cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6t1g1jwv2
title: Data from: Desiccation resistance and pigmentation variation reflects bioclimatic differences in the Drosophila americana species complex

description: Background: Disentangling the selective factors shaping adaptive trait
 variation is an important but challenging task. Many studies—especially in
 Drosophila—have documented trait variation along latitudinal or
 altitudinal clines, but frequently lack resolution about specific
 environmental gradients that could be causal selective agents, and often
 do not investigate covariation between traits simultaneously. Here we
 examined variation in multiple macroecological factors across geographic
 space and their associations with variation in three physiological traits
 (desiccation resistance, UV resistance, and pigmentation) at both
 population and species scales, to address the role of abiotic environment
 in shaping trait variation. Results: Using environmental data from
 collection locations of three North American Drosophila species—D.
 americana americana, D. americana texana and D. novamexicana—we identified
 two primary axes of macroecological variation; these differentiated
 species habitats and were strongly loaded for precipitation and moisture
 variables. In nine focal populations (three per species) assayed for each
 trait, we detected significant species-level variation for both
 desiccation resistance and pigmentation, but not for UV resistance.
 Species-level trait variation was consistent with differential natural
 selection imposed by variation in habitat water availability, although
 patterns of variation differed between desiccation resistance and
 pigmentation, and we found little evidence for pleiotropy between traits.
 Conclusions: Our multi-faceted approach enabled us to identify potential
 agents of natural selection and examine how they might influence the
 evolution of multiple traits at different evolutionary scales. Our
 findings highlight that environmental factors influence functional trait
 variation in ways that can be complex, and point to the importance of
 studies that examine these relationships at both population- and
 species-levels.   
description: Desiccation resistance includes start and end times for
 individuals in survival assays, as well as total minutes survived and dry
 weight in grams.
DOI: 10.5061/dryad.ffbg79cqf
title: Persistence of an endangered native duck, feral mallards, and multiple hybrid swarms across the main Hawaiian Islands

description: Interspecific hybridization is recognized as an important process in the
 evolutionary dynamics of both speciation and the reversal of speciation.
 However, our understanding of the spatial and temporal patterns of
 hybridization that erode versus promote species boundaries is incomplete.
 The endangered, endemic koloa maoli (or Hawaiian duck, Anas wyvilliana) is
 thought to be threatened with genetic extinction through ongoing
 hybridization with an introduced congener, the feral mallard (A.
 platyrhynchos). We investigated spatial and temporal variation in hybrid
 prevalence in populations throughout the main Hawaiian Islands, using
 genomic data to characterize population structure of koloa, quantify the
 extent of hybridization, and compare hybrid proportions over time. To
 accomplish this, we genotyped 3,308 double-digest
 restriction-site-associated DNA (ddRAD) loci in 425 putative koloa,
 mallards, and hybrids from populations across the main Hawaiian Islands.
 We found that despite a population decline in the last century, koloa
 genetic diversity is high. There were few hybrids on the island of Kauaʻi,
 home to the largest population of koloa. By contrast, we report that
 sampled populations outside of Kauaʻi can now be characterized as hybrid
 swarms, in that all individuals sampled were of mixed koloa × mallard
 ancestry. Further, there is some evidence that these swarms are stable
 over time. These findings demonstrate spatial variation in the extent and
 consequences of interspecific hybridization, and highlight how islands or
 island-like systems with small population sizes may be especially prone to
 genetic extinction when met with a congener that is not reproductively
 isolated.
DOI: 10.15468/dl.srv5v2
title: Occurrence Download

description: A dataset containing 3297 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Computarización de las colecciones de vertebrados terrestres de la Escuela Nacional de Ciencias Biológicas, IPN - Fases 3"
 ]
}

 The dataset includes 3297 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001999-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vnbgwf
title: Occurrence Download

description: A dataset containing 5708 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Bryophyta, Marchantiophyta, Anthocerotophyta)",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)",
 "Country is Brazil",
 "StateProvince is Rio Grande do Sul"
 ]
}

