zones. We conclude that multitrophic
 microecosystems, such as lichen holobionts, respond with concerted
 compositional changes to climatic factors that also structure communities
 of macroorganisms, e.g. vascular plants.