cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ht76hdrfn
title: Migration distance is a fundamental axis of the slow-fast continuum of life history in boreal birds

description: Seasonal migration is intrinsically connected to the balance of survival
 and reproduction, but whether migratory behavior influences species’
 position on the slow-fast continuum of life history is poorly understood.
 We found that boreal-breeding birds that migrate long distances exhibit
 higher annual adult survival and lower annual reproductive investment
 relative to co-distributed boreal species that migrate shorter distances
 to winter closer to their breeding grounds. Our study uses “vital rates”
 data on reproductive output and survivorship compiled from the literature
 for a species assemblage of 45 species of mostly passerine birds. These
 species breed sympatrically in North American boreal forests but migrate
 to a diversity of environments for the northern winter. After controlling
 for body size and phylogeny, migration distance and apparent annual adult
 survival are positively related across species. Both migration distance
 and survival are positively correlated with wintering in environments that
 are warmer, wetter and greener. At the same time, longer migrations are
 associated with reduced time spent on the breeding grounds, lower clutch
 sizes, and lower fecundity (clutch size x maximum number of broods per
 year). Although seasonal migration is often associated with high
 mortality, our results suggest that long-distance migration imposes
 selection pressures that both confer and demand high adult survival rates.
 That is, owing to the reproductive cost of long-distance migration, this
 strategy can only persist if balanced by high adult survival. Our study
 supports the idea that migration evolves to promote survival of species
 breeding in seasonal environments. In boreal birds, the evolution of the
 longest migrations yields the highest survival, but at an inherent cost to
 annual fecundity. Our results therefore reveal migratory distance as a
 fundamental axis of the slow-fast continuum that predicts, and is
 inextricable from, the balance of survival and reproduction.
description: Data were collected and compiled from publically available
 sources. All data points for all variables used in the analyses and
 figures in the manuscript are published in Table S1 in the Supplementary
 Material of the manuscript, available through the publisher's
 website. The additional data files published in this Dryad archive include
 upstream and raw data from various sources that were used to compile the
 downstream variables published in Table S1.
description: Usage Notes are described in the file titled "READ
 ME.txt"
DOI: 10.5061/dryad.b5mkkwhd5
title: Channel Islands song sparrow (Melospiza melodia) landscape genomics and adaptation to climate with gene flow dataset

description: Disentangling the effects of neutral and adaptive processes in maintaining
 phenotypic variation across environmental gradients is challenging in
 natural populations. Song sparrows (Melospiza melodia) on the California
 Channel Islands occupy a pronounced east-west climate gradient within a
 small spatial extent, providing a unique opportunity to examine the
 interaction of genetic isolation (gene flow) and the environment
 (selection) in driving variation. We used reduced representation genomic
 libraries to infer the role of neutral processes (drift and restricted
 gene flow) and divergent selection in driving variation in
 thermoregulatory traits with an emphasis on the mechanisms that maintain
 bill divergence among islands. Analyses of 22,029 neutral SNPs confirm
 distinct population structure by island with restricted gene flow and
 relatively large effective population sizes, suggesting bill differences
 are likely not a product of genetic drift. Instead, we found strong
 support for local adaptation using 3,294 SNPs in differentiation-based and
 environmental association analyses coupled with genome-wide association
 (GWA) tests. Specifically, we identified several putatively adaptive and
 candidate loci in or near genes involved in bill development pathways
 (e.g., BMP, CaM, Wnt), confirming the highly complex and polygenic
 architecture underlying bill morphology. Furthermore, we found divergence
 in genes associated with other thermoregulatory traits (i.e., feather
 structure, plumage color, and physiology). Collectively, these results
 suggest strong divergent selection across an island archipelago results in
 genomic changes in a suite of traits associated with thermal adaptation
 over small spatial scales. Future research should move beyond the study of
 univariate traits to better understand the multivariate adaptive responses
 to these complex climate regimes.
description: 100-bp single-end RAD-sequencing data for population and
 landscape genomic analyses of Channel Island song sparrows in comparison
 to mainland California song sparrows.
description: Popmap.txt: Includes the individual IDs for each bird and their
 sampling region (CZ = Santa Cruz, RO = Santa Rosa, MI = San Miguel, AN =
 Anacapa, ML = Mainland California). VCF files for
 neutral analyses, tests for divergent selection, and GWAS with bill
 surface area. Phenotype and environment information for
 all birds used for GWAS and genotype-environmental association (GEAs)
 analyses are included as a .csv.
DOI: 10.6084/m9.figshare.31166176
title: Additional file 1 of Distinct genetic profiles of obesity have different effects on breast cancer risk: leveraging Mendelian randomisation to interrogate causal pathways and identify mediating proteins

