cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tm680
title: Data from: A second New World hover fly, Toxomerus floralis (Fabricius) (Diptera: Syrphidae), recorded from the Old World, with description of larval pollen-feeding ecology

description: Recently (2013–2014), several hoverfly specimens from two localities in
 Benin and Cameroon (West and Central Africa) were caught from a species
 that we could not identify using existing identification keys for
 Afrotropical Syrphidae. Specific identification as Toxomerus floralis
 (Fabricius) was accomplished using morphology and various Neotropical
 identification keys. Corroboration of this identification was made by
 sequencing of the standard COI barcode region and a subsequent BLAST-IDS
 in BOLD that revealed a 100% sequence similarity with Toxomerus floralis
 from Suriname (South America). Species identification was further
 supported by sequencing parts of the nuclear 18S and 28S rRNA genes. The
 species is widespread in Togo, Benin, Nigeria and Cameroon, and eggs,
 larvae and adults are abundant at several localities. Yet, the full extent
 of its geographic distribution within tropical Africa remains to be
 determined. This is only the second known established introduction of a
 non-African hoverfly species in the Afrotropics. Interestingly, the larvae
 of the species have been reported as predators of Aphididae and
 Delphacidae but we found them to be pollenivorous, which is a rare feeding
 mode within the subfamily Syrphinae. Moreover, it is the only known
 Syrphinae species of which the larvae feed on pollen from two plant
 species from different families (Cyperaceae and Orobranchaceae). This
 example illustrates how DNA barcoding may allow a fast and accurate
 identification of introduced species.
description: alignment fasta file for
 18S rRNA, 28S rRNA and COIThis file contains the
 alignments of the 18S rRNA, 28S rRNA, and COI datasets used in the paper,
 respectively. The file is in fasta-format.fasta file 18S - 28S -
 COI.fas
DOI: 10.5061/dryad.fh576k0
title: Data from: A late Pleistocene human footprint from the Pilauco archaeological site, Northern Patagonia, Chile

description: The present study describes the discovery of a singular sedimentary
 structure corresponding to an ichnite that was excavated at the
 paleo-archaeological site Pilauco (Osorno, Chile). The trace fossil is
 associated with megafauna bones, plant material and unifacial lithic
 tools. Here we present a detailed analysis of the Pilauco ichnite and
 associated sedimentary structures, as well as new radiocarbon data. The
 ichnological analysis confidently assigns the trace to the ichnospecies
 Hominipes modernus—a hominoid footprint usually related to Homo sapiens.
 Some particular characteristics of the Pilauco trace include an elongated
 distal hallux, lateral digit impressions obliterated by the collapsed
 sediment, and sediment lumps inside and around the trace. In order to
 evaluate the origin of the ichnite, trackmaking experiments are performed
 on re-hydrated fossil bed sediments. The results demonstrate that a human
 agent could easily generate a footprint morphology equivalent to the
 sedimentary structure when walking on a saturated substrate. Based on the
 evidence, we conclude that the trackmaker might well have been a
 bare-footed adult human. This finding, along with the presence of lithic
 artifacts in the same sedimentary levels, might represent further evidence
 for a pre-Clovis South American colonization of northern Patagonia, as
 originally proposed for the nearby Monte Verde site.
description: Pilauco´s Hominipes
 modernus footprintThree-dimensional model
 of the original sedimentary structure attributed to a human footprint that
 was excavated at the Pilauco site, in dorsal view with a virtual 45° tilt
 toward the south to facilitate the observation of profile lines 1-2, 3-4
 and 5-6 drawn on the 3D model surface (123Catch from Autodesk© and trial
 version of Rhino4, McNeel &Associates©).Huella
 Pilauco.obj
DOI: 10.5061/dryad.sh7rm2pt
title: Data from: Repeatability and contingency in the evolution of a key innovation in phage lambda

