cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h58cm
title: Data from: Evidence for Bergmann's rule and not allopatric subspeciation in the threatened kaka (Nestor meridionalis)

description: Species of conservation concern characterized by small and declining
 populations greatly benefit from proactive management approaches such as
 population translocations. Because they often show intra-specific genetic
 and phenotypic variation, which can result from drift or differential
 selective pressures between habitats, understanding the distribution of
 such variation and its underlying processes is a prerequisite to develop
 effective management guidelines. Indeed, translocations among genetically
 differentiated populations potentially locally adapted are discouraged in
 order to avoid outbreeding depression, while translocations among
 populations characterized by high gene flow with no evidence for local
 adaptation are encouraged. Here, we first test whether 2 recognized
 subspecies, the North Island kaka (Nestor meridionalis septentrionalis)
 and South Island kaka (Nestor meridionalis meridionalis) of New Zealand
 fit a scenario of allopatric subspeciation following the separation of the
 North and South Islands at the end of the Pleistocene using 1 mtDNA (n =
 96) and 9 microsatellite markers (n = 126). We then test whether
 morphological differences among the 2 subspecies support a pattern of
 local adaptation, comparing phenotypic divergence (P ST) and the level of
 divergence by drift alone (F ST) among populations. We find little
 population structure between islands, ruling out allopatric subspeciation
 in kaka. Further, P ST exceeds F ST, supporting an adaptive latitudinal
 size cline consistent with Bergmann’s rule. These results therefore
 suggest that using neutral genetic diversity alone can be misleading when
 identifying management units and that the nature of phenotypic variation
 should be considered in translocations efforts. We finally discuss North
 and South Island management units but suggest that cross-island
 translocation be allowed.
description: Kaka_msat_genotypesNestor meridionalis microsatellite genotypes for 9 loci and 126 samplesKaka_mtDNA_CRNestor meridonalis mitocondrial Control region sequences (940 bp) for 96 sampleskaka morphometricsNestor meridonalis morphometrics with bill length, weight, tarsus length, wing length measured on 627 birdsKaka_population_coordinatesNestor meridonalis samplig locations names and coordinates
DOI: 10.5061/dryad.gs835
title: Data from: Post-spawning sexual selection in red and white Chinook salmon (Oncorhynchus tshawytscha)

description: Post-copulatory processes, including sperm competition and cryptic female
 choice (CFC), can play important roles in the maintenance of
 polymorphisms. In Chinook salmon (Oncorhynchus tshawytscha), color morphs
 (red and white) exist due to genetic polymorphisms affecting carotenoid
 deposition in flesh, skin, and gametes. We investigated the role of
 post-spawning sexual selection in maintaining the polymorphism in a mixed
 population. First, we compared sperm velocity differences in water between
 morphs. Next, we measured color-based CFC via 2 methods: 1) sperm velocity
 in ovarian fluid and 2) in vitro competitive fertilization using paired
 red and white males. We found that red males had marginally faster sperm
 relative to white males in water, suggesting that carotenoid storage may
 affect sperm performance. However, ovarian fluid of red and white females
 influenced sperm velocity of red and white males differently, indicative
 of color-based CFC on sperm velocity. Furthermore, we found evidence of
 color-based CFC on paternity success during in vitro competitive
 fertilizations; however, sperm velocity in ovarian fluid did not predict
 results found under in vitro fertilization. Instead, in our study, sperm
 velocity in water was a significant predictor of fertilization success.
 When we accounted for this difference in sperm velocity (in water) between
 paired males, we partitioned the amount of variation in fertilization
 success that was attributed to individual level CFC (male pair × female)
 and male competitiveness (male pair) as 43% and 16%, respectively. In
 conclusion, post-spawning sexual selection processes represent important
 mechanisms contributing to the maintenance of the color polymorphism in
 nature.
description: SpermVelocityWater_Lehnert-BESperm velocity (VAP, VCL, VSL) of red and white Chinook salmon males at 5 seconds post-activation in water. Each male is represented by replicate velocity measures (if applicable).SpermVelocityOF_Lehnert-BESperm velocity (VAP, VSL, VCL) and sperm path straightness (STR) of red and white Chinook salmon males when sperm is activated in ovarian fluid of red and white females. Sperm metrics were recorded at 5 seconds post-activation in ovarian fluid.PaternityCompetitiveFertilizations_Lehnert-BEPaternity assignment for competitive fertilizations in red and white Chinook salmon. For each competitive fertilization, the number of red sired and white sired eggs are provided Difference between paired males is sperm velocity (VAP) in water and ovarian fluid at 5 seconds post-activation are provided, as well as the sperm density ratio (red:white sperm cells) within each competitive fertilization.
DOI: 10.5061/dryad.fp00p
title: Data from: No evidence for thermal transgenerational plasticity in metabolism when minimizing the potential for confounding effects

