cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r4xgxd28f
title: Demographic fluctuations lead to rapid and cyclic shifts in genetic structure among populations of an alpine butterfly, Parnassius smintheus

description: Many populations, especially in insects, fluctuate in size and periods of
 particularly low population size can have strong effects on genetic
 variation. Effects of demographic bottlenecks on genetic diversity of
 single populations are widely documented. Effects of bottlenecks on
 genetic structure among multiple inter-connected populations are less
 studied, as are genetic changes across multiple cycles of demographic
 collapse and recovery. We take advantage of a long-term dataset comprising
 demographic, genetic, and movement data from a network of populations of
 the butterfly, Parnassius smintheus, to examine the effects of fluctuating
 population size on spatial genetic structure. We build on a previous study
 that documented increased genetic differentiation and loss of spatial
 genetic patterns (isolation by distance and by intervening forest cover)
 after a network-wide bottleneck event. Here, we show that genetic
 differentiation was reduced again and spatial patterns returned to the
 system extremely rapidly, within three years (i.e., generations). We also
 show that a second bottleneck had similar effects to the first, increasing
 differentiation and erasing spatial patterns. Thus, bottlenecks
 consistently drive random divergence of allele frequencies among
 populations in this system, but these effects are rapidly countered by
 gene flow during demographic recovery. Our results reveal a system in
 which the relative influence of genetic drift and gene flow continually
 shift as populations fluctuate in size, leading to cyclic changes in
 genetic structure. Our results also suggest caution in the interpretation
 of patterns of spatial genetic structure, and its association with
 landscape variables, when measured at only a single point in time.
description: The data files provide microsatellite genotypes, in Genepop
 format, for the years 2008 and 2013 for the butterfly <em>Parnassius
 smintheus</em>. Landscape data and microsatellite genotypes for the
 years 1995 and 2005, which are also used in the manuscript, are available
 under the following Dryad entry: Caplins, Serena A. et al. (2015), Data
 from: Landscape structure and the genetic effects of a population
 collapse, v2, Dryad, Dataset,
 https://doi.org/10.5061/dryad.d715g.
DOI: 10.5061/dryad.cjsxksn2r
title: Evolution of a conspicuous melanin-based ornament in gulls Laridae

description: Melanin- and carotenoid-based ornaments often signal different aspects of
 individual quality or similar aspects under different environmental
 conditions and, thus, they may become evolutionarily integrated into a
 composite sexual trait. On the other hand, functionally and
 developmentally different characters (e.g. coloration characters of
 different developmental origin) are more likely to evolve independently
 from each other than more similar traits. Here, we examined evolutionary
 correlations between the occurrence of a conspicuous melanin-based
 ornament (hood) and carotenoid-based bare-part ornaments within gull
 family. We also aimed to identify major ecological, life-history, and
 biogeographical predictors of hood occurrence and reconstruct evolutionary
 history of this ornament. We found that hood occurrence was associated
 with red or dark coloration of unfeathered traits (bill and legs), while
 combinations of hood with yellow carotenoid-based coloration of integument
 were evolutionarily avoided. Also, hood occurrence correlated negatively
 with the occurrence of other melanin-based plumage character (mantle).
 Breeding latitude and habitat were identified as major predictors of hood
 occurrence in gulls, as hoods were recorded more frequently in
 low-latitude and inland (rather than marine) species. Finally, our
 analysis provided support for evolutionary lability in hood occurrence,
 with a dominance of transitions towards hood loss in the evolutionary
 history of gulls. The results of our study provide one of the first
 evidence for a correlated evolution of melanin- and carotenoid-based
 ornaments in an avian lineage, which supports evolutionary modularity of
 developmentally and functionally different coloration traits.
DOI: 10.5061/dryad.6djh9w0xd
title: Kelp forests at the end of the earth: 45 years later

