cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.zpc866t5n
title: A Multi-Type Birth-Death model for Bayesian inference of lineage-specific birth and death rates

description: Heterogeneous populations can lead to important differences in birth and
 death rates across a phylogeny. Taking this heterogeneity into account is
 necessary to obtain accurate estimates of the underlying population
 dynamics. We present a new multi-type birth-death model (MTBD) that can
 estimate lineage-specific birth and death rates. This corresponds to
 estimating lineage-dependent speciation and extinction rates for species
 phylogenies, and lineage-dependent transmission and recovery rates for
 pathogen transmission trees. In contrast with previous models, we do not
 presume to know the trait driving the rate differences, nor do we prohibit
 the same rates from appearing in different parts of the phylogeny. Using
 simulated datasets, we show that the MTBD model can reliably infer the
 presence of multiple evolutionary regimes, their positions in the tree,
 and the birth and death rates associated with each. We also present a
 re-analysis of two empirical datasets and compare the results obtained by
 MTBD and by the existing software BAMM. We compare two implementations of
 the model, one exact and one approximate (assuming that no rate changes
 occur in the extinct parts of the tree), and show that the approximation
 only slightly affects results. The MTBD model is implemented as a package
 in the Bayesian inference software BEAST~2, and allows joint inference of
 the phylogeny and the model parameters.
description: Files contained in this dataset:
 Supplement.pdf: Supplementary methods and results
 code_files.zip: R scripts used to simulate, process and analyze
 the data and make the plots; XML configuration files used to run
 BEAST2 data_files.zip: Simulated datasets and summary
 of the results
DOI: 10.5061/dryad.3xsj3txbw
title: Regulation of olfactory-based sex behaviors in the silkworm by genes in the sex-determination cascade

description: Insect courtship and mating depend on integration of olfactory, visual,
 and tactile cues. Compared to other insects, Bombyx mori, the
 domesticated silkworm, has relatively simple sexual behaviors as it cannot
 fly. Here by using CRISPR/Cas9 and electrophysiological techniques we
 found that courtship and mating behaviors are regulated in male silk moths
 by mutating genes in the sex determination cascade belonging to two
 conserved pathways. Loss of Bmdsx gene expression
 significantly reduced the peripheral perception of the major pheromone
 component bombykol by reducing expression of the product of
 the BmOR1 gene which completely blocked courtship in
 adult males. Interestingly, we found that mating behavior was regulated
 independently by another sexual differentiation gene, Bmfru. Loss
 of Bmfru completely blocked mating, but males displayed
 normal courtship behavior. Lack of Bmfru expression
 significantly reduced the perception of the minor pheromone component
 bombykal due to the down regulation of BmOR3 expression;
 further, functional analysis revealed that loss of the product
 of BmOR3 played a key role in terminating male mating
 behavior. Our results suggest
 that Bmdsx and Bmfru are at the base
 of the two primary pathways that regulate olfactory-based sexual behavior.
description: Illumina sequencing as perfomered as our previous study [47],
 total RNA was isolated from 10 <i>Bmfru<sup>
 </sup></i>mutant and WT antennas using TRIzol (Invitrogen,
 Carlsbad, CA, USA), and the residual DNA was removed with RNase-free DNase
 I (New England BioLabs, Ipswich, MA, USA) for 30 min at 37 °C. For
 RNA-seq, library construction and sequencing using an Illumina HiSeq 2000
 were conducted by BGI Genomic Services (Shenzhen, China), briefly
 described as follows. The mRNA was enriched using oligo (dT) magnetic
 beads samples were mixed with a fragmentation buffer, and the mRNA reduced
 to short fragments (~200 bp). The first strand of the cDNA was synthesized
 using random hexamer primers,buffer, dNTPs, RNase H, and DNA polymerase I
 were added to synthesize the second strand, and the double-stranded cDNA
 was purified with magnetic beads followed by performing end repair and
 3'-end single nucleotide adenine addition. Finally, sequencing
 adaptors were ligated to the fragments which were enriched by PCR
 amplification, and an Agilent 2100 Bioanaylzer and an ABI Step One Plus
 Real-Time PCR System were used to quantify libraries. The library products
 were sequenced using an Illumina HiSeq 2000 (BGI Biotech Co. Ltd.). The
 raw sequencing data were qualified, filtered, and mapped to the reference
 silkworm genome database (http://silkworm.genomics.org.cn/) using
 tophat/bowtie2.
description: no.
DOI: 10.5061/dryad.xwdbrv19g
title: Small fish, large river: surprisingly minimal genetic structure in a dispersal-limited, habitat specialist fish