description: The processes responsible for the evolution of key innovations, whereby
 lineages acquire qualitatively new functions that expand their ecological
 opportunities, remain poorly understood. We examined how a virus,
 bacteriophage λ, evolved to infect its host, Escherichia coli, through a
 novel pathway. Natural selection promoted the fixation of mutations in the
 virus’s host-recognition protein, J, that improved fitness on the original
 receptor, LamB, and set the stage for other mutations that allowed
 infection through a new receptor, OmpF. These viral mutations arose only
 after the host evolved reduced expression of LamB, whereas certain other
 host mutations prevented the phage from evolving the new function. This
 study shows the complex interplay between genomic processes and ecological
 conditions that favor the emergence of evolutionary innovations.
description: DRYAD
 FILESThis is a zipped folder
 of all of the data files and scripts to run the statistical analyses
 associated with the manuscript.
DOI: 10.5061/dryad.b025kp0
title: Data from: Elevational changes in the avian community of a Mesoamerican cloud forest park

description: Harboring many range-restricted and specialized species, high elevation
 tropical cloud forests are diverse habitats represented in many protected
 areas. Despite this, many such areas receive little practical protection
 from deforestation and land conversion. Moreover, montane species may be
 more sensitive to climate change owing to various factors affecting
 community assembly across elevational gradients. Few studies have used
 annual monitoring to assess how biological communities in cloud forests
 may be shifting in response to habitat or climate change or assessed the
 efficacy of protected areas in buffering these effects. We analysed
 avifaunal community trends in a ten-year dataset of constant-effort bird
 point-count data in a cloud forest national park in Honduras, Central
 America. We found that species richness and diversity increased at higher
 elevations, but decreased at lower elevations. Abundances of most dietary
 and forest-dependency groups exhibited similar trends, and many key cloud
 forest species shifted upslope and/or increased in abundance. Taken
 together, our results suggest that the avian community is moving upslope
 and species composition is changing. Results for species richness and
 diversity were similar when only non-degraded transects were considered,
 suggesting the role of climate change as an important driver. At lower
 elevations, however, many species may be negatively affected by increased
 habitat degradation, favoring species with low forest-dependency.
 Continued habitat conversion and climate change could push the cloud
 forest bird community further upslope, potentially resulting in increased
 competition, mortality and even extirpation of some species. Increased
 protection is unlikely to mitigate the effects of climate change.
description: Neate-Clegg et al 2018
 BiotropicaThis is the data upon
 which all analyses were conducted. It contains the counts of every species
 from every transect survey from 2007 to 2016 including abundance and
 species richness. For each transect survey there is also the number of
 point count sites (NoSS), mean elevation, elevational range, year, survey
 occasion and number of observers.
DOI: 10.5061/dryad.sp152
title: Data from: Perceptions of research bronchoscopy in Malawian adults with pulmonary tuberculosis: a cross-sectional study.

description: Bronchoscopy is an established research tool in Malawi, enabling
 collection of pulmonary samples for immunological, pharmacological, and
 microbiological studies. It is, however, an invasive clinical procedure
 that offers no direct benefit to volunteering participants when used in a
 research capacity alone, and thus informed consent is essential. This
 study aimed to explore TB patients’ understanding of research
 bronchoscopy, what would motivate them to participate in research
 bronchoscopy, and their concerns, in order to inform consenting processes
 for future clinical studies. We used a qualitative research design. Two
 focus group discussions were conducted with community members and TB
 patients to understand their perceptions of bronchoscopy. Transcripts were
 coded by multiple co-authors and thematic content analysis was used to
 analyse main findings. We found that Malawian patients with pulmonary TB
 were willing to participate in a study using research bronchoscopy for
 health assessment and access to improved healthcare. We identified
 information of value to potential participants when consenting to help
 assuage some of the anxieties expressed by participants. Patient and
 public involvement is essential to improve informed consent and
 institutional trust.
description: Perceptions of research
 bronchoscopy - focus group discussion 1 transcriptThis is the transcript
 of the first focus group discussion with the relatives / carers of TB
 patients in urban Blantyre, Malawi. The transcript includes the Chichewa
 to English translation. Anonymised data presented.Andrew
 fgd1.DS2_CA_Eng.docxPerceptions of research
 bronchoscopy - focus group discussion 2 transcriptThis is the transcript
 of the second focus group discussion with the TB patients on treatment in
 urban Blantyre, Malawi. The transcript includes the Chichewa to English
 translation. Anonymised data presented.Andrew
 fgd2.DS2_DM_Eng.docx
DOI: 10.5061/dryad.s9f7c
title: Data from: The curious case of the camelthorn: competition, coexistence, and nest-site limitation in a multispecies mutualism

