cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3574r
title: Data from: Chemical composition of preen wax reflects major histocompatibility complex similarity in songbirds

description: In jawed vertebrates, genes of the major histocompatibility complex (MHC)
 play a key role in immunity by encoding cell-surface proteins that
 recognize and bind non-self antigens. High variability at MHC suggests
 that these loci may also function in social signalling such as mate choice
 and kin recognition. This requires that MHC genotype covaries with some
 perceptible phenotypic trait. In mammals and fish, MHC is signalled
 chemically through volatile and non-volatile peptide odour cues,
 facilitating MHC-dependent mate choice and other behaviours. In birds,
 despite evidence for MHC-dependent mating, candidate mechanisms for MHC
 signalling remain largely unexplored. However, feather preen wax has
 recently been implicated as a potential source of odour cues. We examined
 whether the chemical composition of preen wax correlates with MHC class
 IIβ genotypes of wild song sparrows (Melospiza melodia). Pairwise chemical
 distance reflected amino acid distance at MHC for male–female dyads,
 although not for same-sex dyads. Chemical diversity did not reflect MHC
 diversity. We used gas chromatography–mass spectrometry (GC-MS) to
 characterize preen wax compounds, and identified four wax esters that best
 reflect MHC similarity. Provided songbirds can detect variation in preen
 wax composition, this cue may allow individuals to assess MHC
 compatibility of potential mates.
description: Presence of MHC alleles
 in each individual1: allele present. 0:
 allele absent.All_mhc_composition_table.csvRelative peak sizes from GC-FID of preen wax for each individualRelative peak sizes are expressed as a percentage of total chromatogram area.All_raw_preen_composition_table.csvPairwise matrix of chemical distance for female-female dyadsValues are standardized Bray-Curtis distances, calculated from relative areas of peaks on GC-FID chromatogram of preen wax.PreenDistance_female-female-standardized_bray-curtis.csvPairwise matrix of chemical distance for male-male dyadsValues are standardized Bray-Curtis distances, calculated from relative areas of peaks on GC-FID chromatogram of preen wax.PreenDistance_male-male-standardized_bray-curtis.csvPairwise matrix of chemical distance for male-female dyadsValues are standardized Bray-Curtis distances, calculated from relative areas of peaks on GC-FID chromatogram of preen wax.PreenDistance_male-female_standardized_bray-curtis.csvPairwise matrix of MHC dissimilarity for female-female dyadsValues calculated from UniFrac amino acid distances.Unifrac_female-female.csvPairwise matrix of MHC dissimilarity for male-male dyadsValues calculated from UniFrac amino acid distances.Unifrac-male-male.csvPairwise matrix of MHC dissimilarity for male-female dyadsValues are calculated from UniFrac amino acid distances.Unifrac_male-female.csv
DOI: 10.5061/dryad.35s4c
title: Data from: Best of both worlds? Association between outcrossing and parasite loads in a selfing fish

description: Mixed-mating strategies (i.e. intermediate levels of self-fertilization
 and outcrossing in hermaphrodites) are relatively common in plants and
 animals, but why self-fertilization (selfing) rates vary so much in nature
 has proved difficult to explain. We tested the hypothesis that parasites
 help maintain mixed-mating using a partially selfing fish (Kryptolebias
 marmoratus) as a model. We show that outcrossed progeny in the wild are
 genetically more diverse and less susceptible to multiple parasite
 infections than their selfed counterparts. Given that outcrossing in K.
 marmoratus can only be attained by male-hermaphrodite matings, our data
 provides an explanation for the coexistence of males and hermaphrodites in
 androdioecious species where hermaphrodites are unable to outcross among
 themselves. Moreover, our study provides evidence that parasites
 contribute to maintaining mixed-mating in a natural animal population.
description: Dataset_Evolution
 11_0197
DOI: 10.5281/zenodo.10998541
title: CMIP6 tmax and tmin data for 50 most populous cities in USA

