cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.stqjq2bzv
title: Calanus InDel genotypes from: No evidence for hybridization between Calanus finmarchicus and C. glacialis in a subarctic area of sympatry

description: In the North Atlantic and the Arctic Ocean, four species of the copepod
 genus Calanus dominate the zooplankton biomass. Because
 of their morphological resemblance, knowledge of their respective
 distribution range has long been biased by misidentification, until the
 recent use of molecular tools uncovered numerous areas of sympatry. As
 hybridization between Calanus
 finmarchicus and C. glacialis has been claimed
 in the East-Canadian Arctic based on microsatellites, we investigated
 further the potential for interbreeding in newly uncovered areas of
 sympatry. Calanusspecies and stage composition were analyzed
 during winter in two Norwegian subarctic fjords, using molecular markers
 developed specifically for species identification and hybrid detection
 between C. finmarchicus and C. glacialis.
 Overall, Calanus glacialis were the most abundant
 throughout the winter, followed by C.
 finmarchicus and C. hyperboreus with only a few
 records of C. helgolandicus. The presence
 of C. glacialis, C. hyperboreus and C.
 finmarchicus’ nauplii was recorded, indicating that these species
 reproduce locally. In January and February, the simultaneous occurrence of
 males and females of both C.
 finmarchicus and C. glacialis suggested a
 potential for inter-species mating. However, genetic admixture tests
 performed on all 1126 individuals revealed no signal of hybridization,
 implying a strong reproductive isolation mechanism. We conclude that no
 evidence supports a potential for hybridization between C.
 finmarchicus and C. glacialis and suggest that
 the initial claim of hybridization
 between Calanus species may have resulted from the use
 of non-appropriate molecular tools.
description: In the study described above, DNA was extracted from each
 specimen's antennules and used in a PCR reaction of 6 InDels. The
 dataset presented here contains the resulting genotypes, with the
 corresponding species ID attributed to each genotype.
description: The first sheet contains the InDel genotypes from the individuals
 of developmental stages CIV, CV and CVI sampled in the
 Skjerstadfjord. The second sheet contains the InDel
 genotypes from the individuals of developmental stages CIV, CV and CVI
 sampled in the Mistfjord. The third sheet contains the
 InDel genotypes from the nauplii sampled in both fjords
 together. Missing values in genotypes are indicated by
 the value: "0".
DOI: 10.5061/dryad.stqjq2bzw
title: Five-years of ocrelizumab in relapsing multiple sclerosis: OPERA studies open-label extension

description: Objective To assess over 3 years of follow-up, the effects of maintaining
 or switching to ocrelizumab (OCR) therapy on clinical and MRI outcomes and
 safety measures in the open-label extension (OLE) phase of the pooled
 OPERA studies in relapsing multiple sclerosis. Methods After 2 years of
 double-blind, controlled treatment, patients continued OCR (600 mg
 infusions every 24 weeks) or switched from interferon (IFN) β-1a (44 μg 3
 times weekly) to OCR when entering the OLE phase (3 years). Adjusted
 annualized relapse rate, time to onset of 24-week confirmed disability
 progression/improvement (CDP/CDI), brain MRI activity (gadolinium-enhanced
 and new/enlarging T2 lesions), and percentage brain volume change were
 analyzed. Results Of patients entering the OLE phase, 88.6% completed Year
 5. The cumulative proportion with 24-week CDP was lower in patients who
 initiated OCR earlier, vs patients initially receiving IFN β-1a (16.1% vs
 21.3% at Year 5; p=0.014). Patients continuing OCR maintained, and those
 switching from IFN β-1a to OCR attained near complete and sustained
 suppression of new brain MRI lesion activity from Year 3 to 5. Over the
 OLE phase, patients continuing OCR exhibited less whole brain volume loss
 from double-blind study baseline vs those switching from IFN β-1a (–1.87%
 vs –2.15% at Year 5; p&lt;0.01). Adverse events were consistent with
 past reports and no new safety signals emerged with prolonged treatment.
 Conclusion Compared with patients switching from IFN β-1a, earlier and
 continuous OCR treatment up to 5 years provided sustained benefit on
 clinical and MRI measures of disease progression.
DOI: 10.15468/dl.kw3c56
title: Occurrence Download

