cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3d3bq
title: Data from: Predation drives local adaptation of phenotypic plasticity

description: Phenotypic plasticity is the ability of an individual genotype to alter
 aspects of its phenotype depending on the current environment. It is
 central to the persistence, resistance and resilience of populations
 facing variation in physical or biological factors. Genetic variation in
 plasticity is pervasive, which suggests its local adaptation is plausible.
 Existing studies on the adaptation of plasticity typically focus on single
 traits and a few populations, while theory about interactions among genes
 (for example, pleiotropy) suggests that a multi-trait, landscape scale
 (for example, multiple populations) perspective is required. We present
 data from a landscape scale, replicated, multi-trait experiment using a
 classic predator–prey system centred on the water flea Daphnia pulex. We
 find predator regime-driven differences in genetic variation of
 multivariate plasticity. These differences are associated with strong
 divergent selection linked to a predation regime. Our findings are
 evidence for local adaptation of plasticity, suggesting that responses of
 populations to environmental variation depend on the conditions in which
 they evolved in the past.
description: NEE_MetaDataMeta data for filesPhenotypicDataPhenotypic data used in G-matrix analyses and QST-FST analysesPedigree_DriftselPedigree format for DRIFTSEL QST-FST analysesMicrosats_DrifselNeutral marker information (microsatellite data) used in QST-FST analysis.
DOI: 10.5061/dryad.25qg7
title: Data from: Partial support for the central–marginal hypothesis within a population: reduced genetic diversity but not increased differentiation at the range edge of an island endemic bird

description: Large-scale population comparisons have contributed to our understanding
 of the evolution of geographic range limits and species boundaries, as
 well as the conservation value of populations at range margins. The
 central–marginal hypothesis (CMH) predicts a decline in genetic diversity
 and an increase in genetic differentiation toward the periphery of
 species’ ranges due to spatial variation in genetic drift and gene flow.
 Empirical studies on a diverse array of taxa have demonstrated support for
 the CMH. However, nearly all such studies come from widely distributed
 species, and have not considered if the same processes can be scaled down
 to single populations. Here, we test the CMH on a species composed of a
 single population: the Island Scrub-Jay (Aphelocoma insularis), endemic to
 a 250 km2 island. We examined microsatellite data from a quarter of the
 total population and found that homozygosity increased toward the island’s
 periphery. However, peripheral portions of the island did not exhibit
 higher genetic differentiation. Simulations revealed that highly localized
 dispersal and small total population size, but not spatial variation in
 population density, were critical for generating fine-scale variation in
 homozygosity. Collectively, these results demonstrate that
 microevolutionary processes driving spatial variation in genetic diversity
 among populations can also be important for generating spatial variation
 in genetic diversity within populations.
description: Langin et al 2017
 Heredity - empirical dataThis file contains
 genetic and spatial data associated with 544 Island Scrub-Jays that were
 sampled as part of this study.Langin et al 2017
 Heredity - simulation dataThis file contains the
 results of 180 simulations conducted as part of this
 study.
DOI: 10.5061/dryad.806382j
title: Data from: Understanding willingness to use oral pre-exposure prophylaxis for HIV prevention among men who have sex with men in China

