cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pnvx0k6pf
title: Temporal dynamics of range-expander and congeneric native plant responses during and after extreme drought events

description: Current climate change causes range shifts of many species to higher
 latitudes and altitudes, and enhances their exposure to extreme weather
 events. It has been shown that range shifting plant species may perform
 differently in the new soil than related natives, however, little is known
 about how extreme weather events influence range-shifting plants compared
 to related natives. Here, we used outdoor mesocosms to study how
 range-shifting plant species respond to extreme drought in live soil from
 a habitat in the new range with and without live soil from a habitat in
 the original range. During summer drought, shoot biomass of the
 range-expanders was reduced. In spite of this, in the mixed community
 range-expanders produced more shoot biomass than congeneric natives. In
 mesocosms with a history of range-expanders in the previous year, native
 plants produced less biomass. Plant legacy or soil origin effects did not
 change the response of natives or range-expanders to summer drought.
 During rewetting, range-expanders had less biomass than congeneric
 natives, but had higher drought resilience (survival) in soils from the
 new range where in the previous year native plant species had grown. The
 biomass patterns of the mixed plant communities were dominated by
 Centaurea species, however, not all plant species within the groups of
 natives and of range expanders showed the general pattern. Drought reduced
 litter decomposition, microbial biomass and abundances of bacterivorous,
 fungivorous and carnivorous nematodes. Their abundances recovered during
 rewetting. There was less microbial biomass, fungal biomass and there were
 fewer fungivorous nematodes in soils from the original range (Hungary)
 where range-expanders had grown in the previous year. We conclude that in
 mixed plant communities of range-expanders and congeneric natives,
 range-expanders performed better, both under ambient and drought
 conditions, than congeneric natives. However, when considering the
 responses of individual species, we observed variations among couples of
 congenerics, so that under the present-mixed community-conditions there
 was no uniformity in responses to drought of range expanders versus
 congeneric natives. Range-expanding plant species reduced soil fungal
 biomass and numbers of soil fungivorous nematodes, suggesting that effects
 of range-expanding plant species can trickle up in the soil food web.
DOI: 10.5061/dryad.1c59zw3wv
title: Data from: Plasticity drives extreme cold tolerance of emerald ash borer (Agrilus planipennis) during a polar vortex

description: Invasive species must often survive combinations of environmental
 conditions that differ considerably from their native range; however, for
 a given species it is unclear whether improved tolerance is the result of
 phenotypic plasticity or genetic adaptation (or both). Agrilus planipennis
 (Coleoptera: Buprestidae; the emerald ash borer) is an invasive pest of
 Fraxinus trees in North America and Europe. Previous studies in
 southwestern Ontario, Canada, showed that A. planipennis is freeze
 avoidant, preventing internal ice formation by accumulating molar
 concentrations of glycerol in its hemolymph and depressing its
 supercooling point (SCP, the temperature at which it freezes). The cold
 tolerance of these southwestern Ontario animals was used to
 predict potential distribution, revealing that some Canadian cities should
 be too cold to allow populations to persist. However, a small population
 of A. planipennis has persisted in Winnipeg, Manitoba, Canada, through
 several severe ‘polar vortex’ events. In 2018/19, we collected A.
 planipennis larvae and prepupae from Winnipeg, Manitoba and Southern
 Ontario, and found that individuals from Winnipeg were extremely cold
 tolerant – with SCPs as low as -52 °C in prepupae (compared to 32 °C in
 Southern Ontario), and survival of unfrozen individuals exposed to -50 °C
 for one hour. This cold tolerance was accompanied by higher hemolymph
 osmolality and glycerol concentration than in the SW Ontario individuals.
 To distinguish between phenotypic plasticity and local adaptation, in
 2020/21 we overwintered Winnipeg-sourced individuals either outdoors in
 southwestern Ontario or in a simulated Winnipeg winter. Simulated Winnipeg
 winter individuals had cold tolerance similar to those overwintered in
 Winnipeg, while southwestern Ontario overwintered individuals had cold
 tolerance similar to those collected previously in the region. The
 simulated winter individuals had higher hemolymph glycerol concentrations
 than southwestern Ontario overwintered animals, at least in part
 due to greater dehydration. Thus, A. planipennis are cold-tolerant enough
 to survive some of the harshest winters where their host trees can grow,
 and most likely attain this cold tolerance via phenotypic plasticity.
 These findings raise the importance of delineating sensitivity of
 conclusions to unexpected phenotypic plasticity when predicting potential
 distributions of new invasives or responses to climate change. The data in
 this dataset are the SCPs and treatment data for the experimental animals
 used in these cold tolerance experiments. 
description: Methods and processing are described in the associated
 manuscript.
description: Please see ReadMe file.
DOI: 10.5061/dryad.jm63xsjcn
title: Data for sperm numbers as a paternity guard in a wild bird

