cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0gb5mkkzv
title: Indirect comparison between immunotherapy alone and immunotherapy plus chemotherapy as first-line treatment for advanced non-small cell lung cancer: A systematic review

description: Objectives: Use of immune checkpoint inhibitors (ICIs) as first-line
 treatment for advanced (stage IIIB/IV) non-small cell lung cancer (NSCLC)
 remains controversial. Clinical trials comparing single-drug immunotherapy
 (IO) with immunotherapy plus chemotherapy (IC) are lacking. We aimed to
 compare the efficacy of IO alone with that of IC as first-line treatment
 for advanced NSCLC. Design: Systematic review Data sources: PubMed, the
 Cochrane Library, and Embase for related studies on NSCLC;
 ClinicalTrials.gov, American Society of Clinical Oncology Meeting Library,
 and World Conference on Lung Cancer for relevant conference abstracts.
 Eligibility criteria: Articles meeting the following criteria were
 selected: (1) randomized controlled trials on NSCLC treatment, (2) all
 individuals in the studies had not received treatment previously, and (3)
 research on IO monotherapy using programmed death-1/programmed death
 ligand-1 (PD-L1) inhibitors or IC. Data extraction and synthesis: After
 reading the original literature, two reviewers independently extracted the
 relevant information. The primary outcomes were progression-free survival
 (PFS), overall survival (OS), and objective response rate (ORR). We also
 extracted data on treatment-related adverse events and immune-related
 adverse events (irAEs). Results: Overall, 10 randomized controlled
 clinical trials (n = 5765) were included. As first-line treatment for
 advanced NSCLC, IC tended to yield better PFS, OS, and ORR than did IO.
 Furthermore, IC yielded significantly better PFS than IO when tumor PD-L1
 expression was at least 50% (HR: 1.81, 95% CI: 1.18–2.78) and yielded a
 better OS and PFS when tumor PD-L1 expression was at least 1%; IO resulted
 in fewer adverse events than did IC. However, the incidence of irAEs was
 higher for IO than for IC. Conclusions: The findings of the indirect
 comparison indicate that IC as first-line treatment for advanced NSCLC is
 significantly more effective than IO in patients with PD-L1 expression in
 at least 50% of tumor cells.
DOI: 10.5061/dryad.gqnk98skd
title: Water stress and insect herbivory interactively reduce crop yield while the insect pollination benefit is conserved

description: Climate change is predicted to hamper crop production due to precipitation
 deficits and warmer temperatures inducing both water stress and increasing
 herbivory due to more abundant insect pests. Consequently, crop yields
 will be impacted simultaneously by abiotic and biotic stressors. Extensive
 yield losses due to such climate change stressors might, however, be
 mitigated by ecosystem services such as insect pollination. We examined
 the single and combined effects of water stress, insect herbivory and
 insect pollination on faba bean yield components and above- and
 belowground plant biomass under realistic field conditions. We used
 rainout shelters to simulate a scenario in line with climate change
 projections, with adequate water supply at sowing followed by a long
 period without precipitation. This induced a gradually increasing water
 stress, culminating around crop flowering and yield formation. We found
 that gradually increasing water stress combined with insect herbivory by
 aphids interactively shaped yield in faba beans. Individually, aphid
 herbivory reduced yield by 79 % and water stress reduced yield by 52 %.
 However, the combined effect of water stress and aphid herbivory reduced
 yield less (84 %) than the sum of the individual stressor effects. In
 contrast, insect pollination increased yield by 68 % independently of
 water availability and insect herbivory. Our results suggest that yield
 losses can be greatly reduced when both water stress and insect herbivory
 are reduced simultaneously. In contrast, reducing only one stressor has
 negligible benefits on yield as long as the crop is suffering from the
 other stressor. We call for further exploration of interactions among
 ecosystem services and biotic and abiotic stressors that simulate
 realistic conditions under climate change.
DOI: 10.5061/dryad.3xsj3txdz
title: Genetic differentiation and signatures of local adaptation revealed by RADseq for a highly-dispersive mud crab Scylla olivacea in the Sulu Sea