description: Supplementary Material 1 Supplementary Table S1. Information on SNPs included in the MR-clust and the results from the clustering. Supplementary Table S2. Mendelian randomisation results for the effects of the three non-null clusters on protein measurements. Supplementary Table S3. Mendelian randomisation results for the effects of the protein measurements on risk of any type of breast cancer and stratified by ER status.
DOI: 10.6084/m9.figshare.31166176.v1
title: Additional file 1 of Distinct genetic profiles of obesity have different effects on breast cancer risk: leveraging Mendelian randomisation to interrogate causal pathways and identify mediating proteins

description: Supplementary Material 1 Supplementary Table S1. Information on SNPs included in the MR-clust and the results from the clustering. Supplementary Table S2. Mendelian randomisation results for the effects of the three non-null clusters on protein measurements. Supplementary Table S3. Mendelian randomisation results for the effects of the protein measurements on risk of any type of breast cancer and stratified by ER status.
DOI: 10.5061/dryad.p8cz8w9qg
title: Data from: Reversal of the adipostat control of torpor during migration in hummingbirds

description: Many small endotherms use torpor to reduce metabolic rate and manage daily
 energy balance. However, the physiological “rules” that govern torpor use
 are unclear. We tracked torpor use and body composition in ruby-throated
 hummingbirds (Archilochus colubris), a long-distance migrant, throughout
 the summer using respirometry and quantitative magnetic resonance. During
 the mid-summer, birds entered torpor at consistently low fat stores (~5%
 of body mass), and torpor duration was negatively related to evening fat
 load. Remarkably, this energy-emergency strategy was abandoned in the late
 summer when birds accumulated fat for migration. Migrating birds were more
 likely to enter torpor on nights when they had higher fat stores, and fat
 gain was positively correlated with the amount of torpor used. These
 findings demonstrate the versatility of torpor throughout the annual cycle
 and suggest a fundamental change in physiological feedback between
 adiposity and torpor during migration. Moreover, this study highlights the
 underappreciated importance of facultative heterothermy in migratory
 ecology.
description: This metadata describes the data and code used in “Reversal of
 the adipostat control of torpor during migration in hummingbirds".
 The objectives of the study were to clarify the rules of torpor use in
 hummingbirds, by investigating the relationship between body composition
 and torpor use in. We used respirometry to calculate rates of energy
 expenditure, and quantitative magnetic resonance (QMR) to measure body
 composition of captive ruby-throated hummingbirds (<em>Archilochus
 colubris</em>). The included R scripts and datasets are used to
 process, analyze, and plot data described in this study.
DOI: 10.5061/dryad.4b8gthtcj
title: Temporal dynamics of mildly deleterious nonsynonymous substitutions in mitochondrial gene sequences in rodents and moles