 The dataset includes 5708 records from 51 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002000-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.hx3ffbg9d
title: A consensus phylogenomic approach highlights paleopolyploid and rapid radiation in the history of Ericales

description: Premise of study: Large genomic datasets offer the promise of
 resolving historically recalcitrant species relationships.
 However, different methodologies can yield conflicting results, especially when clades have experienced ancient, rapid diversification. Here, we analyzed the ancient radiation of Ericales and explored sources of uncertainty related to species tree inference, conflicting gene tree signal, and the inferred placement of gene and genome duplications. Methods: We used a hierarchical clustering approach, with tree-based homology and orthology detection, to generate six filtered phylogenomic matrices consisting of data from 97 transcriptomes and genomes. Support for species relationships was inferred from multiple lines of evidence including shared gene duplications, gene tree conflict, gene-wise edge-based analyses, concatenation, and coalescent-based methods and is summarized in a consensus framework. Key Results: Our consensus approach supported a topology largely concordant with previous studies, but suggests that the data are not capable of resolving several ancient relationships due to lack of informative characters, sensitivity to methodology, and extensive gene tree conflict correlated with paleopolyploidy. We found evidence of a whole genome duplication before the radiation of all or most ericalean families and demonstrate that tree topology and heterogeneous evolutionary rates impact the inferred placement of genome duplications. Conclusions: We provide several hypotheses regarding the history of Ericales, confidently resolve most nodes, but demonstrate that a series of ancient divergences are unresolvable with these data. Whether paleopolyploidy is a major source of the observed phylogenetic conflict warrants further investigation.
description: See publication for details on data generation and
 processing.
DOI: 10.15468/dl.uzus4c
title: Occurrence Download

description: A dataset containing 333 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "TaxonKey is Araneus venatrix"
 ]
}

 The dataset includes 333 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002002-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.1g1jwstr0
title: PRISM-HD: Patient-Reported Impact of Symptoms in Huntington Disease

description: OBJECTIVE: To determine the frequency and relative importance of symptoms
 experienced by adults with Huntington disease (HD) and to identify factors
 associated with a higher disease burden. METHODS: We performed 40
 qualitative interviews (n = 20 with HD, n = 20 caregivers) and analyzed
 2,082 quotes regarding the symptomatic burden of HD. We subsequently
 performed a cross-sectional study with 389 participants (n = 156 with HD
 [60 of whom were prodromal], n = 233 caregivers) to assess the prevalence
 and relative importance (scale 0-4) of 216 symptoms and 15 symptomatic
 themes in HD. Cross-correlation analysis was performed based on sex,
 disease duration, age, number of CAG repeats, disease burden, Total
 Functional Capacity score, employment status, disease status, and
 ambulatory status. RESULTS: The symptomatic themes with the highest
 prevalence in HD were emotional issues (83.0%), fatigue (82.5%), and
 difficulty thinking (77.0%). The symptomatic themes with the highest
 relative importance to participants were difficulty thinking (1.91),
 impaired sleep or daytime sleepiness (1.90), and emotional issues (1.81).
 High Total Functional Capacity scores, being employed, and having
 prodromal HD were associated with a lower prevalence of symptomatic
 themes. Despite reporting no clinical features of the disease, prodromal
 individuals demonstrated high rates of emotional issues (71.2%) and
 fatigue (69.5%). There was concordance between the prevalence of symptoms
 reported by manifest individuals and caregivers. CONCLUSIONS: Many
 symptomatic themes affect the lives of those with HD. These themes have a
 variable level of importance to the HD population and are identified both
 by those with HD and by their caregivers.
DOI: 10.5061/dryad.3ffbg79db
title: Genomic analysis of the only blind cichlid reveals extensive inactivation in eye and pigment formation genes

