cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.b2rbnzsk9
title: Autumn fueling behavior in passerines in relation to migratory distance and day length

description: Songbirds have evolved diverse strategies to cope with seasonality,
 including long-, medium-, and short-distance migration. There is some
 evidence that birds with a longer migration distance deposit fuel faster.
 However, most studies focus on long-distance migrants. Comparisons between
 species with different migration distances are necessary to broaden our
 understanding of fueling capacity in migratory birds. We present maximum
 fuel deposition rates of five songbird species migrating along the
 southeast coast of Sweden in autumn with migration distances ranging from
 long (neotropical migrant) to short (partial/irruptive migrant) (Willow
 Warbler P. trochilus, Lesser Whitethroat Curruca curruca, Common
 Chiffchaff Phylloscopus collybita, European Robin Erithacus rubecula, and
 Blue Tit Cyanistes caeruleus). The birds were fed ad libitum in captivity
 and were exposed to either extended or natural daylength. All species
 ceased to increase in mass when they reached a certain fuel load,
 generally corresponding to migration distance, despite unlimited access to
 food and ample time for foraging. Blue Tits, Willow Warblers, and Lesser
 Whitethroats had the highest fuel deposition rates with extended daylength
 (19%, 20%, and 20%, respectively), and about 13% with natural daylength,
 which is comparable to the highest rates found in migratory songbirds in
 nature. European Robins and Common Chiffchaffs that winter in the
 temperate Mediterranean had the lowest fuel deposition rates (12% and 12%
 with extended daylength, respectively). Our results suggest that the long-
 and short-distance migrants in this study have developed an extreme
 capacity for rapid refueling for different reasons; speedy migration to
 distant wintering grounds or winter survival in Scandinavia. This study
 contributes to our current knowledge of maximum fuel deposition rates in
 different species and the limitations posed by daylength. We highlight the
 need for future studies of species with different migration strategies in
 order to draw broad conclusions about fueling strategies of migratory
 birds.
description: LBM data: These data were collected as a part of the standardized
 ringing scheme at Ottenby Bird Observatory in Ottenby, Sweden.
 Fueling data: The data are from a fueling experiment where
 juvenile birds were captured during autumn migration and given ad libitum
 meal worms while being exposed to either an extended or natural daylength
 regime for up to 10 days. Maximum 24-hour fueling rates and maximum fuel
 loads were calculated from the data. Lean body mass was estimated using a
 linear regression relating wing length to body size. 
description: LBM data: The data were kindly provided by Ottenby Bird
 Observatory for the purpose of this project. Long-term ringing data can be
 requested from the Swedish Ringing Centre (Ringmärkningscentralen) or from
 Ottenby Bird Observatory.
DOI: 10.5061/dryad.mw6m90610
title: From bottom-up to top-down control of invertebrate herbivores in a retrogressive chronosequence

description: In the long-term absence of disturbance, ecosystems often enter a decline
 or retrogressive phase which leads to reductions in primary productivity,
 plant biomass, nutrient cycling and foliar quality. However, the
 consequences of ecosystem retrogression for higher trophic levels such as
 herbivores and predators, are less clear. Using a post-fire forested
 island-chronosequence across which retrogression occurs, we provide
 evidence that nutrient availability strongly controls invertebrate
 herbivore biomass when predators are few, but that there is a switch from
 bottom-up to top-down control when predators are common. This trophic flip
 in herbivore control probably arises because invertebrate predators
 respond to alternative energy channels from the adjacent aquatic matrix,
 which were independent of terrestrial plant biomass. Our results suggest
 that effects of nutrient limitation resulting from ecosystem retrogression
 on trophic cascades are modified by nutrient-independent variation in
 predator abundance, and this calls for a more holistic approach to trophic
 ecology to better understand herbivore effects on plant communities.
description: This dataset has been collected within the above mentioned study.
 It contains data on invertebrate biomass, herbivore damage and herbivore
 impact as well as information on several characteristics of 30 islands
 within a forested chronosequence. Details on how the data has been
 collected can be obtained from Kempel et al. 2022 (From bottom-up to
 top-down control of invertebrate herbivores in a retrogressive
 chronosequence) in the method section and supporting material. 
description: The code has been run with R version 4.1.2 (2021-11-01) --
 "Bird Hippie".
DOI: 10.5061/dryad.8kprr4xs1
title: Initiation of speciation across multiple dimensions in a rock-restricted, tropical lizard