description: These data were downloaded from Google Earth Engine. Each csv includes Year Month Day CM Scenario and other columns. CM includes three scenario (historical, ssp245 and ssp585). The scenario involves the parameter (tasmax or tasmin). Other columns means the city ID. The city ID and corresponding city name can be seen in the csv file named UID Abbreviation.csv above and the shapefile of cities were used from the open repository (Chen et al. 2022). This global inventory includes 247 cities within the contiguous US. This can be found at: Chen, B., Wu, S., Song, Y. et al. Contrasting inequality in human exposure to greenspace between cities of Global North and Global South. Nat Commun 13, 4636 (2022). https://doi.org/10.1038/s41467-022-32258-4.And to select the 50 populous cities, 1 km X 1 km resolution imagery of population by Wang et. al (2022) was used.[Wang, X., Meng, X. & Long, Y. Projecting 1 km-grid population distributions from 2020 to 2100 globally under shared socioeconomic pathways. Sci Data 9, 563 (2022). https://doi.org/10.1038/s41597-022-01675-x]. Based on this, we ranked 50 cities from those 247 US cities found in Chen et al. 2022.Those data and real names of the cities can be studied from these papers.
DOI: 10.5281/zenodo.10998542
title: CMIP6 tmax and tmin data for 50 most populous cities in USA

description: These data were downloaded from Google Earth Engine. Each csv includes Year Month Day CM Scenario and other columns. CM includes three scenario (historical, ssp245 and ssp585). The scenario involves the parameter (tasmax or tasmin). Other columns means the city ID. The city ID and corresponding city name can be seen in the csv file named UID Abbreviation.csv above and the shapefile of cities were used from the open repository (Chen et al. 2022). This global inventory includes 247 cities within the contiguous US. This can be found at: Chen, B., Wu, S., Song, Y. et al. Contrasting inequality in human exposure to greenspace between cities of Global North and Global South. Nat Commun 13, 4636 (2022). https://doi.org/10.1038/s41467-022-32258-4.And to select the 50 populous cities, 1 km X 1 km resolution imagery of population by Wang et. al (2022) was used.[Wang, X., Meng, X. & Long, Y. Projecting 1 km-grid population distributions from 2020 to 2100 globally under shared socioeconomic pathways. Sci Data 9, 563 (2022). https://doi.org/10.1038/s41597-022-01675-x]. Based on this, we ranked 50 cities from those 247 US cities found in Chen et al. 2022.Those data and real names of the cities can be studied from these papers.
DOI: 10.5061/dryad.n3f4g
title: Data from: Lobelia siphilitica plants that escape herbivory in time also have reduced latex production

description: Flowering phenology is an important determinant of a plant’s reproductive
 success. Both assortative mating and niche construction can result in the
 evolution of correlations between phenology and other reproductive,
 functional, and life history traits. Correlations between phenology and
 herbivore defence traits are particularly likely because the timing of
 flowering can allow a plant to escape herbivory. To test whether herbivore
 escape and defence are correlated, we estimated phenotypic and genetic
 correlations between flowering phenology and latex production in
 greenhouse-grown Lobelia siphilitica L. (Lobeliaceae). Lobelia siphilitica
 plants that flower later escape herbivory by a specialist pre-dispersal
 seed predator, and thus should invest fewer resources in defence.
 Consistent with this prediction, we found that later flowering was
 phenotypically and genetically correlated with reduced latex production.
 To test whether herbivore escape and latex production were costly, we also
 measured four fitness correlates. Flowering phenology was negatively
 genetically correlated with three out of four fitness estimates,
 suggesting that herbivore escape can be costly. In contrast, we did not
 find evidence for costs of latex production. Generally, our results
 suggest that herbivore escape and defensive traits will not evolve
 independently in L. siphilitica.
description: LobeliaDataBasic phenotypic data collected from greenhouse grown Lobelia siphilitica plants. Details of the traits can be found in the main publication.
DOI: 10.5061/dryad.2c1s7
title: Data from: Allometry and growth of eight tree taxa in United Kingdom woodlands