description: Trait loss represents an intriguing evolutionary problem, particularly
 when it occurs across independent lineages. Fishes in light-poor
 environments often evolve “troglomorphic” traits, including reduction or
 loss of both pigment and eyes. Here we investigate the genomic basis of
 trait loss in a blind and depigmented African cichlid, Lamprologus
 lethops, and explore evolutionary forces (selection and drift) that may
 have contributed to these losses. This species, the only known blind
 cichlid, is endemic to the lower Congo River. Available evidence suggests
 it inhabits deep, low-light habitats. Using genome sequencing, we show
 that genes related to eye formation and pigmentation, as well as other
 traits associated with troglomorphism, accumulated inactivating mutations
 rapidly after speciation. A number of the genes affected in L. lethops are
 also implicated in troglomorphic phenotypes in Mexican cavefish (Astyanax
 mexicanus) and other species. Analysis of heterozygosity patterns across
 the genome indicates that L. lethops underwent a significant population
 bottleneck roughly 1 Mya, after which effective population sizes remained
 low. Branch-length tests on a subset of genes with inactivating mutations
 show little evidence of directional selection; however, low overall
 heterozygosity may reduce statistical power to detect such signals.
 Overall, genome-wide patterns suggest that accelerated genetic drift from
 a severe bottleneck, perhaps aided by directional selection for the loss
 of physiologically expensive traits, caused inactivating mutations to fix
 rapidly in this species.
description: Data was collected via PCR and Sanger sequencing (see
 Supplemental methods and results).
DOI: 10.5061/dryad.2v6wwpzh5
title: Context dependence of local adaptation to abiotic and biotic environments: a quantitative and qualitative synthesis

description: Understanding how spatially-variable selection shapes adaptation is an
 area of longstanding interest in evolutionary ecology. Recent
 meta-analyses have quantified the extent of local adaptation, but the
 relative importance of abiotic and biotic factors in driving population
 divergence remains poorly understood. To address this gap, we combined a
 quantitative meta-analysis and a qualitative meta-synthesis to (1)
 quantify the magnitude of local adaptation to abiotic and biotic factors
 and (2) characterize major themes that influence the motivation and design
 of experiments that seek to test for local adaptation. Using local-foreign
 contrasts as a metric of local adaptation (or maladaptation), we found
 that local adaptation was greater in the presence than absence of a biotic
 interactor, especially for plants. We also found that biotic environments
 had stronger effects on fitness than abiotic environments when ignoring
 whether those environments were local versus foreign. Finally, biotic
 effects were stronger at low latitudes and abiotic effects were stronger
 at high latitudes. Our qualitative analysis revealed that the lens through
 which local adaptation has been examined differs for abiotic and biotic
 factors. It also revealed biases in the design and implementation of
 experiments that make quantitative results challenging to interpret and
 provided directions for future research.
DOI: 10.5061/dryad.xgxd254bx
title: Evolutionary impacts differ between two exploited populations of northern bottlenose whale (Hyperoodon ampullatus)

description: Interpretation of conservation status should be informed by an
 appreciation of genetic diversity, past demography, and overall trends in
 population size, which contribute to a species’ evolutionary potential and
 resilience to genetic risks. Low genetic diversity can be symptomatic of
 rapid demographic declines and impose genetic risks to populations, but
 can also be maintained by natural processes. The northern bottlenose whale
 Hyperoodon ampullatus has the lowest known mitochondrial diversity of any
 cetacean and was intensely whaled in the Northwest Atlantic over the last
 century, but whether exploitation imposed genetic risks that could limit
 recovery is unknown. We sequenced full mitogenomes and genotyped 37 novel
 microsatellites for 128 individuals from known areas of abundance in the
 Scotian Shelf, Northern and Southern Labrador, Davis Strait, and Iceland,
 and a newly discovered group off Newfoundland. Despite low diversity and
 shared haplotypes across all regions, both markers supported the
 Endangered Scotian Shelf population as distinct from the combined northern
 regions. The genetic affinity of Newfoundland was uncertain, suggesting an
 area of mixing with no clear population distinction for the region.
 Demographic reconstruction using mitogenomes suggests that the northern
 region underwent population expansion following the last glacial maximum,
 but for the peripheral Scotian Shelf population, a stable demographic
 trend was followed by a drastic decline over a temporal scale consistent
 with increasing human activity in the Northwest Atlantic. Low connectivity
 between the Scotian Shelf and the rest of the Atlantic likely compounded
 the impact of intensive whaling for this species, potentially imposing
 genetic risks affecting recovery of this population. We highlight how the
 combination of historic environmental conditions across the North Atlantic
 and modern exploitation of this species has had very different
 evolutionary impacts on structured populations of northern bottlenose
 whales.
description: Sampling, DNA preparation, sequencing, and assembly methods are
 described in: https://onlinelibrary.wiley.com/doi/full/10.1002/ece3.5813
DOI: 10.5061/dryad.8w9ghx3gr
title: Assessing the feasibility of a rapid, high-volume cervical cancer screening program using HPV self-sampling and digital colposcopy in rural regions of Yunnan, China