description: Population isolation and concomitant genetic divergence, resulting in
 strong phylogeographic structure, is a core aspect of speciation
 initiation. If and how speciation then proceeds and ultimately completes
 depends on multiple factors that mediate reproductive isolation, including
 divergence in genomes, ecology, and mating traits. Here we explored these
 multiple dimensions in two young (Plio-Pleistocene) species complexes of
 gekkonid lizards (Heteronotia) from the Kimberley–Victoria River regions
 of tropical Australia. Using mtDNA screening and exon capture
 phylogenomics, we show that the rock-restricted H. planiceps exhibits
 exceptional fine-scale phylogeographic structure compared to the
 co-distributed habitat generalist H. binoei. This indicates pervasive
 population isolation and persistence in the rock-specialist, and thus a
 high rate of speciation initiation across this geographically complex
 region, with levels of genomic divergence spanning the "grey
 zone" of speciation. Proximal lineages of H. planiceps were often
 separated by different rock substrates suggesting a potential role for
 ecological isolation; however, phylogenetic incongruence and historical
 introgression were inferred between one such pair. Eco-morphological
 divergence among lineages within both H. planiceps and H. binoei was
 limited, except that limestone-restricted lineages of H. planiceps tended
 to be larger than rock-generalists. By contrast, among-lineage divergence
 in the chemical composition of epidermal pore secretions (putative mating
 trait) exceeded eco-morphology in both complexes, but with less trait
 overlap among lineages in H. planiceps. This system — particularly the
 rock-specialist H. planiceps — highlights the role of multidimensional
 divergence during incipient speciation, with divergence in genomes,
 eco-morphology, and chemical signals all at play at very fine spatial
 scales.
DOI: 10.5061/dryad.msbcc2g2k
title: Data for taxon-dependent effects of dispersal limitation versus environmental filters on bryophyte assemblages―Multiple perspective studies in land-bridge islands

description: Aim: To explore the taxon-dependent contribution of dispersal limitation
 vs. environmental filters to bryophyte assemblages. Location: The Thousand
 Island Lake, China Taxon: Bryophytes Methods: We compared the observed
 beta diversity with the expected values based on six null models (EE, EF,
 FE, FF, PE, PF) and detected the partial correlation of beta diversity
 with geographical distances. We quantified the contributions of spatial
 vs. environmental variables, and island isolation per se to species
 composition (SC) by using variance partitioning. We modeled the
 species-area relationships (SARs) for bryophytes and other eight biotas.
 To explore the taxon-dependent effects of spatial vs. environmental
 filters on bryophytes, sixteen taxa including five categories (total
 bryophytes, total mosses, liverworts, acrocarpous and pleurocarpous
 mosses) and eleven species-richest families were included in the analyses.
 Results: The observed beta diversity values were significantly different
 from the predicted values based on the six null models for all 16 taxa.
 For all five categories, the observed partial correlations between beta
 diversity and geographical distance after controlling environmental
 effects were not only positive but also significantly different from the
 predicted values based on the null models. Spatial eigenvectors are more
 important in shaping SC than environmental variables for all 16 taxa
 except Brachytheciaceae and Anomodontaceae. Spatial eigenvectors
 contributed more to SC variation in liverworts than in mosses, and in
 pleurocarpous mosses than in acrocarpous mosses. The effects of island
 isolation on SC were significant for all five categories and varied highly
 at the family level. The z-values of the SARs for the five bryophyte
 categories were all larger than those of the other eight biotas. Main
 conclusions: In subtropical fragmented forests, dispersal limitation
 exerted significant, taxon-dependent effects on bryophyte assemblages. It
 was dispersal limitation rather than environmental filtering that
 predominantly regulated SC patterns of bryophytes.
DOI: 10.5061/dryad.mw6m90612
title: Time-dependent benefits of camouflage strategies on heterogeneous backgrounds