description: In our previous studies, the evolutionary rate (substitutions/site/million
 years) of mitochondrial DNA (mtDNA) in rodents and moles was estimated to
 be approximately 0.11 in more recent divergence times of a few tens of
 thousands of years and declined quickly to approximately 0.03 in more
 distant divergence times. However, the modes and mechanisms associated
 with the time dependency have not been well documented. We addressed the
 abundance of nonsynonymous substitutions that had appeared in the
 protein-coding region of mitochondrial cytochrome b gene
 sequences in rodents and moles, using sequences obtained from the
 nucleotide database. We collected 23 haplogroups with signals of
 late Quaternary population expansion events and categorized them into
 three groups. The expansion events were predicted to have started during
 the last 15,000 years (Group I), ca. 53,000 years ago (Group II), and
 130,000-230,000 years ago (Group III). We counted the numbers of
 nonsynonymous and synonymous substitutions in all haplogroups. The
 nonsynonymous substitution ratios were exclusively low (0.06–0.20) in
 Groups II and III. By contrast, the values in Group I varied markedly, and
 Group I could be further classified into two subgroups based on high
 (0.28–0.43) and low (0.09–0.20) values of the nonsynonymous substitution
 ratio, which were roughly associated with the time expansion started,
 suggesting that the shift from high to low values of the nonsynonymous
 substitution ratio occurred within the last 15,000 years. The Group II and
 III networks exhibited two- or three-step star-shaped structures and a
 trend of frequent nonsynonymous substitutions on exterior branches, which
 were less frequent on interior branches, supporting the idea that
 processing to remove nonsynonymous substitutions occurs over a short
 evolutionary time.  Based on temporal dynamics, nonsynonymous
 mtDNA substitutions in small mammals accounted for 40% of all
 substitutions during the very early evolutionary stage and then rapidly
 declined, dropping to approximately 15%. This process appears to have been
 completed in ca. 15,000 years. This is a good explanation of the
 time-dependent trend in the rate of mtDNA evolution predicted by previous
 studies.
DOI: 10.5061/dryad.zs7h44j8n
title: Data from: Reduced mitochondrial respiration in hybrid asexual lizards

description: The scarcity of asexual reproduction in vertebrates alludes to an inherent
 cost. Several groups of asexual vertebrates exhibit lower endurance
 capacity (a trait predominantly sourced by mitochondrial respiration)
 compared to congeneric sexual species. Here we measure endurance capacity
 in five species of Aspidoscelis lizards and examine mitochondrial
 respiration between sexual and asexual species using
 mitochondrial respirometry. Our results show reduced endurance capacity,
 mitochondrial respiration, and phenotypic variability in asexual species
 compared to parental sexual species along with a positive relationship
 between endurance capacity and mitochondrial respiration. Results of lower
 endurance capacity and lower mitochondrial respiration in asexual
 Aspidoscelis are consistent with hypotheses involving mitonuclear
 incompatibility. This repository includes files with DNA sequence
 alignments, evolutionary relationships, mitochondrial respiration, and
 endurance measurements for five species of whiptail lizards. Code used to
 analyze the data in the context of the study is also included.
DOI: 10.5061/dryad.d7wm37q1k
title: Data from: Heating rates are more strongly influenced by near-infrared than visible reflectance in beetles

description: Adaptations to control heat transfer through the integument are a key
 component of temperature regulation in animals. However, there remain
 significant gaps in our understanding of how different optical and
 morphological properties of the integument affect heating rates. To
 address these gaps, we examined the effect of reflectivity in both
 ultraviolet-visible and near-infrared wavelengths, surface
 micro-sculpturing, effective area (area subjected to illumination) and
 cuticle thickness on radiative heat gain in jewel beetles (Buprestidae).
 We measured heating rate using a solar simulator to mimic natural
 sunlight, a thermal chamber to control the effects of conduction and
 convection, and optical filters to isolate different wavelengths. We found
 that effective area and reflectivity predicted heating rate. The thermal
 effect of reflectivity was driven by variation in near-infrared rather
 than ultraviolet-visible reflectivity. By contrast, cuticle thickness and
 surface rugosity had no detectable effect. Our results provide empirical
 evidence that near-infrared reflectivity has an important effect on
 radiative heat gain. Modulating reflectance of near-infrared wavelengths
 of light may be a more widespread adaptation to control heat gain than
 previously appreciated.
DOI: 10.5061/dryad.66t1g1k26
title: Is phenotypic evolution affected by spiders’ construction behaviors?

