cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.290nr65
title: Data from: Nonlinear responses of soil nematode community composition to increasing aridity

description: Aim: Increasing aridity under global change is predicted to have a
 profound impact on the structure and functioning of terrestrial
 ecosystems, yet we have poor understanding of how belowground communities
 respond. In order to understand the longer-term responses of different
 trophic levels in the soil food web to increasing aridity, we investigated
 the abundance, richness and community similarity of the soil nematode
 community along a 3200-km aridity gradient. Location: A transect across
 semi-arid and arid grasslands in Northern China, where the aridity ranges
 from 0.43 to 0.97. Time period: July and August 2012. Major taxa studied:
 Soil-borne Nematoda. Methods: We used Generalized Additive (Mixed) Models
 to analyze the abundance, richness and community similarity patterns of
 soil nematodes. We used Structural Equation Modelling (SEM) to disentangle
 the direct and indirect environmental drivers (aridity, soil and plant
 variables) of the nematode community. Results: The abundance, richness and
 similarity of nematode communities declined non-linearly with increasing
 aridity. The most pronounced decline in nematode richness and community
 similarity occurred under arid conditions (aridity &gt; 0.80).
 However, the shape of response to aridity differed among nematode feeding
 groups. Under arid conditions, the abundance and richness of bacterial
 feeders were less sensitive to changes in aridity than fungal feeders. The
 SEM analysis revealed that nematode community responses to aridity were
 not mediated via changes in plant and soil variables, but rather were
 directly affected by aridity. Main conclusions: Our results show that in
 mesic grasslands increasing aridity primarily caused decline in nematode
 abundance, whereas increasing aridity in xeric grasslands led to loss of
 nematode diversity. The non-linear responses of nematodes to aridity could
 result in non-linear shifts in ecosystem functioning as well, because soil
 nematodes operate at various trophic levels in the soil food web, thereby
 influencing the performance of plants, soil biodiversity and
 biogeochemical cycling.
description: Nema data of
 grasslandNema data in
 grassland.xlsx
DOI: 10.5061/dryad.tb7055f
title: Data from: Interaction among ploidy, breeding system, and lineage diversification

description: If particular traits consistently affect rates of speciation and
 extinction, broad macroevolutionary patterns can be interpreted as
 consequences of selection at high levels of the biological hierarchy.
 Identifying traits associated with diversification rates is difficult
 because of the wide variety of characters under consideration and the
 statistical challenges of testing for associations from comparative
 phylogenetic data. Ploidy (diploid vs. polyploid states) and breeding
 system (self-incompatible vs. self-compatible states) are both thought to
 be drivers of differential diversification in angiosperms. We fit
 twenty-nine diversification models to extensive trait and phylogenetic
 data in Solanaceae and investigate how speciation and extinction rate
 differences are associated with ploidy, breeding system, and the
 interaction between these traits. We show that diversification patterns in
 Solanaceae are better explained by breeding system and an additional
 unobserved factor, rather than by ploidy. We also find that the most
 common evolutionary pathway to polyploidy in Solanaceae occurs via direct
 breakdown of self-incompatibility by whole-genome duplication, rather than
 indirectly via breakdown followed by polyploidization. Comparing multiple
 stochastic diversification models that include complex trait interactions
 alongside hidden states enhances our understanding of the
 macroevolutionary patterns in plant phylogenies.
description: Solanaceae data files
 and Rev analysesBasicdata folder
 contains data used for publication. Rev_analyses folder contains Rev code
 with resulting output for 29 models of diversification.soldata.zip
DOI: 10.5061/dryad.vs830t1
title: Data from: The genomics of invasion: characterization of red lionfish (Pterois volitans) populations from the native and introduced ranges