description: Objective: Implementation of a novel, rapid, high-volume, see-and-treat
 cervical cancer screening program utilizing self-swab HPV testing and
 digital colposcopy in underserved regions of Yunnan China. Design:
 500-1000 women per day self-swabbed for high-risk HPV (hrHPV+). Four
 careHPVTM machines (Qiagen) were run simultaneously to test the specimens.
 All hrHPV+ patients were contacted the same day and digital colposcopy
 (DC) was performed with the EVA system (MobileODT). Digital images were
 obtained, and all suspected lesions were biopsied and then treated.
 Setting: Rural and underserved areas of the Yunnan province, Kunming
 municipality. Participants: 3600 women, mean age 50.2 years, who had never
 been screened for cervical cancer.  The women were of
 the Yi, Hui, Dai, and Han ethnicities. Interventions: Cryotherapy was
 performed on all lesions suspicious for CIN1 and LEEP was performed on all
 lesions suspicious CIN2+. ECC was performed if the transformation zone was
 not fully visualized. Results: 216 women (6%) were hrHPV+. 168 underwent
 same-day colposcopy (23 CIN1, 17 CIN2+). DC was able to identify 15 of 16
 (93.8%) CIN2+ lesions. Conclusions: Currently, China does not have
 national screening guidelines or services for cervical cancer. Only 20.7%
 of Chinese women reported having ever been screened. This study
 illustrates a cost- effective, rapid and practical strategy that can be
 used to screen-and-treat 400+ million Chinese women for cervical cancer.
 First, HPV self-sampling allows large numbers of women to be screened
 rapidly and inexpensively and only +hrHPV women require further
 evaluation. Digital colposcopy is then performed on +hrHPV women with a
 portable digital colposcope. The high-resolution images obtained during DC
 then facilitates appropriate same-day treatment as they are able to
 accurately distinguish between CIN1 and CIN2+ lesions.
  Additionally, DC adds little to the time and cost of screening
 and produces permanent images that can be used for documentation, quality
 control, and expert consultation via a secure cloud-based portal.
DOI: 10.5061/dryad.547d7wm42
title: “Natural” solutions could speed up climate change mitigation, with risks, compared to emissions reductions alone. Additional options are needed.