description: Background: Oral pre-exposure prophylaxis (PrEP) is recommended as an
 additional prevention choice for men who have sex with men (MSM) at
 substantial risk of HIV. The aim of this study was to evaluate the extent,
 and reasons, for MSM’s willingness to use oral PrEP in Wuhan and Shanghai,
 China. Methods: Between May and December 2015, a cross-sectional survey
 was conducted among 487 MSM recruited through snowball sampling in
 physical locations frequented by MSM and through social media
 applications. Exploratory factor analysis was used to group reasons for
 being willing or not willing to use PrEP. Chi-square tests were used to
 explore bivariate associations between groupings of reasons for being
 willing or unwilling to use PrEP, and key sociodemographic and
 sexual-behavioral characteristics of MSM. Results: Overall, 71.3% of
 respondents were willing to use PrEP. The most commonly reported reasons
 for being willing to use PrEP were preventing HIV infection (91.6%),
 taking responsibility for own sexual health (72.6%) and protecting family
 members from harm (59.4%). The main reasons for being unwilling to use
 PrEP were being worried about side effects (72.9%), the necessity of
 taking PrEP for long periods of time (54.3%) and cost (40.4%). Individual
 characteristics that influenced the type of reasons given for being
 willing or unwilling to use PrEP included being married to a woman, having
 a regular sex partner, rates of condom use with regular and casual sex
 partners, and the number of casual sex partners. Conclusion: The
 introduction of PrEP in China could benefit from promotion campaigns that
 emphasize its role in preventing HIV infection, in taking responsibility
 for own sexual health, and in protecting family members from potential
 harm. To reduce uptake barriers, it will be essential to provide accurate
 information to potential PrEP users about the mild and short-term nature
 of side effects, and the possibility of taking PrEP only during particular
 periods of life when the risk of HIV exposure might be highest.
description: Data from: Understanding
 willingness to use oral pre-exposure prophylaxis for HIV prevention among
 men who have sex with men in ChinaPONE-D-17-15313R2.xlsx
DOI: 10.5061/dryad.8460
title: Data from: Genetics of hybrid male sterility among strains and species in the Drosophila pseudoobscura species group

description: Taxa in the early stages of speciation may bear intraspecific allelic
 variation at loci conferring barrier traits in hybrids such as hybrid
 sterility. Additionally, hybridization may spread alleles that confer
 barrier traits to other taxa. Historically, few studies examine within-
 and between-species variation at loci conferring reproductive isolation.
 Here, we test for allelic variation within Drosophila persimilis and
 within the Bogota subspecies of D. pseudoobscura at regions previously
 shown to contribute to hybrid male sterility. We also test whether D.
 persimilis and the USA subspecies of D. pseudoobscura share an allele
 conferring hybrid sterility in a D. pseudoobscura bogotana genetic
 background. All loci conferred similar hybrid sterility effects across all
 strains studied, though we detected some statistically significant
 quantitative effect variation among D. persimilis alleles of some hybrid
 incompatibility QTLs. We also detected allelism between D. persimilis and
 D. pseudoobscura USA at a 2nd chromosome hybrid sterility QTL. We
 hypothesize that either the QTL is ancestral in D. persimilis and D.
 pseudoobscura USA and lost in D. pseudoobscura bogotana, or gene flow
 transferred the QTL from D. persimilis to D. pseudoobscura USA. We discuss
 our findings in the context of population features that may contribute to
 variation in hybrid incompatibilities.
description: BCbogMSH1_DryadBCbogMSH1-Lim_DryadBCbogMSH3_DryadBCbogMSH3-Lim_DryadBCbogSCI_DryadBCbogSCI-Lim_DryadAllelism_Q2_DryadAllelism_Q2-Lim_Dryad
DOI: 10.5061/dryad.g70nj
title: Data from: Coral settlement on a highly disturbed equatorial reef system