description: The kelp forests of southern South America are some of the least disturbed
 on the planet. The remoteness of this region has, until recently, spared
 it from many of the direct anthropogenic stressors that have negatively
 affected these ecosystems elsewhere. Re-surveys of 11 locations at the
 easternmost extent of Tierra del Fuego originally conducted in 1973 showed
 no significant differences in the densities of adult and juvenile
 Macrocystis pyrifera kelp or kelp holdfast diameter between the two survey
 periods. Additionally, sea urchin assemblage structure at the same sites
 were not significantly different between the two time periods, with the
 dominant species Loxechinus albus accounting for 66.3% of total sea urchin
 abundance in 2018 and 61.1% in 1973. Time series of Landsat imagery of the
 region from 1998 to 2018 showed no long-term trends in kelp canopy over
 the past 20 years. However, ~ 4-year oscillations in canopy fraction were
 observed and were strongly and negatively correlated with the NOAA
 Multivariate ENSO index and sea surface temperature. More extensive
 surveying in 2018 showed significant differences in benthic community
 structure between exposed and sheltered locations. Fish species endemic to
 the Magellanic Province accounted for 73% of all nearshore species
 observed and from 98-100% of the numerical abundance enumerated at sites.
 Fish assemblage structure varied significantly among locations and wave
 exposures. The recent creation of the Yaganes Marine Park is an important
 step in protecting this unique and biologically rich region; however, the
 nearshore waters of the region are currently not included in this
 protection. There is a general lack of information on changes in kelp
 forests over long time periods, making a global assessment difficult. A
 complete picture of how these ecosystems are responding to human pressures
 must also include remote locations and locations with little to no impact.
description: Characterization of the benthos was conducted by scuba divers
 along two 25-m long transects.Transects were run parallel to the
 shoreline. For sessile and mobile invertebrates, the number of individuals
 was estimated on 1-m of either side of the transect line (50
 m<sup>2</sup>). For colonial organisms (sponges, some
 cnidarians, bryozoans, and some tunicates) colonies, rather than
 individuals, were counted. Only non-cryptic invertebrates ≥ 1 cm were
 enumerated. For fish surveys, a scuba diver counted and
 sized all fishes within 1-m of either side of a 25 m transect line (50
 m<sup>2</sup>) at each survey site. The transect extended to
 the surface or as far as visibility allowed, including species associated
 with the kelp canopy and water column. Total fish lengths were estimated
 to the nearest cm. In addition, photographs were taken <i>in
 situ</i> to assist with species identification, document underwater
 coloration, and associated habitat.
DOI: 10.5061/dryad.tmpg4f4vp
title: Identification and characterization of QTLs for fruit quality traits in peach through a multi-family approach

description: Background Fruit quality traits have a significant effect on consumer
 acceptance and subsequently on peach (Prunus persica (L.) Batsch)
 consumption. Determining the genetic bases of key fruit quality traits is
 essential for the industry to improve fruit quality and increase
 consumption. Pedigree-based analysis across multiple peach pedigrees can
 identify the genomic basis of complex traits for direct implementation in
 marker-assisted selection. This strategy provides breeders with
 better-informed decisions and improves selection efficiency and,
 subsequently, saves resources and time. Results Phenotypic data of seven
 F1 low to medium chill full-sib families were collected over 2
 years at two locations and genotyped using the 9 K SNP Illumina array. One
 major QTL for fruit blush was found on linkage group 4 (LG4) at 40–46 cM
 that explained from 20 to 32% of the total phenotypic variance and showed
 three QTL alleles of different effects. For soluble solids concentration
 (SSC), one QTL was mapped on LG5 at 60-72 cM and explained from 17 to 39%
 of the phenotypic variance. A major QTL for titratable acidity (TA)
 co-localized with the major locus for low-acid fruit (D-locus). It was
 mapped at the proximal end of LG5 and explained 35 to 80% of the
 phenotypic variance. The new QTL for TA on the distal end of LG5 explained
 14 to 22% of the phenotypic variance. This QTL co-localized with the QTL
 for SSC and affected TA only when the first QTL is homozygous for high
 acidity (epistasis). Haplotype analyses revealed SNP haplotypes and
 predictive SNP marker(s) associated with desired QTL alleles. Conclusions
 A multi-family-based QTL discovery approach enhanced the ability to
 discover a new TA QTL at the distal end of LG5 and validated other QTLs
 which were reported in previous studies. Haplotype characterization of the
 mapped QTLs distinguishes this work from the previous QTL studies.
 Identified predictive SNPs and their original sources will facilitate the
 selection of parents and/or seedlings that have desired QTL alleles. Our
 findings will help peach breeders develop new predictive, DNA-based
 molecular marker tests for routine use in marker-assisted breeding.
DOI: 10.15139/s3/okyliu
title: Data Management and Sharing Plan for: Design and implementation of a social cognitive theory-based medication adherence coaching intervention