description: Mitigation of climate change by intentionally storing carbon in tropical
 forests, soils and wetlands, and by reducing greenhouse gas fluxes from
 these settings has been promoted as rapidly deployable and
 cost-effective.  This approach, sometimes referred to as
 “natural” mitigation, could keep post-industrialization warming below
 1.5°C, when coupled with reductions in fossil fuel emissions, as confirmed
 here with a simple numerical model of future emissions.  However,
 such mitigation could cease in response to changes in future climate, land
 use or natural resource policies, or there could be CO2 released from
 reservoirs of stored carbon.  Model simulations suggest
 cumulative emissions could be similar, under scenarios where carbon
 storage ceases, or stored carbon is released, to emissions expected in the
 absence of any natural mitigation.  If climate change is to be
 minimized, low-risk natural mitigation (e.g. by reducing deforestation)
 should be considered, as emissions targets that could limit warming to
 1.5°C cannot be met without mitigation of this magnitude. 
 However, additional mitigation options should also be considered that can
 reduce CO2 emissions and remove CO2 from the air (and store it
 permanently) and/or reduce the temperature of the atmosphere or the ocean.
description: This text describes the analysis/simple model simulations of
 annual and cumulative future CO<sub>2</sub> emissions plotted
 and discussed in this commentary in Earth's Future.  The data files
 include the simulations plotted in Fig 1, as well as the “natural”
 mitigation fluxes used in the modeling, derived from Griscom et al, 2017,
 and justified with additional data in Table 1 in the main text.  The
 representative concentration pathways that are presented for perspective
 in Fig 1 include RCP2.6 (van Vuuren et al, 2007)  and RCP4.5 (Clarke et
 al, 2007).  While I do provide those data in the csv file, I obtained the
 RCP data from https://tntcat.iiasa.ac.at/RcpDb/dsd?Action=htmlpage&page=about#.
DOI: 10.5061/dryad.8w9ghx3gs
title: Prey exploits the auditory illusions of eavesdropping predators

description: Mating signals have evolved to attract target receivers, even to the point
 of exploiting receivers through perceptual manipulation. Signals, however,
 can also expose signalers to non-target receivers, including predators and
 parasites, and thus have also evolved to decrease enemy attraction. Here
 we show that male treefrogs (Smilisca sila) reduce their attractiveness to
 eavesdropping enemies (bats and midges) by overlapping their calls at
 near-perfect synchrony with the calls of neighboring conspecifics. By
 producing calls that closely follow those of other males, synchronizing S.
 sila take advantage of an auditory illusion where enemies are more
 attracted to the leading call. Female S. sila, however, are not as
 susceptible to this illusion. Thus, synchronization among signaling males
 can result in acoustic crypsis from predators without affecting female
 attraction. Given the widespread use of conspicuous mating signals and
 eavesdropping enemies, perceptual exploitation of eavesdroppers is likely
 a common driver of signal evolution.
description: Data from laboratory and field acoustic playback
 experiments assessing the leader-follower call preferences in the target
 receiver (female frogs: "pugnosed_l-f_data.csv" and
 "tungara_l-f_data.csv") and non-target eavesdroppers (bats:
 "bat_l-f_data", and midges:
 "midge_l-f_data").
DOI: 10.5061/dryad.wdbrv15j8
title: Extensive paraphyly in the typical owl family (Strigidae)

description: The typical owl family (Strigidae) comprises 194 species in 28 genera, 14
 of which are monotypic. Relationships within and among genera in the
 typical owls have been challenging to discern because mitochondrial data
 have produced equivocal results and because many monotypic genera have
 been omitted from previous molecular analyses. Here, we collected and
 analyzed DNA sequences of ultraconserved elements (UCEs) from 43 species
 of typical owls to produce concatenated and multispecies coalescent-based
 phylogenetic hypotheses for all but one genus in the typical owl family.
 Our results reveal extensive paraphyly of taxonomic groups across
 phylogenies inferred using different analytical approaches and suggest the
 genera Athene, Otus, Asio, Megascops, Bubo, and Strix are paraphyletic,
 whereas Ninox and Glaucidium are polyphyletic. Secondary analyses of
 protein-coding mitochondrial genes harvested from off-target sequencing
 reads and mitochondrial genomes downloaded from GenBank generally support
 the extent of paraphyly we observe, although some disagreements exist at
 higher taxonomic levels between our nuclear and mitochondrial phylogenetic
 hypotheses. Overall, our results demonstrate the importance of taxon
 sampling for understanding and describing evolutionary relationships in
 this group, as well as the need for additional sampling, study, and
 taxonomic revision of typical owl species.  Additionally, our
 findings highlight how both divergence and convergence in morphological
 characters have obscured our understanding of the evolutionary history of
 typical owls, particularly those with insular distributions.