cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5dk62
title: Data from: Species delimitation in Tetraploid, Apomictic Amelanchier (Rosaceae)

description: Diversification in Amelanchier tetraploid apomicts differs from that of
 diploid sexuals and produces groups that are taxonomically difficult.
 Apomixis facilitates expansion of ecologically successful genotypes into
 numerous, narrowly distributed, and often minimally distinct microspecies.
 Residual sexuality in tetraploids creates hybrid swarms and intergradation
 of taxa. This gene flow is evident in DNA sequences from nuclear and
 chloroplast regions that record mostly allotetraploid, convoluted
 histories. Ongoing apomixis in successful tetraploid genotypes fosters
 their expansion into geographically widespread phenotypic clusters. We
 delimit such clusters as species and deny species status to microspecies.
 We demonstrate polyploid complexity and our approach to species
 delimitation in three taxa of Amelanchier. The tetraploid microspecies A.
 “rubra” of southeastern Maine, while morphologically distinct, hybridizes
 with sympatric congeners. Eastern North American A. bartramiana contains
 diploids and polyploids (tetraploids and a few triploids) that are
 sometimes morphologically semi-cryptic. We group all ploidy levels in the
 A. bartramiana agamic complex and recognize as a species the diploid (A.
 bartramiana). The tetraploid is not given species status because it
 intergrades extensively with tetraploid congeners, as exemplified by the
 nothospecies named here, A. × neglecta . Western North American A.
 cusickii is tetraploid, mostly distinct morphologically and ecologically,
 distinct genetically, and merits species status.
description: Cushman14Oct16Figure2rubraMorphDataMorphological data matrix for figure 2 and morphological analysis.Cushman14Oct16Figure3bartramianaMorphDataMorphological data matrix for A. bartramiana complex analysis and figure 3.Cushman14Oct16Figure5cusickiiMorphDataMorphological data matrix for the Amelanchier cusickii morphological analysis and figure 5.Cushman14Oct16Figure6ETSalignmentDNA sequence alignment for ETS region and Figure 6.Cushman14Oct16Figure7Leafy2int2dAlignment 2Trimmed DNA sequence alignment of Leafy2int2d region.Cushman14Oct16Figure8Leafy2int2iAlignment 2Trimmed DNA sequence alignment of Leafy2int2i region.
DOI: 10.5061/dryad.124n0
title: Data from: Intraspecific trait variation and colonization sequence alter community assembly and disease epidemics

description: When individuals from multiple populations colonize a new habitat patch,
 intraspecific trait variation can make the arrival order of colonists an
 important factor for subsequent population and community dynamics. In
 particular, intraspecific priority effects (IPEs) allow early arrivers to
 limit the growth or establishment of later arrivers, even when
 competitively inferior on a per-capita basis. Through their effects on
 genes and traits, IPEs can alter short-term growth and long-term
 evolutionary change in single species metapopulations. Given their
 importance for intraspecific interactions, IPEs in a dominant species have
 the potential to affect the composition of entire communities. We
 conducted an experiment to determine whether and how arrival order and
 IPEs in the zooplankter Daphnia pulex affected its interactions with both
 competitors (the cladoceran Simocephalus vetulus) and parasites (the
 virulent fungus Metschnikowia bicuspidata). We found strong evidence for
 IPEs in Daphnia, as early arrivers inhibited late arrivers even when
 competitively inferior. These IPEs in Daphnia altered both the
 establishment success of interspecific competitors and the size of disease
 epidemics: early colonization by fast-growing D. pulex led to large
 Daphnia populations and low competitor establishment, but large disease
 epidemics. Early colonization by slow-growing D. pulex, on the other hand,
 resulted in small Daphnia populations with high competitor establishment,
 but smaller disease epidemics. Overall, our results demonstrate the
 importance of intraspecific variation and arrival order for community
 dynamics, and highlight IPEs as a general mechanism driving variation in
 natural communities.
description: Dibble_Rudolf_2015_OIK-02373-R1Microsoft excel document containing 3 tabs: 'metadata' is a description of the column headings for 2 tabs: 'sampling-data' contains all population data used in the analysis of this experiment for the current manuscript; 'simoest' is an easier-to use summary of the data that ascribes a '1' to experimental units where simocephalus were present until the end of the experiment (and a 0 otherwise). Column heading descriptions are given in 'metadata'sampling-data.csv version of tab 2, 'sampling-data' from the excel workbook. See 'readme.txt' or tab 1, 'metadata' of the excel workbook for column headings.simoest.csv version of 'simoest' tab from excel workbook. Contains data on simocephalus establishment success in experimental containers (i.e. whether simocephalus were present at the end of the experiment)
DOI: 10.5061/dryad.6f4g4
title: Data from: Pleiotropy in the melanocortin system: expression levels of this system are associated with melanogenesis and pigmentation in the tawny owl (Strix aluco)

