cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.cvdncjt1z
title: Breeding success of Eleonora’s falcon in Cyprus revisited using survey techniques for cliff-nesting species

description: The global breeding population of Eleonora’s Falcon (Falco eleonorae) is
 distributed from the Canary Islands in the west, across the Mediterranean
 Sea, to Cyprus in the east. The remoteness of nesting colonies, which are
 predominantly located on sea cliffs and islets, renders breeding success
 estimation a challenging task, requiring a composite approach to assess
 each of the breeding stages. Early estimates of the breeding success of
 Eleonora’s Falcon suggested that the Akrotiri colony in Cyprus had the
 lowest breeding success among all the colonies throughout the species’
 breeding range, at a level seemingly unsustainable, suggesting the colony
 might have been in danger of gradual extinction. Here we use a diversity
 of survey methods including boat, ground, and aerial surveys, with the
 incorporation of photography and photogrammetry, to reassess the breeding
 success and the effect of nest characteristics on the Eleonora’s Falcon
 breeding population in Cyprus. During a 6-yr study, we found that Cyprus
 hosts ~138 ± 8 breeding pairs and that breeding success equals 1.54 ± 0.85
 fledglings per breeding pair, and thus is considerably higher than
 previous estimates. In addition, by analyzing temporal variation in
 breeding and nest characteristics, we found that early breeding and reuse
 of nests positively influence breeding success, but physical nest
 characteristics have a limited effect on colony productivity. The range of
 survey methods employed, as well as the array of photography techniques
 utilized, enhanced the efficiency and accuracy of this study, allowing us
 to overcome the challenge of inaccessibility of nesting cliffs.
description: The dataset is raw survey data from monitoring Eleonora's
 falcon nest sites using a variety of methods described in the paper. Also
 included in separate sheets are the code used to analyse the data - R code
 for statistical analyses and python code to produce a digital surface
 model of the nesting cliffs.
description: The raw data used in statistical analyses are all provided along
 with the R code. The data have all been combined here into one dataset
 though analyses were performed on subsets of the data as described in the
 manuscript. The script to produce the digital surface model is provided
 but we do not provide exact coordinates because of sensitivity of falcon
 nest sites to disturbance.
DOI: 10.5061/dryad.hhmgqnkdt
title: Escape from natural enemies depends on the enemies, the invader, and competition

description: The enemy release hypothesis (ERH) attributes the success of some exotic
 plant species to reduced top-down effects of natural enemies in the
 non-native range relative to the native range. Many studies have tested
 this idea, but very few have considered the simultaneous effects of
 multiple kinds of enemies on more than one invasive species in both the
 native and non-native ranges. Here, we examined the effects of two
 important groups of natural enemies – insect herbivores and soil biota –
 on the performance of Tanacetum vulgare (native to Europe but invasive in
 the USA) and Solidago canadensis (native to the USA but invasive in
 Europe) in their native and non-native ranges, and in the presence and
 absence of competition. In the field, we replicated full-factorial
 experiments that crossed insecticide, T. vulgare-S. canadensis
 competition, and biogeographic range (Europe vs. USA) treatments. In
 greenhouses, we replicated full-factorial experiments that crossed soil
 sterilization, plant-soil feedback, and biogeographic range treatments. We
 evaluated the effects of experimental treatments on T. vulgare and S.
 canadensis biomass. The effects of natural enemies were idiosyncratic. In
 the non-native range and relative to populations in the native range, T.
 vulgare escaped the negative effects of insect herbivores but not soil
 biota, depending upon the presence of S. canadensis; and S. canadensis
 escaped the negative effects of soil biota but not insect herbivores,
 regardless of competition. Thus, biogeographic escape from natural enemies
 depended upon the enemies, the invader, and competition. By explicitly
 testing the ERH in terms of more than one kind of enemy, more than one
 invader, and more than one continent, this study enhances our nuanced
 perspective of how natural enemies can influence the performance of
 invasive species in their native and non-native ranges.
description: Field and greenhouse studies that manipulated above- and
 belowground enemies were replicated in the native and non-native ranges of
 Solidago canadensis and Tanacetum vulgare.
description: Data was formatted specifically for analysis in R.  
 The files "Jena.csv", "USA.csv", and
 "Hungary.csv" give the data for experimental manipulations of
 aboveground enemies and competition in the field.  The files
 "Soil.csv" and "RAW_Soil.csv" give the data for
 experimental manipulations of soil biota in the greenhouse.
DOI: 10.5061/dryad.0cfxpnvzv
title: Contemporary adaptive divergence of plant competitive traits in urban and rural populations and its implication for weed management