description: Connectivity of marine populations is shaped by complex interactions of
 biological and physical processes across the seascape. The influence of
 environmental features on the genetic structure of populations has key
 implications to the dynamics and persistence of populations, and an
 understanding of spatial scales and patterns of connectivity is crucial
 for management and conservation. This study employed a seascape genomics
 approach combining larval dispersal modeling and population genomic
 analysis using single nucleotide polymorphisms (SNPs) obtained from RADseq
 to examine environmental factors influencing patterns of genetic structure
 and connectivity for a highly-dispersive mud crab, Scylla olivacea
 (Herbst, 1796) in the Sulu Sea. Dispersal simulations reveal widespread
 but asymmetric larval dispersal influenced by persistent southward and
 westward surface circulation features in the Sulu Sea. Despite potential
 for widespread dispersal across the Sulu Sea, significant genetic
 differentiation was detected among eight populations based on 1,655 SNPs
 (FST  = 0.0057, p &lt; 0.001) and a subset of 1,643
 putatively neutral SNP markers (FST = 0.0042, p &lt; 0.001).
 Oceanography influences genetic structure, with redundancy analysis (RDA)
 indicating  significant contribution of asymmetric ocean currents
 to neutral genetic variation (R2adj = 0.133; p = 0.035). Genetic structure
 may also reflect demographic factors, with divergent populations
 characterized by low effective population sizes (Ne &lt; 50).
 Pronounced latitudinal genetic structure was recovered for loci putatively
 under selection (FST = 0.2390, p &lt; 0.001), significantly correlated
 with sea surface temperature variabilities during peak spawning months for
 S. olivacea (R2adj = 0.692-0.763; p &lt; 0.050), suggesting putative
 signatures of selection and local adaptation to thermal clines. While
 oceanography and dispersal ability likely shape patterns of gene flow and
 genetic structure of S. olivacea across the Sulu Sea, the impacts of
 genetic drift and natural selection influenced by sea surface temperature
 also appear as likely drivers of population genetic structure. 
 This study contributes to the growing body of literature documenting
 population genetic structure and local adaptation for highly-dispersive
 marine species, and provides information useful for spatial management of
 the fishery resource.
description: Samples were collected among eight localities in the Sulu Sea and
 two outgroup locations in the Philippines. 146 libraries were prepared
 using ddRAD sequencing. The dataset was processed through the STACKSv2.2
 pipeline and other SNP filtering methods in R.
description: One R script and three GENEPOP datasets are available: all
 markers (1655 SNPs), neutral-only (1,643 SNPs), and outlier loci-only (12
 SNPs).
DOI: 10.5061/dryad.g4f4qrfp1
title: Habitat use of co-occurring burying beetles (genus Nicrophorus) in southeastern Ontario, Canada

description: The coexistence of closely related species plays an important role in
 shaping local diversity. However, competition for shared resources can
 limit the ability of species to coexist. Many species avoid the costs of
 coexistence by diverging in habitat use, known as habitat partitioning. We
 examine patterns of habitat use in seven co-occurring species of burying
 beetles (genus Nicrophorus Fabricius, 1775), testing the hypothesis that
 Nicrophorus species partition resources by occupying distinct habitats. We
 surveyed Nicrophorus abundance and 54 habitat characteristics at 100
 random sites spanning an environmentally diverse region of southeastern
 Ontario, Canada. We found that three species occupied distinct habitat
 types consistent with habitat partitioning. Specifically, Nicrophorus
 pustulatus Herschel, 1807, Nicrophorus hebes Kirby, 1837, and Nicrophorus
 marginatus Fabricius, 1801 appear to be specialists for forest canopy,
 wetlands, and open fields, respectively. In contrast, Nicrophorus
 orbicollis Say, 1825, Nicrophorus sayi Laporte, 1840, and Nicrophorus
 tomentosus Weber, 1801 appear to be generalists with wide breadths of
 habitat use. We were unable to identify the habitat associations of
 Nicrophorus defodiens Mannerheim, 1846. Our findings are consistent with
 habitat acting as an important resource axis along which some Nicrophorus
 species partition; however, divergence along other resource axes (e.g.,
 temporal partitioning) also appears important for Nicrophorus coexistence.
description: Please see manuscript for details.
description: Please see ReadMe file for description of data.
DOI: 10.5061/dryad.80gb5mkpj
title: Data from: Functional genetic diversity in an exploited marine species and its relevance to fisheries management

