cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jdfn2z391
title: Data from: Climate warming prolongs the time interval between leaf-out and flowering in temperate trees: effects of chilling, forcing and photoperiod

description: 1. Leaf-out and flowering are two key phenological events of plants,
 denoting the respective onsets of visible vegetative growth and
 reproduction during the year. For each species, the schedule of vegetative
 growth and reproduction is crucial to the maximization of its fitness.
 Warming-induced advances of leaf-out and flowering have been reported
 frequently, however, it is unclear whether the responses of the two events
 are equal for any given species. 2. Using long-term phenological records
 in Europe, we examined simultaneously the responses of both leaf-out and
 flowering of four common temperate tree species to climate warming and
 further examined the effects of winter chilling, spring forcing and
 photoperiod on the responses of the two events. 3. We found that
 regardless whether flowering or leaf-out occurred first, the first event
 advanced more than the second during 1950 – 2013, resulting in a prolonged
 time interval between the two events. The temporal changes were also
 supported by a similar geographical trend that the time interval between
 the two events increased from cold to warm sites. Due to the
 warming-induced reduction in chilling, the spring forcing accumulated
 until the second event was increased more than the forcing accumulated
 until the first event, and that reduced the temperature sensitivity of the
 second event. In addition to the effect of chilling, the shorter
 photoperiod, associated with the advanced spring phenology, was also
 likely to substantially increase the spring forcing accumulated until the
 second event, which thus slowed down its advance, compared to the advance
 of the first event. The relative contributions of chilling and photoperiod
 to the increased forcing varied between species and events, with chilling
 mostly outweighing photoperiod. 4. Synthesis. This study provides the
 large-scale empirical evidence of prolonged time interval between leaf-out
 and flowering with climate warming. The unequal advances of the two events
 may alter the partition of resources between vegetative growth and
 reproduction and cause different changes of spring frost damage to
 vegetative and reproductive tissues, which may alter species fitness and
 further affect ecosystem structure and function.
DOI: 10.5061/dryad.83bk3j9q6
title: Integrative genomics of the mammalian alveolar macrophage response to intracellular mycobacteria: RNA-seq statistics and results

description: Background: Bovine TB (bTB), caused by infection
 with Mycobacterium bovis, is a major endemic disease affecting
 global cattle production. The key innate immune cell that first encounters
 the pathogen is the alveolar macrophage, previously shown to be
 substantially reprogrammed during intracellular infection by the
 pathogen. Here we use differential expression, and correlation- and
 interaction-based network approaches to analyse the host response to
 infection with M. bovis at the transcriptome level to
 identify core infection response pathways and gene modules. These outputs
 were then integrated with genome-wide association study (GWAS) data sets
 to enhance detection of genomic variants for susceptibility/resistance
 to M. bovis infection. Results: The host gene
 expression data consisted of RNA-seq data from bovine alveolar macrophages
 (bAM) infected with M. bovis at 24 and 48 hours
 post-infection (hpi) compared to non-infected control bAM. These RNA-seq
 data were analysed using three distinct computational pipelines to produce
 six separate gene sets: 1) DE genes filtered using stringent fold-change
 and P-value thresholds (DEG-24: 378 genes, DEG-48: 390 genes); 2)
 genes obtained from expression correlation networks (CON-24: 460 genes,
 CON-48: 416 genes); and 3) genes obtained from differential expression
 networks (DEN-24: 339 genes, DEN-48: 495 genes). These six gene sets were
 integrated with three bTB breed GWAS data sets by employing a new genomics
 data integration tool—gwinteR. Using GWAS summary statistics, this
 methodology enabled detection of 36, 102 and 921 prioritised SNPs for
 Charolais, Limousin and Holstein-Friesian, respectively.
 Conclusions: The results from the three parallel analyses showed
 that the three computational approaches could identify genes significantly
 enriched for SNPs associated with susceptibility/resistance to M.
 bovis infection. Results indicate distinct and significant
 overlap in SNP discovery, demonstrating that network-based integration of
 biologically relevant transcriptomics data can leverage substantial
 additional information from GWAS data sets. These analyses also
 demonstrated significant differences among breeds, with the
 Holstein-Friesian breed GWAS proving most useful for prioritising SNPS
 through data integration. Because the functional genomics data were
 generated using bAM from this population, this suggests that the genomic
 architecture of bTB resilience traits may be more breed-specific than
 previously assumed.
DOI: 10.5061/dryad.xksn02vdw
title: Seed size and capitulum position drive germination and dormancy responses to projected warming for the threatened dune endemic Cirsium pitcheri (Asteraceae)