description: As part of a project to develop predictive ecosystem models of United
 Kingdom woodlands we have collated data from two United Kingdom woodlands
 - Wytham Woods and Alice Holt. Here we present data from 582 individual
 trees of eight taxa in the form of summary variables relating to the
 allometric relationships between trunk diameter, height, crown height,
 crown radius and trunk radial growth rate to the tree’s light environment
 and diameter at breast height. In addition the raw data files containing
 the variables from which the summary data were obtained. Large sample
 sizes with longitudinal data spanning 22 years make these datasets useful
 for future studies concerned with the way trees change in size and shape
 over their life-span.
description: Sapling allometry DBH,
 D10 & HeightContains data on DBH
 (cm), D10 (cm) and Height (m) for a total of 145 saplings for the eight
 taxa under consideration. The year in which the DBH and height and D10
 data were recorded is reported for each individual. Data collected in the
 fieldData
 record 1.txtAdult allometry DBH,
 Height & Crown heightContains data on DBH
 (cm), Height (m), Crown height (m) and Crown radius (m) for a total of 297
 adult trees for the eight taxa under consideration. The year in which DBH,
 height and crown height and radius were recorded are reported for each
 individual. Data collected in the fieldData record
 2.txtSapling
 growthContains data on DBH
 growth rates (cm yr-1) for the periods between measurements, the mean
 growth rate, D10 (cm), and the fraction of ambient light in the tree’s
 environment for 129 individuals representing seven of the eight taxa under
 consideration. The year in which D10 and light were measured is reported.
 Data collected in the field.Data record
 4.txtCanopy
 opennessContains data on canopy
 openness for 165 single taxon stands of the eight taxa under
 consideration. Data collected in the field.Data record
 6.txtAll trees height v
 DBHContains data on DBH
 (cm) and Height (m) for 404 individuals for the eight taxa under
 consideration. Repeated measures on each individual results in 1018
 records, the year of each measurement is reported. Data collected in the
 fieldData
 record 3.txtAll trees
 growthContains data on DBH
 growth rates (cm yr-1) for the periods between measurements and the mean
 growth rate for 439 individuals of the eight taxa under consideration.
 Data collected in the field.Data record
 5.txtSORTIE parameter
 fileContains data on 16
 parameters for each of the eight taxa considered here. These allow the
 instantiation of the equations 1-8 listed in the associated paper. In
 conjunction with parameters on mortality and dispersal they also allow
 SORTIE to be run to produce projections of United Kingdom lowland
 woodlands.Data record
 7.txt
DOI: 10.5061/dryad.n311f
title: Data from: Sympatric population divergence within a highly pelagic seabird species complex (Hydrobates spp.)

description: Both physical and non-physical barriers can restrict gene flow among
 seabird populations. Understanding the relative importance of non-physical
 barriers, such as breeding phenology, is key to understanding seabird
 biodiversity. We investigated drivers of diversification in the Leach’s
 storm-petrel species complex (Hydrobates spp.) by examining population
 genetic structure across its range. Variation in the mitochondrial control
 region and six microsatellite loci was assayed in birds sampled from
 breeding colonies throughout the North Atlantic and North Pacific (H.
 leucorhoa leucorhoa), as well as from San Benito Islands (H. l. chapmani),
 and two seasonal populations in Guadalupe (summer breeding H. socorroensis
 and winter breeding H. cheimomnestes), Mexico. Weak but significant
 differentiation was found between populations of H. l. leucorhoa breeding
 in the Atlantic versus North Pacific, as well as between H. l. chapmani
 and H. l. leucorhoa, and between H. socorroensis and H. cheimomnestes
 within Guadalupe. In contrast, strong differentiation in both
 mitochondrial DNA and microsatellites was found between H. leucorhoa and
 both H. socorroensis and H. cheimomnestes. Phylogenetic reconstruction
 suggested the Guadalupe seasonal breeding populations are sister taxa, at
 least in their mitochondrial DNA. Non-physical barriers to gene flow
 appear to be more important than physical barriers in driving divergence
 within the Leach’s storm-petrel species complex. In particular,
 allochronic speciation may have occurred between the seasonal populations
 within Guadalupe. Further work should include higher resolution sequencing
 to confirm results, and an increased sampling effort, particularly within
 the California area, to fully resolve the relationship between H. l.
 leucorhoa and H. l. chapmani.
description: Leachs_stormpetrels_mitochondroalControlRegion_and_outgroupMitochondrial control region sequences for all Leach's storm-petrels used in our study (including from Hydrobates leucorhoa leucorhoa, H. l. chapmani, H. socorroensis, H. cheimomnestes, and outgroup sequences from H. castro).Leachs_stormpetrel_microsatellite_dataMicrosatellite data from all birds used in our study (including from H. leucorhoa leucorhoa, H. l. chapmani, H. socorroensis and H. cheimomnestes).
DOI: 10.5061/dryad.7t7d9
title: Data from: Abandoning sex: multiple origins of asexuality in the ciliate Tetrahymena