description: The Data Management and Sharing Plan describes the scientific data to be generated and/or used in the research and outlines a strategy for managing and sharing project data.
description: Data Management and Sharing Plan
DOI: 10.5061/dryad.fttdz08pc
title: Additive negative effects of decadal warming and nitrogen addition on grassland community stability

description: 1. Much recent research has explored how global warming and increased
 nitrogen (N) deposition, two important components of global environmental
 changes, influence the structure and functioning of natural ecosystems.
 However, how ecosystem dynamics respond to the combination of long-term
 warming and N enrichment remains largely unexplored. 2. We investigated
 the impact of warming and N addition on the temporal stability of plant
 communities in a decade-long field experiment, conducted in a desert
 steppe in northern China, using a split-plot design with warming as the
 main-plot factor and N addition as the split-plot factor. 3. Long-term
 warming and N addition had additive, negative effects on plant community
 stability. A warming-induced decrease in species richness was not a
 significant driver of decreased community stability, which was instead
 driven by the decreased stability of dominant species under warming. On
 the other hand, a N-induced decrease in community stability was ascribed
 to both decreased stability of dominant and common species and decreased
 asynchronous population dynamics under N addition. 4. Synthesis. Our
 results suggest that ongoing anthropogenic environmental changes may have
 appreciable consequences for the stability of natural grassland functions
 and services while also highlighting the different mechanisms associated
 with the similar effects of climate warming and increased N deposition on
 grassland community stability.
DOI: 10.5061/dryad.gmsbcc2jb
title: Data from: Upper tidal flats are disproportionately important for the conservation of migratory shorebirds

description: Migratory animals are crucial for global ecosystems, yet many species are
 threatened by human activities. Coastal shorebirds along the East
 Asian-Australasian Flyway have experienced precipitous declines over the
 past three decades, primarily due to the rapid development of the tidal
 flats, their major stopover habitat. However, populations of several
 species have declined must faster than the rate of habitat loss. To
 explain this discrepancy, we quantified the foraging distribution of 17
 migratory shorebirds throughout the tidal cycle at two critical stopover
 sites. We found that shorebirds exhibit substantial interspecific and even
 site-specific differences in their foraging distributions. Notwithstanding
 these differences, however, the upper tidal flats prove to be especially
 important to most shorebirds by providing more than 70% of their
 cumulative foraging time, two-fold higher than its proportional area.
 Because coastal development typically starts near the high-tide line and
 proceeds outward, the upper tidal flats are also more prone to
 development, which may help to explain why shorebird populations have
 declined much faster than the overall rate of tidal flat loss. Our work
 highlights the importance of protecting upper tidal flats to conserve
 these migratory shorebirds, and demonstrates the need for detailed
 ecological understanding in effective conservation planning.
DOI: 10.5061/dryad.280gb5mmr
title: Adaptive evolution of honeybee dance dialects

description: Efficient communication is highly important for the evolutionary success
 of social animals. Honeybees (genus Apis) are unique in that they
 communicate the spatial information of resources using a symbolic
 “language”, the waggle dance. Different honeybee species differ in
 foraging ecology but it remains unknown whether this shaped variation in
 the dance. We studied distance dialects – interspecific differences in how
 waggle duration relates to flight distance – and tested the hypothesis
 that these evolved to maximize communication precision over the bees’
 foraging ranges. We performed feeder experiments with Apis cerana, A.
 florea and A. dorsata in India and found that A. cerana had the steepest
 dialect, i.e. a rapid increase in waggle duration with increasing feeder
 distance, A. florea had an intermediate, and A. dorsata had the
 lowest dialect. By decoding dances for natural food sites, we inferred
 that the foraging range was smallest in A. cerana, intermediate in A.
 florea and largest in A. dorsata. The inverse correlation between
 foraging range and dialect was corroborated when comparing six
 (sub)species across the geographic range of the genus including previously
 published data. We conclude that dance dialects constitute adaptations
 resulting from a trade-off between the spatial range and the spatial
 accuracy of communication.
DOI: 10.5061/dryad.dbrv15dxk
title: Whole-genome analysis across ten songbird families within Sylvioidea reveals a novel autosome–sex chromosome fusion

