cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.w6m905qpn
title: DNA sequence data - Bicyclus

description: Compared to other regions, the drivers of diversification in Africa are
 poorly understood. We studied a radiation of insects with over 100 species
 occurring in a wide range of habitats across the Afrotropics to
 investigate the fundamental evolutionary processes and geological events
 that generate and maintain patterns of species richness on the continent.
 By investigating the evolutionary history
 of Bicyclus butterflies within a phylogenetic framework,
 we inferred the group’s origin at the Oligo-Miocene boundary from
 ancestors in the Congolian rainforests of central Africa. Abrupt climatic
 fluctuations during the Miocene (ca. 19–17 Ma) likely fragmented
 ancestral populations, resulting in at least eight early-divergent
 lineages. Only one of these lineages appears to have diversified during
 the drastic climate and biome changes of the early Miocene, radiating into
 the largest group of extant species. The other seven lineages diversified
 in forest ecosystems during the late Miocene and Pleistocene when climatic
 conditions were more favorable—warmer and wetter. Our results suggest
 changing Neogene climate, uplift of eastern African orogens, and biotic
 interactions have had different effects on the various subclades
 of Bicyclus, producing one of the most spectacular butterfly
 radiations in Africa.
description: Of the 102 currently recognized Bicyclus species, 94 (92%) were
 included in this study (Supplementary
 Appendix S1 available on Dryad at http://dx.doi.org/10.5061/dryad.qz612jmcb). The included samples covered all 16 currently recognized species-groups (Aduse-Poku et al. 2017). We also included the two recognized species of its sister genus, <em>Hallelesis</em> (<em>H. halyma</em> and <em>H. asochis</em>) and 11 other closely related satyrinae taxa as outgroups, selected on the basis of evolutionary relationships recovered in two earlier higher-level phylogenetic studies (Espeland et al. 2018; Chazot et al. 2019). We used a total of ten protein-coding loci: one mitochondrial (cytochrome c oxidase subunit I, COI) and nine nuclear (carbamoyl phosphate synthetase domain protein, CAD; ribosomal protein S5, RpS5; ribosomal protein S2, RpS2; wingless, wgl; cytosolic malate dehydrogenase, MDH; glyceraldehyde-3-phosphate dehydrogenase, GAPDH; elongation factor 1 alpha, EF-1αα⁠; and arginine kinase, ArgKin and isocitrate dehydrogenase, IDH) (Wahlberg and Wheat 2008). Most sequences used in this study were obtained from Aduse-Poku et al. (2017); additional sequences from six taxa were obtained using the protocols described in that study. All sequences were aligned manually using BioEdit 7.2 (Hall 1999) with properties and reading frames of protein-coding genes examined in MEGA X 10.0.5 (Kumar et al. 2018). Individual gene trees were first generated using IQ-TREE 1.6.11 (Nguyen et al. 2015) to check for contamination and sequence quality. Cleaned sequences were then concatenated to produce a final matrix of up to 7735 aligned nucleotides from 107 taxa (Supplementary Appendix S1 available on Dryad).
DOI: 10.5061/dryad.kprr4xh4v
title: Gene conversion facilitates the adaptive evolution of self-resistance in highly toxic newts

description: Reconstructing the histories of complex adaptations and identifying the
 evolutionary mechanisms underlying their origins are two of the primary
 goals of evolutionary biology. Taricha newts, which contain high
 concentrations of the deadly toxin tetrodotoxin (TTX) as an antipredator
 defense, have evolved resistance to self-intoxication, which is a complex
 adaptation requiring changes in six paralogs of the voltage-gated sodium
 channel (Nav) gene family, the physiological target of TTX. Here, we
 reconstruct the origins of TTX self-resistance by sequencing the entire
 Nav gene family in newts and related salamanders. We show that moderate
 TTX resistance evolved early in the salamander lineage in three of the six
 Nav paralogs, preceding the proposed appearance of tetrodotoxic newts by
 ~100 million years. TTX-bearing newts possess additional unique
 substitutions across the entire Nav gene family that provide physiological
 TTX resistance. These substitutions coincide with signatures of positive
 selection and relaxed purifying selection, as well as gene conversion
 events, that together likely facilitated their evolution. We also identify
 a novel exon duplication within Nav1.4 encoding an expressed TTX-binding
 site. Two resistance-conferring changes within newts appear to have spread
 via nonallelic gene conversion: in one case, one codon was copied between
 paralogs, and in the second, multiple substitutions were homogenized
 between the duplicate exons of Nav1.4. Our results demonstrate that gene
 conversion can accelerate the coordinated evolution of gene families in
 response to a common selection pressure.
DOI: 10.7280/d14979
title: Methyl bromide atmosphere-ocean box model code, inputs, and outputs