description: A dataset containing 1360942 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Amphibia",
 "Country is one of (Canada, United States of America)",
 "Year is greater than or equal to 2000",
 "Year is less than or equal to 2025",
 "BasisOfRecord is Human Observation",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1360942 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001945-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.98sf7m0dr
title: Genomic data reveal similar genetic differentiation in aquifer species with different dispersal capabilities and life histories

description: Little is known about the life histories, genetic structure, and
 population connectivity of shallow groundwater organisms. We used
 next-generation sequencing (RAD-seq) to analyze population genomic
 structure in two aquifer species: Paraperla frontalis (Banks, 1902), a
 stonefly with groundwater larvae and aerial (winged) adults, and
 Stygobromus sp., a groundwater-obligate amphipod. We found similar genetic
 differentiation in each species between floodplains separated by ~70 river
 km in the Flathead River basin of NW Montana, USA. Given that Stygobromus
 lacks the aboveground life stage of P. frontalis, our findings suggest
 that connectivity and magnitude of genetic structure cannot be
 definitively assumed from life history differences.
DOI: 10.15468/dl.spgjpu
title: Occurrence Download

description: A dataset containing 5101 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "Country is Mexico",
 "OccurrenceStatus is Present",
 "StateProvince is one of (Baja California, Baja California Sur)",
 "TaxonKey is Agave"
 ]
}

 The dataset includes 5101 records from 39 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002005-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18394040
title: aphyosemion_splendopleure_decontaminated_FSCR.fasta.gz
DOI: 10.5281/zenodo.18394041
title: aphyosemion_splendopleure_decontaminated_FSCR.fasta.gz
DOI: 10.5061/dryad.31zcrjdg9
title: Phylogenomic data reveal widespred introgression across the range of an alpine and arctic specialist

description: Understanding how gene flow affects population divergence and speciation
 remains challenging. Differentiating one evolutionary process from another
 can be difficult because multiple processes can produce similar patterns,
 and more than one process can occur simultaneously. While simple
 population models produce predictable results, how these processes balance
 in taxa with patchy distributions and complicated natural histories is
 less certain. These types of populations might be highly connected through
 migration (gene flow), but can experience stronger effects of genetic
 drift and inbreeding, or localized selection. While different signals can
 be difficult to separate, the application of high throughput sequence data
 can provide the resolution necessary to distinguish many of these
 processes. We present whole genome sequence data for an avian species
 group with an alpine and arctic tundra distribution to examine the role
 that different population genetic processes have played in their
 evolutionary history. Rosy-finches inhabit high elevation mountaintop sky
 islands and high-latitude island and continental tundra. They exhibit
 extensive plumage variation coupled with low levels of genetic variation.
 Additionally, the number of species within the complex is debated, making
 them excellent for studying the forces involved in the process of
 diversification, as well as an important species group in which to
 investigate species boundaries. Total genomic variation suggests a broadly
 continuous pattern of allele frequency changes across the mainland taxa of
 this group in North America. However, phylogenomic analyses recover
 multiple distinct, well supported, groups that coincide with previously
 described morphological variation and current species-level taxonomy.
 Tests of introgression using D-statistics and approximate Bayesian
 computation reveal significant levels of introgression between multiple
 North American taxa. These results provide insight into the balance
 between divergent and homogenizing population genetic processes, and
 highlight remaining challenges in interpreting conflict between different
 types of analytical approaches with whole genome sequence data.
description: Shallow whole genome sequence data of 67 rosy-finch individuals
 across 4 species. VCF file includes quality filtered snps, but no other
 filters have been applied. See NCBI SRA BioProject PRJNA659436 for raw
 fastqs, and TreeBASE for alignments and tree files
 (http://purl.org/phylo/treebase/phylows/study/TB2:S26830).
DOI: 10.5061/dryad.9mf02
title: Data from: Mammal diversity and metacommunity dynamics in urban green spaces: implications for urban wildlife conservation