description: Sex chromosomes in birds have long been considered to be extremely stable.
 However, this notion has lately been challenged by findings of independent
 autosome–sex chromosome fusions within songbirds, several of which occur
 within a single clade, the superfamily Sylvioidea. To understand what
 ecological and evolutionary processes drive changes in sex chromosome
 systems, we need complete descriptions of sex chromosome diversity across
 taxonomic groups. Here, we characterize the sex chromosome systems across
 Sylvioidea using whole-genome data of species-representatives of ten
 different families, including two published and eight new genomes. We
 describe a novel fusion in the family Cisticolidae (represented by
 Cisticola juncidis) involving a part of chromosome 4. We also confirm the
 previously identified fusion between chromosome Z and a part of chromosome
 4A in all ten families and show that fusions involving parts of chromosome
 3 and 5 are not found outside the families where they were first
 discovered (Alaudidae and Panuridae). These findings add to the complexity
 of the sex chromosome system in Sylvioidea, where four independent
 autosome–sex chromosome fusions have now been identified.
DOI: 10.5061/dryad.kprr4xh1r
title: All or nothing: switch to high current reproductive investment under risk of starvation in male kelp crab

description: One of the key features in reproduction of polygynous species is seminal
 recovery after mating. However, it is poorly known how environmental
 factors affect the recuperation period of seminal material. This study
 aims to test plasticity in recovery of seminal reserves in response to
 distinct environmental conditions of the kelp crab Taliepus dentatus. Male
 crabs were maintained after depletion of seminal reserves in one of eight
 different treatments in a factorial design of temperature (12°C and 16°C),
 food availability (with alimentation and food deprivation) and time period
 (15 and 30 days), simulating different environmental situations in the
 laboratory to which the crab might be exposed to along its distribution.
 Temperature and food availability modulated the seminal recovery period in
 T. dentatus. Complete replenishment was reached within 30 days in all
 treatments (i.e., 12°C and 16°C each with alimentation and food
 deprivation) but the highest recovery index was found in crabs without
 food provision (16°C). In this condition, the recovery index was twice as
 high compared to males maintained at a similar temperature but with
 feeding. Prolonged starvation at 16°C may be extremely stressful
 conditions for male crabs, during which risk to die probably triggered a
 concentration of the reproductive effort in favor of immediate
 reproduction. This suggests that plasticity of energy allocation towards
 reproduction may be expressed during extremely suboptimal conditions,
 which might be a similar strategy as proposed by the terminal investment
 hypothesis. The generally relatively fast seminal recovery regardless of
 the temperature may explain the kelp crab´s continuous mating throughout
 the year.
description: Methods are descriped in detail in the published
 article. The dataset corresponds to Figures 3a/b and
 4a/b and to the relationship between the vasa deferentia dry weight and
 carapace length.
description: <strong>Column electroejaculation:</strong>
 0 = crabs without initial electroejaculation.
 1 = crabs initially electroejaculated.
DOI: 10.5061/dryad.zcrjdfn76
title: Description and classification of echolocation clicks of Indian Ocean humpback (Sousa plumbea) and Indo-Pacific bottlenose (Tursiops aduncus) dolphins from Menai Bay, Zanzibar, East Africa