description: This dataset contains the source code and necessary inputs to run the
 6-box atmosphere ocean model described in Saltzman et al., 2021 and
 Nicewonger et al., 2021. The model outputs described in Saltzman et al.
 are also described.
DOI: 10.5061/dryad.34tmpg4kc
title: Data for: Transgenerational plasticity in the eye size of Daphnia

description: It is well established that environmental signals can induce phenotypic
 responses that persist for multiple generations. The induction of such
 'transgenerational plasticity' (TGP) depends upon the ability of
 organisms to accurately receive and process information from environmental
 signals. Thus, sensory systems are likely intertwined with TGP. 
 Here we tested the link between an environmental stressor and
 transgenerational responses in a component of the sensory system (eye
 size) that is linked to enhanced vision and ecologically-relevant
 behaviors. We reared 45 clones of Daphnia pulicaria in the presence and
 absence of a low-quality resource (cyanobacteria) and evaluated shifts in
 relative eye size in offspring. Our results revealed divergent shifts in
 relative eye size within- and across-generations. Parental Daphnia that
 were fed cyanobacteria produced a smaller eye than Daphnia fed high
 quality algae. Such differences were then reversed in the offspring
 generation; Daphnia whose mothers were fed cyanobacteria produced larger
 eyes than Daphnia that were continually fed green algae. We discuss the
 extent to which this maternal effect on eye size is an adaptive response
 linked to improved foraging.
DOI: 10.5061/dryad.dfn2z351q
title: Data from: Reference genome of Lumpfish Cyclopterus lumpus Linnaeus provides evidence of male heterogametic sex determination through the AMH pathway

description: Teleosts exhibit extensive diversity of sex determination (SD) systems and
 mechanisms, providing the opportunity to study the evolution of sex
 determination and sex chromosomes. Here we sequenced the genome of the
 Common Lumpfish (Cyclopterus lumpus Linnaeus), a species of increasing
 importance to aquaculture, and identified the SD region and master SD
 locus using a 70K SNP array and tissue-specific expression data. The
 chromosome-level assembly identified 25 diploid chromosomes with a total
 size of 572.89 Mb, a scaffold N50 of 23.86 Mb, and genome annotation
 predicted 21,480 protein-coding genes. Genome wide association analysis
 located a highly sex-associated region on chromosome 13, suggesting that
 anti-Müllerian hormone (AMH) is the putative SD factor. Linkage
 disequilibrium and heterozygosity across chromosome 13 support a
 proto-XX/XY system, with an absence of widespread chromosome divergence
 between sexes. We identified three copies of AMH in the Lumpfish primary
 and alternate haplotype assemblies localized in the SD region. Comparison
 to sequences from other teleosts suggested a monophyletic relationship and
 conservation within the Cottioidei. One AMH copy showed similarity to
 AMH/AMHY in a related species and was also the only copy with expression
 in testis tissue, suggesting this copy may be the functional copy of AMH
 in Lumpfish. The two other copies arranged in tandem inverted duplication
 were highly similar, suggesting a recent duplication event. This study
 provides a resource for the study of early sex chromosome evolution and
 novel genomic resources that benefits Lumpfish conservation management and
 aquaculture.
DOI: 10.5281/zenodo.18397119
title: BEYOND "DOING NOTHING": IVANHOE'S RENDERING OF WUWEI IN THE DAODEJING (CHS. 1, 3, 37, 48), WITH LAU, HENRICKS, AND AMES AND HALL AS CONTEXT
DOI: 10.5281/zenodo.18397118
title: BEYOND "DOING NOTHING": IVANHOE'S RENDERING OF WUWEI IN THE DAODEJING (CHS. 1, 3, 37, 48), WITH LAU, HENRICKS, AND AMES AND HALL AS CONTEXT
DOI: 10.6076/d1js3z
title: DEPP: Deep learning enables extending species trees using single genes