description: As urban growth expands and natural environments fragment, it is essential
 to understand the ecological roles fulfilled by urban green spaces. To
 evaluate how urban green spaces function as wildlife habitat, we estimated
 mammal diversity and metacommunity dynamics in city parks, cemeteries,
 golf courses, and natural areas throughout the greater Chicago, IL, USA
 region. We found similar a-diversity (with the exception of city parks),
 but remarkably dissimilar communities in different urban green spaces.
 Additionally, the type of urban green space greatly influenced species
 colonization and persistence rates. For example, coyotes (Canis latrans)
 had the highest, but white-tailed deer (Odocoileus virginianus) the
 lowest, probability of persistence in golf courses compared to other green
 space types. Further, most species had a difficult time colonizing city
 parks even when sites were seemingly available. Our results indicate that
 urban green spaces contribute different, but collectively important,
 habitats for maintaining and conserving biodiversity in cities.
description: Gallo_et_al_2017_Ecological_ApplicationsR script, JAGS model, and data used to estimate diversity and community and population dynamics in urban green spaces in the Chicago metropolitan area, IL USA.DataS1.zip
DOI: 10.15468/dl.de7swk
title: Occurrence Download

description: A dataset containing 13338 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Breeding records of birds in Greenland"
 ]
}

 The dataset includes 13338 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002004-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.80gb5mkn4
title: Historical allopatry and secondary contact or primary intergradation in the Puerto Rican Crested Anole, Anolis cristatellus, on Vieques Island

description: Recent work revealed surprisingly deep mitochondrial genetic divergence in
 the lizard Anolis cristatellus among samples obtained from the small
 Caribbean island of Vieques. We sought to determine whether this had
 resulted from natural or anthropogenic causes, and (if the former),
 whether divergence occurred in a biogeographic context of allopatry
 followed by secondary contact, or via isolation-by-distance across the
 species’ historical range. We first estimated a mitochondrial gene tree
 for 379 samples and then genotyped 3,407 single nucleotide polymorphic
 sites from 48 individuals using a modified genotyping-by-sequencing
 approach. We found that Anolis cristatellus samples from Vieques belong to
 two highly divergent mitochondrial subclades, but the geographic
 distribution of these haplogroups indicates that this pattern is
 most-likely natural in origin. Analysis of our SNP dataset revealed
 differentiation that is consistent with isolation-by-distance between the
 western and eastern ends of Vieques, suggesting that the overall pattern
 of divergence likely reflects primary intergradation with a mitochondrial
 break on the historical Puerto Rico Bank paleo-island that happened to
 coincide with the present-day island of Vieques. Our findings help
 underscore the growing consensus that results from a single genetic marker
 can prove highly misleading in studies of historical population genetic
 structure.
DOI: 10.5061/dryad.pg4f4qrj6
title: Differential contributions of the two human cerebral hemispheres to action timing

description: Rhythmic actions benefit from synchronization with external events.
 Auditory-paced finger tapping studies indicate the two cerebral
 hemispheres preferentially control different rhythms. It is unclear
 whether left-lateralized processing of faster rhythms and
 right-lateralized processing of slower rhythms bases upon hemispheric
 timing differences that arise in the motor or sensory system or whether
 asymmetry results from lateralized sensorimotor interactions. We measured
 fMRI and MEG during symmetric finger tapping, in which fast tapping was
 defined as auditory-motor synchronization at 2.5 Hz. Slow tapping
 corresponded to tapping to every fourth auditory beat (0.625 Hz). We
 demonstrate that the left auditory cortex preferentially represents the
 relative fast rhythm in an amplitude modulation of low beta oscillations
 while the right auditory cortex additionally represents the internally
 generated slower rhythm. We show coupling of auditory-motor beta
 oscillations supports building a metric structure. Our findings reveal a
 strong contribution of sensory cortices to hemispheric specialization in
 action control.
DOI: 10.6086/d1q378
title: Data from: What's that smell? Hummingbirds avoid foraging on resources with defensive insect compounds

