cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.wm37pvmnm
title: Immigration credit of temperate forest herbs in fragmented landscapes – implications for restoration of habitat connectivity

description: 1. In many agricultural landscapes, it is important to restore networks of
 forests to provide habitat and stepping stones for forest specialist taxa.
 More knowledge is, however, needed on how to facilitate the immigration of
 such taxa in restored forest patches. Here, we present the first
 chronosequence study to quantify the dynamics of immigration credits of
 forest specialist plants in post-arable forest patches. 2. We studied the
 distribution of herbaceous forest specialist plant species in 54
 post-arable broadleaved forest patches along gradients of age (20-140
 years since forest establishment), distance from ancient forest (0-2600 m)
 and patch area (0.5-9.6 ha). With Linear Mixed Models we estimated the
 effects of these factors on species richness, patch means of four
 dispersal-related plant traits and with Generalized Linear Models on the
 occurrence of 20 individual species. 3. Post-arable forest patch age and
 spatial isolation from ancient forest, but not patch size, were important
 predictors for species richness of forest specialists, suggesting that
 also small patches are valuable for habitat connectivity. Compared to
 species richness in ancient forest stands, the immigration credit was
 reduced by more than 90% after 80 years in post-arable forest patches
 contiguous to ancient forest compared to 40% after 80 years and 60% after
 140 years in isolated patches (at least 100 m to next forest).
 Tall-growing species with adaptations to long-distance dispersal were
 faster colonizers while species with heavy diaspores and clonal growth
 were slower to colonize. 4. Synthesis and applications: We show that
 post-arable oak plantations have a high potential for restoration of
 forest herb vegetation. Dispersal-related plant traits play a key role in
 explaining interspecific differences among forest specialists. To
 facilitate forest herb immigration across all functional groups in
 agricultural landscapes, we suggest to create clusters of relatively small
 new forest patches nearby older forest with source populations.
description: The data on the vascular plant flora were collected by the first
 author during field inventories between the years 2002 and 2018. Details
 on the inventories and collection of other data are given in the paper and
 the Supporting Information files.
description: Data on soil pH are missing for several post-arable forest
 patches. The missing values are indicated by n/a in excel file 1. However,
 soil pH was only used in preliminary data analysis and not in the final
 models.
DOI: 10.5061/dryad.6djh9w11q
title: Ancestral sperm ecotypes reveal multiple invasions of a non-native fish in northern Europe

description: For externally fertilising organisms in the aquatic environment, the
 abiotic fertilisation medium can be a strong selecting force. Among bony
 fishes, sperm are adapted to function in a narrow salinity range. A
 notable exception is the family Gobiidae, where several species reproduce
 across a wide salinity range. The family also contains several wide-spread
 invasive species. To better understand how these fishes tolerate such
 varying conditions, we measured sperm performance in relation to salinity
 from a freshwater and a brackish population within their ancestral
 Ponto-Caspian region of the round goby, Neogobius melanostomus. These two
 ancestral populations were then compared to nine additional invaded sites
 across northern Europe, both in terms of their sperm traits and by using
 genomic SNP markers. Our results show clear patterns of ancestral
 adaptations to freshwater and brackish salinities in their sperm
 performance. Population genomic analyses show that the ancestral ecotypes
 have generally established themselves in environments that fit their sperm
 adaptations. Sites close to ports with intense shipping show that both
 outbreeding and admixture can affect the sperm performance of a population
 in a given salinity. Rapid adaptation to local conditions is also
 supported at some sites. Historical and contemporary evolution in the
 traits of the round goby sperm cells is tightly linked to the population
 and seascape genomics as well as biogeographic processes in these invasive
 fishes. Since the risk of a population establishing in an area is related
 to the genotype by environment match, port connectivity and the ancestry
 of the round goby population can likely be useful for predicting the
 species spread.
description: See associated study for details.
description: See readme file and associated study for details.
DOI: 10.5061/dryad.jdfn2z3bm
title: Supplemental information for: Annual tropical-rainforest productivity through two decades: Complex responses to climatic factors, CO2 and storm damage

