cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25338/b8mw7p
title: High quality, chromosome-scale genome assemblies: Comparisons of three Diaphorina citri (Asian Citrus Psyllid) geographic populations

description: The Asian citrus psyllid, Diaphorina citri, is the insect vector of the
 causal agent of huanglongbing (HLB), a devastating bacterial disease of
 commercial citrus. Few genomic resources exist for D. citri. In this
 study, we utilized PacBio HiFi and chromatin confirmation contact (Hi-C)
 sequencing to sequence, assemble, and compare three high quality,
 chromosome-scale genome assemblies of D. citri collected from California,
 Taiwan, and Uruguay. Our assemblies had final sizes of 282.67 Mb
 (California), 282.89 Mb (Taiwan), and 266.67 Mb (Uruguay) assembled into
 13 pseudomolecules – a reduction in assembly size of 41% to 45% compared
 to previous assemblies which we validated using flow cytometry. We
 identified the X chromosome in D. citri and found it to use an XX/X0
 sex-determination system. Annotation of repetitive elements revealed
 differing repeat class content between assemblies and showed that the bulk
 of repeat DNA is found on chromosomes 8 through 13. We annotated between
 19,083 and 20,357 protein-coding genes and orthologous clustering of these
 suggested Taiwan and Uruguay D. citri are more closely related. Structural
 variant analyses identified chromosome 1 as having the largest variation
 in size between assemblies. We provide new python scripts to predict and
 filter endogenous viral elements (EVEs), finding 30 EVEs in California, 40
 EVEs in Taiwan, and 32 EVEs in Uruguay, including a large, conserved
 integration with a closest BLASTx hit to Diaphorina citri flavi-like virus
 (DcFLV). We predicted differing numbers and sizes of piwi-interacting RNA
 (piRNA) clusters in each assembly, identifying 29 clusters in California,
 41 in Taiwan, and 11 in Uruguay. Mitochondrial haplotype networks indicate
 that Taiwan and Uruguay D. citri are closely related, while California is
 related to Florida D. citri. These high quality, chromosome-scale
 assemblies provide new genomic resources to researchers to further D.
 citri and HLB research.
DOI: 10.34894/5qod0i
title: Replication Data for: How important are user-generated data for search result quality?

description: Do search engines produce better results because their algorithms are better or because they can access more data from past searches? We document that the algorithm of a small search engine can produce nonpersonalized results that are of similar quality to those of the dominant firm (Google) for certain types of search queries. Overall differences in the quality of search results are explained by searches for rare queries, which constitute 74 percent of the traffic in our data. We conduct an experiment in which we keep the algorithm of a small search engine fixed and only vary the amount of data it uses as input. Our results show that giving small search engines access to more data about rare queries improves the quality of their results. This suggests that mandatory data sharing by large search engines is a necessary condition, yet probably not a sufficient one, to increase competition in the search market.
DOI: 10.5061/dryad.pnvx0k6pp
title: Reduced pollinator service in small populations of Arabidopsis lyrata at its southern range limit

description: Even though a high fraction of angiosperm plants depend on animal
 pollinators for sexual reproduction, little is known how pollinator
 service changes across the ranges of plant species’ and whether it may
 contribute to range limits. Here, we tested for variation in pollinator
 service in the North American Arabidopsis lyrata from its southern to
 northern range edge and evaluated the driving mechanisms. We monitored
 insect pollinators using time-lapse cameras in 13 populations over two
 years and spotted 67 pollinating insect taxa, indicating the generalist
 nature of this plant-pollinator system. Pollinator service was highest at
 intermediate local flower densities and higher in large compared to small
 plant populations. Southern populations had generally smaller population
 sizes, and visitation rate and pollination ratio decreased with latitude.
 We also found that pollinator visitation was positively correlated with
 the richness of other flowering plants. Synthesis: This study indicates
 that plant populations at southern range edges receive only marginal
 pollinator service if they are small, and the effect of lower pollination
 is also detectable within populations across the range when the local
 flower density is low. Results therefore suggest the potential for an
 Allee effect in pollination that manifests itself across spatial scales.
description: Data was collected in the field, and processed using R
DOI: 10.5061/dryad.02v6wwq5b
title: Using GBIF to Demonstrate Colonial Legacies on Biodiversity Data

description: Biologists recognize the Caribbean archipelago as a biodiversity hotspot
 and employ it for their research as a “natural laboratory”, but do not
 always appreciate that these ecosystems are in fact palimpsests shaped by
 multiple human cultures over millennia. We discuss two case studies of the
 Caribbean’s fragmented natural history collections, the effects of
 differing legislation and governance by the region’s multiple nation
 states. We use digital natural history specimen data from GBIF to
 demonstrate how colonial history has influenced specimen collection
 patterns in Trinidad & Tobago, The Bahamas, and the Greater
 Antilles.
description: Data on digitized natural history specimen comes from the GBIF
 database through the GBIF API using the R package `rgbif`.
 Institution locations were gathered partially through the GBIF
 API, and partially manually.
DOI: 10.5061/dryad.z8w9ghxf1
title: Chloroplast haplotypes and main haplotypes of nrITS clones of Gentiana crassicaulis