description: 1. Competition among neighboring plants plays essential roles in growth,
 reproduction, population dynamics, and community assembly, but how
 competition drives local adaptation and the traits underlying the
 adaptation remain unclear. Here, we focused on populations of the
 aggressive weed Digitaria ciliaris from urban and rural habitats as low-
 and high-competition environments for light resources and examined how
 competitive interaction drove contemporary adaptive divergence of
 competitive traits. 2. To examine local adaptation to different
 competitive environments in D. ciliaris and the specific traits that have
 been selected for, we compared growth rate and competitive traits in
 plants from farmland and urban populations between high- and
 low-competition treatments. Furthermore, we conducted a field tillage
 experiment with drone (UAV) monitoring to examine the possibility that
 trait evolution in farmland habitats might influence weed management
 practices in crop fields. 3. Plants from farmland populations had higher
 growth rates than plants from urban populations in high-competition
 treatments, and vice versa in low-competition treatments. Among
 populations, those with larger height/width ratios (farmland populations)
 were more tolerant of aboveground competition in high-competition
 treatments, but among individuals, those with larger ratios had lower
 growth rates in low-competition treatments. More plants from farmland
 populations, which had thicker stems (and larger height/width ratios),
 survived after experimental tillage than plants from urban habitats with
 thinner stems. 4. Synthesis. Our study empirically demonstrated adaptive
 divergence in competitive traits in aboveground competitors and its
 underlying traits. Moreover, contemporary adaptive divergence between
 urban and rural plant populations has practical implications for weed
 control. The urban–rural model system can thus contribute to both basic
 and applied research in plant evolutionary ecology. Further research is
 required to understand adaptive divergence in plants between urban and
 rural environments, and the traits underlying the adaptation, not only
 aboveground, but also belowground.
DOI: 10.5061/dryad.2jm63xsm6
title: Shade alters grass growth and architecture by reducing root biomass

description: Variable tree cover characterizes tropical grassy biomes. Light
 availability in the ground layer becomes increasingly limited as tree
 cover increases while open canopy environments are associated with a
 flammable grassy ground layer. Grass species dominating the ground layer
 of these ecosystems have adopted strategies to persist and proliferate
 with frequent fire. However, there is limited understanding of how grass
 growth and flammability traits respond to changes in light availability.
 We experimentally grew 14 grass species characteristic of the Malagasy
 Central Highlands for one year with four treatments of light exclusion
 ranging from 0 – 60%. Six plant functional traits and four leaf
 flammability traits were measured: plant height, bulk density, aboveground
 biomass, belowground biomass, ratio of root to shoot biomass, specific
 leaf area, leaf heat release capacity, temperature of maximum
 decomposition, total heat release and peak heat release rate. Belowground
 biomass, the ratio of root to shoot biomass and bulk density were
 substantially negatively affected by decreasing light availability while
 aboveground biomass showed no significant change although, there was a
 trend towards smaller plants at high shade. Specific leaf area increased
 with declining light availability. In terms of leaf flammability,
 unexpectedly, only leaf total heat release was significantly positively
 affected and the other traits were not. These suggest that any field
 alterations in grass flammability would be primarily underpinned by
 changes in plant architecture and potentially microclimate. The reductions
 observed in belowground biomass suggests that grasses would be rapidly
 lost from shaded environments with a diminished competitive capacity to
 resprout.
DOI: 10.5061/dryad.xgxd254dj
title: Fossil microbodies are melanosomes: evaluating and rejecting the ‘fossilised decay-associated microbes’ hypothesis