description: Sperm competition is thought to impose strong selection on males to
 produce competitive ejaculates to outcompete rival males under competitive
 mating conditions. Our understanding of how different sperm traits
 influence fertilization success, however, remains limited, especially in
 wild populations. Recent literature highlights the importance of
 incorporating multiple ejaculate traits and pre-copulatory sexually
 selected traits in analyses aimed at understanding how selection acts on
 sperm traits. However, variation in a male’s ability to gain fertilization
 success may also depend upon a range of social and ecological factors that
 determine the opportunity for mating events both within and outside of the
 social pair-bond. Here, we test for an effect of sperm quantity and sperm
 size on male reproductive success in the red-back fairy-wren (Malurus
 melanocephalus) while simultaneously accounting for pre-copulatory sexual
 selection and potential socio-ecological correlates of male mating
 success. We found that sperm number (i.e., cloacal protuberance volume),
 but not sperm morphology, was associated with reproductive success in male
 red-backed fairy-wrens. Most notably, males with large numbers of sperm
 available for copulation achieved greater within-pair paternity success.
 Our results suggest that males use large sperm numbers as a defensive
 strategy to guard within-pair paternity success in a system where there is
 a high risk of sperm competition and female control of copulation.
 Finally, our work highlights the importance of accounting for
 socio-ecological factors that may influence male mating opportunities when
 examining the role of sperm traits in determining male reproductive
 success.
DOI: 10.5061/dryad.wstqjq2p2
title: Effects of pollen supply on Apis mellifera worker longevity and body weight in the presence and absence of an intact gut microbiota

description: Gut microbiota are known to foster pollen digestion in honey bee workers,
 Apis mellifera, thereby enhancing longevity and body weight gain. However,
 it is currently not known how longevity and body weight gain are effected
 when gut microbiota are reduced in bees with or without access to pollen.
 Here, using a hoarding cage set-up with freshly emerged summer workers, we
 manipulated the gut microbiota of half the bees with the antibiotic
 tetracycline (ABX), and left the other half untreated on a sucrose
 solution diet. Afterwards, all bees were assigned to either sucrose diets
 or sucrose plus ad libitum access to pollen (N=4 treatments, N=26
 bees/treatment, N=10 replicates/treatment, N=1040 total workers). The data
 confirm that pollen has a positive effect on longevity and body weight in
 workers with an unmanipulated gut microbiota. Surprisingly, the
 antibiotics alone also improved the longevity and body weight of the
 workers fed a strictly sucrose diet, potentially explained by the
 reduction of harmful bacteria. However, this positive effect was always
 reversed in the presence of pollen, underscoring the innate value of
 natural microbiota on pollen digestion. In conclusion, a combination of
 adequate pollen supply and an intact gut microbiota appears crucial to
 honey bee worker health, calling for respective efforts to ensure both in
 managed colonies.
DOI: 10.5061/dryad.6wwpzgn19
title: Cryptosporidium and Blastocystis sp infections in wild primates from urban and peri-urban centres in Kenya