description: The adaptive function of melanin-based coloration is a long-standing
 debate. A recent genetic model suggested that pleiotropy could account for
 covariations between pigmentation, behaviour, morphology, physiology and
 life history traits. We explored whether the expression levels of genes
 belonging to the melanocortin system (MC1R, POMC, PC1/3, PC2 and the
 antagonist ASIP), which have many pleiotropic effects, are associated with
 melanogenesis (through variation in the expression of the genes MITF,
 SLC7A11, TYR, TYRP1) and in turn melanin-based coloration. We considered
 the tawny owl (Strix aluco) because individuals vary continuously from
 light to dark reddish, and thus, colour variation is likely to stem from
 differences in the levels of gene expression. We measured gene expression
 in feather bases collected in nestlings at the time of melanin production.
 As expected, the melanocortin system was associated with the expression of
 melanogenic genes and pigmentation. Offspring of darker reddish fathers
 expressed PC1/3 to lower levels but tended to express PC2 to higher
 levels. The convertase enzyme PC1/3 cleaves the POMC prohormone to obtain
 ACTH, while the convertase enzyme PC2 cleaves ACTH to produce
 α-melanin-stimulating hormone (α-MSH). ACTH regulates glucocorticoids,
 hormones that modulate stress responses, while α-MSH induces
 eumelanogenesis. We therefore conclude that the melanocortin system,
 through the convertase enzymes PC1/3 and PC2, may account for part of the
 interindividual variation in melanin-based coloration in nestling tawny
 owls. Pleiotropy may thus account for the covariation between phenotypic
 traits involved in social interactions (here pigmentation) and life
 history, morphology, behaviour and physiology.
description: Emaresi
 Data
DOI: 10.5061/dryad.s8p44
title: Data from: Erosion of beta diversity under interacting global change impacts in a semiarid grassland

description: 1. Human impacts are often thought of as homogenizing natural communities,
 but it is unclear how these impacts interact to alter the beta diversity
 (spatial variability) of plant communities. 2. In a grassland with high
 beta diversity along a soil fertility gradient, we asked which
 combinations of nutrient enrichment, precipitation enhancement, and
 disturbance would homogenize communities along the gradient by allowing
 dominant species from one part of the gradient to increase their
 abundances in other parts of the gradient. In particular, joint addition
 of nutrients and water might especially benefit resource acquisitive
 and/or exotic species, which have been observed to compete well in
 resource-rich conditions; this would tend to reduce variation in species
 composition across the gradient. To alleviate dispersal limitation as a
 constraint on treatment responses, we added seeds of 15 species abundant
 in different parts of the soil fertility gradient to our 132 plots. 3.
 Fertilization and water addition allowed species from fertile soils to
 increase their abundance in infertile soils, an effect that strengthened
 with time. Disturbance permitted species from infertile soils to increase
 in abundance in infertile soils, but only transiently. Plant height,
 specific leaf area, and exotic status best predicted the abilities of
 species to attain greater cover in harsh habitats under ameliorated
 conditions. Among-habitat beta diversity of seeded species was reduced by
 the interactive effect of fertilization and watering, although not by
 watering alone. 4. Synthesis. Our findings are a novel demonstration of
 how interacting global change factors reduce beta diversity by eroding the
 biotic and abiotic resistances that control community structure along soil
 fertility gradients.
description: seedingdata
DOI: 10.5061/dryad.628f242
title: Data from: Bionomics and insecticide resistance of the arboviral vector Aedes albopictus in northern Lao PDR