description: Invasive species are one of the greatest threats to global biodiversity
 and ecosystem health, and population genetics provides promising tools for
 understanding the evolutionary process of successful invaders. The
 well-documented introduction of the red lionfish (Pterois volitans) to the
 western Atlantic, Gulf of Mexico and Caribbean has decimated native fauna
 due to the invader’s voracious predation and growth rate. We tested
 whether our samples were within the region of the source of invasion into
 the Atlantic and Caribbean and investigated whether hybridization in the
 native or introduced range was responsible for the success of this
 invasive species. We used a reduced representation sequencing method to
 generate over 50,000 single nucleotide polymorphisms and sequence data
 from two mitochondrial DNA genes to analyze the population patterns. We
 found one location in the southeastern Pacific that was genetically
 similar to one location the southwestern Atlantic and evidence of the
 subsequent spread south to the Gulf of Mexico and the Caribbean, which
 supports previous findings. Within the native range, we found genetic
 divergences commensurate with distinct species and evidence of
 hybridization. We found limited structure within the introduced range and
 no evidence of Pterois miles or hybrids within this range. Finally, we
 found signatures of selection between the native and introduced range that
 may be a result of the introduction. Overall, this study of the red
 lionfish showed the pattern of introduction and suggested a deeper
 sampling of genomic data from individuals within the native range may
 reveal hybridization between species as the source of the aggressive
 invasion.
description: ddRAD Sequence data for
 lionfish from STACKSThis is the VCF file (v.
 4.0) from the Stacks (v.1.24) population pipeline following the parameters
 set in the manuscript.lionfish8pops_ddRADseq.vcflionfish8pops_ddRADseq.vcf
DOI: 10.5061/dryad.k8t37j5
title: Data from: Assessing precision and requirements of three methods to estimate roe deer density

description: Roe deer (Capreolus capreolus) is the most abundant cervid in Europe and,
 as such, has a considerable impact over several human activities. Accurate
 roe deer population size estimates are useful to ensure their proper
 management. We tested 3 methods for estimating roe deer abundance (drive
 counts, pellet-group counts, and camera trapping) during two consecutive
 years (2012 and 2013) in the Apennines (Italy) in order to assess their
 precision and applicability. During the study period, population density
 estimates were: drive counts 21.89±12.74 roe deer/km2 and pellet-group
 counts 18.74±2.31 roe deer/km2 in 2012; drive counts 19.32±11.12 roe
 deer/km2 and camera trapping 29.05±7.48 roe deer/km2 in 2013. Precision of
 the density estimates differed widely among the 3 methods, with
 coefficients of variation ranging from 12% (pellet-group counts) to 58%
 (drive counts). Drive counts represented the most demanding method on
 account of the higher number of operators involved. Pellet-group counts
 yielded the most precise results and required a smaller number of
 operators, though the sampling effort was considerable. When compared to
 the other two methods, camera trapping resulted in an intermediate level
 of precision and required the lowest sampling effort. We also discussed
 field protocols of each method, considering that volunteers, rather than
 technicians, will more likely be appointed for these tasks in the near
 future. For this reason, we strongly suggest that for each method managers
 of population density monitoring projects take into account ease of use as
 well as the quality of the results obtained and the resources required.
description: Drive_countsThe file contains the raw data regarding the drive counts: surface of the sampling area, the correction factor (see text for details), the number of roe deer counted and the estimated density for each drive counts area sampled.Pellet_Group_CountThe file contains the raw data regarding the pellet-group counts: the vegetation category of the sampling plot, the time window the results refer to (in days), and the number of pellet-group found for each sampling plot.Random_Encounter_MethodThe file contains the raw data for the Random Encounter Method sampling: the number of days the camera trap has been in the field, the number of single-encounter events, the vegetation category of the camera location, and the brand of the camera for each camera trap location sampled.REM.csv
DOI: 10.5061/dryad.221f9g2
title: Personality predicts foraging site fidelity and trip repeatability in a marine predator