description: The Himalaya-Hengduan Mountain region is one of the hotspots of
 biodiversity research. The uplift of the Qinghai-Tibetan Plateau (QTP) and
 the Quaternary glaciation caused great environmental changes in this
 region, and the responses of many species in the QTP to the Quaternary
 climate are still largely unknown. The genetic structure and
 phylogeographical history of Gentiana crassicaulis Duthie ex Burk, an
 endemic Chinese alpine species in this area, were investigated based on
 four chloroplast fragments and internal transcribed spacer region of the
 nuclear ribosomal DNA (nrITS) sequences of 11 populations. The populations
 with highly diverse chloroplast haplotypes were mainly found at the edge
 of the QTP. There were two main haplotypes of nrITS clones, one shared by
 the Yunnan and Guizhou populations, and the other by the remaining
 populations. The population with the highest diversity was the Gansu
 population, located at the edge of the plateau. Based on molecular dating,
 the diversification of G. crassicaulis at the edge of the plateau occurred
 before the Last Glacial Maximum (LGM), and the species may have completed
 its expansion from the edge to the platform. Ecological Niche Models were
 conducted to predict the distributional ranges of G. crassicaulis at
 present, during the LGM, and during the last interglacial (LIG) period.
 The results demonstrated that G. crassicaulis survived on the QTP platform
 and at the edge during the LGM but afterward retreated from the platform
 to the southern edge, followed by expansion to the platform.
description: Total genomic DNA was
 extracted from the silica-gel–dried leaves.
 Four chloroplast fragments
 were amplified and sequenced, including
 rpl33, rpl33-rps18, rpl16 intron, and trnC-GCA-petN. The four
 fragments were concatenated, and a total of 6 haplotypes (H1–H6) were
 identified from 113 individuals of Gentiana crassicaulis.
 The ITS region was amplified
 and the PCR products were cloned using the pUCm-T Vector PCR
 Products Cloning Kit (Sangon, Shanghai, China), and 10 clones per
 individual were sequenced. From 11 populations of Gentiana crassicaulis,
 330 ITS cloning sequences were obtained. The haplotypes shared among the
 populations were S1 and S2, which accounted for 44.8% (148/330) and 11.2%
 (37/330) of all the cloning sequences, respectively.
DOI: 10.5061/dryad.kprr4xh67
title: Expansion of non-native plant Flaveria bidentis (L.) Kuntze driven by range of factors leading to patchy distribution patterns

description: Given the growing concern over the ecological impacts of non-native
 species, exploring these species’ expansion edge and distribution patterns
 and their driving factors is important for developing suitable management
 measures. Flaveria bidentis (L.) Kuntze, a non-native plant that was
 introduced to China in the 1990s, has spread from southern Hebei Province,
 where it first took root, to the surrounding regions and has become one of
 the most notorious invasive weeds in northern China. Based on 15 years
 (2006-2021) of extensive field investigations, the spatial distribution of
 sampling and occurrence points were mapped in the recently expanded region
 of F. bidentis’ population. Then, nearest neighbor analysis used to
 characterize the spatial pattern differences between samplings and
 occurrences. An exponential decay function was used to elucidate the
 driving factors contributing to the presence and absence of F. bidentis.
 Our results demonstrated an effective random sampling setup, a
 heterogeneous spatial distribution of F. bidentis, and a multi-regional
 independent aggregation distribution pattern (p&lt;0.01). There were
 significant spatial correlations between the aggregation areas of plant
 occurrence points and the locations of roads and construction sand
 distribution centers. These findings suggest that human activities
 involving major roads and construction sand distribution centers were
 driving factors contributing to this long-distance dispersal and spatially
 discontinuous distribution patterns. The presence of these patchy
 distribution patterns has important implications for ongoing efforts to
 manage populations of non-native species.
DOI: 10.5061/dryad.931zcrjmz
title: Automatic analysis of cochlear response using electrocochleography signals during cochlear implant surgery