description: Processes occurring early in the life stages of corals can greatly
 influence the demography of coral populations, and successful settlement
 of coral larvae that leads to recruitment is a critical life history stage
 for coral reef ecosystems. Although corals in Singapore persist in one the
 world’s most anthropogenically impacted reef systems, our understanding of
 the role of coral settlement in the persistence of coral communities in
 Singapore remains limited. Spatial and temporal patterns of coral
 settlement were examined at 7 sites in the southern islands of Singapore,
 using settlement tiles deployed and collected every 3 months from 2011 to
 2013. Settlement occurred year round, but varied significantly across time
 and space. Annual coral settlement was low (~54.72 spat m-2 yr-1) relative
 to other equatorial regions, but there was evidence of temporal variation
 in settlement rates. Peak settlement occurred between March–May and
 September–November, coinciding with annual coral spawning periods
 (March–April and October), while the lowest settlement occurred from
 December–February during the northeast monsoon. A period of high
 settlement was also observed between June and August in the first year
 (2011/12), possibly due to some species spawning outside predicted
 spawning periods, larvae settling from other locations or extended larval
 settlement competency periods. Settlement rates varied significantly among
 sites, but spatial variation was relatively consistent between years,
 suggesting the strong effects of local coral assemblages or environmental
 conditions. Pocilloporidae were the most abundant coral spat (83.6%),
 while Poritidae comprised only 6% of the spat, and Acroporidae &lt;1%.
 Other, unidentifiable families represented 10% of the coral spat. These
 results indicate that current settlement patterns are reinforcing the
 local adult assemblage structure (‘others’; i.e. sediment-tolerant coral
 taxa) in Singapore, but that the replenishment capacity of Singapore’s
 reefs appears relatively constrained, which could lead to less resilient
 reefs.
description: Singapore coral
 settlement raw data 2015Two years of coral
 settlement data from Singapore (September 2011 to 2013) at seven sites.
 Data broken down into three families (Acroporidae, Pocilloporidae,
 Poritidae), and all other coral spat categorized as
 'others'.Singapore coral cover
 raw data 2015Percent cover hard coral
 at seven sites in Singapore.
DOI: 10.5061/dryad.g2028
title: Data from: Local adaptation to salinity in the three-spined stickleback?

description: Different lines of evidence suggest that the occurrence and extent of
 local adaptation in high gene flow marine environments – even in mobile
 and long-lived vertebrates with complex life cycles – may be more
 widespread than earlier thought. We conducted a common garden experiment
 to test for local adaptation to salinity in Baltic Sea sticklebacks
 (Gasterosteus aculeatus). Fish from three different native salinity
 regimes (high, mid and low) were subjected to three salinity treatments
 (high, mid and low) in a full-factorial experimental design. Irrespective
 of their origin, fish subjected to low (and mid) salinity treatments
 exhibited higher juvenile survival, grew to largest sizes and were in
 better condition than fish subjected to the high salinity treatment.
 However, a significant interaction between native and treatment salinities
 – resulting mainly from the poor performance of fish native to low
 salinity in the high salinity treatment – provided clear cut evidence for
 adaptation to local variation in salinity. Additional support for this
 inference was provided by the fact that the results concur with an earlier
 demonstration of significant differentiation in a number of genes with
 osmoregulatory functions across the same populations and that the
 population-specific responses to salinity treatments exceeded that to be
 expected by random genetic drift.
description: Size_dryadFirst tab: size (cm) at 2 months. Second tab: size (cm) at 4, 6 and 8 months.Population codes follow those listed in the manuscript. Values listed in native and treatment salinity correspond to 5, 10 and 20 ppt.
DOI: 10.5061/dryad.s7576
title: Data from: Spinosity, regeneration, and targeting among Paleozoic crinoids and their predators

description: Evolving interactions between predators and prey constitute one of the
 major adaptive influences on marine animals during the Paleozoic. Crinoids
 and fish constitute a predator-prey system that may date back to at least
 the Silurian, as suggested by patterns of crinoid regeneration and
 spinosity in concert with changes in the predatory fauna. Here we present
 data on the frequency of breakage and regeneration in the spines of the
 Middle Devonian camerate Gennaeocrinus and Late Paleozoic cladids, as well
 as an expanded survey of the prevalence of spinosity and infestation by
 platyceratid gastropods on crinoid genera during the Paleozoic. Spine
 regeneration frequency in the measured populations is comparable to arm
 regeneration frequencies from Mississippian Rhodocrinites and from modern
 deep-water crinoid populations. The prevalence of spinosity varies by
 taxon, time, and anatomy among Paleozoic crinoids; notably, spinosity in
 camerates increased from the Silurian through the Mississippian and
 decreased sharply during the Pennsylvanian, whereas spines were uncommon
 in cladids until their late Mississippian diversification. Among
 camerates, tegmen spinosity is positively correlated with the presence of
 infesting platyceratids. These results allow us to evaluate several
 hypotheses for the effects of predation on morphological differences
 between early, middle, and late Paleozoic crinoid faunas. Our data
 corroborate the hypothesis that predators targeted epibionts on camerate
 crinoids and anal sacs on advanced cladids, and suggest that the
 replacement of shearing predators by crushing predators after the
 Hangenberg extinction affected the locations of spines in Mississippian
 camerates.
description: Measurements of all
 spinesThis is an XLSX file
 with three sheets. The first contains the specimen numbers (field numbers
 only, as the specimens have not been accessioned), measurements, and
 regeneration status for all eucladid anal sac spines used in this study;
 the second contains the same for eucladid calyx spines, and the third for
 spines of Gennaeocrinus goldringae.Supp-A.xlsxSpinosity, anal sac, and infestation dataThis is a .XLSX file that contains all the genera considered in this study, including those which were left out of the final analyses due to lack of data. For each genus, it gives all the available data on temporal range, spinosity, presence of anal structure, infestation, and regeneration.Supp-B.xlsx
DOI: 10.5061/dryad.50kc9
title: Data from: The simultaneous inducibility of phytochemicals related to plant direct and indirect defences against herbivores is stronger at low elevation