description: In the last four decades there has been a staggering increase in the
 geographical range of the arboviral vector Aedes albopictus (Skuse, 1894).
 This species is now found in every continent except Antarctica, increasing
 the distribution of arboviral diseases such as dengue and chikungunya. In
 Lao PDR dengue epidemics occur regularly, with cases of chikungunya also
 reported. As treatment methods for arboviral diseases is limited, the
 control of the vector mosquitoes are essential. There is a paucity of
 information on the bionomics and resistance status of this mosquito for
 successful vector control efforts. Here we describe the bionomics and
 insecticide resistance status of Ae. albopictus in Laos to identify
 opportunities for control. Adult Ae. albopictus were collected using
 human-baited double bed net (HDN) traps in forests, villages and rubber
 plantations and tested for alpha- and flaviviruses with RT-PCR. Surveys
 were also conducted to identify larval habitats. Seven adult and larval
 populations originating from Vientiane Capital and Luang Prabang province
 were tested against DDT, malathion, permethrin, deltamethrin and, temephos
 following WHO protocols. Aedes albopictus were found throughout the year,
 but were six-fold greater in the rainy season than the dry season. Adult
 females were active for 24 hours, with peak of behaviour at 18.00 h. The
 secondary forest and rubber plantation samples showed evidence of
 Pan-flaviviruses, while samples from the villages did not. More than half
 of the emerged Ae. albopictus were collected from mature rubber
 plantations (53.9%; 1,533/2,845). Most Ae. albopictus mosquitoes emerged
 from latex collection cups (19.7%; 562/2,845), small water containers
 (19.7%; 562/2,845) and tyres (17.4%; 495/2,845). Adult mosquitoes were
 susceptible to pyrethroids, apart from one population in Vientiane city.
 All populations were resistant to DDT (between 27–90% mortality) and all
 except one were resistant to malathion (20–86%). Three of the seven larval
 populations were resistant to temephos (42–87%), with suspected resistance
 found in three other populations (92–98%).This study demonstrates that
 rural areas in northern Laos are potential hot spots for arboviral disease
 transmission. Multiple-insecticide resistance was found. Aedes albopictus
 control efforts in villages need to expand to include secondary forests
 and rubber plantations, with larval source management and limited use of
 insecticides.
description: POne_Laos_Albo_bionomics_rawdata_IR_adultPOne_Laos_Albo_bionomics_rawdata_IR_larvaePOne_Laos_Albo_bionomics_rawdata_LarvalsurveyRaw data of the Ae. albopictus larval surveyPOne_Laos_Albo_bionomics_rawdata_AdultsurveyRaw data of the Ae. albopictus adult survey
DOI: 10.5061/dryad.70ng4
title: Data from: Is pairing with a relative heritable? estimating female and male genetic contributions to the degree of biparental inbreeding in song sparrows (Melospiza melodia)

description: The degree of inbreeding expressed within populations can profoundly shape
 evolutionary dynamics. The degree to which individuals inbreed is
 frequently assumed to evolve in response to selection, for example
 resulting from inbreeding depression. Such evolutionary responses require
 additive genetic variance (VA) in the degree to which individuals inbreed.
 However, the magnitude of VA in the degree of biparental inbreeding has
 never been estimated. We devised a quantitative genetic model to estimate
 sex-specific VA in the degree to which individuals inbreed, while
 accounting for effects of individuals' own coefficients of inbreeding
 and genetic effects stemming from immigration. We applied this model to
 the degree of inbreeding expressed through social pairing in free-living
 song sparrows (Melospiza melodia). VA estimates for both sexes appreciably
 exceeded zero and the cross-sex genetic covariance was strongly positive,
 creating substantial total VA in the degree of inbreeding. Our analyses
 also revealed inbreeding depression in the degree of inbreeding such that
 more inbred individuals paired with closer relatives, and immigrant
 effects such that individuals with greater genomic contributions from
 immigrants paired with more distant relatives. We thereby demonstrate that
 the degree of biparental inbreeding can show substantial VA in nature and
 might consequently evolve in response to selection.
description: ASReml-R
 analysisData, inverse A-matrix,
 and R code to conduct the analysis using ASReml in R.asreml.tarWOMBAT analysisData, inverse A-matrix, and code to run the quantitative genetic analyses using the WOMBAT software. Also, code is included to conduct the Monte Carlo simulations to obtain model parameter sampling distributions.wombat.tarSimulation code from Supporting Informationsimulations.tar
DOI: 10.5061/dryad.68vs3
title: Data from: Competition-driven niche segregation on a landscape scale: evidence for escaping from syntopy toward allotopy in two coexisting sibling passerine species

