cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.z08kprrgm
title: From common gardens to candidate genes: Exploring local adaptation to climate in red spruce

description: Local adaptation to climate is common in plant species and has been
 studied in a range of contexts, from improving crop yields to predicting
 population maladaptation to future conditions. The genomic era has brought
 new tools to study this process, which was historically explored through
 common garden experiments.  In this study, we combine genomic
 methods and common gardens to investigate local adaptation in red spruce
 and identify environmental gradients and loci involved in climate
 adaptation. We first use climate transfer functions to estimate the impact
 of climate change on seedling performance in three common gardens. We then
 explore the use of multivariate gene-environment association (GEA) methods
 to identify genes underlying climate adaptation, with particular attention
 to the implications of conducting genome scans with and without correction
 for neutral population structure. This integrative approach uncovered
 phenotypic evidence of local adaptation to climate and identified a set of
 putatively adaptive genes, some of which are involved in three main
 adaptive pathways found in other temperate and boreal coniferous species:
 drought tolerance, cold hardiness, and phenology. These putatively
 adaptive genes segregated into two “modules” associated with different
 environmental gradients. This study nicely exemplifies the multivariate
 dimension of adaptation to climate in trees.
DOI: 10.15468/dl.8cubrm
title: Occurrence Download

description: A dataset containing 82 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Echinospartum barnadesii",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 82 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003264-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8cz8w9gv1
title: Data from: When perfection isn’t enough: host egg signatures are an effective defence against high-fidelity African cuckoo mimicry

description: Most mimicry systems involve imperfect mimicry, whereas perfect and
 high-fidelity mimicry are rare. When the fidelity of mimicry is high,
 mimics might be expected to have the upper hand against their antagonists.
 However, in coevolving systems, diversification of model phenotypes may
 provide an evolutionary escape, because mimics cannot simultaneously match
 all model individuals in the population. Here we investigate high-fidelity
 mimicry in a highly specialised, Afrotropical brood parasite-host system:
 the African cuckoo and fork-tailed drongo. Specifically, we test whether
 host egg polymorphisms are an effective defence against such mimicry. We
 show, using a combination of image analysis, field experiments, and
 simulations, that 1) egg colour and pattern mimicry of fork-tailed drongo
 eggs by African cuckoos is near-perfect on average; 2) drongos show
 fine-tuned rejection of foreign eggs, exploiting unpredictable pattern
 differences between parasitic eggs and their own; and 3) the high degree
 of interclutch variation (polymorphic egg ‘signatures’) exhibited by
 drongos gives them the upper hand in the arms race, with 93.7% of cuckoo
 eggs predicted to be rejected, despite cuckoos mimicking the full range of
 drongo egg phenotypes. These results demonstrate the effectiveness of
 model diversification as a defence against mimics, even when mimicry is
 highly accurate.
description: Field work took place in
 September–November 2009, 2010, 2011, and 2019 within a ~3,500 hectare area
 centred at 16°45' S, 26°54' E in the Choma district, southern
 Zambia. Fork-tailed drongo and African cuckoo egg phenotypes were measured
 from nests found at this study site. Eggshell pattern was
 quantified from photographs of eggs. Eggshell background colour (i.e.
 avoiding pattern) was measured using spectrophotometry. Egg length and
 width were measured with digital calipers. Egg
 rejection experiments on fork-tailed drongos were performed in 2009, 2010,
 2011, and 2019 (n = 14, 19, 19, and 65 respectively). To simulate a
 parasitism event, we replaced a host egg with a conspecific egg from
 another female (hereafter ‘experimental egg’; a surrogate for a cuckoo
 egg). We monitored experiments daily in 2019 and daily when possible in
 2009–2011, for four days to determine whether the experimental egg was
 rejected or accepted. We took the disappearance of the experimental egg to
 be evidence of host rejection.
description: Code is implemented in R version 4.2.1.
DOI: 10.5061/dryad.sn02v6x7b
title: Metabolic rate and foraging efficiency