description: The timing of reproduction influences key evolutionary and ecological
 processes in wild populations. Variation in reproductive timing may be an
 especially important evolutionary driver in the marine environment, where
 the high mobility of many species and few physical barriers to migration
 provide limited opportunities for spatial divergence to arise, and where
 many species synchronize their reproduction to seasonal cycles of
 planktonic productivity. Using genomic data collected from spawning
 aggregations of Pacific herring (Clupea pallasii) across 1,600 km of
 coastline, we show that reproductive timing drives population structure in
 these pelagic fish. Within a specific spawning season we observed
 isolation by distance, indicating that gene flow is limited over our study
 area. These results emphasize the importance of considering both seasonal
 and spatial variation in reproductive timing when delineating management
 units for Pacific herring. On several chromosomes we detected linkage
 disequilibrium extending over millions of base pairs, suggesting the
 presence of chromosomal rearrangements. The frequencies of putative
 chromosomal rearrangements differed between populations spawning at
 different times of year. Spawning phenology was highly correlated with
 polymorphisms in several genes, in particular SYNE2, which influences the
 development of retinal photoreceptors in vertebrates. SYNE2 is likely
 within a chromosomal rearrangement in Pacific herring and is also
 associated with spawn timing in Atlantic herring (Clupea harengus). The
 observed genetic diversity likely underlies resource waves provided by
 spawning herring and demonstrates how population-level genetic diversity
 can influence ecosystem processes. Given the ecological, economic, and
 cultural significance of herring, our results support that conserving
 intraspecific genetic diversity is important for maintaining current and
 future ecosystem processes.
description: This supplemental data set contains filtered genotypes in
 standard vcf file format for 1,104 herring collected from active spawning
 aggregations. Details on sample collection, laboratory work, and
 bioinformatic analyses can be found in the manuscript.
description: The genotype data are in standard vcf file format. Missing data
 are denoted by this character: ./.
DOI: 10.5061/dryad.crjdfn32s
title: Coregonus spp. opsin amplicon sequence alignments

description: Local adaptation can drive diversification of closely related species
 across environmental gradients and promote convergence of distantly
 related taxa that experience similar conditions. We examined a potential
 case of adaptation to novel visual environments in a species flock (Great
 Lakes salmonids, genus Coregonus) using a new amplicon genotyping protocol
 on the Oxford Nanopore Flongle. Five visual opsin genes were sequenced for
 individuals of C. artedi, C. hoyi, C. kiyi, and C. zenithicus. Comparisons
 revealed species-specific differences in a key spectral tuning amino acid
 in rhodopsin (Tyr261Phe substitution), suggesting local adaptation of C.
 kiyi to the blue-shifted depths of Lake Superior. Ancestral state
 reconstruction demonstrates that parallel evolution and “toggling” at this
 amino acid residue has occurred several times across the fish tree of
 life, resulting in identical changes to the visual systems of distantly
 related taxa across replicated environmental gradients. Our results
 suggest that ecological differences and local adaptation to distinct
 visual environments are strong drivers of both evolutionary parallelism
 and diversification.
description: Visual opsin genes from 18 <em>Coregonus artedi</em>,
 19 <em>C. hoyi</em>, 21 <i>C. kiyi</i>, and
 16 <em>C. zenithicus</em> were PCR amplified and sequenced
 using the Oxford Nanopore Flongle. Reads were aligned to version 1 of
 the <em>Coregonus</em> sp. 'balchen' assembly
 (De-Kayne et al. 2020) using bwa mem. Raw sequence data is deposited in
 SRA, under BioProject #PRJNA664981. Raw Sanger
 sequencing data is also included here, in .ab1 file formats. For each of
 13 samples, we sequenced a ~700 bp segment
 of <em>rhodopsin </em>using Sanger sequencing, to verify the
 results of our nanopore sequencing. These sequence files (both forward and
 reverse for each sample) are included here, in the format (SAMPLE
 ID)_RH_A_A_(Fwd/Rev).ab1. 
description: Alignments of reads are in BAM format, and are named according to
 the sample ID, which is also available on NCBI (BioProject
 #PRJNA664981) (i.e. CA01.bam is sample #
 of <em>Coregonus</em><em> artedi</em>). BAM index
 files (*.bam.bai) are also included.  A VCF file
 containing called SNPs for all samples is also included
 (FINAL_filtered_opsins.vcf). This file contains called SNPs for 80
 samples, 74 of which were used in the present study (these 74 sample names
 correspond to the names of the BAM files that are also included in this
 repository). The file has been filtered to remove genotype calls that were
 made at &lt;100x coverage, as this was the point at which genotyping
 was determined to be unreliable.
DOI: 10.5061/dryad.tmpg4f4wx
title: Biogeographic parallels in thermal tolerance and gene expression variation under temperature stress in a widespread bumble bee