description: Myrmecophyte plants house ants in domatia in exchange for protection from
 herbivores. Ant-myrmecophyte mutualisms exhibit two general patterns due
 to competition between ants for plant occupancy: i) domatia nest-sites are
 a limiting resource and ii) each individual plant hosts one ant species at
 a time. However, individual camelthorn trees (Vachellia erioloba)
 typically host two to four ant species simultaneously, often coexisting in
 adjacent domatia on the same branch. Such fine-grain spatial coexistence
 questions the conventional wisdom on ant-myrmecophyte mutualisms.
 Camelthorn ants appear not to be nest-site limited, despite low abundance
 of suitable domatia, and have random distributions of nest-sites within
 and across trees. These patterns suggest a lack of competition between
 ants for domatia and contrast strongly with other ant-myrmecophyte
 systems. Comparison of this unusual case with others suggests that spatial
 scale is crucial to coexistence or competitive exclusion involving
 multiple ant species. Furthermore, coexistence may be facilitated when
 co-occurring ant species diverge strongly on at least one niche axis. Our
 conclusions provide recommendations for future ant-myrmecophyte research,
 particularly in utilising multispecies systems to further our
 understanding of mutualism biology.
description: Vachellia erioloba
 ant-domatia survey resultsThese data were
 collected during field work conducted at Kuzikus Wildlife Reserve
 (23°13'S, 18°24'E, elevation 1340m) in Namibia (for full site
 description see Campbell et al. 2013, African Journal of Ecology
 51:590-598). Surveys were completed in April, September and October 2011
 for ant occupants within swollen-thorn domatia of camelthorn trees,
 Vachellia erioloba. Using secateurs, branches were removed from trees and
 thorns opened in the field to examine the contents. Thorns were surveyed
 from the tip of the branch inwards towards the trunk. We recorded
 microsite data on branch and thorn variables, and for the contents of a
 thorn we recorded ant species, an estimate of number of ants at each life
 stage (workers, alates, queens, and brood) and other thorn
 occupants.Vachellia erioloba Ant-Thorn
 Survey Results - Kuzikus 2011.xlsx
DOI: 10.5061/dryad.b0733
title: Data from: Phylogeny of the Detarioid Genera Cynometra and Maniltoa (Leguminosae)

description: The genus Cynometra (Leguminosae, Detarioideae) is a large, pantropical
 group of woody plants ranging in size from 5-50 meters. While many recent
 advances have been made in higher level legume systematics, many large
 genera still require more study to test their monophyly. Further, its
 relationship to the much smaller Pacific genus Maniltoa is unclear. Here
 we present the first broadly-sampled phylogeny of Cynometra and Maniltoa,
 based on molecular data from three chloroplast loci: matK, the trnL intron
 and the trnL intergenic spacer. Our analyses indicate that Cynometra is
 not monophyletic as currently circumscribed, as several researchers had
 previously suspected. We recover two strongly supported clades of
 Cynometra sensu lato; one that is most closely related to a clade
 consisting of the genera Dicymbe and Polystemonanthus and is composed of
 exclusively African taxa and another clade that is pantropical and is
 nested in a larger clade with the Scorodolphoeus group and the genera
 Normandiodendron, Neochevalierodendron, and Zenkerella. Futhermore, the
 genus Maniltoa is nested within the pantropical Cynometra clade and is
 also non-monophyletic. The two clades are each supported by several
 morphological characters that can be used to distinguish between them
 (e.g. inflorescence structure, pedicel articulation, fruit dehiscence).
 These results will be used to modify the classification by moving the
 relevant African taxa to a new genus and placing Maniltoa in synonymy with
 Cynometra.
description: cyno_matk_10Jan2017cyno_trnL_intron10Jan2017cyno_trnl_spacer_10Jan2017
DOI: 10.5061/dryad.fp861
title: Data from: The magnitude of behavioral isolation is affected by characteristics of the mating community