description: What happens when organisms actively modify their environment? Clarifying
 the role of construction behavior on a macroevolutionary scale is crucial
 to interpreting phenotypic evolution. Spiders, an extremely successful
 group of animals exhibiting a wide variety of functional, morphological,
 and behavioral diversity, are ideal candidates to test whether animal
 behaviors are related to their phenotypic evolution. Herein, we
 reconstructed the phylogenomic relationships of 303 spiders covering 105
 families with 99 newly developed molecular markers that universally apply
 across Araneae, and explicitly tested the potential link between
 construction behavior and somatic evolution based on extensive
 morphological data from 3,342 extant species and 682 fossil species. Our
 dated molecular phylogeny provides the backbone for analyses, revealing
 the behavioral and ecological processes behind these spiders’
 morphological adaptations. Evolutionary model analyses showed the
 artifacts constructed by spiders, especially the suspending webs, expand
 the spider’s ability to inhabit different habitats. These artifacts have
 more substantial impacts on their somatic traits than habitats and promote
 different trajectories of morphological evolution. Specifically, for
 spiders, silk-lined burrowing produced larger bodies, relatively shorter
 legs, and longer patellae, while web-building produced smaller bodies,
 relatively long legs, and shorter patellae, and hunting promoted an
 intermediate morphological size. Molecular convergence analysis showed
 that genes related to morphogenesis or response to stimulus and stress are
 enriched in spiders with construction behavior. Our study demonstrated
 that the construction behavior of an animal plays a crucial role in
 determining the direction and intensity of the selection pressure imposed
 on it and provides strong evidence that construction behaviors are
 associated with phenotypic evolution on macroevolutionary timescales.
DOI: 10.5061/dryad.cc2fqz661
title: Wolbachia manipulate fitness benefits of olfactory associative learning in a parasitoid wasp

description: Upon encountering a host, a female parasitoid wasp has to decide whether
 to learn positive or negative cues related to a host. The optimal female
 decision will depend on the fitness costs and benefits of learned stimuli.
 Reward quality is positively related to the rate of behavioral acquisition
 in processes such as associative learning. Wolbachia, an endosymbiotic
 bacterium, often plays an impressive role in the manipulation of its
 arthropod host’s biology. Here we studied the responses of two natural
 Wolbachia infected/uninfected Trichogramma brassicae populations to
 theoretically high- and low- reward values during a conditioning process
 and the consequences of their responses in terms of memory duration.
 According to our results, uninfected wasps showed an attraction response
 to high value rewards, but showed aversive learning in response to low
 value rewards. Memory span of uninfected wasps after conditioning by
 low-value rewards was significantly shorter compared to high-value
 rewards. As our results revealed, responses to high quality hosts will
 bring more benefits (bigger size, increased fecundity and enhanced
 survival) compared to low-quality hosts for uninfected wasps. Infected
 wasps were attracted to conditioned stimuli with the same memory duration
 after conditioning by both types of hosts. This was linked to the fact
 that parasitoids emerging from both types of hosts present the same
 life-history traits. Therefore, these hosts represent the same quality
 reward for infected wasps. According to obtained results it can be
 concluded that Wolbachia manipulates the learning ability of its host
 resulting in the wasp responding to all reward values similarly.
DOI: 10.5061/dryad.3tx95x6gb
title: Videos related to: Noise matters: Elephants show risk-avoidance behaviour in response to human-generated seismic cues