description: Metabolic rate is the rate at which organisms process energy and is often
 considered as the fundamental driver of life history processes. The link
 between metabolic rate and life history is critically mediated via
 foraging, which shapes the energy acquisition patterns of an individual.
 This predicts that individuals with different metabolic rates likely vary
 in their foraging strategies, although such a link has rarely been
 empirically investigated in the context of optimal foraging theory - a
 powerful framework for understanding how animals maximize their foraging
 returns. Many central place foragers such as honeybees maximize their
 energetic efficiency rather than the rate of energetic gain, given the
 critical role of energetic costs on foraging decisions. We therefore
 tested if individuals of low and high metabolic rates differ in efficiency
 maximization, using genetic lines of honeybees with different metabolic
 rates. Our results show that low metabolic rate foragers visit more
 flowers during a foraging trip and have a higher energetic efficiency than
 high metabolic rate foragers in both low and high resource conditions. We
 discuss the significance of these results in the context of division of
 labor and the adaptive role of phenotypic diversity in metabolic rate in a
 social insect colony.
DOI: 10.5281/zenodo.18393458
title: scATAC-seq for paper: "Mechanical load protects the heart from cancer "
title: scATAC-seq

description: scATAC-sequencing supporting Analysis for Paper
DOI: 10.5281/zenodo.18393459
title: scATAC-seq for paper: "Mechanical load protects the heart from cancer "
title: scATAC-seq

description: scATAC-sequencing supporting Analysis for Paper
DOI: 10.5061/dryad.w0vt4b8vj
title: Feeding habits influence species habitat associations at the landscape scale in a diverse clade of Neotropical fishes

description: Aim. A primary goal of community ecology is to understand the mechanisms
 that drive species’ spatial distribution and habitat associations.
 Species' geographic distribution can be influenced by the
 distribution of their prey partly because consumers' behavior is
 oriented to optimal energy use during foraging. We analyzed how
 differences in dietary preferences influence the spatial distribution and
 habitat associations of species at the landscape scale. We hypothesized
 that differences in feeding guilds will lead to divergent habitat
 association patterns among species. Location. Amazon River
 drainage basin.  Taxon. Characiform fishes in the family
 Serrasalmidae (piranhas and pacus).  Methods. We used
 diet data to classify species into feeding guilds (frugivores, herbivores,
 piscivores, fin and scale feeders, and planktivores). We used three
 proxies of habitat association derived from satellite products: floodplain
 extent, landscape heterogeneity, and flood duration, in three distance
 buffers. We implemented Phylogenetic Generalized Least Squares models to
 evaluate the relationship between habitat association and feeding guilds.
 Results. Frugivores, piscivores, and fin and scale feeders
 presented similar patterns of habitat associations, with frugivores
 occupying wider areas of floodplain and greater landscape heterogeneity.
 Herbivores and planktivores were associated with smaller floodplain
 extents and lower landscape heterogeneity. All feeding guilds were
 associated with similar levels of flood duration. Main conclusions.
 Differences in resource distribution (assessed through feeding guilds) can
 influence habitat association.  Considering the hydrological
 variability (i.e., floodplain extent) and landscape heterogeneity that
 characterize floodplains, the patterns of habitat association vary with
 the spatial scale considered. This work highlights the importance of
 understanding species habitat associations by fish as well as food
 resource dynamics and floodplain dependence. This realization is critical
 for assessing the impact of anthropogenic activities on freshwater
 ecosystems.
DOI: 10.5061/dryad.rjdfn2zf8
title: Conflict over fertilization underlies the transient evolution of reinforcement