description: Background-matching camouflage is a well-established strategy to reduce
 detection, but implementing this on heterogeneous backgrounds is
 challenging. For prey with fixed colour patterns, solutions include
 specialising on a particular visual microhabitat or adopting a compromise
 or generalist appearance, matching multiple backgrounds imperfectly.
 Existing studies suggest both approaches can succeed, but most consider
 relatively simple scenarios, where artificial prey appear against two
 backgrounds differing in a single visual characteristic. Here, we used
 computer-based search tasks with human participants to test the relative
 benefits of specialising and generalising for complex targets, displayed
 on either two or four types of naturalistic backgrounds. Overall, across
 two background types, specialisation was beneficial, though its success
 varied with search duration, such that generalist targets could outperform
 specialists in the first seconds of each search event. Against four
 different backgrounds, the initial cost to specialisation was greater, so
 specialists and generalists ultimately experienced similar survival.
 Generalists performed better when their patterning was a compromise
 between backgrounds that were more similar to each other than when
 backgrounds were more different, with similarity in luminance more
 relevant than pattern differences. Time-dependence in the relative success
 of these strategies suggests that predator search behaviour may affect
 optimal camouflage in real-world situations.
DOI: 10.5061/dryad.51c59zwcb
title: Global warming facilitates the nesting of the loggerhead turtle on the Mediterranean coast of Spain

description: Temperature data loggers were deployed in 2015, 2016 and 2017 at simulated
 loggerhead sea turtle nests in 52 beaches scattered along the
 Mediterranean coast of Spain. Results demonstrated that sand temperature
 is currently high enough to allow the incubation of loggerhead
 turtles' clutches in most Spanish beaches. The data set provides with
 average sand temperature in simulated nests at 40 cm deep (one simulated
 net per beach, one beach in each sheet, each year in a different column).
 Data are missing for some years at certain beaches because the data logger
 did not work or was not recovered.
description: Data loggers recorded sand temperature every 30 minutes. Daily
 average is provided. Only data from June 1st to October 31st were analyzed
 by Cardona et al. (2022). Cells
 highlighted in yellow denote the onset and the end of the viable
 incubation window.
description: Excel file.
DOI: 10.5061/dryad.h70rxwdnk
title: Seasonal pigment fluctuation in diploid and polyploid Arabidopsis revealed by machine learning-based phenotyping method PlantServation (Part 2/2)

description: Long-term field monitoring of leaf pigment content is informative for
 understanding plant responses to environments distinct from regulated
 chambers but is impractical by conventional destructive measurements. We
 developed PlantServation, a method incorporating robust image-acquisition
 hardware and deep learning-based software that extracts leaf color by
 detecting plant individuals automatically. As a case study, we applied
 PlantServation to examine environmental and genotypic effects on the
 pigment anthocyanin content estimated from leaf color. We analyzed
 &gt;4 million images of small individuals of four Arabidopsis species
 in the field, where the plant shape, color, and background vary over
 months. Past radiation, coldness, and precipitation significantly affected
 the anthocyanin content. The synthetic allopolyploid A. kamchatica
 recapitulated the fluctuations of natural polyploids by integrating
 diploid responses. The data support a long-standing hypothesis stating
 that allopolyploids can inherit and combine the traits of progenitors.
 PlantServation facilitates the study of plant responses to complex
 environments termed “in natura”.
description: Top-view images of <em>Arabidopsis</em> were
 collected multiple times per day using commercial RGB cameras in a common
 garden in Japan for three seasons. Labelling data were
 generated by manually marking the areas of target plants in
 images. Scripts were produced for analyzing the images
 and color and size information of the target plants extracted from the
 images. 
description: Labelling data (.json files) can be opened using labelme in
 python. R scripts (.r files) can be opened in R or as a
 text file. Python scripts (in
 script_7_for_Dataset_8_Fig_S29) can be opened in Python or as a text
 file.
DOI: 10.5061/dryad.7m0cfxpzf
title: Incomplete reproductive barriers and genomic differentiation impact the spread of resistance mutations between green- and red-colour morphs of a cosmopolitan mite pest