description: Placing new sequences onto reference phylogenies is increasingly used for
 analyzing environmental samples, especially microbiomes. However, existing
 placement methods have a fundamental limitation: they assume that query
 sequences have evolved using specific models directly on the reference
 phylogeny. Thus, they can place single-gene data (e.g., 16S rRNA
 amplicons) onto their own gene tree. This practice is a proxy for a more
 ambitious goal: extending a (genome-wide) species tree given data from
 individual genes. No algorithm currently addresses this challenging
 problem. Here, we introduce Deep-learning Enabled Phylogenetic Placement
 (DEPP), an algorithm that learns to extend species trees using single
 genes without pre-specified models. We show that DEPP updates the
 multi-locus microbial tree-of-life with single genes with high accuracy.
 We further demonstrate that DEPP can achieve the long-standing goal of
 combining 16S and metagenomic data onto a single tree, enabling community
 structure analyses that were previously impossible and producing robust
 patterns.
description: Visit this link to view the most recent version of this dataset:
 https://doi.org/10.6076/D14G68
DOI: 10.5061/dryad.7wm37pvsv
title: Dietary vitamin E reaches the mitochondria in the flight muscle of zebra finches but only if they exercise

description: Whether dietary antioxidants are effective for alleviating oxidative costs
 associated with energy-demanding life events first requires they are
 successfully absorbed in the digestive tract and transported to sites
 associated with reactive species production (e.g. the mitochondria).
 Flying birds are under high energy and oxidative demands, and although
 birds commonly ingest dietary antioxidants in the wild, the
 bioavailability of these consumed antioxidants is poorly understood. We
 show for the first time that an ingested lipophilic antioxidant,
 α-tocopherol, reached the mitochondria in the flight muscles of a songbird
 but only if they regularly exercise (60 min of perch-to-perch flights two
 times in a day or 8.5 km day-1). Deuterated α-tocopherol was found in the
 blood of exercise-trained zebra finches within 6.5 hrs and in isolated
 mitochondria from pectoral muscle within 22.5 hrs, but never reached the
 mitochondria in caged sedentary control birds. This rapid pace (within a
 day) and extent of metabolic routing of a dietary antioxidant to muscle
 mitochondria means that daily consumption of such dietary sources can help
 to pay the inevitable oxidative costs of flight muscle metabolism, but
 only when combined with regular exercise.
DOI: 10.6076/d1f300
title: Data-driven versus consensus diagnosis of MCI: enhanced sensitivity for detection of dementia progression, biomarker status, and neuropathological outcomes