description: Cochlear implants (CIs) provide an opportunity for the hearing impaired to
 perceive sound through electrical stimulation of the hearing (cochlear)
 nerve. However, there is a high risk of losing a patient's natural
 hearing during CI surgery, which has been shown to reduce speech
 perception in noisy environments as well as music appreciation. This is a
 major barrier to the adoption of CIs by the hearing impaired.
 Electrocochleography (ECochG) has been used to detect intra-operative
 trauma that may lead to loss of natural hearing. There is early evidence
 that ECochG can enable early intervention to save natural hearing of the
 patient. However, detection of trauma by observing changes in the ECochG
 response is typically carried out by a human expert. Here, we discuss a
 method of automating the analysis of cochlear responses during CI surgery.
 We establish, using historical patient data, that the proposed method is
 highly accurate (~94% and ~95% for sensitivity and specificity
 respectively) when compared to a human expert. The automation of real-time
 cochlear response analysis is expected to improve the scalability of
 ECochG and improve patient safety.
DOI: 10.15468/dl.np8m8w
title: Occurrence Download

description: A dataset containing 33374 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Living Specimen, Machine Observation)",
 "Continent is Europe",
 "License is CC-BY 4.0",
 "TaxonKey is Ovis aries"
 ]
}

 The dataset includes 33374 records from 145 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003063-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.51c59zw9t
title: Tectaria danangensis (Tectariaceae), a new fern species from Vietnam

description: A new fern species, Tectaria danangensis (Tectariaceae)
 is described and illustrated from Vietnam, which had long been
 misreported as T. crenata. The new species somewhat
 resembles T. poilanei, a species long neglected in the
 fern flora of Indochina, in the frond shape and sori arrangement
 but differs by its sori irregularly in two rows (versus regularly
 2-rowed, distantly and evenly arranged) between lateral veins of
 pinnae, fronds being more or less dimorphic (versus monomorphic), and
 basal pinnae each having a base-joined (versus free) branch. Phylogenetic
 analyses of selected sequences of cpDNA suggested T.
 danangensis has close affinity to T.
 harlandii. Tectaria danangensis appears to be
 an intermediate species between T.
 harlandii and T. poilanei.
description: 1. The "T" or "T." in species naming is an
 abbreviation of Tectaria. 2. In the sequence
 alignments, "N"or "?" stands for unsequenced
 character. 3. Phylogenetic tree of Tectaria is obtained
 from Bayesian inference, maximum likelihood and maximum parsimony analysis
 of combined plastid regions of rbcL, atpB, rps16-matK, ndhF-trnN and
 trnL-F.
DOI: 10.5061/dryad.f1vhhmgzp
title: Distribution records: Reconciling biodiversity conservation and flood risk reduction: the new strategy for freshwater protected areas

description: Aim: Natural disaster risk reduction (DRR) is becoming a more important
 function of protected area (PAs) for current and future global warming.
 However, biodiversity conservation and DRR have been handled separately
 and their interrelationship has not been explicitly addressed. This is
 mainly because, due of prevailing strategies and criteria for PA
 placement, a large proportion of PAs are currently located far from
 human-occupied areas, and habitats in human-occupied areas have been
 largely ignored as potential sites for conservation despite their high
 biodiversity. If intensely developed lowland areas with high flooding risk
 overlap with important sites for biodiversity conservation, it would be
 reasonable to try to harmonize biodiversity conservation and human
 development in human-inhabited lowland areas. Here, we examined whether
 extant PAs can conserve macroinvertebrate and freshwater fish biodiversity
 and whether human-inhabited lowland flood risk management sites might be
 suitable to designate as freshwater protected areas (FPAs). Location:
 Across Japan Methods: We examined whether extant PAs can conserve
 macroinvertebrate and freshwater fish biodiversity and analyzed the
 relationship between candidate sites for new FPAs and flood disaster risk
 and land use intensity at a national scale across Japan based on
 distribution data for 131 freshwater fish species and 1395
 macroinvertebrate species. Results: We found that extant PAs overlapped
 with approximately 30% of conservation-priority grid cells (1 km2) for
 both taxa. Particularly for red-listed species, only one species of
 freshwater fish and three species of macroinvertebrate achieved the
 representation target within extant PAs. Moreover, more than 40% of
 candidate conservation-priority grid cells were located in flood risk and
 human-occupied areas for both taxa. Main conclusions: Floodplain
 conservation provides suitable habitat for many freshwater organisms and
 helps control floodwaters, so establishing new FPAs in areas with high
 flood risk could be a win-win strategy for conserving freshwater
 biodiversity and enhancing ecosystem-based DRR (eco-DRR).
DOI: 10.5061/dryad.3xsj3txj8
title: The mere presence of cuckoos in breeding area alters egg-ejection decisions in Daurian redstarts