description: 1. The role of interspecific competition for generating patterns in
 species’ distribution is hotly debated and studies taking into account
 processes occurring at both large and small spatial scales are almost
 missing. Theoretically, competition between species with overlapping
 niches should result in divergence of their niches in sympatry to reduce
 the costs of competition. Many species show a mosaic distribution within
 sympatric zones, with the syntopic sites occupied by both species, and
 allotopic sites where only one species occurs. It is unclear whether such
 mosaics arise as a consequence of competition-driven niche segregation or
 due to the decline of their abundances towards range edges driven by
 environmental gradients. 2. If the interspecific competition matters, we
 should observe (i) a shift in habitat preferences of one or both species
 between syntopy and allotopy, and (ii) between allopatry and allotopy.
 Moreover, (iii) species should show greater divergence in their habitat
 preferences in allotopy than in allopatry where (iv) no differences in
 habitat preferences may occur. Finally, (v) shifts should be generally
 greater in the competitively subordinate species than in the dominant
 species. 3. We used a unique dataset on abundance of two closely related
 passerine species, the Common Nightingale (Luscinia megarhynchos) and the
 Thrush Nightingale (Luscinia luscinia), collected across their syntopy,
 allotopy and allopatry. The predictions were tested within a generalized
 mixed-effects modelling framework. 4. After accounting for environmental
 gradients perpendicular to the species’ contact zone, we found a strong
 support for all but one prediction. Habitat preferences of both species
 shifted markedly between syntopy and allotopy, as well as between
 allopatry and allotopy. Whereas the species preferred the same habitats in
 allopatry, their preferences became strikingly different in allotopy where
 the abundance of the Common Nightingale increased towards dry and warm
 sites with low coverage of pastures, while the abundance of the Thrush
 Nightingale showed exactly opposite trends. Fifth prediction was not
 supported. 5. Our results indicate that the competition between closely
 related species can result in considerable changes in habitat use across
 their geographic ranges accompanied with divergence in their habitat
 preferences in sympatry. Here the species “escape” from competition to
 allotopic sites covered by habitats avoided by the competitor. Therefore,
 we argue that the interspecific competition is an important driver of
 species’ distribution at both large and small spatial scales.
description: Nightingale’s abundance
 and co-occurrence statusnightingales.csv
DOI: 10.5061/dryad.16860
title: Data from: C4 photosynthesis boosts growth by altering physiology, allocation and size

description: C4 photosynthesis is a complex set of leaf anatomical and biochemical
 adaptations that have evolved more than 60 times to boost carbon uptake
 compared with the ancestral C3 photosynthetic type1,​2,​3. Although C4
 photosynthesis has the potential to drive faster growth rates4,5,
 experiments directly comparing C3 and C4 plants have not shown consistent
 effects1,6,7. This is problematic because differential growth is a crucial
 element of ecological theory8,9 explaining C4 savannah responses to global
 change10,11, and research to increase C3 crop productivity by introducing
 C4 photosynthesis12. Here, we resolve this long-standing issue by
 comparing growth across 382 grass species, accounting for ecological
 diversity and evolutionary history. C4 photosynthesis causes a 19–88%
 daily growth enhancement. Unexpectedly, during the critical seedling
 establishment stage, this enhancement is driven largely by a high ratio of
 leaf area to mass, rather than fast growth per unit leaf area. C4 leaves
 have less dense tissues, allowing more leaves to be produced for the same
 carbon cost. Consequently, C4 plants invest more in roots than C3 species.
 Our data demonstrate a general suite of functional trait divergences
 between C3 and C4 species, which simultaneously drive faster growth and
 greater investment in water and nutrient acquisition, with important
 ecological and agronomic implications.
description: Experiment data DOI
 10.1038_NPLANTS.2016.38Experimental data used
 for the comparative growth analysis reported by Atkinson et al. (2016) DOI
 10.1038_NPLANTS.2016.38. The phylogeny used for this analysis is included
 as supplementary data with the paper.Experiment data
 DOI0.1038_NPLANTS.2016.38.csv
DOI: 10.5061/dryad.1v0tb
title: Data from: Host-associated genomic differentiation in congeneric butterflies: now you see it, now you don’t