description: Unlike many other vertebrates, the presence and role of functional
 olfactory systems in birds are only recently attracting attention. For
 example, hummingbirds utilize visual cues to locate flowers, but little is
 known about the role olfaction plays in foraging despite observations that
 hummingbirds avoid resources occupied by certain insects. We investigated
 the behavioural responses of both wild and captive hummingbirds to
 olfactory cues of hymenopteran floral visitors, including native wood ants
 (Formica francoeuri), invasive Argentine ants (Linepithema humile) and
 European honeybees (Apis mellifera). Although not known for their sense of
 smell, hummingbirds in this study exhibited the ability to distinguish
 insect chemical cues in different ecological contexts. Both wild and
 captive hummingbirds avoided foraging on feeders with defensive chemicals
 of F. francoeuri and aggregation pheromones of L. humile. Interestingly,
 no response to honeybee cuticular hydrocarbons was observed. Understanding
 the contexts in which these cues are perceived and how olfaction can shape
 foraging behaviour of hummingbirds adds to our understanding of foraging
 ecology in general.
description: We observed hummingbird vistiation to feeders to assess how they
 responded to different insect-derived chemicals. Birds were presented with
 control feeder (no odor or just a solvent control) and a treatment feeder
 (with one of 3 odors). We compared the number of visits to each feeder and
 time spent on each feeder between treatments
description: All columns and variables are explained in the metadata tab and
 readme,txt, including species codes. The aviary tab provides the data from
 the individual birds observed in aviaries and the wild tab provides the
 data from the wild, free-foraging birds observed in the field. Please
 refer to the meta
DOI: 10.25338/b86k7v
title: Data from: Evolution of sexually dimorphic pheromone profiles coincides with increased number of male-specific chemosensory organs in Drosophila prolongata

description: Binary communication systems that involve sex-specific signaling and
 sex-specific signal perception play a key role in sexual selection and in
 the evolution of sexually dimorphic traits. The driving forces and genetic
 changes underlying such traits can be investigated in systems where
 sex-specific signaling and perception have emerged recently and show
 evidence of potential coevolution. A promising model is found in
 Drosophila prolongata, which exhibits a species-specific increase in the
 number of male chemosensory bristles. We show that this transition
 coincides with recent evolutionary changes in cuticular hydrocarbon (CHC)
 profiles. Long-chain CHCs that are sexually monomorphic in the closest
 relatives of D. prolongata (D. rhopaloa, D. carrolli, D. kurseongensis,
 and D. fuyamai) are strongly male-biased in this species. We also identify
 an intraspecific female-limited polymorphism, where some females have
 male-like CHC profiles. Both the origin of sexually dimorphic CHC profiles
 and the female-limited polymorphism in D. prolongata involve changes in
 the relative amounts of three mono-alkene homologs, 9-Tricosene,
 9-Pentacosene and 9-Heptacosene, all of which share a common biosynthetic
 origin and point to a potentially simple genetic change underlying these
 traits. Our results suggest that pheromone synthesis may have coevolved
 with chemosensory perception, and open the way for reconstructing the
 origin of sexual dimorphism in this communication system.
DOI: 10.5061/dryad.8sf7m0ch8
title: Data from: Reproduction has different costs for immunity and parasitism in a wild mammal

description: Life history theory predicts that reproductive
 allocation
 draws resources away from immunity, resulting in increased parasitism. However, studies of reproductive tradeoffs rarely examine multiple measures of reproduction, immunity, and parasitism. It is therefore unclear whether the immune costs of reproductive traits correlate with their resource costs, and whether increased parasitism emerges from weaker immunity. We examined these relationships in wild female red deer (Cervus elaphus) with variable reproductive allocation and longitudinal data on mucosal antibody levels and helminth parasitism. We noninvasively collected faecal samples, counting propagules of strongyle nematodes (order: Strongylida), the common liver fluke Fasciola hepatica and the red deer tissue nematode Elaphostrongylus cervi. We also quantified both total and anti-strongyle mucosal IgA to measure general and specific immune allocation. Contrary to our predictions, we found that gestation was associated with decreased total IgA but with no increase in parasitism. Meanwhile, the considerable resource demand of lactation had no further immune cost but was associated with higher counts of strongyle nematodes and Elaphostrongylus cervi. These contrasting costs arose despite a negative correlation between antibodies and strongyle count, which implied that IgA was indicative of protective immunity. Our findings suggest that processes other than classical resource allocation tradeoffs are involved in mediating observed relationships between reproduction, immunity, and parasitism in wild mammals. In particular, reproduction-immunity tradeoffs may result from hormonal regulation or maternal antibody transfer, with parasitism increasing as a result of increased exposure arising from resource acquisition constraints. We advocate careful consideration of resource-independent mechanistic links and measurement of both immunity and parasitism when investigating reproductive costs.
DOI: 10.5061/dryad.j0zpc8692
title: Data from: Diving into divergence: differentiation in swimming performances, physiology and gene expression between locally-adapted sympatric cichlid fishes