description: Background: By segregating somatic and germinal functions into large,
 compound macronuclei and small diploid micronuclei, respectively, ciliates
 can explore sexuality in ways other eukaryotes cannot. Sex, for instance,
 is not for reproduction but for nuclear replacement in the two cells
 temporarily joined in conjugation. With equal contributions from both
 conjugants, there is no cost of sex which theory predicts should favor
 asexuality. Yet ciliate asexuality is rare. The exceptional Tetrahymena
 has abandoned sex through loss of the micronucleus; its amicronucleates
 are abundant in nature where they reproduce by binary fission but never
 form conjugating pairs. A possible reason for their abundance is that the
 Tetrahymena macronucleus does not accumulate mutations as proposed by
 Muller’s ratchet. As such, Tetrahymena amicronucleates have the potential
 to be very old. This study used cytochrome oxidase-1 barcodes to determine
 the phylogenetic origin and relative age of amicronucleates isolated from
 nature. Results: Amicronucleates constituted 25% of Tetrahymena-like wild
 isolates. Of the 244 amicronucleates examined for cox1 barcodes, 237
 belonged to Tetrahymena, seven to other genera. Sixty percent originated
 from 12 named species or barcoded strains, including the model Tetrahymena
 thermophila, while the remaining 40% represent 19 putative new species,
 eight of which have micronucleate counterparts and 11 of which are known
 only as amicronucleates. In some instances, cox1 haplotypes were shared
 among micronucleate and amicronucleates collected from the same source.
 Phylogenetic analysis showed that most amicronucleates belong to the
 “borealis” clade in which mating type is determined by gene rearrangement.
 Some amicronucleate species were clustered on the SSU phylogenetic tree
 and had longer branch lengths, indicating more ancient origin.
 Conclusions: Naturally occurring Tetrahymena amicronucleates have multiple
 origins, arising from numerous species. Likely many more new species
 remain to be discovered. Shared haplotypes indicate that some are of
 contemporary origin, while phylogeny indicates that others may be millions
 of years old. The apparent success of amicronucleate Tetrahymena may be
 because macronuclear assortment and recombination allow them to avoid
 Muller’s ratchet, incorporate beneficial mutations, and evolve
 independently of sex. The inability of amicronucleates to mate may be the
 result of error(s) in mating type gene rearrangement.
description: SSU phylogeny of
 amicronucleate TetrahymenaSSU amicronucleate tree
 .nexSSU amicronucleate tree
 Newick formatSSU amicronucleate tree
 in Newick formatSSU amicronucleate
 tree.nwk
DOI: 10.5061/dryad.4pm81
title: Data from: Filters of floristic exchange: how traits and climate shape the rainforest invasion of Sahul from Sunda

description: Aim To evaluate how biogeographic and ecological processes influenced
 species distributions and community assembly in a continental rainforest
 flora with mixed biogeographic origins. Location Continental Australia.
 Methods We identified 795 species with Sahul ancestry (Australian
 rainforest flora of Gondwanan origin) and 604 species with Sunda ancestry
 (rainforest plant lineages of Indo-Malesian origin) from a total of 1872
 free-standing Australian woody rainforest taxa. We then compared the
 distribution of Sunda to Sahul species in relation to variation in species
 richness and phylogenetic endemism at continental scale, and local species
 distributions in available plot data from the Tropics (Cape York and the
 Australian Wet Tropics in northern Queensland) and subtropics
 (Nightcap-Border Ranges, Washpool and Dorrigo, in northern New South
 Wales). We compared the dispersal and persistence characteristics, and key
 functional traits (leaf size, fruit size, wood density and maximum height
 at maturity) of the Sunda and Sahul components of the continental
 rainforest flora. The influence of climate (temperature) and local
 environmental (altitude) factors in driving fine-scale distributional
 patterns were evaluated. Results Sunda rainforest species richness
 decreased with increasing latitude but maintained high levels of endemism,
 including in the south. Sunda species traits suggest more efficient
 dispersal and faster growth than Sahul lineages. Resprouting (persistence)
 was less evident in species with Sunda than Sahul ancestry. We show that
 Sunda lineage distributions were influenced by interacting environmental
 and climatic factors, as well as historical contingencies. Main
 conclusions Efficient dispersal and relatively fast growth likely
 facilitated the establishment and spread of Sunda lineages in Australia.
 However, the Sunda invasion was resisted in stable, saturated communities
 of Sahul lineages, and in the temperate south where climate acted as a
 strong filter. The results highlight the importance of integrating
 historical biogeography and contemporary ecological processes to study
 continental-scale rainforest distribution and assembly.
description: Sunda_Sahul
 listList of Australian
 rainforest species allocated with biogeographic origin.certainty in SundaSahul
 speciesFile contains a list of
 Sunda and Sahul species with a verdict given (i.e. how certain an ancestry
 was allocated). Verdict is based on the published studies relating to each
 species with further comments from an Australian rainforest
 expert.
DOI: 10.5061/dryad.6m3n9
title: Data from: Pigmented anatomy in Carboniferous cyclostomes and the evolution of the vertebrate eye