description: We studied patterns of genetic differentiation and barriers to gene flow
 within and between morphs of T. urticae in
 order to understand the factors that influence the spread of
 resistance mutations across its populations. We derived multiple
 iso-female lines from Tetranychus populations collected
 from agricultural crops. We generated genomic and morphological data,
 characterized their bacterial communities, and performed controlled
 crosses.
description: The datasets were collected in controlled laboratory experiments
 involving reciprocal crosses and morphological measurements using
 different populations of <em>Tetranychus</em> mites.
DOI: 10.5061/dryad.95x69p8ph
title: High virulence is associated with pathogen spreadability in a songbird-bacterial system

description: How directly-transmitted pathogens benefit from harming hosts is key to
 understanding virulence evolution. It is recognized that pathogens benefit
 from high within-host loads, often associated with virulence. However,
 high virulence may also directly augment spread of a given amount of
 pathogen, here termed “spreadability”. We used house finches and the
 conjunctival pathogen Mycoplasma gallisepticum to test
 whether two components of virulence– the severity of conjunctival
 inflammation and behavioral morbidity produced– predict pathogen
 spreadability. We applied ultraviolet powder around the conjunctiva of
 finches that were inoculated with pathogen treatments of
 distinct virulence and measured within-flock powder spread, our proxy for
 “spreadability”. When compared to uninfected controls, birds infected with
 a high-virulence, but not low-virulence, pathogen strain, spread
 significantly more powder to flockmates. Relative to controls,
 high-virulence treatment birds both had more severe conjunctival
 inflammation– which potentially facilitated powder shedding– and longer
 bouts on feeders, which serve as fomites. However, food peck rates and
 displacements with flockmates were lowest in the high-virulence treatment
 relative to controls, suggesting inflammatory rather than behavioral
 mechanisms likely drive augmented spreadability at high virulence. Our
 results suggest that inflammation associated with virulence can facilitate
 pathogen spread to conspecifics, potentially favoring virulence evolution
 in this system and others.
description: The dataset was collected using 45 wild-caught house finches that
 were housed in groups in an outdoor aviary. One bird per flock  (termed
 the "index" bird) was treated with one of three pathogen
 treatments: sham inoculation controls, infection with a low-virulence
 strain of the bacterial pathogen Mycoplasma gallisepticum, or infected
 with a high-virulence strain of Mycopasma gallisepticum. We have three
 types of data collection that resulted in three .csv files: first birds
 were captured at multiple timepoints to assess eye scores in response to
 treatment, take swabs for pathogen load, and to apply or collect data on
 UV powder spread as our metric of spreadability. Second, we collected
 behavioral data (foraging bout lengths at feeder ports and displacement
 interactions at feeder ports) via Radio Frequency Identification Devices
 that were present at each feeding port, and recorded the presence and
 duration of any bird at the feeder port via the PIT tags embedded in each
 birds color bands. Finally, we took video data and, by watching videos,
 collected information on the number of times that each bird stuck its head
 into the feeder port during the time it sat on the feeder port.
description: R (open-source) is the only program needed to process and our
 data files, which are all in .csv or .txt format.
DOI: 10.5061/dryad.3j9kd51nv
title: Female great tits (Parus major) reproduce earlier when paired with a male they prefer