description: When two species meet in secondary contact, the production of low-fitness
 hybrids may be prevented by the adaptive evolution of increased prezygotic
 isolation, a process known as reinforcement. Theoretical challenges to the
 evolution of reinforcement are generally cast as a coordination problem,
 i.e. "how can statistical associations between traits and preferences
 be maintained in the face of recombination?" However, the evolution
 of reinforcement also poses a potential conflict between mates. For
 example, the opportunity costs to hybridization may differ between the
 sexes or species. This is particularly likely for reinforcement based on
 postmating prezygotic (PMPZ) incompatibilities, as the ability to
 fertilize both conspecific and heterospecific eggs is beneficial to male
 gametes, but heterospecific mating may incur a cost for female gametes. We
 develop a population genetic model of interspecific conflict over
 reinforcement inspired by "gametophytic factors'', which
 act as PMPZ barriers among Zea mays subspecies. We demonstrate that this
 conflict results in the transient evolution of reinforcement––after
 females adaptively evolve to reject gametes lacking a signal common in
 conspecific gametes, this gamete signal adaptively introgresses into the
 other population. Ultimately the male gamete signal fixes in both species,
 and isolation returns to pre-reinforcement levels. We interpret geographic
 patterns of isolation among Z. mays subspecies considering these findings
 and suggest when and how this conflict can be resolved. Our results
 suggest that sexual conflict over fertilization may pose an understudied
 obstacle to the evolution of reinforcement. 
description: Data as generated by iteration of a deterministic code posted on
 the associated GitHub repo, https://github.com/carushworth/gameto-theory across the relevant parts of parameter space.
description: Data as generated by iteration of a deterministic code posted on
 the associated GitHub repo, https://github.com/carushworth/gameto-theory gf_sims.R was used to generate all results for figures with only one gametophytic factor (all figures but fig S7). gf_two_gfs.R was used to generate all results for the two gametophytic factor model (fig S7).
DOI: 10.5061/dryad.dz08kps10
title: Changes in habitat suitability for wintering dabbling ducks during dry conditions in the Central Valley of California

description: In arid and Mediterranean regions, landscape-scale wetland conservation
 requires understanding how wildlife responds to dynamic freshwater
 availability and human actions to enhance wetland habitat. Taking
 advantage of the Landsat satellite time series (2007–2016) and structured
 and community science bird survey data, we built species distribution
 models to describe how three duck species – Northern Pintail (Anas acuta),
 Green-winged Teal (A. crecca), and Northern Shoveler (A. clypeata) –
 respond to freshwater supply and food resources on different flooded land
 cover types in the Central Valley of California. Specifically, our models
 were designed to compare duck habitat suitability between the wettest to
 driest conditions in each month from September through April. Using
 abundance-weighted boosted regression trees, we created three sets of
 species occurrence models based on different covariates: (i) near
 real-time (hereafter “real-time”) covariates in which duck observations
 were matched to the surface water availability within the 16-day window of
 a Landsat observation, (ii) a combination of real-time covariates and
 waterfowl food resource covariates describing annual corn and rice biomass
 and managed wetland moist soil seed yield estimates derived from Landsat
 data, and (iii) long-term average covariates – the most common approach to
 species distribution modeling – in which long-term average surface water
 availability was used. We modeled the monthly occurrence of three duck
 species as a function of surface water availability, land cover type, road
 density, temperature, and bird data source. We found that dry conditions
 result in reduced habitat suitability, with the biggest reductions in
 November through January and in agricultural fields; in contrast,
 suitability of flooded wetland habitat was relatively robust to overall
 surface water availability. When models of habitat suitability based on
 the long-term average climate conditions were compared to models based on
 real-time conditions, the highest long-term suitability values occurred in
 areas where suitability was high regardless of whether it was a wet or a
 dry year. While all models performed well, the inclusion of crop and
 wetland plant yield covariates resulted in slightly more accurate models.
 Overall, species distribution models created using data on the
 environmental conditions present at the time of bird observations can aid
 conservation efforts under extreme conditions over large spatial scales.
description: Please see mansucript [currently in revision] with the same title
 for the full description of methods and results.
DOI: 10.5061/dryad.b2rbnzsjr
title: Testing hypotheses of hybrid taxon formation in the shrubby beardtongues (Penstemon subgenus Dasanthera)