description: The supplemental files in this deposition contribute additional
 information useful for understanding the analyses in the associated
 manuscript.  Two files contain the annual (CARBONO Project
 measurement-year) data for productivity and for environmental conditions
 that were analyzed in the paper.  The annual productivity metrics
 were derived from the CARBONO Project litterfall and tree-growth data that
 were provided and documented in prior Dryad data depositions.  A
 third file in this deposition provides the daily data underlying the
 analyzed meteorological factors. The fourth file lists the standardized
 set of 66 test models that were used to test each of the five productivity
 metrics for environmental responses.  The fifth file is an
 auxiliary table documenting tree mortality by year. The included README
 file documents the information in these files.
description: The methods used to produce the productivity and soil-moisture
 and tree mortality and growth data were detailed in the respective prior
 CARBONO Project data depositions.  The daily climatic data were based on
 data generated by the Organization for Tropical Studies’ meteorological
 station at the La Selva Biological Station.  D.A. Clark screened and where
 necessary gap-filled the climatic records, using cross-record regressions
 (e.g., manual vs. automated temperature or rainfall data).  The
 calculations of the daily and yearly climatic metrics are detailed in the
 accompanying README file. 
description: The metrics in this supplemental information are explained and
 documented in the accompanying README file.
DOI: 10.5061/dryad.k3j9kd57q
title: Data used in the study: Sinking Slab Stress and Seismo-tectonics of the Indo-Burmese Arc: A Reappraisal

description: Differing views on the north-eastern Indian plate subduction and its
 seismic potential place the subduction process as a relict, ceased,
 creeping, or fully locked, challenging the seismic hazard uncertainty
 estimates of Indo-Burmese Arc (IBA) at either extreme. To clear some of
 these contentions, we re-examine the state of the IBA stress field using
 available earthquake faulting mechanism solutions. Our stress inversion
 results underline the tectonic complexity and emphasize that the stress of
 this subduction is primarily driven by the northward oblique motion of the
 Indian Plate. Models highlight the presence of the least compressive
 stresses as the margin-normal component all along the shallow sinking
 slab. Furthermore, solutions link the shallow strike-slip earthquakes with
 the lateral slab shear due to oblique slip-partitioning. Spatial
 variations in the Indian slab stress field indicate higher margin-parallel
 compression at the Naga versus the Chin and Rakhaine-Arakan segments,
 implying resistance to the northward motion of India, illuminating the
 buttressing effects on IBA. Models also depict active ∼E-W shortening
 across the Kabaw fault. Inversion solutions bring out a higher
 compressional environment towards the south, along the Sagaing Fault.
 Finally, based on the overall stress field variations, we speculate that
 the Rakhine Bangladesh Megathrust could be a low-stress forearc, as across
 the arc interacting stress fields are weak, capable of generating
 megathrust ruptures with long replenishment intervals. Due to the spatial
 stress field variations and buttressing effects, the interface may also
 exhibit a variable rupture mode.
DOI: 10.5061/dryad.cfxpnvx5n
title: Intercontinental dispersal and whole‐genome duplication contribute to loss of self‐incompatibility in a polyploid complex