description: Environmental change may cause phenotypic changes that are inherited
 across generations through transgenerational plasticity (TGP). If TGP is
 adaptive, offspring fitness increases with an increasing match between
 parent and offspring environment. Here we test for adaptive TGP in somatic
 growth and metabolic rate in response to temperature in the clonal
 zooplankton Daphnia pulex. Animals of the first focal generation
 experienced thermal transgenerational ‘mismatch’ (parental and offspring
 temperatures differed), whereas conditions of the next two generations
 matched the (grand)maternal thermal conditions. Adjustments of metabolic
 rate occurred during the lifetime of the first generation (i.e.
 within-generation plasticity). However, no further change was observed
 during the subsequent two generations, as would be expected under TGP.
 Furthermore, we observed no tendency for increased juvenile somatic growth
 (a trait highly correlated with fitness in Daphnia) over the three
 generations when reared at new temperatures. These results are
 inconsistent with existing studies of thermal TGP, and we describe how
 previous experimental designs may have confounded TGP with
 within-generation plasticity and selective mortality. We suggest that the
 current evidence for thermal TGP is weak. To increase our understanding of
 the ecological and evolutionary role of TGP, future studies should more
 carefully identify possible confounding factors.
description: Data metabolism and
 growth, daphnia pulexData for all figures
 used in the main document, as well as electronic supplementary material S2
 and S3.Dryad
 data.xlsx
DOI: 10.5061/dryad.5qv85
title: Data from: Low reproductive isolation and highly variable levels of gene flow reveal limited progress toward speciation between European river and brook lampreys

description: Ecologically based divergent selection is a factor that could drive
 reproductive isolation even in the presence of gene flow. Population pairs
 arrayed along a continuum of divergence provide a good opportunity to
 address this issue. Here we used a combination of mating trials,
 experimental crosses and population genetics analyses to investigate the
 evolution of reproductive isolation between two closely related species of
 lampreys with distinct life histories. We used microsatellite markers to
 genotype over 1000 individuals of the migratory parasitic river lamprey
 (Lampetra fluviatilis) and freshwater-resident nonparasitic brook lamprey
 (L. planeri) distributed in 10 sympatric and parapatric population pairs
 in France. Mating trials, parentage analyses and artificial fertilizations
 demonstrated a low level of reproductive isolation between species even
 though size assortative mating may contribute to isolation. Most
 parapatric population pairs were strongly differentiated due to the joint
 effects of geographic distance and barriers to migration. In contrast, we
 found variable levels of gene flow between sympatric populations ranging
 from panmixia to moderate differentiation, which indicates a gradient of
 divergence with some population pairs that may correspond to alternative
 morphs or ecotypes of a single species and others that remain partially
 isolated. Ecologically-based divergent selection may explain these
 variable levels of divergence among sympatric population pairs but
 incomplete genome swamping following secondary contact could have also
 played a role. Overall, this study illustrates how highly differentiated
 phenotypes can be maintained despite high levels of gene flow that limit
 the progress toward speciation.
description: DatasetRougemont_et_al_2015JEBDataset of 13 microsatellite and 1023 individualsDatasetRougemont_et_al2015.xlsx
DOI: 10.5061/dryad.6bf38
title: Data from: The extent and meaning of hybridization and introgression between Siberian spruce (Picea obovata) and Norway spruce (Picea abies): cryptic refugia as stepping stones to the west?

