cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.95x69p8mr
title: Data from: Evolutionary transition from a single RNA replicator to a multiple replicator network

description: In prebiotic evolution, self-replicating molecules are believed to have
 evolved into complex living systems by expanding their information and
 functions open-endedly. Theoretically, such evolutionary complexification
 could occur through successive appearance of novel replicators that
 interact with one another to form replication networks. Here we perform
 long-term evolution experiments of RNA that replicates using a
 self-encoded RNA replicase. The RNA diversifies into multiple coexisting
 host and parasite lineages, whose frequencies in the population initially
 fluctuate and gradually stabilize. The final population, comprising five
 RNA lineages, forms a replicator network with diverse interactions,
 including cooperation to help the replication of all other members. These
 results support the capability of molecular replicators to spontaneously
 develop complexity through Darwinian evolution, a critical step for the
 emergence of life.
description: Please refer to README.txt.
DOI: 10.5061/dryad.h70rxwdkp
title: Whence came these plants most foul? Phylogenomics and biogeography of Lowiaceae (Zingiberales)

description: Lowiaceae (order Zingiberales) is a small family of forest herbs in
 Southeast Asia. All species belong to the genus Orchidantha. They are
 known for possessing orchid-like flowers that are smelly, apparently
 mimicking dead animals, feces, or mushrooms. Little is known of the
 biogeographic patterns or character evolution of the family. We sampled
 the family extensively, including many recently discovered species, and
 reconstructed the phylogeny of the family using HybSeq with
 Lowiaceae-specific RNA baits. Our phylogenetic reconstructions confirm
 that the family is most closely related to Strelitziaceae, and that
 species with dark, foul-smelling flowers form a grade in which a clade of
 species with paler smelling flowers are embedded. The pale-flowered
 species produce a distinct odor, resembling edible mushrooms. Apart from a
 single species, the species from Borneo form a clade, and the same is true
 for Indochinese species. The remaining species form a more widespread
 clade. A biogeographic analysis shows that the distribution of Lowiaceae
 can explained by vicariance and gradual dispersal from a shared ancestral
 range of Borneo and Indochina. There is no evidence of long-distance
 dispersal, only a later extension in distribution to Peninsular Malaysia
 which coincides with the presence of a land bridge. Different directions
 of spread are possible, but none require long-distance dispersal. The
 results are consistent with the geological history of Southeast Asia. In
 particular, the relatively early isolation between Indochina and Borneo
 could be explained by the presence of a sea barrier that developed 10–15
 MYA, and the continuous movement of plant species between Borneo and
 Peninsular Malaysia could be explained by a land bridge that existed until
 c. 5 MYA. The lack of an extensive land bridge with a suitable habitat may
 explain the absence of this genus from Sumatra and other Indonesian
 islands aside from Borneo. The strict reliance on a continuous habitat for
 the range expansion of Lowiaceae can be explained by their fruits and
 seeds, which lack obvious adaptations for long-distance dispersal. The
 inability to disperse to new areas may also explain why the extant species
 have very restricted distributions.
description: DNA sequence data, phylogenetic analyses, and trait data.
DOI: 10.5061/dryad.3xsj3txhr
title: Raw coordinates and measurements from: Like parent, like child -Ontogenetic development of claws of intertidal arthropods (Acari, Oribatida) from different ecological niches

description: The shape of claws of adult air-breathing intertidal oribatid mites shows
 a strong correlation with ecology. As nothing is known about juvenile
 characteristics of this trait, the ontogenetic development of these
 attachment devices was studied for the first time with comprehensive
 geometric morphometric methods. In nine investigated species, claws of
 immature stages can be classified into the same ecological categories as
 adults, i.e. juveniles of several rock-dwelling species already show
 higher and stronger curved claw shapes with smaller claw angles, while
 juvenile instars of the single investigated mangrovedwelling species
 possess lower and less curved claws with wider claw angles. For each
 species, claw curvature is almost static during the complete development
 and claw length grows directly proportional with increasing body size.
 Developmental changes in body size and weight are thus mainly compensated
 by a simple relative growth in size. Despite the finding that claw shapes
 of early developmental stages are already classifiable into ecological
 categories, their shapes also change slightly during development to become
 more ‘rock’, ‘mix’ or ‘mangrove’-like, respectively. The present results
 demonstrate that ecology is also the most important factor in shaping the
 claws of immatures and that attachment in the intertidal environment is
 vital for the survival of each mobile stage.
DOI: 10.5061/dryad.v6wwpzgxd
title: Earth and life evolve together- a comment on Yamahira et al.