description: Melanosomes are membrane-bound organelles of varying geometry, commonly
 found within a range of vertebrate tissues, that contain the pigment
 melanin. Melanosomes have been identified in the fossil record in many
 exceptionally preserved fossils allowing reconstructions of the coloration
 of many extinct animals. However, these microstructures have also been
 interpreted as “microbial cells” or melanin producing bacteria based on
 their geometric similarities to melanosomes. Here we test these two
 conflicting hypotheses experimentally. Our results demonstrate multiple
 lines of evidence that these fossil microbodies are indeed melanosomes:
 the geometry of decay-associated microbes differs significantly from
 fossil microbodies; fossil microbodies are very strongly localized to in
 vivo melanized tissues and are absent in tissues typically unmelanized in
 vivo, in all fossils examined regardless of lithology or age. On the basis
 of these results, as well as a thorough review of existing literature on
 melanin like pigments, we are able to rule out a bacterial origin for
 fossil microbodies and demonstrate that fossil microbodies associated with
 exceptional vertebrate fossils are in fact preserved melanosomes.
description: This raw dataset has been
 collected by measuring modern melanosome samples, fossil microbodies in
 exceptionally preserved fossils and experimental decay microbial consortia
 from scanning electron micrographs. The variables measured and tabulated
 in this dataset are length, diameter and aspect ratio (length/diameter).
 Summary statistics of raw data are included in Sheet 9.
description: Guide to Dataset Usage File Name:
 DATA_Dryad_Roy et al. 2020 File organisation
 |- Sheet 1: Fig 1 - Shape and size profiles of modern
 melanosomes, fossil microbodies and microbes from decay
 experiments. |- Sheet 2: Modern melanosome
 samples |- Sheet 3: Microbodies from isolated fossil
 feathers |- Sheet 4: Microbodies from fossil feathers
 attached to skeletal material |- Sheet 5: Microbes from
 experimental decay of isolated feathers |- Sheet 6:
 Microbes from experimental decay of bird carcasses (1 week of
 decay) |- Sheet 7: Microbes from experimental decay of
 bird carcasses (2 weeks of decay) |- Sheet 8: Microbes
 from experimental decay of tadpoles |- Sheet 9: Summary
 statistics There are missing values in Sheet 6 and
 Sheet 7 due to failure of microbial growth during the decay
 experiments.
DOI: 10.5061/dryad.f7m0cfxsz
title: Data from: What’s in a colluvial deposit? New perspectives from archaeopedology.

description: Colluvial deposits are considered as sedimentary archives for the
 reconstruction of soil erosion history, Holocene climate, past pedogenesis
 and land use. However, the human contribution to the formation of
 colluvial deposits is mainly based on quantitative assumptions derived
 from the local chronostratigraphy and archaeology. For this reason, there
 is often a substantial gap in the qualitative identification of specific
 land use practices that caused prehistoric soil erosion. We use an
 archaeopedological multi-proxy approach on a multi-layered colluvial
 deposit (six colluvial horizons) at the prehistoric site of Fürstenberg
 (Southwest Germany) to gain detailed insights into the soil erosion
 history, past pedogenesis and land use practices since the Neolithic. Soil
 and geochemical analyses such as X-ray fluorescence (XRF), X-ray
 diffraction (XRD), pedogenic oxides, pH-value and calcium carbonate
 content support the chronostratigraphy based on ages from optically
 stimulated luminescence (OSL) and AMS 14C dating. Further, biogeochemical
 analyses of phytoliths, charcoal spectra, black carbon (BC), soil organic
 matter (SOM) composition by using pyrolysis-field ionization mass
 spectroscopy (Py-FIMS), urease activity, steroid biomarker and heavy
 metals (HM) are used as land use proxies. The OSL and 14C ages indicate
 five phases of colluvial deposition and land use comprising the Early to
 Younger Neolithic, the Urnfield to Hallstatt period, the Iron to Roman
 Age, the High Middle Ages and the pre-modern period. The soil and
 geochemical proxies correlate with a phase of geomorphodynamic stability
 between the Early to Younger Neolithic and the Urnfield to Hallstatt
 period. The high abundance of grass morphotypes since the Neolithic and
 the increase of Juniperus species since the Urnfield to Hallstatt period
 indicate a persistent anthropogenic impact on the vegetation. Considerable
 amounts of burned OM (up to 1600 g BC kg-1 SOC, also identified as
 thermally stabilized SOM compounds by Py-FIMS) at greater soil depths
 provide information that fire clearing (e.g. slash-and-burn) was
 especially used to open and maintain the landscape until the Roman Age.
 The absence of phytolith species originating from cereals, the occurrence
 of Juniperus and the evidence from the analysis of urease activity and
 faecal biomarkers indicate that the slopes of the Fürstenberg were mainly
 used for livestock farming and wood procurement. Thus, the application of
 specific soil-biogeochemical proxies to colluvial deposits provide new
 information on the nature of past land use practices that caused soil
 erosion and the formation of colluvial deposits at that time. In general,
 archaeopedological multi-proxy analyses of colluvial deposits, integrating
 the local archaeological record, contributes to a refined understanding of
 how humans have shaped the landscape since the Neolithic.
DOI: 10.15468/dl.gum5w4
title: Occurrence Download