description: Sympatric speciation occurs without strict vicariance and is thought to
 often be driven by ecological specialization of subpopulations that
 eventually diverge genetically and phenotypically. Distinct morphologies
 between sympatric populations occupying different niches have been
 interpreted as such differentiating adaptive phenotypes, yet differences
 in performance and thus adaptiveness between them were rarely tested.
 Here, we investigated if divergent body shapes of two sympatric crater
 lake cichlid species from Nicaragua, one being a shore-associated
 (benthic) species while the other prefers the open water zones (limnetic),
 affect cruising and sprinting swimming abilities - performances
 particularly relevant to their respective lifestyles. Furthermore, we
 investigated species differences in oxygen consumption across different
 swimming speeds and compare gene expression in gills and white muscle at
 rest and during exercise. We found a superior cruising ability in the
 limnetic Amphilophus zaliosus compared to the benthic A. astorquii, while
 sprinting was not different, suggesting that their distinct morphologies
 affect swimming performance. Increased cruising ability in A. zaliosus was
 however linked to a higher oxygen demand, during activity (but not rest),
 indicating different metabolic rates during exercise - a hypothesis
 supported by coinciding gene expression patterns of gill transcriptomes.
 We identified differentially expressed genes linked to swimming
 physiology, regulation of swimming behaviour and oxygen intake. A
 combination of physiological and morphological differences may thus
 underlie adaptations to these species’ distinct niches. This complex
 ecological specialization likely resulted in morphological and
 physiological trade-offs that contributed to the rapid establishment and
 maintenance of divergence with gene flow.
DOI: 10.5061/dryad.xpnvx0kb3
title: Intracranial haemodynamic relationships in patients with cerebral small vessel disease

description: Objective To investigate cerebrovascular reactivity (CVR), blood flow,
 vascular and cerebrospinal fluid (CSF) pulsatility, and their independent
 relationship to cerebral small vessel disease (SVD) features, in patients
 with minor ischaemic stroke and MRI evidence of SVD. Methods We recruited
 patients with minor ischaemic stroke and assessed CVR using Blood Oxygen
 Level Dependent (BOLD) MRI during a hypercapnic challenge, cerebral blood
 flow, vascular and CSF pulsatility using phase contrast MRI, and
 structural MR brain imaging to quantify white matter hyperintensities
 (WMH) and perivascular spaces (PVS). We used multiple regression to
 identify parameters associated with SVD features, controlling for patient
 characteristics. Results 53 of 60 patients completed the study with a full
 dataset (age 68.0±8.8, 74% male, 75% hypertensive). After controlling for
 age, gender and systolic BP, lower white matter CVR was associated with
 higher WMH volume (-0.01%/mmHg per log10 increase in WMH volume, p=0.02),
 basal ganglia PVS (-0.01%/mmHg per point increase in PVS score, p=0.02)
 and higher venous pulsatility (superior sagittal sinus -0.03%/mmHg,
 p=0.02, per unit increase in pulsatility index) but not with cerebral
 blood flow (p=0.58). Lower foramen magnum CSF stroke volume was associated
 with worse white matter CVR (0.04%/mmHg per ml increase in stroke volume,
 p=0.04) and more severe basal ganglia PVS (p=0.09). Conclusions Lower CVR,
 higher venous pulsatility and lower foramen magnum CSF stroke volume
 indicate that dynamic vascular dysfunctions underpin PVS dysfunction and
 WMH development. Further exploration of microvascular dysfunction and CSF
 dynamics may uncover new mechanisms and intervention targets to reduce SVD
 lesion development, cognitive decline and stroke.