description: Premise of the Study Angiosperm species often shift from
 self-incompatibility to self-compatibility following population
 bottlenecks. Across the range of a species, population bottlenecks may
 result from multiple factors, each of which may affect the geographic
 distribution and magnitude of mating-system shifts. We describe how
 intercontinental dispersal and genome duplication facilitate loss of
 self-incompatibility. Methods Self and outcross pollinations were
 performed on plants from 24 populations of the Campanula rotundifolia
 polyploid complex. Populations spanned the geographic distribution and
 three dominant cytotypes of the species (diploid, tetraploid, hexaploid).
 Key Results Loss of self-incompatibility was associated with both
 intercontinental dispersal and genome duplication. European plants were
 largely self-incompatible, whereas North American plants were
 intermediately to fully self-compatible. Within both European and North
 American populations, loss of self-incompatibility increased as ploidy
 increased. Ploidy change and intercontinental dispersal both contributed
 to loss of self-incompatibility in North America, but range expansion did
 not affect self-incompatibility within Europe or North America.
 Conclusions When species are subject to population bottlenecks arising
 through multiple factors, each factor can contribute to
 self-incompatibility loss. In a widespread polyploid complex, the loss of
 self-incompatibility can be predicted by the cumulative effects of
 whole-genome duplication and intercontinental dispersal.
description: We performed paired (i.e. both performed on the same maternal
 plant) self- and outcrosses on a series of Campanula rotundifolia plants
 from 24 populations across the European and North American ranges. Each
 pair was then used to calculate a ratio of selfed seed to outcrossed seed,
 which was in turn used to calculate an Index of Self-Incompatibility
 (1-ratio). We also assigned the ploidy level and location (Europe vs.
 North America) as discrete values. We then calculated
 the linear distance from each population to a hypothesized origin in the
 Czech Republic. While it is now suspected that the origin is farther south
 (which was determined after the publication of this paper), that
 difference does not change the outcome of the analyses in this
 paper. The dataset included here contains the following
 data columns: Population ID (which corresponds to the supplemental data
 file), Ploidy (2X, 4X, or 6X), Continent (1 = Europe, 2 = North America),
 Distance from origin (km), Selfed_seed
 (number of selfed seed), Outcrossed_seed (number of outcrossed), and Ratio (self/out).              
description: The population numbers referred to in the dataset are listed in
 the supplemental file available on the AJB website for this article.
 Localities and coordinates are available there.
DOI: 10.5061/dryad.8w9ghx3mw
title: Histology, TNF-alpha, and collagen score, body weight, and ulcer size

description: Background: Areca nut (Areca catechu L.) is the seed of the fruit of the
 oriental palm that is commonly used among Southeast Asian communities.
 Chrysanthemum (Dendrathema grandiflora) is a flowering plant originating
 from East Asia and dominantly grows in China. Both of these plants have
 strong antioxidant activities. To investigate the mechanism of their wound
 healing activities, we prepared areca nut and chrysanthemum polyethylene
 oral gel and performed several in vivo assays using Sprague-Dawley rats.
 Methods:  Sprague Dawley rats were divided into five groups:
 Negative control group (rats with base gel treatment), positive control
 group (rats treated with triamcinolone acetonide), F1 (treatment with 20%
 areca nut:80% chrysanthemum), F2 (treatment with 50% areca nut:50%
 chrysanthemum), and F3 (treatment with 80% areca nut:20% chrysanthemum).
 Traumatic ulcers were performed on the buccal mucosa of all experimental
 animals that received topical oral gel and triamcinolone acetonide twice a
 day for seven days. The clinical and histological characteristics were
 analyzed and scored. Results: During the six days, the ulcerated area
 receded linearly over time and was completely cicatrized in F2 and
 positive control group (Dependent t-test, p&lt;0.05). There were a
 significant increase in body weight in F2 and positive control groups.
 There were no significant differences between groups in histology
 examination (Kruskal Wallis test, p&lt;0.05). The moderate score of
 TNF-α levels was seen in F2 and positive control groups (ANOVA/Tukey
 test). Similar results were seen in the collagenases assay. Conclusions: A
 balanced combination of areca nut and chrysanthemum extract in the oral
 gel can optimize the healing of traumatic oral ulcers in rats through the
 increase of TNF-α and collagen deposition.
description: The data set was collected from the biopsy of the ulceration on
 buccal mucosa of Sprague-Dawley rats that have been treated with areca nut
 and chrysan oral gel.  The histology characteristics,
 TNF-alpha, and collagen scores were analyzed according to ulcer phase. The
 body weights were measured by digital scale. The oral ulcers were measured
 by digital calliper.
description: There are no missing values.
DOI: 10.25338/b86d27
title: Drosophila enhancer adult bristle expression assay using UAS sv-RNAi