description: Genetic connectivity is expected to be lower in species with limited
 dispersal ability and a high degree of habitat specialization (intrinsic
 factors). Also, gene flow is predicted to be limited by habitat conditions
 such as physical barriers and geographic distance (extrinsic factors). We
 investigated the effects of distance, intervening pools, and rapids on
 gene flow in a species, the Tuxedo Darter (Etheostoma lemniscatum), a
 habitat specialist that is presumed to be dispersal-limited. We predicted
 that the interplay between these intrinsic and extrinsic factors would
 limit dispersal and lead to genetic structure even at the small spatial
 scale of the species range (a 38.6 km river reach). The simple linear
 distribution of E. lemniscatum allowed for an ideal test of how these
 factors acted on gene flow and allowed us to test expectations (e.g.,
 isolation-by-distance) of linearly distributed species. Using 20
 microsatellites from 163 individuals collected from 18 habitat patches, we
 observed low levels of genetic structure that were related to geographic
 distance and rapids, though these factors were not barriers to gene flow.
 Pools separating habitat patches did not contribute to any observed
 genetic structure. Overall, E. lemniscatum maintains gene flow across its
 range and is comprised of a single population. Due to the linear
 distribution of the species, a stepping stone model of dispersal best
 explains the maintenance of gene flow across its small range. In general,
 our observation of higher than expected connectivity likely stems from an
 adaptation to disperse due to temporally unstable and patchy habitat.
description: PCR products were genotyped using
 an ABI3730 sequencer with LIZ600 as the size standard at the University of
 Florida Interdisciplinary Center for Biotechnology Research. Allele sizes
 were scored automatically using the panel editor function in GeneMarker
 v1.6 (SoftGenetics LLC) and then confirmed manually. Any allele that did
 not fit the expected repeat pattern for that locus was closely examined,
 and then, if necessary, edited manually or re-amplified and re-genotyped.
 To ensure consistency of allele sizes across reactions, three positive
 controls were included on each genotyping run.
description: Missing alleles are denoted with a 0. The spreadsheet includes
 each sampled individual’s identification name, and the individual’s
 corresponding locality and reach numbers. Each locus is spread over two
 columns (denoted as Elem0##) and the allele calls for each individual is
 given for each locus and individual.
DOI: 10.5061/dryad.dncjsxkvt
title: The last pteraspids (Agnatha, Heterostraci): New material from the Middle Devonian of Alberta and Idaho

description: This report documents the last pteraspids, (armored, jawless members of
 the Heterostraci), which are otherwise only known from the Early Devonian
 of the Old Red Sandstone Continent. Tuberculate pteraspid heterostracans
 are described from the Middle Devonian beds of two formations in western
 North America. The late Givetian Yahatinda Formation of Alberta and
 British Columbia consists of channels cut into lower Paleozoic rocks and
 represents deposition in marine to littoral environments. Clavulaspis
 finis new genus new combination, is redescribed from additional material
 from the Yahatinda Formation and renamed, as the original genus name has
 proved to be invalid.  The Eifelian Spring Mountain beds of Idaho
 consist of a large channel that represents a clastic dominated estuarine
 environment. It contains Scutellaspis wilsoni new genus new species, and
 the previously described species from the Spring Mountain beds is
 redescribed as Ecphymaspis idahoensis new genus new combination, prompted
 by new material and a review of the validity of the original genus name.
 Phylogenetic analysis shows that these three new taxa form part of the
 derived clade Protaspididae.
description: The dataset is derived from observations of new taxa and
 historical documents describing other species of Heterostraci. The matrix
 of characters and taxa was copied into a text file, translated into NEXUS
 and TNT files by Mesquite. The example TNT (*.tnt) and PAUP* (*.nex) files
 include basic commands for replicating the results.
description: Standard notations are used with '?' meaning no data is
 available to determine the transition state for the character for this
 species. A dash indicates that this entry is not applicable as the
 contingent state was not met in another field. See character lists and
 descriptions.
DOI: 10.5061/dryad.qbzkh18d9
title: Male harassment leads to fitness costs for females by disrupting oviposition site preferences