description: Ecotypic variation among populations may become associated with widespread
 genomic differentiation, but theory predicts that this should happen only
 under particular conditions of gene flow, selection and population size.
 In closely related species, we might expect the strength of
 host-associated genomic differentiation (HAD) to be correlated with the
 degree of phenotypic differentiation in host-adaptive traits. Using
 microsatellite and Amplified Fragment Length Polymorphism (AFLP) markers,
 and controlling for isolation by distance between populations, we sought
 HAD in two congeneric species of butterflies with different degrees of
 host plant specialization. Prior work on Euphydryas editha had shown
 strong interpopulation differentiation in host-adapted traits, resulting
 in incipient reproductive isolation among host-associated ecotypes. We
 show here that Euphydryas aurinia had much weaker host-associated
 phenotypic differentiation. Contrary to our expectations, we detected HAD
 in Euphydryas aurinia, but not in E. editha. Even within an E. aurinia
 population that fed on both hosts, we found weak but significant sympatric
 HAD that persisted in samples taken 9 years apart. The finding of
 significantly stronger HAD in the system with less phenotypic
 differentiation may seem paradoxical. Our findings can be explained by
 multiple factors, ranging from differences in dispersal or effective
 population size, to spatial variation in genomic or phenotypic traits and
 to structure induced by past histories of host-adapted populations. Other
 infrequently measured factors, such as differences in recombination rates,
 may also play a role. Our result adds to recent work as a further caution
 against assumptions of simple relationships between genomic and adaptive
 phenotypic differentiation.
description: Result from alternative
 partitioning of dataRaw output R script
 testing for host associated differentiation, partitioned with either
 microsatellite data only, or AFLP data only.alt
 analysis.docxRaw R
 outputRaw output from the R
 script used to run the main analysis.R
 output.docxScript containing
 R-based analysis, data matrixes and plotting codeThis archive contains
 the main analysis and plotting functions, and the data matrixes used in
 the analysis.euphy.zip
DOI: 10.5061/dryad.nq36d
title: Data from: Ontogenetic stage-specific quantitative trait loci contribute to divergence in developmental trajectories of sexually dimorphic fins between medaka populations

description: Sexual dimorphism can evolve when males and females differ in phenotypic
 optima. Genetic constraints can, however, limit the evolution of sexual
 dimorphism. One possible constraint is derived from alleles expressed in
 both sexes. Because males and females share most of their genome, shared
 alleles with different fitness effects between sexes are faced with
 intralocus sexual conflict. Another potential constraint is derived from
 genetic correlations between developmental stages. Sexually dimorphic
 traits are often favoured at adult stages, but selected against as
 juvenile, so developmental decoupling of traits between ontogenetic stages
 may be necessary for the evolution of sexual dimorphism in adults.
 Resolving intralocus conflicts between sexes and ages is therefore a key
 to the evolution of age-specific expression of sexual dimorphism. We
 investigated the genetic architecture of divergence in the ontogeny of
 sexual dimorphism between two populations of the Japanese medaka (Oryzias
 latipes) that differ in the magnitude of dimorphism in anal and dorsal fin
 length. Quantitative trait loci (QTL) mapping revealed that few QTL had
 consistent effects throughout ontogenetic stages and the majority of QTL
 change the sizes and directions of effects on fin growth rates during
 ontogeny. We also found that most QTL were sex-specific, suggesting that
 intralocus sexual conflict is almost resolved. Our results indicate that
 sex- and age-specific QTL enable the populations to achieve optimal
 developmental trajectories of sexually dimorphic traits in response to
 complex natural and sexual selection.
description: R_script_
 for_Legendre_polynomialR script for Legendre
 orthogonal polynomial analysis of growth and allometric
 curve.Legendre_polynomial_for_Dryad.Rmedaka_SNP_assay_designCustom SNP assay design for the Japanese medaka (Illumina VeraCode Golden Gate assay).pure_crossRaw morphological data of the pure cross.OFAM_M_pheno_allRaw morphological data of F2 male.OFAM_M_SNPSNP data of F2 male; A indicates the southern homozygote, while B indicates the northern homozygote.OFAM_F_pheno_allMorphological data of F2 female.OFAM_F_SNPSNP data of F2 female; A indicates the southern homozygote, while B indicates the northern homozygote.
DOI: 10.5281/zenodo.18381822
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Mont A. Cazier, http://www.wikidata.org/entity/Q21392418. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q21392418