description: Data from manuscript "Sex-specific evolution of a Drosophila sensory
 system via interacting cis- and trans-regulatory changes" by D
 Luecke, G Rice, and A Kopp. This study examines the regulation of
 expression for the chemosensory bristle specifier gene
 Pox neuro, which has expanded expression into ancestrally mechanosensory
 bristles in male D. prolongata. Flourescent assays show
 qualitativetly expanded expression driven by the D.
 prolongata allele relative to enhancers from sister species in
 the developing pupal leg. Adult bristle disruption assays
 using shavenoid RNAi show
 quantitative expression expansion by the D.
 prolongata allele into specific mechanosensory bristles on the
 dorso-anterior leg of the first tarsi.
description: <em>Pox neuro</em> enhacer regions were cloned into
 Gal4 reporter vector pBPGUw and inserted site-specifically into the attP2
 docking site. Homozygous reporter-Gal4 flies were crossed to UAS-dcr2;
 UAS-svRNAi flies. T1 legs from the F1 of this cross were mounted in PVA
 clearing media and examined under light microscopy. Individual bristles
 were scored as 0 for missing, 0.5 for truncated, and 1 for
 intact. Comparisons between number of effected bristle per species
 enhancer allele were done by pairwise t test, with bonferonni correction
 for multiple tests.
description: Bristle identities are based on the included first tarsus
 diagram, modified from Tokunagu 1962. Missing values represent intact
 bristles, and are treated as such (1s) by the accompanying
 R script.
DOI: 10.5061/dryad.70rxwdbxz
title: Behavioural change during dispersal and its relationship to survival and reproduction in a cooperative breeder

description: (1) The ability of dispersing individuals to adjust their behaviour to
 changing conditions is instrumental in overcoming challenges and reducing
 dispersal costs, consequently increasing overall dispersal success.
 Understanding how dispersers’ behaviour and physiology change during the
 dispersal process, and how they differ from resident individuals, can shed
 light on the mechanisms by which dispersers increase survival and maximise
 reproduction. (2) By analysing individual behaviour and concentrations of
 faecal glucocorticoid metabolites (fGCM), a stress-associated biomarker,
 we sought to identify the proximate causes behind differences in survival
 and reproduction between dispersing and resident meerkats (Suricata
 suricatta). (3) We used data collected on 67 dispersing and 108 resident
 females to investigate (i) which individual, social, and environmental
 factors are correlated to foraging and vigilance, and whether the role of
 such factors differs among dispersal phases, and between dispersers and
 residents; (ii) how time allocated to either foraging or vigilance
 correlated to survival in dispersers and residents; and (iii) the link
 between aggression and change in fGCM concentration, and their
 relationship with reproductive rates in dispersing groups and resident
 groups with either long-established or newly established dominant females.
 (4) Time allocated to foraging increased across dispersal phases, while
 time allocated to vigilance decreased. Time allocated to foraging and
 vigilance correlated positively, and negatively respectively, with
 dispersers’ group size. We did not find a group size effect for residents.
 High proportions of time allocated to foraging correlated with high
 survival, and more so in dispersers, suggesting that maintaining good
 physical condition may reduce mortality during dispersal. Further, while
 subordinate individuals rarely reproduced in resident groups, the
 conception rate of subordinates in newly formed dispersing groups was
 equal to that of their dominant individuals. Mirroring conception rates,
 in resident groups, fGCM concentrations were lower in subordinates than in
 dominants, whereas in disperser groups, fGCM concentrations did not differ
 between subordinates and dominants. (5) Our results, which highlight the
 relationship between behavioural and physiological factors and demographic
 rates, provide insights into some of the mechanisms that individuals of a
 cooperative species can use to increase overall dispersal success.
DOI: 10.5281/zenodo.18391002
title: Dataset for climate-driven LSTM-SIR Modeling of dengue transmission in Guangdong, China (2016-2024)

description: This dataset contains the processed time-series data used to drive and validate the LSTM - SIR hybrid model in a study on dengue transmission dynamics. It comprises monthly dengue case counts and aggregated daily meteorological variables(maximum, mean, and minimum temperature, precipitation, and relative humidity) at the provincial level for Guangdong, China, along with quantified indicators of non-pharmaceutical intervention (NPI) intensity. The collection further incorporates semi - monthly Aedes mosquito surveillance data and corresponding daily meteorological variables from ten prefecture - level cities in the Province.
DOI: 10.5281/zenodo.18391003
title: Dataset for climate-driven LSTM-SIR Modeling of dengue transmission in Guangdong, China (2016-2024)

description: This dataset contains the processed time-series data used to drive and validate the LSTM - SIR hybrid model in a study on dengue transmission dynamics. It comprises monthly dengue case counts and aggregated daily meteorological variables(maximum, mean, and minimum temperature, precipitation, and relative humidity) at the provincial level for Guangdong, China, along with quantified indicators of non-pharmaceutical intervention (NPI) intensity. The collection further incorporates semi - monthly Aedes mosquito surveillance data and corresponding daily meteorological variables from ten prefecture - level cities in the Province.
DOI: 10.5061/dryad.hqbzkh1gp
title: Effects of glaciation and whole genome duplication on the distribution of the Campanula rotundifolia polyploid complex