description: 1. Animal populations are often comprised of both foraging specialists and
 generalists. For instance, some individuals show higher foraging site
 fidelity (spatial specialisation) than others. Such individual differences
 in degree of specialisation can persist over timescales of months or even
 years in long-lived animals, but the mechanisms leading to these different
 individual strategies are not fully understood. 2. There is accumulating
 evidence that individual variation in foraging behaviour is shaped by
 animal personality traits, such as boldness. Despite this, the potential
 for boldness to drive differences in the degree of specialisation is
 unknown. 3. In this study, we used novel object tests to measure boldness
 in black-legged kittiwakes (Rissa tridactyla) breeding at four colonies in
 Svalbard, and deployed GPS loggers to examine their at-sea foraging
 behaviour. We estimated the repeatability of foraging trips, and used a
 hidden Markov model to identify locations of foraging sites in order to
 quantify individual foraging site fidelity. 4. Across the breeding season,
 bolder birds were more repeatable than shy individuals in the distance and
 range of their foraging trips, and during the incubation period (but not
 chick rearing), bolder individuals were more site faithful. Birds
 exhibited these differences while showing high spatial similarity in
 foraging areas, indicating that site selection was not driven by
 personality-dependent spatial partitioning. 5. We instead suggest that a
 relationship between boldness and site fidelity may be driven by
 differences in behavioural flexibility between bold and shy individuals.
 Together, these results provide a potential mechanism by which widely
 reported individual differences in foraging specialisation may emerge.
description: Harris_etal_2019_boldnessSiteFidelity_JAE_data_archiveThis data package contains (i) data from personality tests used to calculate individual boldness estimates, (ii) foraging trip distances, durations and ranges used to estimate foraging trip repeatability, (iii) locations of foraging sites used to test for personality-dependent spatial partitioning, and (iv) estimates of individual foraging site fidelity used to test for a relationship between site fidelity and boldness. See README file for column details.Harris_etal_2019_JAE_data_archive.zip
DOI: 10.5061/dryad.6v78j4c
title: Using genomic information for management planning of an endangered perennial, Viola uliginosa

description: Species occupying habitats subjected to frequent natural and/or
 anthropogenic changes are a challenge for conservation management. We
 studied one such species, Viola uliginosa, an endangered perennial wetland
 species typically inhabiting sporadically flooded meadows alongside
 rivers/lakes. In order to estimate genomic diversity, population structure
 and history, we sampled five sites in Finland, three in Estonia, and one
 each in Slovenia, Belarus, and Poland using genomic SNP data with
 double-digest restriction site associated DNA sequencing (ddRAD-seq). We
 found monophyletic populations, high levels of inbreeding (mean population
 FSNP = 0.407 – 0.945), low effective population sizes (Ne = 0.8 – 50.9),
 indications of past demographic expansion and rare long-distance
 dispersal. Our results are important in implementing conservation
 strategies for Viola uliginosa, which should include founding of seed
 banks, ex situ cultivations, and re-introductions with individuals of
 proper origin, combined with continuous population monitoring and habitat
 management.
description: Supporting/Supplemental
 informationViola_Supplementary.docx
DOI: 10.5061/dryad.gk100m1
title: Data from: Long-term persistence of monotypic dengue transmission in small size isolated populations, French Polynesia, 1978-2014

description: Understanding the transition of epidemic to endemic dengue transmission
 remains a challenge in regions where serotypes co-circulate and there is
 extensive human mobility. French Polynesia, an isolated group of 72
 inhabited islands, distributed among five geographically separated
 subdivisions, has recorded mono-serotype epidemics since 1944, with long
 inter-epidemic periods of circulation. Laboratory confirmed cases have
 been recorded since 1978, enabling exploration of dengue epidemiology
 under monotypic conditions in an isolated, spatially structured
 geographical location. A database was constructed of confirmed dengue
 cases, geolocated to island for a 35-year period. Statistical analyses of
 viral establishment, persistence and fade-out as well as synchrony among
 subdivisions were performed. Seven monotypic and one heterotypic dengue
 epidemic occurred, followed by low-level viral circulation with a
 recrudescent epidemic occurring on one occasion. Incidence was
 asynchronous among the subdivisions. Complete viral die-out occurred on
 several occasions with invasion of a new serotype, but also in the absence
 of any novel serotype. Island population size had a strong impact on the
 establishment, persistence and fade-out of dengue cases and endemicity was
 estimated achievable only at a population size in excess of 175 000.
 Despite island remoteness and low population size, dengue cases were
 observed somewhere in French Polynesia almost constantly, in part due to
 the spatial structuration generating asynchrony among subdivisions.
 Long-term persistence of dengue virus in this group of island populations
 may be enabled by island hopping, although could equally be explained by a
 reservoir of sub-clinical infections on the most populated island, Tahiti.
description: Dengue case
 dataLaboratory confirmed
 dengue cases by day by island from 1979 until 2014Teissier et al
 data.xlsx
description: Laboratory confirmed cases performed at the Institut Louis
 Malardé from samples sent by clinicians
DOI: 10.5061/dryad.29rt7n0
title: Data from: No consistent effects of humans on animal genetic diversity worldwide