description: In many species, a difference in the optimal number of copulations for
 males and females leads to sexual conflict. This is well-documented in the
 bean beetle, Callosobruchus maculatus, where both sexes mate multiply and
 females incur fitness costs from injuries caused by the male genitalia.
 Here we demonstrate that sexual conflict also decreases female fitness due
 to male harassment. We hypothesized that harassment costs would come as
 (1) decreased clutch size, egg size, or both and by (2) disruption of
 female preference for higher quality oviposition substrate. 
 Mated females were housed with two bean types – cowpeas, their preferred
 natal hosts, and toxic pinto beans. They were then submitted to either no,
 moderate, or high male harassment in the oviposition site. Females under
 harassment produced smaller clutch sizes, but not smaller eggs, resulting
 in the absence of an egg size/clutch size tradeoff. Additionally, females
 did not exhibit a preference for their natal cowpeas hosts over toxic
 pinto beans when males were present at the oviposition site, although they
 do so when harassing males are not present. Harassment disrupted female
 responses to variation in oviposition substrate quality, resulting in
 considerable fitness consequences in the form of lower offspring
 production and survival.
DOI: 10.5061/dryad.rxwdbrv4j
title: Rapid evolution by sexual selection in a wild, invasive mammal

description: Sexual selection theory provides a framework for investigating the
 evolution of traits involved in attracting and competing for mates. We
 show that ecological factors can strongly influence the adaptive value of
 these traits, and changes to these factors can lead to rapid evolutionary
 change. We compared sexually selected traits in the small Indian mongoose
 (Urva auropunctata) between their sparsely-populated native range and four
 tropical islands to which they were introduced within the last 150 years
 and where, due to a lack of interspecific competition and predation, they
 have become invasive and densely populated. Because of a likely increase
 in encounter rate, we predicted that selection on long-distance chemical
 advertisement by males would relax in the introduced range. Accordingly,
 male, but not female, anal pads (used in scent marking) decreased in size
 in relation to both time since introduction and population density, and
 their relationship to body size and condition weakened. Concurrently, as
 predicted by intensified sperm competition, testis size increased
 following introduction. The small Indian mongoose thus experienced an
 inversion in the relative contributions to fitness of two sexual traits,
 followed by their rapid evolution in line with ecological changes.
description: Missing values (i.e., blank cells) are primarily due to either a)
 measurements for that particular morphological trait were not collected in
 that location, or b) the specific animal was missing the measured
 trait.
DOI: 10.15468/dl.yqy3z6
title: Occurrence Download

description: A dataset containing 3698 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Retropinna retropinna",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 3698 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002154-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tu3rze
title: Occurrence Download

description: A dataset containing 9458 records in GBIF matching the query:
SELECT
 '422' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 37.42857426825602
 AND decimalLatitude &lt;= 41.89415215079384
 AND decimalLongitude &gt;= 109.37183140870387
 AND decimalLongitude &lt;= 119.88149504725064
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 9458 records were derived from 101 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002132-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.4qrfj6q6g
title: Evaluating the role of predatory fish controlling the invasion of the Asian golden mussel (Limnoperna fortunei) in a subtropical river