description: Gene exchange between species occurs in areas of secondary contact, where
 two species have the opportunity to hybridize. If heterospecific males are
 more common than conspecific males, females will experience more
 encounters with males of other species. These encounters might increase
 the likelihood of heterospecific matings, and lead to the production of
 hybrid progeny. I studied the mating behavior of two pairs of sibling
 species endemic to Africa: Drosophila yakuba/D. santomea and D.
 simulans/D. sechellia. Drosophila yakuba and D. simulans are cosmopolitan
 species widely distributed in the African continent, while D. santomea and
 D. sechellia are island endemics. These pairs of species hybridize in
 nature and have the potential to exchange genes in natural conditions. I
 used these two pairs of Drosophila species, and constructed mating
 communities of different size and different heterospecific:conspecific
 composition. I found that both the total number of potential mates and the
 relative frequency of conspecific vs. heterospecific males affect female
 mating decisions in the cosmopolitan species but not in the island
 endemics. These results suggest that the population characteristics in
 which mating occurs may affect the magnitude of premating isolation.
 Community composition might thus facilitate, or impair, gene flow between
 species.
description: Raw data and analytical
 codeRaw_data_density_Matute.zip
DOI: 10.5061/dryad.3hc80
title: Data from: Fire coral clones demonstrate phenotypic plasticity among reef habitats

description: Clonal populations are often characterized by reduced levels of genotypic
 diversity, which can translate into lower numbers of functional
 phenotypes, both of which impede adaptation. Study of partially clonal
 animals enables examination of the environmental settings under which
 clonal reproduction is favoured. Here, we gathered genotypic and
 phenotypic information from 3,651 georeferenced colonies of the fire coral
 Millepora platyphylla in five habitats with different hydrodynamic regimes
 in Moorea, French Polynesia. In the upper slope where waves break, most
 colonies grew as vertical sheets (“sheet tree”) making them more
 vulnerable to fragmentation. Nearly all fire corals in the other habitats
 are encrusting or massive. The M. platyphylla population is highly clonal
 (80% of the colonies are clones), while characterized by the highest
 genotype diversity ever documented for terrestrial or marine populations
 (1,064 genotypes). The proportion of clones varies greatly among habitats
 (≥58%–97%) and clones (328 clonal lineages) are distributed
 perpendicularly from the reef crest, perfectly aligned with wave energy.
 There are six clonal lineages with clones dispersed in at least two
 adjacent habitats that strongly demonstrate phenotypic plasticity. Eighty
 per cent of the colonies in these lineages are “sheet tree” on the upper
 slope, while 80%–100% are encrusting or massive on the mid slope and back
 reef. This is a unique example of phenotypic plasticity among
 reef-building coral clones as corals typically have wave-tolerant growth
 forms in high-energy reef areas.
description: RawDataSummary table of all colonies genotyped with relevant corresponding data, including microsatellite genotypes at twelve loci and phenotypes.
DOI: 10.5061/dryad.nm61g
title: Data from: Sex-specific allelic transmission bias suggests sexual conflict at MC1R