description: Evidence of pathogen cross transmission between humans and primates has
 raised concerns about the potential impact of zoonotic pathogen
 transmission on primate and human health, and primate conservation.
 Cryptosporidium infection has been recorded in many primate species,
 indicating that they are likely to serve as potential reservoirs for human
 infections. We conducted molecular characterization of Cryptosporidium
 species infecting wild primates for insights into the little-known
 zoonotic transmission cycles in urban and peri-urban centres in Kenya.
 Rectal swabs were collected from a total of 65 primates, DNA extracted and
 screened by nested polymerase chain reaction. Overall, 43.08% of all the
 primates sampled were found positive for Cryptosporidium species with most
 infections occurring in adults. Positive cases of Cryptosporidium sp
 infection were distributed across all the study sites. Three of four
 sampled primate species (Papio anubis, Chlorocebus aethiops, Cercopithecus
 mitis) were positive for Cryptosporidium infections; one (Cercopithecus
 ascanius schmidts) was not. Sequencing results further revealed the
 presence of Blastocystis species. Strong bootstrap support showed a clear
 clustering of both Cryptosporidium and Blastocystis species obtained from
 this study with human isolates. In conclusion, both parasites have
 zoonotic potential and our findings highlight the importance of periodic
 surveillance of wild primate populations for zoonoses.
description: We trapped free-raging
 nonhuman primates (NHPs) in 2018 and 2019 from natural urban wildlife
 populations within five urban and peri-urban centres of selected towns in
 Kenya:<b> </b>in the western part of the country Kisumu,
 Kakamega, central Murang’a and on along the coast Mombasa and
 Kilifi. Sampling was carried out as previously described
 (Maamun
 <i>et al.,</i> 2011, Jeneby <i>et al.,</i>,
 2011).
 To avoid
 re-trapping of study subjects, we applied a non-toxic dye to the fur to
 identify sampled individuals, An authorised wildlife
 veterinarian physically examined the animals under
 anaesthesia and recorded their general health, sex and age group as
 described Nyamota <i>et al.,</i>
 (2020) and Mbuthia
 <i>et al.,</i> (2021).
 Sampled primates
 included <i>Papio
 anubis</i>
 (olive baboon), <i>Chlorocebus aethiops</i> (African green
 monkey), <i>Cercopithecus mitis</i> (Sykes monkeys) and
 <i>Cercopithecus ascanius schmidts</i> (red-tailed
 monkey). Faecal samples were collected from the
 rectum via swabbing and stored in 70% ethanol for molecular assays.
DOI: 10.5061/dryad.h70rxwdkv
title: A preliminary comparison of a songbird's song repertoire size and other song measures between an urban and a rural site