description: Human impacts on genetic diversity are poorly understood yet critical to
 biodiversity conservation. We used 175,247 COI sequences collected between
 1980 and 2016 to assess the global effects of land use and human density
 on the intraspecific genetic diversity of 17,082 species of birds, fishes,
 insects, and mammals. Human impacts on mtDNA diversity were taxon and
 scale-dependent, and were generally weak or non-significant. Spatial
 analyses identified weak latitudinal diversity gradients as well as
 negative effects of human density on insect diversity, and negative
 effects of intensive land use on fish diversity. The observed effects were
 predominantly associated with species turnover. Time series analyses found
 nearly an equal number of positive and negative temporal trends in
 diversity, resulting in no net monotonic trend in diversity over this time
 period. Our analyses reveal critical data and theory gaps and call for
 increased efforts to monitor global genetic diversity.
description: Raw fasta and coordinate
 filesThese data contain the
 raw unfiltered COI fasta and accompanying coordinate files of all species
 (birds, fishes, insects, and mammals) in the publication. A separate
 folder contains a summary of the species excluded from analyses following
 filtering and processing steps. See associated code on GitHub
 (https://github.com/VFugere/GenDivProject) for filtering and
 processing.Millette_etal_EcolLett_DATA.zip
DOI: 10.5061/dryad.52vq8t5
title: Data from: Accelerate low water corrosion: the microbial sulphur cycle in microcosm

description: Accelerated low water corrosion is a form of marine steel corrosion caused
 by bacterial activity. It has a global spread and is potentially
 responsible for billions of pounds of damage. We have determined in detail
 both the chemistry of corrosion products and the associated microbiology
 at a UK site. The corrosion products form a layered structure with iron
 sulphides at the steel surface and iron oxides and sulphates in contact
 with water. The iron sulphides are formed by reaction of steel with
 hydrogen sulphide formed by sulphate reducing bacteria and are oxidised
 through a series of sulphur oxidation states by sulphide oxidising
 bacteria, forming acid at all stages and encompassing the whole of the
 bacterial sulphur cycle. The bacteria involved are endemic in anoxic bed
 sediment, and the process is a response to the presence of steel as an
 electron donor, and the generation of anoxic microenvironments within
 corrosion products.
description: 16s RNA and Microarray
 data from 'Accelerated Low Water Corrosion: The mcirobial sulphur
 cycle in microcosmExcel data file
 including processed data from GeoChip microarray, and 16s RNA
 sequencing.Smith et al MatDeg2019
 metagenomics database.xlsx
DOI: 10.5061/dryad.5qf75h2
title: Data from: Effects of the colour of photophase light on locomotor activity in a nocturnal and a diurnal South African rodent

description: Many physiological and behavioural responses to varying qualities of
 light, particularly during the night (scotophase) have been well
 documented in rodents. We used varying wavelengths of daytime (photophase)
 lighting to assess daily responses in locomotor activity in the nocturnal
 Namaqua rock mouse (Micaelamys namaquensis) and diurnal four-striped field
 mouse (Rhabdomys pumilio). Animals were exposed to three light-dark cycle
 regimes: a short-wavelength- (SWLC), a medium-wavelength- (MWLC) and a
 long-wavelength light-dark cycle (LWLC). Overall, daily locomotor activity
 of both species changed according to different wavelengths of light, the
 diurnal species displayed most activity under SWLC and the nocturnal
 species exhibited the highest levels of activity under LWLC. Both species
 showed an increase in diurnal activity and a decrease in nocturnal
 activity under LWLC. These results indicate an attenuated responsiveness
 to long wavelength light in the nocturnal species, but this does not
 appear to be true for the diurnal species. These results emphasize that
 the effect of light on the locomotor activity of animals depends on both
 the properties of the light and the temporal organization of activity of a
 species.
description: RSBL-2019-0597
 dataLocomotor activity data
 for 14 days of three light wavelengths for two South African mouse
 species, one diurnal and one nocturnal.
DOI: 10.5061/dryad.mr36sp2
title: Data from: Impact of plant functional group and species removals on soil and plant nitrogen and phosphorus across a retrogressive chronosequence