description: The provocative study by Yamahira et al. hypothesizes that one
 species, Oryzias setnai, endemic to coastal areas of west-flowing streams
 of the Western Ghats, is the sister species of all other ricefishes and
 that it diverged in the late Mesozoic. They conclude India is the center
 of origin of ricefishes, the ancestral lineage of which subsequently
 diversified and dispersed to occupy its current broad range throughout
 Asia and Southeast Asia. This scenario is presented as the only possible
 conclusion from the molecular phylogenetic analysis. We challenge their
 scenario and conclusions based on a reanalysis of their data.
description: Reanalyses of an existing data set with varying parameters. Data
 set comprises four phylogenetic tree files with different scaling factors,
 a species distribution file and 20 result files from RASP analyses
 differing in various parameter settings.
DOI: 10.5061/dryad.6hdr7sr2c
title: Climate and land-use effects on dung beetle assemblages

description: This dataset contains data from a field study conducted in 2019 and
 described in the paper "Dung beetle diversity is mainly affected by
 land use, while community specialization is driven by climate" by
 Englmeier et al. To test the effects of land use and climate on
 α-diversity, local community specialization (H2'), and γ-diversity of
 dung beetles, we used pitfall traps baited with four different dung types
 at 114 study sites, distributed over a spatial extent of 300 km x 300 km
 and 1000 m in elevation. Study sites were established in four local
 land-use types: forests, grasslands, arable sites, and settlements,
 embedded in near-natural, agricultural, or urban landscapes. We used
 negative-binomial generalized linear models for alpha-diversity,
 calculated community specialization on dung resources by using the
 standardized two-dimensional Shannon entropy (H2'), and assessed
 γ-diversity by Hill-numbers. Our results show that intensive land use
 i.e., agriculture and urban areas, strongly reduced dung beetle α- and
 γ-diversity, respectively. Dung beetle abundance and species density were
 strongly affected by agricultural land use on both spatial scales, whereas
 γ-diversity on a local scale was mainly affected by settlements and on a
 landscape scale equally by agricultural and urban land use. Increasing
 precipitation diminished dung beetle abundance, and higher temperatures
 reduced community specialization and γ-diversity. These results indicate
 that intensive land use and higher temperatures may cause a loss in dung
 beetle diversity and alter community networks of dung beetle assemblages.
 A decrease in dung beetle diversity may disturb decomposition processes at
 both local and regional scales and alter ecosystem functioning, which
 leads to drastic ecological and economic damage.
description: Pitfall traps; Statistics were conducted in R.
description: Data can be opened by R and Excel.
DOI: 10.5061/dryad.8cz8w9grp
title: Bryosphere loss impairs litter decomposition consistently across moss species, litter types, and micro-arthropod abundance

description: The bryosphere (i.e., ground mosses and their associated biota) is a key
 driver of nutrient and carbon dynamics in many terrestrial ecosystems, in
 part because it regulates litter decomposition. However, we have a poor
 understanding of how litter decomposition responds to changes in the
 bryosphere, including changes in bryosphere cover, moss species, and
 bryosphere-associated biota. Specifically, the contribution of
 micro-arthropods to litter decomposition in the bryosphere is unclear.
 Here, we used a 16-month litterbag field experiment in two boreal forests
 to investigate bryosphere effects on litter decomposition rates among two
 moss species (Pleurozium schreberi and Hylocomium splendens), and two
 litter types (higher-quality Betula pendula litter and lower-quality P.
 schreberi litter). Additionally, we counted all micro-arthropods in the
 litterbags and identified them to functional groups. We found that
 bryosphere removal reduced litter decomposition rates by 28% and
 micro-arthropod abundance by 29%, and led to a colder micro-climate.
 Litter decomposition rates and micro-arthropod abundance were uncorrelated
 overall, but were positively correlated in B. pendula litterbags.
 Bryosphere effects on litter decomposition rates were consistent across
 moss species, litter types, and micro-arthropod abundances and community
 compositions. These findings suggest that micro-arthropods play a minor
 role in litter decomposition in the boreal forest floor, suggesting that
 other factors (e.g., micro-climate, nutrient availability) likely drive
 the positive effect of the bryosphere on decomposition rates. Our results
 point to a substantial and consistent impairment of litter decomposition
 in response to loss of moss cover, which could have important implications
 for nutrient and carbon cycling in moss-dominated ecosystems.
description: Detailed methods are given in the paper "Bryosphere loss
 impairs litter decomposition consistently across moss species, litter
 types, and micro-arthropod abundance" published by Ecosystems. The
 files included here relate to three data sets: - Litter
 mass loss, measured using the litterbag method. -
 Meso-fauna abundance, extracted from litterbags using Tullgren
 funnels. - Ground temperature, recorded using iButton
 loggers.
DOI: 10.5061/dryad.h9w0vt4k3
title: Prioritizing terrestrial invasive alien plant species for management in urban ecosystems