description: African elephants (Loxodonta africana) use many sensory modes to gather
 information about their environment, including the detection of seismic,
 or ground-based, vibrations. Seismic information is known to include
 elephant-generated signals, but also potentially encompasses biotic cues
 that are commonly referred to as ‘noise’. To investigate seismic
 information transfer in elephants beyond communication, here we tested the
 hypothesis that wild elephants detect and discriminate between seismic
 vibrations that differ in their noise types, whether elephant- or
 human-generated. We played three types of seismic vibrations to elephants:
 seismic recordings of elephants (elephant-generated), white noise
 (human-generated), and a combined track (elephant & human
 generated). We found evidence of both detection of seismic noise and
 discrimination between the two treatments containing human-generated
 noise. In particular, we found evidence of retreat behaviour, where
 seismic tracks with human-generated noise caused elephants to move further
 away from the trial location. We conclude that seismic noise are cues that
 contain biologically-relevant information for elephants that they can
 associate with risk. This expands our understanding of how elephants use
 seismic information, with implications for elephant sensory ecology and
 conservation management.
description: Video data was collected during seismic playback experiments from
 a car separate from the car playing the seismic treatment (Figure 2a in
 main manuscript). Seismic playback was 6 minutes long, with 2 minutes of
 silence (a1 period), 2 minutes of seismic treatment (WN, Ele or
 Ele&WN, b period), then 2 minutes of silence (a2 period; Figure 1
 in main manuscript). Videos were cropped into these 2 minute segments (a1,
 b or a2) and assigned a random number for blind analysis of elephant
 behaviour. These two minute videos have been uploaded (in either .ts or
 .mp4 format) along with a key for their treatment type, family/sub-family
 group and focal individual identity (see
 'notes_on_videos.xlsx'). One video (33) uploaded was not used as
 elephant behavioural data in the main manuscript, but gives an example
 recording of car noise (Supplementary Figure 3).
description: Spreadsheet 'notes_on_videos' has three tabs.
 Treatment_key tab gives the number/title of the video and its
 corresponding family/sub-family group and the seismic treatment given. It
 also gives a key for the terms 'WN' 'Ele'
 'Ele&WN' (seismic playback treatments) 'a1'
 'b' and 'a2' (experimental periods). Focal_individuals
 tab gives details of which elephant in the video was the focal elephant,
 how visible they are in the video, notes on their identity,
 family/subfamily group and seismic treatment. Supp_Fig_3 tab gives more
 information on the videos that match the example recordings given in
 Supplementary Figure 3 - the elephant families, period, start and end
 times, distance from source and terrain related to these example
 recordings.
DOI: 10.5061/dryad.02v6wwq34
title: Data and code for Caves, Dixit, Colebrook-Robjent, Hamusikili, Stevens, Thorogood, and Spottiswoode: Hosts elevate either within-clutch consistency or between-clutch distinctiveness of egg phenotypes in defence against brood parasites

description: In host-parasite arms races, hosts can evolve signatures of identity to
 enhance detection of parasite mimics. In theory, signatures are most
 effective when within-individual variation is low (“consistency”), and
 between-individual variation is high (“distinctiveness”). However,
 empirical support for positive covariation in signature consistency and
 distinctiveness across species is mixed. Here we attempt to resolve this
 puzzle by partitioning distinctiveness according to how it is achieved:
 (1) greater variation within each trait, contributing to elevated
 “absolute distinctiveness” or (2) combining phenotypic traits in
 unpredictable combinations (“combinatorial distinctiveness”). We tested
 how consistency covaries with each type of distinctiveness by measuring
 variation in egg colour and pattern in two African bird families
 (Cisticolidae and Ploceidae) that experience mimetic brood parasitism.
 Contrary to predictions, parasitised species, but not unparasitised
 species, exhibited a negative relationship between consistency and
 combinatorial distinctiveness. Moreover, regardless of parasitism status,
 consistency was negatively correlated with absolute distinctiveness across
 species. Together, these results suggest that (i) selection from parasites
 acts on how traits combine rather than absolute variation in traits, (ii)
 consistency and distinctiveness are alternative rather than complementary
 elements of signatures, and (iii) mechanistic constraints may explain the
 negative relationship between consistency and absolute distinctiveness
 across species.
description: Please see associated Readme file.
description: Please see associated Readme file.
DOI: 10.6084/m9.figshare.31166229
title: Additional file 2 of Sorghum embryos undergoing B chromosome elimination express B-variants of mitotic-related genes

description: Additional file 2. Supplementary Table: Tables S1-S7 (file contains A chromosomes or B chromosome contigs length, +B and 0B counts in k-mer analysis and A/B contig identities (Table S1), B-contigs located genes together with their gene ontologies (Table S2), information about the samples used for RNA sequencing (Table S3), differential expression data (Table S4), GSEA results in whole embryo groups and sections RNA-seq data (Table S5), PISA analysis results (Table S6), sequencies of CENH3 proteins (Table S7)).
DOI: 10.6084/m9.figshare.31166229.v1
title: Additional file 2 of Sorghum embryos undergoing B chromosome elimination express B-variants of mitotic-related genes

description: Additional file 2. Supplementary Table: Tables S1-S7 (file contains A chromosomes or B chromosome contigs length, +B and 0B counts in k-mer analysis and A/B contig identities (Table S1), B-contigs located genes together with their gene ontologies (Table S2), information about the samples used for RNA sequencing (Table S3), differential expression data (Table S4), GSEA results in whole embryo groups and sections RNA-seq data (Table S5), PISA analysis results (Table S6), sequencies of CENH3 proteins (Table S7)).