description: Brood parasitic cuckoos and their hosts serve as model systems for
 studying host-parasite coevolution. Egg-rejection behavior constitutes an
 effective defense against brood parasitism, but some host species show
 phenotypic plasticity in egg-rejection behavior. Direct exposure
 to a cuckoo near the nest can increase egg-rejection likelihood, and
 long-term studies have shown that increased the egg-rejection rates
 generally correlate with higher parasite prevalence. However, it remains
 unclear whether such increases result from interactions between parasites
 and hosts, as these can be surprisingly common, or whether the mere
 presence of cuckoos in the breeding area is sufficient. Daurian
 redstarts Phoenicurus auroreus are a common
 host of the common cuckoo Cuculus canorus that defend
 against cuckoo parasitism mainly by ejecting the parasitic egg from the
 nest. This species is unique, as its first breeding attempt of the year
 takes place before the arrival of cuckoos, excluding the possibility for
 direct interactions. We simulated the ambient presence of cuckoos or
 hoopoes Upupa epops (control) in sub-populations of
 redstarts during their first egg-laying period by presenting
 taxidermic models and playing back vocalizations. Redstarts in
 cuckoo-treated plots showed significantly higher egg-ejection rates than
 individuals in control plots, even though females in both groups were
 equally likely to recognize the parasitic egg. Among females that did
 recognize the parasitic egg, those exposed to the cuckoo treatment were
 more likely to eject it than those exposed to the control treatment. Our
 results demonstrate unequivocally that the mere presence of cuckoos in the
 environment is sufficient to provoke egg-ejection behavior.
DOI: 10.5061/dryad.m37pvmd41
title: Sex-based differences in the use of post-fire habitats by invasive cane toads (Rhinella marina)

description: Wildfires can modify habitat attributes, and those changes may
 differentially affect males versus females within a species if there is
 pre-existing niche divergence between the sexes. We used radio-tracking
 and dissections to study invasive cane toads (Rhinella marina), and
 performed transect counts on native frogs and cane toads 12 months after
 extensive fires in forests of eastern Australia. Both toads and native
 frogs were encountered more frequently in burned sites than in unburned
 sites. Most microhabitat features were similar between burned versus
 unburned areas, but fire had differential impacts on the ecology of male
 versus female toads. In burned areas females were less numerous but were
 larger, in better body condition, and had consumed more prey (especially,
 coleopterans and myriapods). The impact of fire on attributes of
 retreat-sites (e.g., temperature, density of vegetation cover) also
 differed between the sexes. More generally, intraspecific divergence in
 ecological traits within a species (as a function of body size as well as
 sex) may translate into substantial divergences in the impacts of habitat
 change.
description: Information regarding how the data was collected and processed is
 included in the README.txt file. Usage notes are also included in the
 file.
DOI: 10.5061/dryad.m905qfv32
title: Thermal plasticity and evolution shape predator-prey interactions differently in clear and turbid water

description: Warming and eutrophication negatively affect freshwater ecosystems by
 modifying trophic interactions and increasing water turbidity. We need to
 consider their joint effects on predator-prey interactions, and how these
 depend on the thermal evolution of both predator and prey. We quantified
 how 4°C warming and algae-induced turbidity (that integrates turbidity per
 se and increased food for zooplankton prey) affect functional response
 parameters and prey population parameters in a common-garden experiment.
 We did so for all combinations of high- and low-latitude predator
 (damselfly larvae) and prey (water fleas) populations to assess the
 potential impact of thermal evolution of predators and/or prey at a high
 latitude under warming using a space-for-time substitution. We then
 modelled effects on the system stability (i.e. tendency to oscillate)
 under different warming, turbidity and evolutionary scenarios. Warming and
 turbidity had little effect on the functional response parameters of
 high-latitude predators. In contrast, warming and turbidity reduced the
 handling times of low-latitude predators. Moreover, warming increased the
 search rates of low-latitude predators in clear water but instead
 decreased these in turbid water. Warming increased stability (i.e.
 prevented oscillations) in turbid water (except for the “high-latitude
 predator & high-latitude prey” system), mainly by decreasing the
 prey’s carrying capacity and partly also by decreasing search rates, while
 it did not affect stability in clear water. Algae-induced turbidity
 generally decreased stability, mainly by increasing the prey’s carrying
 capacity and partly also by increasing search rates. This resembles
 findings that nutrient enrichment can reduce the stability of trophic
 systems. The expected stability of the high-latitude trophic system under
 warming was dependent on the turbidity level: our results suggest that
 thermal plasticity tends to destabilize the high-latitude trophic system
 under warming in clear water but not in turbid water, and that thermal
 evolution of the predator will stabilize the high-latitude system under
 warming in turbid water but less so in clear water. The extent to which
 thermal plasticity and evolution shape trophic system stability under
 warming may strongly differ between clear and turbid water bodies, with
 their contributions having a more stabilizing role in turbid water.
description: The methods for data collection and processing are described in
 the Materials and methods and the appendix of the manuscript.
description: FR.csv contains data of functional response of the predatory
 damselfy larvae feeding on their daphnid prey. r.csv
 contains data used for estimating the intrinsic population growth rate of
 the prey. K.csv contains data used for estimating the
 carrying capacity of the prey. README_file.txt contains
 information for the headers of the attached csv files.