description: A dataset containing 981 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Biserrula pelecinus",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 981 records from 70 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002439-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5dv41ns43
title: The genetic ancestry of American Creole cattle inferred from uniparental and autosomal genetic markers

description: Cattle imported from the Iberian Peninsula spread throughout America in
 the early years of discovery and colonization to originate Creole breeds,
 which adapted to a wide diversity of environments and later received
 infuences from other origins, including zebu cattle in more recent years.
 We analyzed uniparental genetic markers and autosomal microsatellites in
 DNA samples from 114 cattle breeds distributed worldwide, including 40
 Creole breeds representing the whole American continent, and samples from
 the Iberian Peninsula, British islands, Continental Europe, Africa and
 American zebu. We show that Creole breeds difer considerably from each
 other, and most have their own identity or group with others from
 neighboring regions. Results with mtDNA indicate that T1c-lineages are
 rare in Iberia but common in Africa and are well represented in Creoles
 from Brazil and Colombia, lending support to a direct African infuence on
 Creoles. This is reinforced by the sharing of a unique Y-haplotype between
 cattle from Mozambique and Creoles from Argentina. Autosomal
 microsatellites indicate that Creoles occupy an intermediate position
 between African and European breeds, and some Creoles show a clear Iberian
 signature. Our results confrm the mixed ancestry of American Creole cattle
 and the role that African cattle have played in their development.
DOI: 10.5061/dryad.ghx3ffbkw
title: Data from: Study of regional differences in GC content values in chromosomes of the guppy and related fish species

description: Genetic and physical mapping of the guppy (P. reticulata) have shown that
 recombination patterns differ greatly between males and females. Crossover
 events occur evenly across the chromosomes in females, but in male meiosis
 they are restricted to the tip furthest from the centromere of each
 chromosome, creating very high recombination rates per megabase, similar
 to the high rates in of pseudo-autosomal regions (PARs) of mammalian sex
 chromosomes. We here used the intronic GC content to indirectly infer the
 recombination patterns on guppy chromosomes. This is based on evidence
 that recombination is associated with GC-biased gene conversion, so that
 genome regions with high recombination rates should be detectable by high
 GC content. We used intron sequences and 3rd positions of codons,
 in order to make comparisons between sequences that are matched,
 as far as possible, with respect to selective constraints. Both these
 types of sites are likely to be under weak selection. Almost all guppy
 chromosomes, including the sex chromosome (LG12), prove to have very high
 GC values near their assembly ends, suggesting high recombination rates
 due to strong crossover localisation in male meiosis. Our test does not
 suggest that the guppy XY pair has stronger crossover localisation than
 the autosomes, or than the homologous chromosome in a closely related
 fish, the platyfish (Xiphophorus maculatus). We therefore conclude that
 the guppy XY pair has not recently undergone an evolutionary change to a
 different recombination pattern, or reduced its crossover rate, but that
 the guppy evolved Y-linkage due to acquiring a male-determining factor
 that also conferred the male crossover pattern. The results also identify
 the centromere ends of guppy chromosomes, which were not determined in the
 guppy genome assembly. 
description: Python and r code files for intronic GC analyses in the chromosomes of 3 fish species, based on published and unpublished short-read genome sequences and annotated genes.
description: No other files are needed. The files include 2 files with scripts
 for the analysis, and the files with results after analyses.
DOI: 10.5061/dryad.05qfttf0w
title: Population genomic, olfactory, dietary, and gut microbiota analyses demonstrate the unique evolutionary trajectory of feral pigs