description: 1. Invasive alien plant species (IAPs) in urban areas can have detrimental
 effects on biodiversity, ecosystem services and human well-being. Urban
 areas are complex social management mosaics with high land-use diversity,
 complex land tenure patterns, and many different stakeholder groups, some
 of which derive benefits from invading species. Urban conservation
 practitioners face complex decisions about which IAPs require management.
 Yet most IAPs prioritization frameworks have been designed for and
 implemented in natural or rural areas and are generally inadequate for
 guiding effective and sustainable interventions in urbanized areas. 2. We
 modified an existing prioritization scheme to develop a framework for
 prioritizing terrestrial IAPs in urban areas which applies evidence-based
 (data-driven) and stakeholder-based (local knowledge) assessments to score
 and rank alien plant species in terms of their priority for management
 using an objective set of criteria. 3. The framework consists of forty-six
 criteria, grouped into eight modules which assess invasion status, habitat
 requirements, biological characteristics, dispersal ability, distribution,
 impact (positive and negative), and potential for control for each alien
 plant species under consideration. 4. We use the city of Toronto, Canada
 as a case study to test our framework – a list of 50 IAPs were effectively
 scored and ranked in order of high to low priority for control. Species
 with the highest total prioritization scores were Vincetoxicum rossicum
 (Dog Strangling Vine), Convolvulus arvensis (Field Bindweed) and Taraxacum
 officinale (Common Dandelion) (ranked 1, 2 and 3, respectively). 5. Many
 of the identified high priority species align with the those previously
 flagged as of management concern by conservation practitioners, but also
 include those that are not actively managed due to their perceived lower
 ecological impacts. These species still require high resource investment
 for other objectives such as aesthetics. This highlights the complexity of
 alien plant species management in urban areas. 6. Synthesis and
 applications. Prioritizing invasive alien plants for management in urban
 areas is particularly challenging due to often conflicting ecological,
 economic, and social objectives. We use available evidence and local
 stakeholder knowledge to develop an objective and systematic
 prioritization tool which can assist conservation practitioners in
 selecting priority species for management action in complex urban
 landscapes.
DOI: 10.15468/dl.38j2dt
title: Occurrence Download

description: A dataset containing 668 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Unaspis citri)"
 ]
}

 The dataset includes 668 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003013-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.qfttdz0jh
title: Data from: PMSeeker: A Scheme for paternity marker set mining

description: The paternity test is a genetic test that analyzes genetic characteristics
 (mostly molecular markers) to identify whether two individuals have a
 parent-child relationship. It is frequently employed in judicial
 identification and economic species breeding. Because a single
 marker's discriminability is restricted, numerous markers are
 typically utilized to produce an accurate result. Obviously, having an
 excessive number of redundant markers wastes time and resources, and
 adequate approaches are required to screen reduced and efficient paternity
 marker sets (PMS). This study established a non-redundant PMS-screening
 scheme based on the exhaustive algorithm and greedy algorithm. When
 screening PMS, the greedy algorithm selects markers based on the parental
 dispersity index (PDI), a uniquely defined metric that outperforms
 polymorphic information content (PIC) and probability of exclusion (PE).
 With the conjunctive use of the two algorithms the optimal solutions were
 found for more than 99.7% of solvable cases in three groups of random
 sample experiments in this study. This scheme effectively reduces the
 number of markers in PMS, so conserving people and experimental resources
 and laying the groundwork for the widespread implementation of paternity
 assignment technology in economic species breeding.
DOI: 10.5061/dryad.3ffbg79k8
title: 3D models of Artibeus jamaicensis and Rhinolophus pusillus hyoid apparatus and tympanic bones

description: The morphology of the stylohyal-tympanic bone articulation found in
 laryngeally echolocating 7 bats is highly indicative of a function
 associated with signal production. One untested hypothesis is that 8 this
 morphology allows the transfer of a sound signal from the larynx to the
 tympanic bones (auditory 9 bulla) via the hyoid apparatus during signal
 production by the larynx. We used µCT data and finite 10 element analysis
 (FEA) to model the propagation of sound through the hyoid chain into the
 tympanic 11 bones to test this hypothesis. We modeled sound pressure (dB)
 wave propagation from the basihyal to the 12 tympanic bones, vibratory
 behavior (m) of the stylohyal – tympanic bone unit, and the stylohyal and
 13 tympanic bones when the stylohyal bone is allowed to pivot on the
 tympanic bone. Sound pressure wave 14 propagation was modeled using the
 harmonic acoustics solver in ANSYS and vibratory behavior was 15 modeled
 using coupled modal and harmonic response analyses in ANSYS. For both
 analyses (harmonic 16 acoustics and harmonic response), the input
 excitation on the basihyal and thyrohyals was modeled as the 17 estimated
 pressure (Pa) imposed by the collision of the vibrating thyroid cartilage
 of the larynx against 18 these bones during signal production. Our models
 support the hypothesis that this stereotypical hyoid 19 morphology found
 in laryngeally echolocating bats can transfer sound to the auditory bullae
 at an 20 amplitude that is likely heard for the species Artibeus
 jamaicensis and Rhinolophus pusillus
description: The 3D models were rendered from micoCT scans and processed in
 Fusion 360 and SpaceClaim and saved as STL and STEP files.
DOI: 10.5061/dryad.cjsxksn6x
title: Data from: Titmice are a better indicator of bird density in Northern European than in Western European forests