description: 1. The invasive Asian golden mussel (Limnoperna fortunei) is continuously
 expanding through South America, altering the aquatic ecosystem structure
 and functioning. While several native fish species predate on this mussel,
 these interactions, and their consequences for the food web, have not been
 studied in depth. 2. We combine a survey of the fish assemblage trophic
 structure using gut contents and stable isotope analysis with an in situ
 exclusion experiment in order to: (i) determine the main fish species
 predating on L. fortunei; (ii) estimate the contribution of L. fortunei to
 the biomass of fish assemblage; and (iii) evaluate the role of fish on the
 density and maximum shell length of L. fortunei in the lower Uruguay River
 (the Río de La Plata Basin). 3. We found that about one-third of the fish
 species in the assemblage (28 out of 81 species) consumed L. fortunei,
 which was an important food item (&gt;10% of the dietary volume and
 &gt;30% of frequency of occurrence) for 11 fish species. Stable
 isotope mixing models consistently suggested that &gt;14 % of the
 total biomass of the fish assemblage was derived directly from carbon
 derived from L. fortunei tissues. In addition, the exclusion experiment
 demonstrated that fish predation reduces the mussel density by ca. 70% and
 the mussel maximum shell length by ca. 40%. 4. Synthesis and Applications.
 Our research suggests a top-down effect of fish on the mussel’s abundance,
 highlighting the need to preserve the fish communities of Uruguay River,
 where migratory fish are of key relevance. In the light of these findings,
 actions such as implementing efficient fish passage technologies in the
 actual (and projected) dams of the Uruguay River basin become essential to
 avoid local extinctions of these natural controls of the invasion upstream
 of the dams.10-Jan-2020
DOI: 10.5061/dryad.6hdr7sqwr
title: Enhanced Heterogenous Hydration of SO2 Through Immobilization of Pyridinic-N on Carbon Materials

description: Carbon materials doped with nitrogen has long been utilized for SO2
 removal from flue gases for the benefits of environment. The role of water
 is generally regarded as hydration of SO3 which is formed through the
 oxidization of SO2. However, the hydrolysis of SO2, especially on the
 surface of N doped carbon materials, was almost ignored. In this study,
 the hydrolysis of SO2 was investigated in detail on the pyridinic nitrogen
 (PyN) doped graphene (GP) surfaces. It is found that, compared to the
 homogenous hydrolysis of SO2 assisted with NH3 in gas phase, the
 heterogeneous hydrolysis is much more thermodynamically and kinetically
 favorable. Specifically, when a single H2O molecule is involved, the
 energy barrier for SO2 hydrolysis is as low as 0.15 eV, with 0.59 eV
 released, indicating the hydrolysis of SO2 can occur at rather low water
 concentration and temperature. Thermodynamic integration molecular
 dynamics results show the feasibility of the hydrogenated substrate
 recovery and the immobilized N acting as a catalytic site for SO2
 hydrolysis. Our findings show that the heterogeneous hydrolysis of SO2
 should be universal and potentially uncover the puzzling reaction
 mechanism for SO2 catalytic oxidation at low temperature by N doped carbon
 materials.
DOI: 10.5061/dryad.v9s4mw6r9
title: Unexpectedly diverse forest dung beetle communities in degraded rainforest landscapes in Madagascar

description: Tropical forests, which harbor high levels of biodiversity, are being lost
 at an alarming speed. Madagascar, a biodiversity hotspot, has lost more
 than half of its original forest cover. Most of the remaining forests are
 small fragments of primary and secondary forest with differing degrees of
 human impact. These forests, as well as coffee and fruit plantations, may
 be important in supporting the forest dependent biodiversity in Madagascar
 but this has been little studied. In Madagascar dung beetles, which offer
 important ecosystem services, are largely restricted to forests. We
 examined the ability of fragmented and degraded forests to support dung
 beetle diversity, compared to the large areas of primary forest in eastern
 Madagascar. We found a general trend of a reduction of species with a loss
 of forest connectivity. In contrast, a higher level of forest disturbance
 was associated with higher species diversity. In several sites of
 low-quality forest as many or more species were found as in less disturbed
 and primary forests. The average size of dung beetles was smaller in the
 lower quality localities than in the primary forests. These findings
 suggest that many forest dung beetles in Madagascar are better adapted to
 forest disturbance than earlier expected, although they require some level
 of connectivity to surrounding forest.
DOI: 10.6084/m9.figshare.31162471
title: VESM source data

description: Source data for reproducing the results in the manuscript <b>VESM: Compressing the collective knowledge of ESM into a single protein language model</b> by <i>Tuan Dinh, Seon-Kyeong Jang, Noah Zaitlen and Vasilis Ntranos.</i>
DOI: 10.6084/m9.figshare.31162471.v1
title: VESM source data