description: Objective: Given prior work demonstrating that mild cognitive impairment
 (MCI) can be empirically differentiated into meaningful cognitive
 subtypes, we applied actuarial methods to comprehensive neuropsychological
 data from the University of California San Diego (UCSD) Alzheimer’s
 Disease Research Center (ADRC) in order to identify cognitive subgroups
 within nondemented ADRC participants, and to examine cognitive, biomarker,
 and neuropathological trajectories. Methods: Cluster analysis was
 performed on baseline neuropsychological data (n=738; mean age=71.8).
 Survival analysis examined progression to dementia (mean follow-up=5.9
 years). CSF AD biomarker status and neuropathological findings at
 follow-up were examined in a subset with available data. Results: Five
 clusters were identified: "optimal" cognitively normal
 (CN; n=130) with above-average cognition, "typical" CN
 (n=204) with average cognition, non-amnestic MCI (naMCI; n=104), amnestic
 MCI (aMCI; n=216), and mixed MCI (mMCI; n=84). Progression to dementia
 differed across MCI subtypes (mMCI&gt;aMCI&gt;naMCI), with the
 mMCI group demonstrating the highest rate of CSF biomarker positivity and
 AD pathology at autopsy. Actuarial methods classified 29.5% more of the
 sample with MCI and outperformed consensus diagnoses in capturing those
 who had abnormal biomarkers, progressed to dementia, or had AD pathology
 at autopsy. Conclusions: We identified subtypes of MCI and CN with
 differing cognitive profiles, clinical outcomes, CSF AD biomarkers, and
 neuropathological findings over more than 10 years of follow-up. Results
 demonstrate that actuarial methods produce reliable cognitive phenotypes,
 with data from a subset suggesting unique biological and neuropathological
 signatures. Findings indicate that data-driven algorithms enhance
 diagnostic sensitivity relative to consensus diagnosis for identifying
 older adults at risk for cognitive decline.
DOI: 10.5061/dryad.3tx95x6gg
title: Immunocompetent birds choose larger breeding colonies

description: The optimal size of social groups may vary between individuals, depending
 on their phenotypic traits, such as dominance status, age, or personality.
 Larger social groups often enhance transmission rates of pathogens and
 should be avoided by individuals with poor immune defenses. In contrast,
 more immunocompetent individuals are expected to take advantage of larger
 group sizes (e.g. better protection, information transfer) with smaller
 extra costs from pathogen or parasite pressure. Here, we hypothesized that
 immunocompetence may be a key determinant of group size choice and tested
 this hypothesis in a colonial waterbird, the common tern Sterna hirundo.
 For this purpose, we used a unique experimental framework, where formation
 of breeding colonies of different sizes was induced under uniform
 environmental conditions. For this purpose, different-size patches of
 attractive nesting substrate (artificial floating rafts) were provided at
 a single site with limited availability of natural nesting habitat. Colony
 size was identified as the only significant predictor of both innate
 (natural antibody mediated complement activation) and adaptive
 (immunoglobulin concentrations) immunological traits in the common terns,
 as more immunocompetent birds settled in larger experimental colonies. In
 contrast, we found no significant associations between colony size and
 genetic diversity of key pathogen-recognition receptors, toll-like
 receptors (TLRs) and the major histocompatibility complex (MHC) or
 genome-wide heterozygosity. We conclude that settlement decisions may be
 flexible within individuals and, thus, are likely to be primarily
 determined by the current immunological status, rather than fixed
 immunogenetic traits. Our study sheds new light on the complex interface
 between immunity and sociality in animals.
DOI: 10.5061/dryad.k6djh9w6c
title: Dataset: Reproductive ageing and pace-of-life syndromes

description: A common pattern of reproductive ageing is that reproductive performance
 increases during early life and reaches a peak, followed by a decline with
 age. Such quadratic reproductive ageing patterns can differ among
 individuals. Moreover, if individual differences in reproductive ageing
 patterns reflect individual-specific life-history trade-off strategies,
 they are also predicted to be associated with behaviour according to the
 pace-of-life syndrome. For example, more active, aggressive or bolder
 individuals may invest more in early reproduction, resulting in more rapid
 reproductive ageing. In this study, we estimated individual differences in
 quadratic reproductive ageing patterns and the relationship between
 reproductive ageing and the activity of the virgin female bean bug
 (Riptortus pedestris) in the absence of mating costs. We found that the
 egg production of virgin females followed a parabolic trajectory with age
 and that individuals varied significantly in their quadratic reproductive
 ageing patterns. In addition, we found that females that were relatively
 more active during early life invested in egg production more heavily at a
 young age and suffered from a sharper decline in egg production later in
 life. Thus, our results indicate that individual reproductive ageing
 patterns may be a key component in the study of pace-of-life syndromes. We
 suggest that within-individual plastic characteristics of life-history
 traits such as reproductive ageing patterns may explain the mixed results
 from multiple studies on pace-of-life syndromes.
DOI: 10.5061/dryad.dfn2z351r
title: Biweekly fine litterfall in the 18 CARBONO Project plots, La Selva Biological Station, October 1997-October 2018