description: Population sizes of many birds are declining alarmingly and methods for
 estimating fluctuations in species’ abundances at a large spatial scale
 are needed. The possibility to derive indicators from the tendency of
 specific species to co-occur with others has been overlooked. Here we
 tested whether the abundance of resident titmice can act as a general
 ecological indicator of forest bird density in European forests. Titmice
 species are easily identifiable and have a wide distribution, which makes
 them potentially useful ecological indicators. Migratory birds often use
 information on the density of resident birds, such as titmice, as a cue
 for habitat selection. Thus, the density of residents may potentially
 affect community dynamics. We examined spatio-temporal variation in
 titmouse abundance and total bird abundance, each measured as biomass, by
 using long-term citizen science data on breeding forest birds in Finland
 and France. We analyzed the variation in observed forest bird density
 (excluding titmice) in relation to titmouse abundance. In Finland, forest
 bird density linearly increased with titmouse abundance. In France, forest
 bird density non-linearly increased with titmouse abundance, the
 association weakening towards high titmouse abundance. We then analyzed
 whether the abundance (measured as biomass) of random species sets could
 predict forest bird density better than titmouse abundance. Random species
 sets outperformed titmice as an indicator of forest bird density only in
 4.4% and 24.2% of the random draws, in Finland and France, respectively.
 Overall, the results suggest that titmice could act as an indicator of
 bird density in Northern European forest bird communities, encouraging the
 use of titmice observations by even less-experienced observers in citizen
 science monitoring of general forest bird density.
DOI: 10.5061/dryad.fttdz08v1
title: Freshwater floodplain habitats buffer native food webs from negative effects of non-native centrarchids and bullfrogs

description: Species introductions are common in freshwater environments, with the
 potential to transform community and ecosystem structure. Predatory fishes
 and American bullfrogs (Rana catesbeiana = Lithobates catesbeianus) are
 both widespread aquatic invaders implicated in native amphibian declines.
 In lowland ecosystems, co-occurrence between native and non-native fishes
 and larval amphibians appears more common than in high-elevation
 ecosystems, though community interactions there are poorly studied. In
 this study, we used stable isotope analysis of carbon (δ13C) and nitrogen
 (δ15N) to examine native fish and amphibian trophic structure in lowland,
 floodplain waterbodies with and without non-native centrarchid fishes and
 bullfrogs. In the presence of non-native taxa, three-spine stickleback
 (Gasterosteus aculeatus), two native salamander larvae, and one of two
 native frog species shifted their food resources and/or fed lower on the
 food web, with only one species exhibiting a decline in niche size. The
 observed trophic shifts reflect changes in habitat and/or food resources,
 which may reduce competition or predation, and promote co-occurrence.
 Collectively, our study suggests that the co-occurrence of native and
 non-native amphibians and fishes in lowland, floodplain habitats may be
 facilitated by broad food resource availability and complex habitat
 structure.
description: Our study system was the Chehalis River Basin in southwestern
 Washington, USA. The Chehalis River floodplain contains extensive
 off-channel habitats, including oxbow ponds, wetlands, and seasonally
 flooded fields and forests. We sampled 16 sites in spring (18 April – 4
 May 2017) and resampled eight of those sites in summer (20 June – 6 July
 2017), with one site sampled in the spring excluded from further study as
 we observed none of our focal taxa. At each site, we examined a suite of
 habitat characteristics, collected water samples for chemical analysis,
 and sampled the biotic community. Specifically, we collected the following
 organisms for food web analysis: dominant macrophytes, seston (from water
 samples; see above), filamentous algae (where present), zooplankton,
 macroinvertebrates, amphibians, and fishes (where present). Vertebrates
 were weighed and measured prior to isotopic analysis. All isotope samples
 were analyzed for percent carbon (C), percent nitrogen (N),
 δ<sup>13</sup>C, and δ<sup>15</sup>N values.
 Details are provided in the associated manuscript (currently in review
 at Freshwater Science).
description: Three datasets are provided: 1. Environmental
 characteristics of the 15 study sites 2. Vertebrate
 measurements (e.g., mass and length) for the fishes and larval amphibians
 collected for the project 3. Stable isotope results,
 including percent C, percent N, δ<sup>13</sup>C, and
 δ<sup>15</sup>N values Each file has
 associated metadata.