description: Characteristics of birdsong, especially minimum frequency, have been shown
 to vary for some species between urban and rural populations and along
 urban-rural gradients. However, few urban-rural comparisons of song
 complexity—and none that we know of based on the number of distinct song
 types in repertoires—have occurred. Given the potential ability of song
 repertoire size to indicate bird condition, we primarily sought to
 determine if number of distinct song types displayed by Song Sparrows
 (Melospiza melodia) varied between an urban and a rural site. We
 determined song repertoire size of 24 individuals; 12 were at an urban
 (‘human-dominated’) site and 12 were at a rural (‘agricultural’) site.
 Then, we compared song repertoire size, note rate, and peak frequency
 between these sites. Song repertoire size and note rate did not vary
 between our human-dominated and agricultural sites. Peak frequency was
 greater at the agricultural site. Our finding that peak frequency was
 higher at the agricultural site compared to the human-dominated site,
 contrary to many previous findings pertaining to frequency shifts in
 songbirds, warrants further investigation. Results of our pilot study
 suggest that song complexity may be less affected by anthropogenic factors
 in Song Sparrows than are frequency characteristics. Additional
 study, however, will be required to identify particular causal factors
 related to the trends that we report and to replicate, ideally via
 multiple urban-rural pairings, so that broader generalization is possible.
description: The data reported herein were collected as described in the open
 access published article. Briefly overviewed: we recorded the
 vocalizations of Song Sparrows in an urban and in a rural environment.
 Then, we compared song type repertoire size, peak frequency, and note rate
 between the sites. We report these measures for each bird in the
 'BrewerFudickar_SongData' csv file. The other three data files
 present 1) noise levels at both sites, 2) impervious surface coverage at
 both sites, and 3) song types recorded as a function of song instances
 recorded for a subset of birds.
description: We have presented all of the files required to reproduce the
 analysis and data figures presented in our study. There are four text
 files which present the metadata; one for each of the four data files.
 There are three .R files (BrewerFudickar_ImpervStats.R,
 BrewerFudickar_NoiseStats.R, and BrewerFudickar_SongStats.R) that present
 code used for the analyses. There are three .R files
 (BrewerFudickar_EffortCurves.R, BrewerFudickar_SongBoxPlots.R and
 BrewerFudickar_NoiseImpervFig.R) that present the code for making
 the data-based figures from our study. There are no missing
 data.
DOI: 10.5061/dryad.70rxwdc05
title: Differences in feather structure between urban and forest great tits – constraint or adaptation?

description: Urbanization is one of the strongest habitat transforming processes today
 that has resulted in changes in the ecological conditions for wild
 populations. In birds, the limitation of natural food sources and a warmer
 microclimate in cities can potentially influence the development and
 functioning of the plumage that may have important fitness consequences.
 Despite its potential significance, the plumage structure of urban birds
 are largely unexplored and it is unclear whether and how they respond to
 urban ecological processes such as different constraints and selection
 pressures. In this study, we compared several structural properties of
 contour, primary and tail feathers between two forest and two urban great
 tit (Parus major) populations. Our results show that the urban environment
 affects only a few structural properties of feathers and only in the
 plumage of first-year birds. We found that both the plumulaceous and the
 pennaceous parts of their contour feathers are longer and have lower barb
 density in the urban than in the forest habitat. We also found that the
 primaries of first-year birds have narrower rachis and higher barbule
 density in the cities than in the forests, but there were no differences
 in other wing feather traits and in any tail feather traits between
 habitats. We did not find differences in the feather structure of urban
 versus forest adult birds. The habitat differences in first-year birds may
 indicate nutritional constraints or the effects of the warmer microclimate
 of the urban environment. These differences seem to disappear completely
 in adulthood that can be explained by the selective mortality of
 first-year birds, or by adults being less sensitive than first-year birds
 to environmental effects during their molt.
DOI: 10.5061/dryad.zgmsbccd0
title: Amplicon_sorter: a tool for reference-free amplicon sorting based on sequence similarity and for building consensus sequences

description: Oxford Nanopore Technologies (ONT) is a third-generation sequencing
 technology that is gaining popularity in ecological research for its
 portable and low-cost sequencing possibilities. Although the technology
 excels at long-read sequencing, it can also be applied to sequence
 amplicons. The downside of ONT is the low quality of the raw reads. Hence,
 generating a high-quality consensus sequence is still a challenge. We
 present Amplicon_sorter, a tool for reference-free sorting of ONT
 sequenced amplicons based on their similarity in sequence and length and
 for building solid consensus sequences.
description: Oxford Nanopore sequencing was done on a 9.4.1 MinION Flow cell
 and basecalling was done in Guppy 4.2.2 (HAC) and Guppy 5.0.7
 (supHAC).
description: <b>Amplicon_sorter: a
 tool for reference-free amplicon sorting based on sequence similarity and
 for building consensus sequences</b> Andy
 Vierstraete<sup>*</sup>, Bart P. Braeckman Laboratory of aging physiology
 and Molecular Evolution, University of Gent, 9000 Gent, Belgium
 andy.vierstraete@ugent.be These data files were used for the above publication. Barcode_sequences.xlsx: contains the sequence of the different barcodes. Barcodes_species.xlsx: list of species and their corresponding barcodes. Sanger_references.fasta: the sanger references of the used species. HAC_data.zip: the fastq file basecalled with the High Accuracy option in Guppy. supHAC_data.zip: the fastq file basecalled with the Super Accuracy option in Guppy. The data files contain more barcodes and data than used in the publication.  The testrun was combined with samples from another lab that is working with fungi.
DOI: 10.5061/dryad.37pvmcvmt
title: Blast output from: Lost in dead wood? Environmental DNA sequencing from dead wood shows little signs of saproxylic beetles