description: This publication presents the 21-year record of fine-litterfall (leaves,
 reproductive materials, twigs &lt; 1 cm diameter) in the 18 plots of
 the CARBONO Project in the old-growth tropical rainforest at La Selva
 Biological Station, Costa Rica.  The CARBONO Project (1997-2018)
 was a multidisciplinary long-term research program to quantify forest
 carbon cycling at the landscape scale in the old-growth upland
 forest. The dataset is complete and has been through extensive
 qa/qc based on internal checks and readbacks.
description: To study carbon-cycle processes at the landscape scale, a network
 of 18 0.5-ha permanent plots was established across the old-growth forest
 at La Selva, using an unbiased, random-block design based on
 pre-determined coordinates drawn from the soils and topographic coverages
 of La Selva’s geographic information system.  This network was designed to
 sample the upland old-growth forest with replication on each of the three
 dominant edaphic conditions (younger oxisol alluvial terrace, older oxisol
 plateau, and older oxisol slope; six plots each).  Biweekly through the
 period October 1997 – October 2018, fine litterfall was collected from
 nine paired standing basket-traps and ground traps arrayed across each of
 the 18 plots.  In the lab, the materials were then separated by category
 and dried to constant weight.  When a trap was found to be compromised by
 blockage or trap damage from falling wood or by animals, its contents were
 discarded and the trap was immediately repaired or replaced.  The
 plot-level litterfall in each biweekly collection period was based on the
 actual number of active traps in that collection period. 
description: A ReadMe file provides detailed documentation.  The only missing
 values are in blanks in  the comments variable in the data set.
DOI: 10.25338/b80341
title: Nucleation sites and forest recovery under high shrub competition

description: Forests currently face numerous stressors, raising questions about
 processes of forest recovery as well as the role of humans to stimulate
 recovery through planting trees that might not otherwise regenerate.
 Theoretically, planted trees can also provide a seed source for further
 recruitment once the planted trees become reproductive, acting as
 “nucleation” sites; however, it is unclear whether changing site
 conditions over time (e.g., through the growth of competitors like woody
 shrubs) influences establishment in the long term, even if seed
 availability increases. We tested the nucleation concept in a system where
 shrub competition is known to influence tree establishment and growth,
 performing an observational study of sites within and close to newly
 reproductive planted stands in yellow-pine and mixed-conifer ecosystems in
 the Sierra Nevada, CA. We surveyed and then modeled both seedling
 occurrence and density as a function of distance to seed sources,
 competing woody vegetation, and other environmental characteristics. We
 found that proximity to a planted stand is associated with an increase in
 the probability of yellow pine (YP) seedlings (species more likely to
 originate from the planted stand) from 0.33 at 35 meters from the planted
 stand to 0.56 directly adjacent to the stand and 0.65 within the stand.
 However, we did not find a significant effect of proximity on YP seedling
 density. This proximity effect suggests that seed availability continues
 to be a driver of recruitment several decades post-wildfire, though other
 processes may influence the expected density of recruits. Proxies for
 competitive pressure (shrub volume and shrub cover) were not significant,
 suggesting that competing vegetation did not have a major influence on
 recruitment. While seedling presence and density appeared to be
 independent of shrub impacts, we did find that shrubs were significantly
 taller than seedlings. Therefore, we suggest that shrubs may not limit
 seedling establishment, but they may negatively affect seedlings’ ability
 to grow and serve as a seed source for further recruitment and forest
 expansion. Altogether, we find that planting may provide a statistically
 significant but small role in driving recruitment outside of the planted
 site.
description: See Ursell and Safford (2022) Nucleation sites and forest
 recovery under high shrub competition. Ecological Applications.