description: Premise Hybridization is increasingly being identified in the genomes of
 species across the tree of life. This has led to a general recognition
 that hybridization plays an important role in the generation of species
 diversity. While hybridization may increase species diversity directly via
 the formation of new taxa through hybrid speciation, it may also act
 indirectly via the exchange of phenotypic and genetic variance between
 species, which may in turn stimulate future speciation events.  
 Methods Using high-throughput sequence data, we resolve phylogenetic
 relationships and investigate the role of hybridization as a
 diversification mechanism in the shrubby beardtongues (Penstemon subgenus
 Dasanthera), a group of North American wildflowers that has undergone a
 recent and rapid adaptive radiation. Specifically, we test four hypotheses
 of hybrid taxon formation resulting from hybridization between P.
 davidsonii and P. fruticosus.   Key Results Species tree
 inference supports the monophyly of subgenus Dasanthera and elucidates
 relationships between taxa distributed in the Cascades and Sierra Nevada
 Mountains. Results also provide evidence of gene flow between P.
 davidsonii and P. fruticosus and support at least one hybrid origin
 hypothesis (P. davidsonii var. menziesii) in a region of contemporary
 distributional overlap. Hybridization may have also been facilitated by
 historical overlap in geographic distribution caused by species’ responses
 to climatic changes during the Pleistocene.   Conclusions Our
 results support a history of hybridization between focal taxa in a rapidly
 radiating clade of plants and more broadly contribute to our growing
 understanding of the role of hybridization as a diversification mechanism
 in plants.
DOI: 10.5061/dryad.3n5tb2rm4
title: Data and scripts for: Phylogeny of the Poritiinae (Lepidoptera: Lycaenidae), butterflies with ant assocations and unusual lichenivorous diets

description: The Poritiinae are a diverse subfamily of lycaenid butterflies with about
 700 species divided into two major groups: the Asian endemic tribe
 Poritiini, and the African endemic tribe Liptenini. Among these, the
 Liptenini are notable for their lichenivorous diet and the strong but
 apparently non-mutualistic ant associations of many species. We present
 the first molecular phylogeny for this subfamily, based on data from 14
 gene regions and including 218 representatives from 177 taxa
 (approximately 25% of species) in 50 of the 58 (86%) recognized genera.
 From this analysis, we confirm the division of the subfamily into two
 tribes, and we rearrange the Liptenini tribe into six subtribes,
 Durbaniina, Pentilina, Liptenina, Iridanina, and Epitolina, plus a new
 tribe, Cooksoniina subtrib. n., to fill a gap in the nomenclature revealed
 by the phylogenetic analysis. We also point to several genera in need of
 further taxonomic revision. Ancestral range reconstruction could not infer
 the range of the common ancestor of the Poritiinae; however, the common
 ancestor of the Poritiini was likely Asian, while that of the Liptenini
 was likely African, with subsequent narrowing of ranges in several
 lineages.
description: Methods described in Boyle <em>et al.</em>, Phylogeny
 of the Poritiinae (Lepidoptera: Lycaenidae), butterflies with ant
 associations and unusual lichenivorous diets.
description: Script files ending in .sh are bash scripts run on a cluster; by
 removing any lines beginning "#SBATCH" or "module
 load" they should run in any environment that runs bash
 scripts. Script files ending in .R are R
 scripts. Also included are the final aligned and
 trimmed DNA sequences, both separately (in clipped_fasta.zip) and combined
 (concatenated_alignments.fas), all in fasta format.
 Range and determination data used in ancestral range
 reconstruction may be found in .phy and .txt files. The
 tree produced by IQ-TREE is provided as a .tre file.
DOI: 10.5061/dryad.tx95x6b1w
title: An abundant sea anemone from the Carboniferous Mazon Creek Lagerstӓtte, U.S.A.: Representative specimens examined

description: Sea anemones (Actiniaria) are among the rarest of recognized fossil
 organisms, even rarer than jellyfish. Here we demonstrate that the most
 abundant fossil in the Pennsylvanian Mazon Creek Lagerstätte of Illinois,
 Essexella asherae, is an infaunal or semi-infaunal anemone. Essexella is
 redescribed based on a taphonomic analysis of thousands of specimens, as
 well as associated medusae and trace fossils. Specimens of Essexella (also
 known as the “blobs”) were long believed to be medusae, but we reassign
 Essexella to the order Actiniaria and reinterpret the putative jellyfish
 Reticulomedusa as the pedal or oral disc of Essexella. We also implicate
 Essexella as a producer of Conostichus, a widespread plug-shaped trace
 fossil that occurs in coeval strata in the same region. Radiate structures
 comparable to the bases of Conostichus and the ichnofossil Bergaueria, as
 well as the pedal discs of modern anemones, characterize Reticulomedusa.
 Bona fide medusae are present in the Mazon Creek biota, and include
 Anthracomedusa turnbulli and Octomedusa pieckorum, whereas the soft-bodied
 fossil Lascoa mesostaurata is referred to Problematica.
description: We examined thousands of specimens of
 <em>Essexella</em>, principally in the collections of the
 Field Museum, Yale Peabody Museum, Royal Ontario Museum, Manitoba Museum,
 and the University of Illinois at Chicago (UIC), as well as in private
 collections. Scores of specimens were selected for more detailed
 examination and are listed here.
DOI: 10.25349/d9w32d
title: Data for: Axisymmetric Displacement Flows in Flow-driven Fractures