description: Global temperature changes have emphasized the need to understand how
 species adapt to thermal stress across their ranges. Genetic mechanisms
 may contribute to variation in thermal tolerance, providing evidence for
 how organisms adapt to local environments. We determine physiological
 thermal limits and characterize genome-wide transcriptional changes at
 these limits in bumble bees using laboratory-reared Bombus
 vosnesenskii workers. We analyze bees reared from latitudinal
 (35.7–45.7°N) and altitudinal (7–2154 m) extremes of the species’
 range to correlate thermal tolerance and gene expression among populations
 from different climates. We find that critical thermal minima (CTMIN)
 exhibit strong associations with local minimums at the location of queen
 origin, while critical thermal maximum (CTMAX) was invariant among
 populations. Concordant patterns are apparent in gene expression data,
 with regional differentiation following cold exposure, and expression
 shifts invariant among populations under high temperatures. Furthermore,
 we identify several modules of co-expressed genes that tightly correlate
 with critical thermal limits and temperature at the region of origin. Our
 results reveal that local adaptation in thermal limits and gene expression
 may facilitate cold tolerance across a species range, whereas high
 temperature responses are likely constrained, both of which may have
 implications for climate change responses of bumble bees.
description: The datasets include read-count data generated by processing the
 raw poly-A amplified directional 50 bp paired-end RNAseq reads (see SRA
 accession below) using TrimGalore v0.4.2, aligning them to
 the <em>Bombus impatiens</em> genome v2.0 (BIMP2.0) with
 TopHat v2.1.1, and counting read alignments to the transcripts on a
 gene_name basis with HTSeq v0.9.1.  Also included
 are:  <em>Bombus
 impatiens</em> genome v2.0 (BIMP2.0) and <em>Drosophila
 melanogaster</em> (Release_6_plus_ISO1_MT) genomic.gff and
 protein.faa files for reciprocal best blast hit annotation.
 WorldClim data relevant to the samples
 Critical thermal test results Alignment
 results Pheontype tables for samples
 a <em>D. melanogaster </em>GO file for use in
 R Filtering files Analytical R
 scripts
description: To repeat the analyses in the paper, please go to the
 'Scripts' folder. Please run the following scripts in R in this
 order. In a new session:
 WCGNA_complete_script.R Close session (all relevant
 results will be saved) In a new
 session: Limma_BlockedAnalysis_complete_script.R In
 the same session: DGE_WCGNA.comparison.R
DOI: 10.5061/dryad.4qrfj6q88
title: Demographic responses to climate change in a threatened Arctic species