description: Source data for reproducing the results in the manuscript <b>VESM: Compressing the collective knowledge of ESM into a single protein language model</b> by <i>Tuan Dinh, Seon-Kyeong Jang, Noah Zaitlen and Vasilis Ntranos.</i>
DOI: 10.6084/m9.figshare.31162471.v2
title: VESM source data

description: Source data for reproducing the results in the manuscript <b>VESM: Compressing the collective knowledge of ESM into a single protein language model</b> by <i>Tuan Dinh, Seon-Kyeong Jang, Noah Zaitlen and Vasilis Ntranos.</i>
DOI: 10.5281/zenodo.18394540
title: EASTERN IMAGERY IN EIGHTEENTH-CENTURY ENGLISH POETRY

description: The eighteenth century witnessed a significant expansion of English literary engagement with the East, particularly in poetry, where Oriental imagery became a powerful aesthetic, philosophical, and symbolic resource. This article examines the representation and function of Eastern motifs in the poetry of Thomas Gray, William Collins, and selected contemporaries, situating their work within the broader cultural context of Enlightenment curiosity, imperial expansion, and early Orientalist discourse. Through close textual analysis, the study explores how Eastern imagery was employed not merely as exotic ornamentation, but as a means of interrogating emotion, imagination, morality, and the limits of rationalism. By drawing on Persian, Arabic, and Asian symbolic traditions—often filtered through translations, travel literature, and classical analogies—eighteenth-century poets reshaped English poetic language and sensibility. The article argues that Oriental imagery in this period functioned as a transitional aesthetic bridge between neoclassical restraint and Romantic emotional depth, contributing to the evolution of English poetic forms and themes.
DOI: 10.5061/dryad.05qfttdzr
title: Plant carbohydrate-active enzymes in bamboo (Neosinocalamus affinis): identification, classification and function in lignocellulose biosynthesis in herbivore defence

description: Neosinocalamus affinis, a type of cluster bamboo, is a good
 candidate feedstock for biomass energy. In the study, we found a total of
 686 genes were identified as belonging to CAZyme families in the
 N. affinis transcriptome, including 222 glycoside hydrolases
 (GHs), 288 glycosyltransferases (GTs), 64 carbohydrate esterases (CEs), 70
 auxiliary activities (AAs), 37 carbohydrate binding modules (CBMs) and
 five polysaccharide lyases (PLs). Expression profiles revealed that
 several CAZyme genes were up-regulated after insect infestation,
 particularly the GT, GH, AA and CE family members. Lignocellulose assays
 showed that the contents of three components, cellulose, hemicellulose and
 lignin, increased after insect infestation. Our findings showed that
 CAZyme genes were abundant in the N. affinis transcriptome and
 were involved in the response to herbivory. These findings could be
 applied to protect bamboo against herbivores, such as the bamboo snout
 beetle Cyrtotrachelus buqueti, and develop low-cost chemical feedstock
 from bamboo.
description: <b>Transcriptome data from
 </b><b><i>Neosinocalamus
 affinis</i></b><b> and CAZyme family
 analysis</b> The<i> N. affinis</i> transcriptome data were retrieved from the National Center for Biotechnology Information (NCBI) database Sequence Read Archive (SRA; BioProject PRJNA396472), accessed through the accession number SRX3051434 using NCBI (https://www.ncbi.nlm.nih.gov/) and focused on CAZyme genes. To identify CAZyme genes, coding sequences of all the assembled unigenes were submitted for local BLASTx search using the dbCAN CAZyme annotation algorithm, which provides the hidden Markov model index files of various carbohydrate enzyme domains by hmmscan,<sup>16</sup> with an E-value cutoff of 1E−5. <b>Phylogenetic analysis of the </b><b>CAZymes</b> ClustalX 2.1 program and DNAMAN software version 8.0 (Lynnon Biosoft) were used to align CAZyme protein sequences with default parameters. The MEGA 7.0 program<sup>17</sup> was used to establish a tree between <i>N. affinis</i> and <i>A.</i><i> thaliana</i> to survey the phylogenetic relationships using the Neighbor-Joining method with 1000 bootstrap replicates.