description: The raw data presented in the associated manuscript entitled
 "Axisymmetric displacement flows in fluid-driven
 fractures" are included here. For experiments 1 through 16
 (see table 3 for experimental parameters), we measure (1) the radius of
 the fracture during the formation of the pre-fracture, (2) the radius of
 the fracture during the displacement flow (i.e. when the second fluid is
 injected), and (3) the radial position of the interface during the two
 fluids, during the displacement flow.  We also measured the
 fracture thickness in the viscous and toughness regimes using absorbance
 measurements. The raw data presented in figures 4(b) and 8 for the
 toughness regime, 5(b) and 9 for the viscous regime are
 included.
DOI: 10.5061/dryad.05qfttf5w
title: Data from: Relating pupil diameter and blinking to cortical activity and hemodynamics across arousal states

description: Arousal state affects neural activity and vascular dynamics in the cortex,
 with sleep associated with large changes in the local field potential
 (LFP) and increases in cortical blood flow. We investigated the
 relationship between pupil diameter and blink rate with neural activity
 and blood volume in the somatosensory cortex in male and female
 unanesthetized, head-fixed mice. We monitored these variables while the
 mice were awake, during periods of rapid eye movement (REM), and during
 non-rapid eye movement (NREM) sleep. Pupil diameter was smaller during
 sleep than in the awake state. Changes in pupil diameter were coherent
 with both gamma-band power and blood volume in the somatosensory cortex,
 but the strength and sign of this relationship varied with arousal state.
 We observed a strong negative correlation between pupil diameter and both
 gamma-band power and blood volume during periods of awake rest and NREM
 sleep, though the correlations between pupil diameter and these signals
 became positive during periods of alertness, active whisking, and REM.
 Blinking was associated with increases in arousal and decreases in blood
 volume when the mouse was asleep. Bilateral coherence in gamma-band power
 and in blood volume dropped following awake blinking, indicating a
 'reset' of neural and vascular activity. Using only eye metrics
 (pupil diameter and eye motion), we could determine the mouse’s arousal
 state (‘Awake’, ‘NREM’, ‘REM’) with greater than 90% accuracy with a
 5-second resolution. There is a strong relationship between pupil diameter
 and hemodynamics signals in mice, reflecting the pronounced effects of
 arousal on cerebrovascular dynamics.
description: See the methods section of the manuscript.
description: MATLAB v2022a
DOI: 10.5061/dryad.zcrjdfngq
title: Data for: Phylogenomics and historical biogeography of Hydrangeeae (Hydrangeaceae) elucidate the effects of geologic and climatic dynamics on diversification

description: Demonstrating the process of transregional biogeography and mechanisms
 underlying evolutionary radiations is crucial to understanding biological
 evolution. Here, we use Hydrangeeae (Hydrangeaceae), a tribe with a unique
 disjunct distribution and complex trait variations, using a solid
 phylogenetic framework, to investigate how geographical and climatic
 factors interact with functional traits to trigger plant evolutionary
 radiations. We constructed the first highly supported and dated
 phylogenetic framework using 79 protein-coding genes obtained from 81
 plastomes, representing 63 species and all major clades, and found that
 most extant species originated from asynchronous diversification of two
 lineages undergoing repeated expansion and retraction, at middle and high
 latitudes of the Northern Hemisphere between East Asia and North America,
 during the Eocene to Pleistocene (driven by geologic and climatic
 dynamics). In accordance with these drivers, interactions of flora between
 central-eastern China and Japan occurred frequently after the Late
 Tertiary. We found that resource limitation and range fragmentation likely
 accelerated the diversification of Hydrangeeae, which supports the
 resource-use hypothesis. Our study sheds light on the evolutionary
 radiation and assembly of flora within East Asia, and the East Asian-North
 American disjunction, through integration of phylogenomic and
 biogeographic data with functional trait and ecological data.