description: Passive acoustic monitoring (PAM) is a powerful method to study the
 occurrence, movement and behavior of echolocating odontocetes (toothed
 whales) in the wild. However, in areas occupied by more than one species,
 echolocation clicks need to be classified into species. The present study
 investigated whether the echolocation clicks produced by small, at-risk,
 resident sympatric populations of Indian Ocean humpback dolphin (Sousa
 plumbea) and Indo-Pacific bottlenose dolphin (Tursiops aduncus) in Menai
 Bay, Zanzibar, East Africa, could be classified to allow species specific
 monitoring. Underwater sounds of S. plumbea and T. aduncus groups were
 recorded using a SoundTrap 202HF in January and June-August 2015. Eight
 acoustic parameters, i.e. -10 dB duration, peak, centroid, lower -3 and
 lower -10 dB frequencies, and -3 dB, -10 dB and root-mean-squared
 bandwidth, were used to describe and compare the two species’ echolocation
 clicks. Statistical analyses showed that S. plumbea clicks had
 significantly higher peak, centroid, lower -3 and lower -10 dB frequencies
 compared to T. aduncus, whereas duration and bandwidth parameters were
 similar for the two species. Random Forest (RF) classifiers were applied
 to determine parameters that could be used to classify the two species
 from echolocation clicks and achieved 28.6% and 90.2% correct species
 classification rates for S. plumbea and T. aduncus, respectively. Both
 species were classified at a higher rate than expected at random, however
 the identified classifiers would only be useful for T. aduncus monitoring.
 The frequency and bandwidth parameters provided most power for species
 classification. Further study is necessary to identify useful classifiers
 for S. plumbea. This study represents a first step in acoustic description
 and classification of S. plumbea and T. aduncus in the western Indian
 Ocean region, with potential application for future acoustic monitoring of
 species-specific temporal and spatial occurrence in these sympatric
 species.
DOI: 10.5061/dryad.2bvq83bm8
title: Data from: Thalamus and focal to bilateral seizures: a multi-scale cognitive imaging study

description: Objective To investigate the functional correlates of recurrent
 secondarily generalized seizures in temporal lobe epilepsy (TLE), using
 task-based fMRI as a framework to test for epilepsy-specific network
 rearrangements. As the thalamus modulates propagation of temporal-lobe
 onset seizures and promotes cortical synchronization during cognition, we
 hypothesized that occurrence of secondarily generalized, i.e. focal to
 bilateral tonic-clonic seizures (FBTCS), would relate to thalamic
 dysfunction, altered connectivity and whole-brain network centrality.
 Methods FBTCS occur in a third of patients with TLE and are a major
 determinant of disease severity. In this cross-sectional study, we
 analyzed 113 patients with drug-resistant TLE (55 left/58 right), who
 performed a verbal fluency fMRI task that elicited robust thalamic
 activation. Thirty-three patients (29%) had experienced at least one FBTCS
 in the year preceding the investigation. We compared patients with
 TLE-FBTCS to those without FBTCS via a multi-scale approach, entailing
 analysis of SPM12-derived measures of activation, task-modulated thalamic
 functional connectivity (psychophysiological interaction), and
 graph-theoretical metrics of centrality.  Results Individuals
 with TLE-FBTCS had less task-related activation of bilateral thalamus,
 with left-sided emphasis, and left hippocampus than those without FBTCS.
 In TLE-FBTCS, we also found greater task-related thalamotemporal and
 thalamo-motor connectivity, and higher thalamic degree and betweenness
 centrality. Receiver operating characteristic curves, based on a combined
 thalamic functional marker, accurately discriminated individuals with and
 without FBTCS. Conclusions In TLE-FBTCS, impaired task-related thalamic
 recruitment coexists with enhanced thalamotemporal connectivity and
 whole-brain thalamic network embedding. Altered thalamic functional
 profiles are proposed as imaging biomarkers of active secondary
 generalization.
description: Details in relation to data collection and processing details are
 provided in the main manuscript text. The uploaded material
 contains: -Supplementary Methods (Appendix
 e-1) -Supplementary Results (Appendix e-2)
 -Two supplementary Figures (Figure e-1, Figure e-2)
 -Two supplementary Tables (Table e-1, Table e-2)
 -Additional references (e-References), cited in the supplementary
 material only.
description: No specific usage notes.