description: Ecological theory indicates that warmer and more stable climates should
 result in stronger biotic interactions. Therefore, plant species growing
 at lower elevations and experiencing greater herbivore pressure, should
 invest in higher levels of defences than those at higher elevations.
 Nonetheless, there are a number of studies that have found no effect of
 elevational gradients on plant defensive traits. Several factors might
 explain the lack of consistency for the altitude-defence relationships;
 including 1) the reduction of all defensive traits into one measure of
 resistance; 2) not considering plant defence as the simultaneous
 expression of several defensive traits; and 3) not considering the
 relative influence of biotic (e.g. herbivory) and abiotic (e.g. climate
 and soil conditions) factors associated with the ecological gradient.
 Here, we present a comprehensive test of the effects of elevation and its
 associated biotic and abiotic factors on the individual and simultaneous
 expression of constitutive direct and indirect defences and their
 inducibility (i.e. expression of defences after herbivore attack).
 Specifically, we estimated climatic and soil variables and measured
 herbivore damage and constitutive and jasmonic acid-induced glucosinolate
 levels in the leaves as a proxy for direct defences, and volatile emission
 as a proxy for indirect defences in 16 Cardamine species naturally growing
 along the steep elevational gradient of the Alps. Within a phylogenetic
 comparative framework, we found that species growing at lower elevations
 invested more in the simultaneous inducibility of both direct and indirect
 defences, whereas species growing at higher elevations invested more in
 constitutive direct defences. Although we found strong elevation gradients
 in herbivory and climatic and soil variables, these biotic and abiotic
 factors only partially explained elevational patterns in plant defences.
 Synthesis - These results highlight that the complex regulation of
 multiple defence traits strongly vary across elevational gradients and
 build towards a better understanding of the multiple mechanisms underlying
 trait evolution and species interactions along ecological gradients.
description: glucosinolate and
 volatile data for Pellissier et althree sheets: 1) leaf
 glucosinolate data for each species sampled from either control
 (undamaged) or JA-induced (JA) plants. 2) volatile organic compounds from
 the leaves of the same plants. 3) average values for glucosinolates and
 volatiles, plus average elevation, herbivore attack, and Landolt value for
 soil fertility for each speciesdryad.xlsx
DOI: 10.5061/dryad.948k7j42
title: Data from: Genetic rediscovery of an ‘extinct’ Galápagos giant tortoise species