description: Premise Of The Study Both intrinsic and extrinsic factors contribute to a
 species distribution. Among plants, the extrinsic effects of glaciation
 and intrinsic effects of whole genome duplication are powerful drivers of
 biogeographical patterns, but the interplay of these factors is poorly
 understood. Here, we investigate the roles glaciation and whole-genome
 duplication have played in the evolution of the widespread polyploid
 complex Campanula rotundifolia. Methods We assessed the cytotype of 37
 populations that spanned the geographic and cytotypic range of the C.
 rotundifolia complex. We constructed a chloroplast phylogeny for these
 populations and used RAD-seq to create nuclear phylogenies and networks
 for a subset of 23 populations; and estimated divergence times of major
 clades using Bayesian estimation of substitution rates. Key Results
 Campanula rotundifolia originated in south-central Europe and underwent
 range expansion throughout much of Europe and North America. Multiple
 genome duplications have occurred in C. rotundifolia—at least two
 tetraploid and three hexaploid formations. Conclusions Nuclear and
 chloroplast phylogenies are largely congruent with a history of
 populations surviving glacial maxima in known Pleistocene refugia in
 Europe and North America. Divergent European clades are consistent with
 two disjunct glacial refugia within Europe. North America was colonized by
 hexaploids derived from Western European lineages. A glacial refugium in
 Midwestern North America likely facilitated post-glacial recolonization of
 North America and limited genetic divergence. These results implicate both
 glaciation and whole-genome duplication as contributing factors to the
 extant biogeography of C. rotundifolia.
description: This dataset consists of two DNA sequence alignments, one nuclear
 sdRAD DNA, one chloroplast DNA. All individual sequences are also archived
 in NCBI. Nuclear RADseq sequences are in the SRA archive (Accession
 SRP151156) and chloroplast sequences are in GenBank (Accessions: MH509220
 – MH509381). RADseq data was generated for 26 pooled populations (6-10
 individuals / population) using the SacI restriction enzyme and sequenced
 on an Illumina HiSeq 2500. Chloroplast sequences were generated using
 Sanger sequencing for up to three individuals per 37 populations.
 Chloroplast sequences were aligned using CodonCode Aligner and proofread
 by hand. RADseq sequences were first screened using Stacks for SNPs that
 varied between populations but were fixed within populations, because we
 sequenced pooled data. These retained reads were than concatenated into
 one sequence by population and aligned.
description: If others wish to perform their own alignments, the individual
 reads are available on NCBI (Accessions MH509220 – MH509381).
DOI: 10.5061/dryad.j6q573nf5
title: Cost-effective library preparation for whole genome sequencing with feather DNA

description: Samples from avian species of high conservation concern are often low in
 total genomic DNA (gDNA).  Feathers are collected more frequently
 than blood, yet they contain low total gDNA which can present challenges
 in using them for genomics. Whole Genome Sequencing (WGS) can provide many
 insights that can be used to aid in species conservation, but current
 methods for working with feathers are cost prohibitive for population
 level genomic analyses.  Thus, there is a need for a
 cost-effective method of preparing WGS libraries from feathers. To bridge
 the gap between sampling techniques commonly used in avian conservation
 genetics that yield low total gDNA and the powerful tool of WGS, we
 developed a method that successfully produces WGS libraries from feather
 gDNA with as low input as 0.48 ng of DNA and an average final library size
 of 300-500 base pairs.  Sequencing results suggest high
 sequencing quality using our protocol with feather DNA.  We
 conclude that our method will facilitate high-throughput WGS on low total
 gDNA samples, like feathers, thus expanding the power of genomic tools in
 critical avian conservation research.
description:  See manuscript for modified method for library preparation of
 samples.
description: The BAM files are binary files of the Sequence Alignment/Map
 format for sequence data. The BAM files can be viewed and analyzed with
 open-source software such as Samtools (http://www.htslib.org/) and Picard Tools (https://broadinstitute.github.io/picard/).