description: Sexual conflict arises when selection in one sex causes the displacement
 of the other sex from its phenotypic optimum, leading to an inevitable
 tension within the genome – called intralocus sexual conflict. Although
 the autosomal melanocortin-1-receptor gene (MC1R) can generate colour
 variation in sexually dichromatic species, most previous studies have not
 considered the possibility that MC1R may be subject to sexual conflict. In
 the barn owl (Tyto alba), the allele MC1RWHITE is associated with whitish
 plumage coloration, typical of males, and the allele MC1RRUFOUS is
 associated with dark rufous coloration, typical of females, although each
 sex can express any phenotype. Because each colour variant is adapted to
 specific environmental conditions, the allele MC1RWHITE may be more
 strongly selected in males and the allele MC1RRUFOUS in females. We
 therefore investigated whether MC1R genotypes are in excess or deficit in
 male and female fledglings compared with the expected Hardy–Weinberg
 proportions. Our results show an overall deficit of 7.5% in the proportion
 of heterozygotes in males and of 12.9% in females. In males, interannual
 variation in assortative pairing with respect to MC1R explained the
 year-specific deviations from Hardy–Weinberg proportions, whereas in
 females, the deficit was better explained by the interannual variation in
 the probability of inheriting the MC1RWHITE or MC1RRUFOUS allele.
 Additionally, we observed that sons inherit the MC1RRUFOUS allele from
 their fathers on average slightly less often than expected under the first
 Mendelian law. Transmission ratio distortion may be adaptive in this
 sexually dichromatic species if males and females are, respectively,
 selected to display white and rufous plumages.
description: BreedingPairsMC1RJuvenilesMicrosatellitesJuvenilesScript Chi2 Simulationscript FIS SimulationScript proportion of assortative pairing
DOI: 10.5061/dryad.v2818
title: Data from: Plant functional groups within a tropical forest exhibit different wood functional anatomy

description: Understanding the anatomical basis of plant water transport in forest
 ecosystems is crucial for contextualizing community-level adaptations to
 drought, especially in life-form-rich tropical forests. To provide this
 context, we explored wood functional anatomy traits related to plant
 hydraulic architecture across different plant functional groups in a
 lowland tropical rain forest. We measured wood traits in 90 species from
 six functional groups (mature-phase, understorey and pioneer trees;
 understorey and pioneer shrubs; vines) and related these traits to
 intrinsic water-use efficiency (WUEi) as a measure of physiological
 performance. We also examined vessel size distribution patterns across
 groups to determine trade-offs in theoretical hydraulic safety vs.
 efficiency. Some plant functional groups exhibited significant differences
 in vessel parameters and WUEi. Vessel diameters in vines and pioneer trees
 were two- to threefold greater on average than in understorey trees and
 shrubs. Contrastingly, vessels in understorey trees and shrubs fell within
 the smaller size classes, suggesting greater safety mechanisms. In
 addition to these trends, large vessel dimensions were important
 predictors of WUEi among the functional groups. We conclude that wood
 functional anatomy profiles varied across plant functional groups in a
 tropical rain forest. These groups can therefore serve as a framework for
 further investigations on structure–function relationships and a sound
 basis for modelling species responses to drought.
description: Wood density, vessel
 characteristics and water use efficiency for 90 tropical
 speciesWood density, vessel
 characteristics and water use efficiency for 90 tropical
 speciesVessel and WUE 90
 species.xlsx
DOI: 10.5061/dryad.1qs20
title: Data from: Oceanographic connectivity and environmental correlates of genetic structuring in Atlantic herring in the Baltic Sea

description: Marine fish often show little genetic structuring in neutral marker genes,
 and Atlantic herring (Clupea harengus) in the Baltic Sea are no exception;
 historically, very low levels of population differentiation (FST ≈ 0.002)
 have been found, despite a high degree of interpopulation environmental
 heterogeneity in salinity and temperature. Recent exome sequencing and SNP
 studies have however shown that many loci are under selection in this
 system. Here, we combined population genetic analyses of a large number of
 transcriptome-derived microsatellite markers with oceanographic modelling
 to investigate genetic differentiation and connectivity in Atlantic
 herring at a relatively fine scale within the Baltic Sea. We found
 evidence for weak but robust and significant genetic structuring (FST =
 0.008) explainable by oceanographic connectivity. Genetic differentiation
 was also associated with site differences in temperature and salinity,
 with the result driven by the locus Her14 which appears to be under
 directional selection (FST = 0.08). The results show that Baltic herring
 are genetically structured within the Baltic Sea, and highlight the role
 of oceanography and environmental factors in explaining this structuring.
 The results also have implications for the management of herring
 fisheries, the most economically important fishery in the Baltic Sea,
 suggesting that the current fisheries management units may be in need of
 revision.
description: Genepop 60
 3Genepop formatted file
 for 60 microsatellite loci, for 15 sampling locations.