description: The Arctic is undergoing rapid and accelerating change in response to
 global warming, altering biodiversity patterns and ecosystem function
 across the region. For Arctic endemic species, our understanding of the
 consequences of such change remains limited. Spectacled eiders (Somateria
 fischeri), a large Arctic sea duck, use remote regions in the Bering Sea,
 Arctic Russia, and Alaska throughout the annual cycle making it difficult
 to conduct comprehensive surveys or demographic studies. Listed as
 Threatened under the U.S. Endangered Species Act, understanding the
 species response to climate change is critical for effective conservation
 policy and planning. Here, we developed an integrated population model to
 describe spectacled eider population dynamics using
 capture-mark-recapture, breeding population survey, nest survey, and
 environmental data collected between 1992 and 2014. Our intent was to
 estimate abundance, population growth, and demographic rates, and quantify
 how changes in the environment influenced population dynamics. Abundance
 of spectacled eiders breeding in western Alaska has increased since
 listing in 1993 and responded more strongly to annual variation in first
 year survival than adult survival or productivity. We found both adult
 survival and nest success were highest in years following intermediate sea
 ice conditions during the wintering period, and both demographic rates
 declined when sea ice conditions were above or below average. In recent
 years sea ice extent has reached new record lows and has remained below
 average throughout the winter for multiple years in a row. Sea ice
 persistence is expected to further decline in the Bering Sea. Our results
 indicate spectacled eiders may be vulnerable to climate change and the
 increasingly variable sea ice conditions throughout their wintering range
 with potentially deleterious effects on population dynamics. Importantly,
 we identified that different demographic rates responded similarly to
 changes in sea ice conditions, emphasizing the need for integrated
 analyses to understand population dynamics.
description: Data were collected through a number of different methods and
 collated here for analysis in an integrated population model. Field
 collection methods include aerial survey data (waterfowl breeding pair
 survey), nest plot survey, and capture-mark-recapture. Details on
 processing are available in the "read_me" sheet within the
 "spei_data" excel file and in the forthcoming manuscript.
 Additional files include ".RDS" for the capture-history and
 multi-state m-array based on capture-mark-recapture data. Two R files are
 included with the code to load the data, the jags model, and the code to
 fit the jags model.
description: The ".RDS" files are ready to use as-is in an analysis
 of capture-mark-recapture data with state-assignment details in the
 accompanying code. Data in the excel files require minimal manipulation
 which is documented in the accompanying code.
DOI: 10.5061/dryad.0zpc866w9
title: Data from: Ecological and social drivers of neighbor recognition and the dear enemy effect in a poison frog

description: Navigating social relationships frequently rests on the ability to
 recognize familiar individuals using phenotypic characteristics. Across
 diverse taxa, animals vary in their capacities for social recognition but
 the ecological and social sources of selection for recognition are often
 unclear. In a comparative study of two closely related species of poison
 frogs, we identified a species difference in social recognition of
 territory neighbors and investigated potential sources of selection
 underlying this difference. In response to acoustic playbacks, male golden
 rocket frogs (Anomaloglossus beebei) recognized the calls of neighbors and
 displayed a “dear enemy effect” by responding less aggressively to
 neighbors’ calls than strangers’ calls. In contrast, male Kai rocket frogs
 (Anomaloglossus kaiei) were equally aggressive to the calls of neighbors
 and strangers. This species difference in behavior is associated with key
 differences in reproductive ecology and characteristics of territories.
 Golden rocket frogs defend reproductive resources in the form of
 bromeliads, which is expected to create a threat asymmetry between
 neighbors and strangers favoring decreased aggression to neighbors. In
 contrast, Kai rocket frogs do not defend reproductive resources. Further,
 compared with Kai rocket frog territories, golden rocket frog territories
 occur at higher densities and are defended for longer periods of time,
 creating a more complex social environment with more opportunities for
 repeated but unnecessary aggression between neighbors, which should favor
 the ability to recognize and exhibit less aggression towards neighbors.
 These results suggest that differences in reproductive ecology can drive
 changes in social structure that select for social recognition.
description: These data were collected by James Tumulty in the field in
 Kaieteur National Park in Guyana. Included are data on aggressive
 thresholds of male golden rocket frogs (Anomaloglossus beebei) and Kai
 rocket frogs (Anomaloglossus kaiei) in response to acoustic playback
 experiments. Also included are spatial data from long term monitoring of
 territorial males of both species as well as egg clutches, tadpoles, and
 reproductive resources (bromeliads). Spatial data have been processed as
 described in the manuscript to produce home range estimates, nearest
 neighbor distances, and spatial associations between territorial males and
 egg clutches, tadpoles, and bromeliads. Additionally, simulated spatial
 association data are included.
description: Please see README files associated with each data set.