description: eDNA metabarcoding has become a standard method for assessing
 wood-inhabiting fungi and bacteria, yet determination of
 dead-wood-inhabiting beetles still relies on time-consuming collection of
 beetle specimens. We thus tested whether beetle species can be identified
 by eDNA sequencing of wood in a mesocosm experiment that manipulated
 species assemblages. Dead wood samples were taken at exit holes of beetles
 and DNA was extracted and analyzed using two comparative methods: (i)
 metabarcoding with standard arthropod primers (421 bp) and (ii) using
 short species-specific primers (120-264 bp) with Sanger sequencing.
 Results showed that beetle DNA was amplified by each of the two
 approaches, however, with (i) we detected only one non-target saproxylic
 beetle species. In addition, we identified 80 different OTUs with four
 non-targeted species of arthropods. For (ii) we detected the targeted
 species in two fresh beetle exit holes out of 20 samples. We suggest that,
 in contrast to fungi and bacteria, this eDNA metabarcoding approach is not
 able to reliably detect saproxylic beetles from wood samples, likely due
 to rapid degradation of their target DNA. Adapting such an approach for
 large scale analyses thus requires a better knowledge of degradation
 processes affecting DNA quality and quantity in wood.
DOI: 10.25338/b86s6j
title: The causes and consequences of pest population variability in agricultural landscapes

description: Variability in population densities is key to the ecology of natural
 systems but also has great implications for agriculture. Farmers’
 decisions are heavily influenced by their risk-aversion to pest outbreaks
 that result in major yield losses. However, the need for long-term pest
 population data across many farms has prevented researchers from exploring
 the drivers and implications of pest population variability. Here, we
 demonstrate the critical importance of population variability for
 sustainable farming by analyzing 13-yrs of pest densities across
 &gt;1300 Spanish olive orchards and vineyards. Variable populations
 were more likely to cause major yield losses, but also occasionally
 created temporal windows when densities fell below insecticide spray
 thresholds. Importantly, environmental factors regulating pest variability
 were very distinct from factors regulating mean density, suggesting
 variability needs to be uniquely managed. Finally, we found diversifying
 landscapes may be a win-win for conservation and farmers, as diversified
 landscapes promote less abundant and less variable pest populations.
 Therefore, we encourage agricultural stakeholders to increase complexity
 of the landscapes surrounding their farms through conserving/restoring
 natural habitat and/or diversifying crops.
description: The Andalusian Government
 provides this large database containing pest and field management data for
 13 years (2006-2018) across Andalusia, Spain. This is an unusually rich
 data resource, as it contains detailed, long-term, and well-replicated
 pest observations. Specifically, personnel within the RAIF network (Red de
 Información y Alerta Fitosanitaria) monitor pest populations on
 privately-owned fields across the Andalusian region of Spain and advise
 farmers about when and how to manage pests based on economic injury
 thresholds and integrated pest management rules. Farmers in the RAIF
 network are encouraged to use integrated management criteria, such that
 insecticides are only applied when pest populations exceed economic injury
 thresholds (described below). The RAIF database also records several pest
 management practices, including applications of insecticides, herbicides,
 and fungicides, as well as tillage events. Finally, the database includes
 the identities of the crop cultivars, the cooperatives in which farmers
 are members, and the regions in which the fields are
 located.