description: Mate choice is a key component of reproductive biology. Females often
 prefer certain males but do females modulate their reproductive investment
 depending on whether they are mated with their preferred partner? We
 investigated this question in great tits (Parus major) where we subjected
 36 females to a six-choice mate preference test. Male morphological traits
 and the female’s own characteristics did not influence the preference
 females expressed. We did find that females spent significantly more time
 near more exploratory males. We then paired them with one of the males in
 aviaries and subsequently monitored their reproductive investment (through
 measurement of plasma 17β-oestradiol concentrations, first egg date,
 clutch size, and egg size). Females that were mated with a male for which
 they had a strong preference laid their first clutch significantly earlier
 in the season than females paired with a male they less preferred. Our
 results show that mate preference influences reproductive investment in
 great tits, thereby linking mate choice to bird reproductive decisions.
DOI: 10.15468/dl.ahrhez
title: Occurrence Download

description: A dataset containing 37 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gigasiphon macrosiphon",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 37 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003371-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.k6djh9w9w
title: Recovery from heat-induced infertility: A study of reproductive tissue responses and fitness consequences in male Drosophila melanogaster

description: The predicted temperature increase caused by climate change is a threat to
 biodiversity. Across animal taxa, male reproduction is often sensitive to
 elevated temperatures leading to fertility loss and in more adverse
 scenarios, this can result in sterility when males reach their upper
 thermal fertility limit. Here we investigate temperature-induced changes
 in reproductive tissues, fertility reduction, sterility, and the
 associated fitness loss during the subsequent recovery phase in male
 Drosophila melanogaster. We heat-stressed males during development and
 either allowed them to recover or not in early adulthood, while measuring
 several determinants of male reproductive success. We found significant
 differences in recovery rate, organ sizes, sperm production, and other key
 reproductive traits among males from our different temperature treatments.
 Sperm maturation was impaired before reaching the upper thermal sterility
 threshold. While some effects were reversible, this did not compensate for
 the fitness loss due to damage imposed during development. Surprisingly,
 developmental heat stress was damaging to accessory gland growth, and
 female post-mating responses mediated by seminal fluid proteins were
 impaired regardless of the possibility of recovery. We suggest that
 sub-lethal thermal sterility and the subsequent fertility reduction is
 caused by a combination of inefficient functionality of both the accessory
 gland and testes.
description: We add to the novel and
 rapidly increasing field conduction investigations into the consequences
 of elevated temperature on reproductive performance in insects. We used
 the model <em>Drosophila melanogaster</em> for a comprehensive
 study and measured multiple determinants of male reproductive success to
 understand the impact of elevated temperatures on the functionality of
 both reproductive tissues: the testis and the accessory
 gland.
DOI: 10.5061/dryad.f4qrfj70k
title: Early diversification of avian limb morphology and the role of modularity in the locomotor evolution of crown birds

description: High disparity among avian forelimb and hind limb segments in crown birds
 relative to non-avialan theropod dinosaurs, potentially driven by the
 origin of separate forelimb and hind limb locomotor modules, has been
 linked to the evolution of diverse avian locomotor behaviors. However,
 this hypothesized relationship has not been quantitatively investigated in
 a phylogenetic framework. We assessed the relationship between the
 evolution of limb morphology and locomotor behavior by comparing a
 numerical proxy for locomotor diversity to morphospace sizes derived from
 a dataset of 1241 extant species. We then estimated how limb disparity
 accumulated during the crown avian radiation. Lastly, we tested whether
 limb segments evolved independently between each limb module using
 phylogenetically informed regressions. Disparity increased significantly
 with behavioral diversity after accounting for clade age and species
 richness. We found that forelimb disparity accumulated rapidly early in
 avian evolution, whereas hindlimb disparity accumulated later, in more
 recent divergences. We recovered little support for strong correlations
 between forelimb and hind limb morphology. We posit that these findings
 support independent evolution of locomotor modules that enabled the
 striking morphological and behavioral diversity of extant birds.