description: Among coastal plant species at risk from rapid environmental changes is
 the North American Great Lakes dune endemic Cirsium pitcheri. Despite
 being listed as federally threatened, little is known about how C.
 pitcheri seed attributes influence germination and dormancy-break patterns
 in the context of climate change. Following a previous work where we found
 differences in the number and weight of C. pitcheri seeds among capitulum
 positions and study sites, here we examine the effects of seed attributes
 (capitulum position, seed weight and site of origin) on the proportion and
 timing of C. pitcheri seed germination under temperature treatments that
 simulate projected warming in the Great Lakes (20/10°C, 25/10°C and
 30/10°C day/night). Our results demonstrate that C. pitcheri produces
 diverse cohorts of seeds with seed attributes that significantly influence
 the timing and probability of germination over a three-year soil seed
 bank. C. pitcheri seed germination proportions were highest at 20°C and
 decreased successively at 25°C and 30°C. Seeds from terminal capitula had
 higher germination proportions and took longer to germinate than those
 from secondary capitula. The effect of seed weight on germination
 probability also depended on site of origin and capitulum position, with
 all effects varying in size and significance over time. Our results
 highlight the considerable differences in germination patterns exhibited
 by seeds from different capitulum positions and sites of origin and
 provide insight into the dormancy-break patterns that C. pitcheri might
 experience under the predicted temperature rise in the Great Lakes region
 of North America.
DOI: 10.5061/dryad.rn8pk0p85
title: Data from: Synchronous effects produce cycles in deer populations and deer-vehicle collisions

description: Population cycles are fundamentally linked with spatial synchrony, the
 prevailing paradigm being that populations with cyclic dynamics are easily
 synchronized. That is, population cycles help give rise to spatial
 synchrony. Here we demonstrate this process can work in reverse, with
 synchrony causing population cycles. We show that timescale-specific
 environmental effects, by synchronizing local population dynamics on
 certain timescales only, cause major population cycles over large areas in
 white-tailed deer. An important aspect of the new mechanism is specificity
 of synchronizing effects to certain timescales, which causes local
 dynamics to sum across space to a substantial cycle on those timescales.
 We also demonstrate, to our knowledge for the first time, that synchrony
 can be transmitted not only from environmental drivers to populations
 (deer), but also from there to human systems (deer-vehicle collisions).
 Because synchrony of drivers may be altered by climate change, changes to
 population cycles may arise via our mechanism.
description: See the included ReadMe.pdf file for information on each
 comma-delimited (.csv) data file.
DOI: 10.5061/dryad.34tmpg4hx
title: Data and R Markdown files for: Estimating the capacity of Chamaecrista fasciculata for adaptation to change in precipitation

description: Adaptation through natural selection may be the only means by which small
 and fragmented plant populations will persist through present day
 environmental change. A population’s additive genetic variance for fitness
 (VA(W)) represents its immediate capacity to adapt to the environment in
 which it exists. We evaluated this property for a population of the annual
 legume Chamaecrista fasciculata through a quantitative genetic experiment
 in the tallgrass prairie region of the Midwest USA, where changing climate
 is predicted to include more variability in rainfall. To reduce incident
 rainfall, relative to controls receiving ambient rain, we deployed rain
 exclusion shelters. We found significant VA(W) in both treatments. We also
 detected a significant genotype-by-treatment interaction for fitness which
 suggests that the genetic basis of the response to natural selection will
 differ depending on precipitation. For the trait specific leaf area, we
 detected maladaptive phenotypic plasticity and an interaction between
 genotype and environment. Selection for thicker leaves was detected with
 increased precipitation. These results indicate capacity of this
 population of C. fasciculata to adapt in situ to environmental change.
description: Fitness (number of seeds produced) and trait data (specific leaf
 area) were collected in an urban grassland in Minneapolis, Minnesota on a
 pedigreed population of the prairie annual legume, <em>Chamaecrista
 fasiculata</em> (partridge pea). Fitness was anlyzed in R using
 aster models. Quantitative genetic variance components of specific leaf
 area were estimated using the program Quercus
 (https://cbs.umn.edu/academics/departments/eeb/quercus). See manuscript
 for details.
DOI: 10.5061/dryad.dz08kprwb
title: Male fairy-wrens produce and maintain vibrant breeding colours irrespective of individual quality

description: Conspicuous colours may signal individual quality if high-quality
 individuals produce more elaborate colours or have a greater capacity to
 invest in colour maintenance. We investigate these hypotheses using
 repeated within-individual observations and experimentally-induced colour
 production in a wild bird, the superb fairy-wren (Malurus cyaneus). Male
 superb fairy-wrens undergo an annual moult from brown, non-breeding
 plumage to an ultraviolet-blue and black breeding plumage. Colour
 maintenance is especially relevant for this species because structural,
 ultraviolet-blue plumage colours are particularly susceptible to fading.
 Further, only the most sexually attractive males moult to breeding plumage
 early (before spring) and thereby keep their colours for an extended time
 before the breeding season. Our results show that (i) sexually attractive,
 early-moulting males do not have higher quality breeding colours and (ii)
 breeding colours are not impacted by experimentally inducing males to
 moult early and while in low body condition. We found that (iii) breeding
 colours do not fade but remain consistent or become more saturated within
 individuals over time. Despite this, (iv) males do not spend more time
 preening while in breeding plumage. Instead, males keep their colours in
 pristine condition by re-moulting parts of their breeding plumage
 throughout the breeding season, suggesting an alternative, potential cost
 of maintaining ornamental colours. We conclude that variation in
 structural breeding colours is unlikely to indicate individual quality in
 superb fairy-wrens.
DOI: 10.15468/dl.nmdczf
title: Occurrence Download