description: The success of vertebrates is linked to the evolution of a camera-style
 eye and sophisticated visual system. In the absence of useful data from
 fossils, scenarios for evolutionary assembly of the vertebrate eye have
 been based necessarily on evidence from development, molecular genetics
 and comparative anatomy in living vertebrates. Unfortunately, steps in the
 transition from a light-sensitive ‘eye spot’ in invertebrate chordates to
 an image-forming camera-style eye in jawed vertebrates are constrained
 only by hagfish and lampreys (cyclostomes), which are interpreted to
 reflect either an intermediate or degenerate condition. Here, we
 report—based on evidence of size, shape, preservation mode and localized
 occurrence—the presence of melanosomes (pigment-bearing organelles) in
 fossil cyclostome eyes. Time of flight secondary ion mass spectrometry
 analyses reveal secondary ions with a relative intensity characteristic of
 melanin as revealed through principal components analyses. Our data
 support the hypotheses that extant hagfish eyes are degenerate, not
 rudimentary, that cyclostomes are monophyletic, and that the ancestral
 vertebrate had a functional visual system. We also demonstrate integument
 pigmentation in fossil lampreys, opening up the exciting possibility of
 investigating colour patterning in Palaeozoic vertebrates. The examples we
 report add to the record of melanosome preservation in Carboniferous
 fossils and attest to surprising durability of melanosomes and
 biomolecular melanin.
description: Character
 descriptionsDescriptions of
 characters from the phylogenetic analysisCharacter_descriptions.docxGabbott_et_al_2016_mtxData matrix in NEXUS format
DOI: 10.5061/dryad.dj2bf
title: Data from: Opposing effects of allogrooming on disease transmission in ant societies

description: To prevent epidemics, insect societies have evolved collective disease
 defences that are highly effective at curing exposed individuals and
 limiting disease transmission to healthy group members. Grooming is an
 important sanitary behaviour—either performed towards oneself
 (self-grooming) or towards others (allogrooming)—to remove infectious
 agents from the body surface of exposed individuals, but at the risk of
 disease contraction by the groomer. We use garden ants (Lasius neglectus)
 and the fungal pathogen Metarhizium as a model system to study how
 pathogen presence affects self-grooming and allogrooming between exposed
 and healthy individuals. We develop an epidemiological SIS model to
 explore how experimentally observed grooming patterns affect disease
 spread within the colony, thereby providing a direct link between the
 expression and direction of sanitary behaviours, and their effects on
 colony-level epidemiology. We find that fungus-exposed ants increase
 self-grooming, while simultaneously decreasing allogrooming. This
 behavioural modulation seems universally adaptive and is predicted to
 contain disease spread in a great variety of host–pathogen systems. In
 contrast, allogrooming directed towards pathogen-exposed individuals might
 both increase and decrease disease risk. Our model reveals that the effect
 of allogrooming depends on the balance between pathogen infectiousness and
 efficiency of social host defences, which are likely to vary across
 host–pathogen systems.
description: grooming in 5 days per
 replicategrooming in days per
 replicategrooming in 5 days per
 interactionsurvival day
 12