description: Genes from recently extinct species can live on in the genomes of extant
 individuals of mixed ancestry. Recently, Poulakakis et al. detected
 genetic signatures of the giant Galápagos tortoise once endemic to
 Floreana Island (Chelonoidis elephantopus) within eleven hybrid
 individuals of otherwise pure C. becki on Volcano Wolf, Isabela Island.
 Movement of tortoises among islands by pirate and whaling ships was not
 uncommon during the 1800’s, representing a likely mechanism by which
 individuals from Floreana were translocated to northern Isabela, despite
 being presumed extinct soon after Charles Darwin’s historic voyage to the
 Galápagos Islands in 1835. These eleven hybrid individuals with C.
 elephantopus ancestry were thought to be the last genetic vestiges of a
 unique evolutionary lineage in the wild. Here we report that
 reproductively mature purebred tortoises of the recently ‘extinct’ C.
 elephantopus from Floreana Island are very likely still alive today, as
 identified and tracked through the genetic footprints’ left in the genomes
 of very recent hybrid offspring on Volcano Wolf, Isabela Island. If found,
 these purebred C. elephantopus individuals could constitute core founders
 of a captive breeding program directed towards resurrecting this species.
description: Garrick_et_al_CurrBiol_DRYADGalapagos tortoise microsatellite genotypes and mitchondrial DNA control region haplotypes
DOI: 10.5061/dryad.8jt10
title: Data from: The remarkable convergence of skull shape in crocodilians and toothed whales

description: The striking resemblance of long-snouted aquatic mammals and reptiles has
 long been considered an example of morphological convergence, yet the true
 cause of this similarity remains untested. We addressed this deficit
 through three-dimensional morphometric analysis of the full diversity of
 crocodilian and toothed whale (Odontoceti) skull shapes. Our focus on
 biomechanically important aspects of shape allowed us to overcome
 difficulties involved in comparing mammals and reptiles, which have
 fundamental differences in the number and position of skull bones. We
 examined whether diet, habitat and prey size correlated with skull shape
 using phylogenetically informed statistical procedures. Crocodilians and
 toothed whales have a similar range of skull shapes, varying from
 extremely short and broad to extremely elongate. This spectrum of shapes
 represented more of the total variation in our dataset than between
 phylogenetic groups. The most elongate species (river dolphins and
 gharials) are extremely convergent in skull shape, clustering outside of
 the range of the other taxa. Our results suggest the remarkable
 convergence between long-snouted river dolphins and gharials is driven by
 diet rather than physical factors intrinsic to riverine environments.
 Despite diverging approximately 288 million years ago, crocodilians and
 odontocetes have evolved a remarkably similar morphological solution to
 feeding on similar prey.
description: Landmark
 Data.pts files for crania
 and mandibles.
DOI: 10.5061/dryad.d8080
title: Data from: MHC class II assortative mate choice in European badgers (Meles meles)

description: The major histocompatibility complex (MHC) plays a crucial role in the
 immune system, and in some species, it is a target by which individuals
 choose mates to optimize the fitness of their offspring, potentially
 mediated by olfactory cues. Under the genetic compatibility hypothesis,
 individuals are predicted to choose mates with compatible MHC alleles, to
 increase the fitness of their offspring. Studies of MHC-based mate choice
 in wild mammals are under-represented currently, and few investigate more
 than one class of MHC genes. We investigated mate choice based on the
 compatibility of MHC class I and II genes in a wild population of European
 badgers (Meles meles). We also investigated mate choice based on
 microsatellite-derived pairwise relatedness, to attempt to distinguish
 MHC-specific effects from genomewide effects. We found MHC-assortative
 mating, based on MHC class II, but not class I genes. Parent pairs had
 smaller MHC class II DRB amino acid distances and smaller functional
 distances than expected from random pairings. When we separated the
 analyses into within-group and neighbouring-group parent pairs, only
 neighbouring-group pairs showed MHC-assortative mating, due to similarity
 at MHC class II loci. Our randomizations showed no evidence of
 genomewide-based inbreeding, based on 35 microsatellite loci; MHC class II
 similarity was therefore the apparent target of mate choice. We propose
 that MHC-assortative mate choice may be a local adaptation to endemic
 pathogens, and this assortative mate choice may have contributed to the
 low MHC genetic diversity in this population.
description: candidate males (MHC
 class I)candidate males (MHC
 class II DRB)candidate males MHC
 class I genotypescandidate males MHC
 class II DRB genotypesmicrosatellite
 genotyping dataneighboring social
 groupsparent pairs MHC
 genotyping data (class I)parent pairs MHC
 genotyping data (class II DRB)