description: A dataset containing 450 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Codariocalyx motorius",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 450 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002643-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.qnk98sff2
title: Evaluating the genetic variation of the COI gene of Insecta: Implications for DNA barcoding, metabarcoding and species delimitation studies

description: The genetic variation of the COI gene has a great effect on the final
 results of the species delimitation studies. However, little research has
 comprehensively investigated the genetic divergence in COI among Insecta.
 The fast-growing COI data in BOLD provide an opportunity for
 comprehensively appraising the genetic variation in COI among Insecta. We
 calculated the K2P distance of 64,414 insect species downloaded from BOLD.
 The match ratios of the clustering analysis based on different thresholds
 were compared among 4,288 genera (35,068 species). Besides, we also
 compared the match ratios obtained from two species delimitation methods:
 the clustering analysis (distance-based method) and the bPTP analysis
 (tree-based method). Furthermore, the effectiveness of two different
 results of the bPTP analysis: bPTP_h and bPTP_ml was also tested.
 Approximately one-quarter of the species of Insecta showed high
 intraspecific genetic variation (&gt; 3%), and a conservative estimate
 of this value is 12.05-22.58%. The application of empirical thresholds
 (e.g., 2% and 3%) in the clustering analysis may result in the
 overestimation of species diversity. In metabarcoding studies, a threshold
 of 3% can only be used to estimate the insect diversity roughly. As for
 the clustering analysis, the "threshOpt" or
 "localMinima" algorithms can provide a priori value for the
 researcher. Nevertheless, if the minimum interspecific genetic distance of
 congeneric species was greater than or equal to 2%, it is possible to
 avoid overestimating the species diversity based on the empirical
 thresholds. Besides, the match ratios of the bPTP_ml results were higher
 than those of the bPTP_h results. As for the bPTP analysis, the bPTP_ml
 results were recommended. If a proper threshold was selected, the
 clustering analysis may outperform the bPTP analysis.
description: <strong>Fasta_Files_Datasets1</strong><br> The
 sequence files of 64,414 species after data filtering
 <strong>Fasta_Files_Datasets2</strong><br> The
 sequence files of 4,288  genera after data filtering
DOI: 10.5061/dryad.s1rn8pk66
title: Data from: Anthropogenic extinctions conceal widespread evolution of flightlessness in birds

description: Human-driven extinctions can affect our understanding of evolution,
 through the nonrandom loss of certain types of species. Here, we
 explore how knowledge of a major evolutionary transition—the evolution of
 flightlessness in birds—is biased by anthropogenic extinctions. Adding
 data on 581 known anthropogenic extinctions to the extant avifauna
 increases the number of species by 5%, but quadruples the number of
 flightless species. The evolution of flightlessness in birds is a
 widespread phenomenon, occurring in more than half of bird orders and
 evolving independently at least 150 times. Thus, we estimate that this
 major evolutionary transition occurred at a rate four times higher than it
 would appear based solely on extant species. Our analysis of
 preanthropogenic avian diversity shows how anthropogenic effects can
 conceal the frequency of major evolutionary transitions in life forms and
 highlights that macroevolutionary studies with only small amounts of
 missing data can still be highly biased.
description: To obtain a list of all known bird extinctions during the rise of
 humans (i.e., from the Late Pleistocene onward), we reviewed the published
 literature on the topic. First, for historic extinctions (after 1500 CE),
 we extracted the information from the IUCN Red List of Threatened Species
 (Accessed on June 2019), which includes 162 species that are categorized
 as extinct (EX) or extinct in the wild (EW). To search for older
 extinctions or undescribed species, we carried out a literature search
 using Google Scholar including the terms “geographical location AND
 (extinct OR fossil) AND (avian OR bird)” up to August 2019. For the
 geographical locations, we used all the main island archipelagos in the
 world as well as the continents. After accessing relevant studies, we also
 checked extinct species or archaeological sites cited within these papers.
 We complemented the search with scrutiny of relevant books on the subject.
 For the prehistoric extinctions, we only included species that were
 extinct after the last interglacial during the Late Pleistocene (126,000
 years B.P.), which is determined by their presence in fossil deposits of
 later age or by contemporary records of the species.
description: This dataset includes: <strong>Data File
 S1</strong><b>. </b>Complete list of all known extinct
 species (N=581) that have gone extinct during the rise of humans (i.e.
 from the Late Pleistocene and onwards), including their taxonomic
 classification, extinction period, flight ability, island endemicity, and
 geographical origin. <strong>Data File
 S2</strong>. Complete list of all extant bird species (N=10964),
 including their conservation status, flight ability, and island
 endemicity. <b>Data
 File S3. </b>List of islands where extant or extinct flightless
 species are found, including their archipelago and geographical
 coordinates. <b>Data
 File S4. </b>A matrix showing the archipelagos or landmasses (in
 rows) where each flightless species (in columns) is found.
DOI: 10.5061/dryad.51c59zw6r
title: Data from: Connecting the data landscape of long-term ecological studies: the SPI-Birds data hub