description: 1. In the prolonged absence of catastrophic disturbance, ecosystem
 retrogression occurs, which is characterized by declining soil nitrogen
 (N) and phosphorus (P) availability, increasing plant and soil N to P
 ratios, and reduced plant biomass and productivity. It is, however,
 largely unknown as to how the effects of plant communities on soil
 nutrients change during retrogression or might contribute to declining
 nutrient availability as retrogression proceeds. 2. We studied a well
 characterized system of 30 lake islands in northern Sweden that
 collectively represent a 5000-year post-fire retrogressive chronosequence.
 For each island, we established an experiment that involved full factorial
 removal of three plant functional groups (tree roots, dwarf shrubs and
 mosses), and of three species of dwarf shrub (Vaccinium myrtillus, V.
 vitis-idaea and Empetrum hermaphroditum). After 19 years, we took various
 measures of soil N and P availability, and measured foliar N and P for
 each dwarf shrub species, for each plot in the experiment. 3. Although
 plant removal effects (and particularly removal of tree roots, shrubs, and
 Vaccinium species) on belowground N and P measures sometimes changed
 during retrogression, this seldom happened in a way that explains the
 decline in nutrient availability and increase in N to P ratios that
 characterizes ecosystem retrogression. The only exceptions were that the
 positive effects of tree roots on soil mineral N and P, and of V.
 myrtillus on soil mineral P, declined during retrogression. 4. Plant
 removal effects on community-level measures of shrub N and P varied
 greatly across the chronosequence, but these effects again did not align
 with the changes in soil nutrient availability or N to P ratios that
 characterize ecosystem retrogression. 5. Synthesis. Our results suggest
 that retrogression, and associated changes in nutrient availability and
 soil N to P ratios, is driven mainly by longer-term pedogenic processes as
 opposed to shorter-term effects of plant communities on soil N and P
 availability. More generally, they illustrate the value of long-term and
 large-scale experimental manipulations of plant communities for showing
 how effects of biodiversity loss on ecosystem properties vary across
 contrasting ecosystems.
description: raw data for Wardle et
 al. (J Ecol)File contains three
 pages, i.e., (1) metadata, (2) soil data, (3) plant
 dataWardle-2020-for-dryad.xlsx
DOI: 10.5061/dryad.5qj63hm
title: Data from: Rapid change from migration to residence in relation to climate in a long-distance migratory bird

description: Recent changes in climate have advanced the timing of long-distance
 migration in birds, although there are still no studies showing a change
 from migration to residence in previously migratory populations. Barn
 swallows Hirundo rustica are long-distance migrant songbirds with an
 almost global breeding distribution and with resident populations in Egypt
 and possibly in south China. In Europe, they have been exclusively
 migratory with wintering populations in Africa where they also undergo an
 annual moult. In December 2015, barn swallows started wintering in large
 numbers in Portugal resulting in these individuals also moulting there.
 Here, we tested the origin of these novel resident European birds by using
 measurements of feather deuterium (δ2Hf) of juveniles that had grown their
 feathers at the breeding grounds in Europe and in adults that had grown
 their feathers in the winter quarters to test for a difference in moult
 distribution of these two individual categories of barn swallows. Second,
 we tested the prediction that barn swallows have changed their migratory
 habits from wintering in Africa to wintering in Portugal as revealed by
 differences in δ2Hf compared to known Palearctic-Afrotropical migrants.
 Third, we tested whether moult phenology had changed following recent
 residency in Portugal. Our results confirm the existence of an entirely
 resident population of barn swallows in Europe with a shorter and earlier
 moult period.
description: Barn swallow
 residency All data
 AVEIROFILE-17032019.xls