description: Domestication is an intriguing evolutionary process. Many domestic
 populations are subjected to strong human-mediated selection, and when
 some individuals return to the wild, they are again subjected to selective
 forces associated with new environments. Generally, these feral
 populations evolve into something different from their wild predecessors
 and their members typically possess a combination of both wild and human
 selected traits.  Feralisation can manifest in different forms on
 a spectrum from a wild to a domestic phenotype. This depends on how the
 re-wilded domesticated populations can re-adapt to natural environments
 based on how much potential and flexibility the ancestral genome retains
 after its domestication signature. Whether feralisation leads to
 the evolution of new traits that do not exist in the wild or to
 convergence with wild forms, however, remains unclear. To address this
 question, we performed population genomic, olfactory, dietary, and gut
 microbiota analyses on different populations of Sus
 scrofa (wild boar, hybrid, feral and several domestic pig
 breeds). Porcine Single Nucleotide Polymorphisms (SNPs) analysis shows
 that the feral population represents a cluster distinctly separate from
 all others. Its members display signatures of past artificial selection,
 as demonstrated by values of FST in specific regions of
 the genome and bottleneck signature, such as the number and length of runs
 of homozygosity. Generalised FST values, re-acquired
 olfactory abilities, diet, and gut microbiota variation show current
 responses to natural selection. Our results suggest that feral pigs are an
 independent evolutionary unit which can persist so long as levels of human
 intervention remain unchanged.
DOI: 10.5061/dryad.7sqv9s4qg
title: Data from: Evolution of starvation resistance in an invasive insect species, Aethina tumida (Coleoptera: Nitidulidae)

description: Starvation resistance, or the ability to survive periods without food, can
 shed light on selection pressure imposed by food scarcity, including
 chances to invade new regions as a result of human transport. Surprisingly
 little information is known about starvation resistance for invasive
 insect species. Given that native and invasive populations differ in
 starvation resistance, this would suggest different selection scenarios
 and adaptive shifts fostering invasion success. Here, we show striking
 differences in starvation resistance of adult small hive beetles Aethina
 tumida (SHB) between native and invasive populations. In the laboratory,
 starvation resistance of freshly-emerged laboratory-reared and
 field-collected adult females and males was evaluated in the beetle’s
 native African range and in their invasive North American range. SHB in
 their native African range survived longer than SHB in their invasive
 North American range. Across ranges, females survived longer than males.
 Field-collected SHB survived in Africa longer than freshly-emerged ones,
 but not in the invasive range. This suggests no selection for starvation
 resistance in the invasive range, possibly due to differences between
 African and European-derived honey bee hosts facilitating a tradeoff
 scenario between reproduction and starvation resistance. The ability of
 adult females to survive up to two months without food appears to be one
 factor contributing to the invasion success of this species. Assuming food
 availability is usually high in the invasive ranges, and trade-offs
 between starvation resistance and fecundity/reproduction are common, it
 seems as if selection for starvation resistance during transport could set
 up potential trade-offs that enhance reproduction after invasion. It would
 be interesting to see if this is a possible general pattern for invasive
 insect species.
DOI: 10.5061/dryad.pzgmsbchp
title: Data from: Comparing the indirect effects between exploiters in predator-prey and host-pathogen systems

description: DataS1 These files are Maple and Matlab scripts for analyzing the
 predator-prey and host-pathogen models in "Comparing the indirect
 effects between exploiters in predator-prey and host-pathogen
 systems" and generating the figures in that study.