description: 1. The integration and synthesis of the data in different areas of science
 is drastically slowed and hindered by a lack of standards and networking
 programmes. Long-term studies of individually marked animals are not an
 exception. These studies are especially important as instrumental for
 understanding evolutionary and ecological processes in the wild. Further,
 their number and global distribution provides a unique opportunity to
 assess the generality of patterns and to address broad-scale global issues
 (e.g. climate change). 2. To solve data integration issues and enable a
 new scale of ecological and evolutionary research based on long-term
 studies of birds, we have created the SPI-Birds Network and Database
 (www.spibirds.org) – a large-scale initiative that connects data from, and
 researchers working on, studies of wild populations of individually
 recognizable (usually ringed) birds. Within year and a half since the
 establishment, SPI-Birds has recruited over 120 members, and currently
 hosts data on almost 1.5 million individual birds collected in 80
 populations over 2000 cumulative years, and counting. 3. SPI-Birds acts as
 a data hub and a catalogue of studied populations. It prevents data loss,
 secures easy data finding, use and integration, and thus facilitates
 collaboration and synthesis. We provide community-derived data and
 meta-data standards and improve data integrity guided by the principles of
 Findable, Accessible, Interoperable, and Reusable (FAIR), and aligned with
 the existing metadata languages (e.g. ecological meta-data language). 4.
 The encouraging community involvement stems from SPI-Bird's
 decentralized approach: research groups retain full control over data use
 and their way of data management, while SPI-Birds creates tailored
 pipelines to convert each unique data format into a standard format. We
 outline the lessons learned, so that other communities (e.g. those working
 on other taxa) can adapt our successful model. Creating community-specific
 hubs (such as ours, COMADRE for animal demography, etc.) will aid
 much-needed large-scale ecological data integration.
description: This dataset and code can be used to reproduce Figure 2 in the
 Manusript. Figure 2 represents the summary information on the number of
 populations hosted at SPI-Birds that (A) collect data on a certain
 species; (B) collect different types of data on individuals (alongside
 basic breeding parameters); (C) have been studied for a certain period of
 time; as of October 2020.
DOI: 10.5061/dryad.3tx95x6dx
title: Resource-driven colonization by cod in a high Arctic food web

description: Climate change is commonly associated with many species redistributions
 and the influence of other factors may be marginalized, especially in the
 rapidly warming Arctic. The Barents Sea, a high latitude large marine
 ecosystem in the Northeast Atlantic has experienced above average
 temperatures since the mid 2000’s with divergent bottom temperature trends
 at sub-regional scales. Concurrently, the Barents Sea stock of Atlantic
 cod Gadus morhua, one of the most important commercial fish stocks in the
 world, increased following a large reduction in fishing pressure and
 expanded north of 80°N. We examined the influence of food availability and
 temperature on cod expansion using a comprehensive data set on cod stomach
 fullness stratified by sub-regions characterized by divergent temperature
 trends. We then tested whether food availability, as indexed by cod
 stomach fullness, played a role in cod expansion in sub-regions that were
 warming, cooling or showed no trend. The greatest increase in cod
 occupancy occurred in three northern sub-regions with contrasting
 temperature trends. Cod apparently benefited from initial high food
 availability in these regions that previously had few large-bodied fish
 predators. The stomach fullness in the northern sub-regions declined
 rapidly after a few years of high cod abundance, suggesting that the
 arrival of cod caused a top down effect on the prey base. Prolonged cod
 residency in the northern Barents Sea is, therefore, not a certainty.
description: Data from the Joint Russian
 Norwegian Ecosystem survey in the Barents Sea. The data are aggregated by
 sub-regions, see file data_script.txt and main paper for explanation. The
 raw data at the station level sampled by Norwegian boats at the
 surveys can be obtained from the Institute of Marine Research, Norway upon
 reasonable request. Special legal restrictions apply to Russian raw data.
 These can only be shared under contracted agreements.