description: Boreal species were repeatedly exposed to ice ages and went through cycles
 of contraction and expansion while sister species alternated periods of
 contact and isolation. The resulting genetic structure is consequently
 complex, and demographic inferences are intrinsically challenging. The
 range of Norway spruce (Picea abies) and Siberian spruce (Picea obovata)
 covers most of northern Eurasia; yet their geographical limits and
 histories remain poorly understood. To delineate the hybrid zone between
 the two species and reconstruct their joint demographic history, we
 analysed variation at nuclear SSR and mitochondrial DNA in 102 and 88
 populations, respectively. The dynamics of the hybrid zone was analysed
 with approximate Bayesian computation (ABC) followed by posterior
 predictive structure plot reconstruction and the presence of barriers
 across the range tested with estimated effective migration surfaces. To
 estimate the divergence time between the two species, nuclear sequences
 from two well-separated populations of each species were analysed with
 ABC. Two main barriers divide the range of the two species: one
 corresponds to the hybrid zone between them, and the other separates the
 southern and northern domains of Norway spruce. The hybrid zone is centred
 on the Urals, but the genetic impact of Siberian spruce extends further
 west. The joint distribution of mitochondrial and nuclear variation
 indicates an introgression of mitochondrial DNA from Norway spruce into
 Siberian spruce. Overall, our data reveal a demographic history where the
 two species interacted frequently and where migrants originating from the
 Urals and the West Siberian Plain recolonized northern Russia and
 Scandinavia using scattered refugial populations of Norway spruce as
 stepping stones towards the west.
description: SSR genotypes of Picea
 abies and P. obovataTsuda_Pabies_obovata.txt: The input file of STRUCTURE analysis based on 10loci of 1599 individuals. Missing data is coded as -9. Tsuda_Pabies_obovata_sampleInfo.xlsx: This file includes a list of population code, group, longitude (E) and latitude (N) which are corresponding to "Tsuda_Pabies_obovata.txt".Tsuda_Pabies_obovata_2016.txtTsuda_Picea_sampleInfo_2016
DOI: 10.5061/dryad.36j5d
title: Data from: Silver nanoparticles as a medical device in healthcare settings: a five-step approach for candidate screening of coating agents

description: Silver nanoparticle-based antimicrobials can promote a long lasting
 bactericidal effect without detrimental toxic side effects. However, there
 is not a clear and complete protocol to define and relate the properties
 of the particles (size, shape, surface charge, ionic content) with their
 specific activity. In this paper, we propose an effective multi-step
 approach for the identification of a ‘purpose-specific active
 applicability window’ to maximize the antimicrobial activity of medical
 devices containing silver nanoparticles (Ag NPs) (such as surface
 coaters), minimizing any consequent risk for human health (safety by
 design strategy). The antimicrobial activity and the cellular toxicity of
 four types of Ag NPs, differing in their coating composition and
 concentration have been quantified. Through the implementation of
 flow-field flow fractionation, Ag NPs have been characterized in terms of
 metal release, size and shape. The particles are fractionated in the
 process while being left unmodified, allowing for the identification of
 biological particle-specific contribution. Toxicity and inflammatory
 response in vitro have been assessed on human skin models, while
 antimicrobial activity has been monitored with both non-pathogenic and
 pathogenic Escherichia coli. The main benefit associated with such
 approach is the comprehensive assessment of the maximal effectiveness of
 candidate nanomaterials, while simultaneously indexing their properties
 against their safety.
description: RAW data
 manuscriptFigure raw data and
 statitistical analysisRAW DATA
 RSOS-REF17113.xlsx
DOI: 10.5061/dryad.d433j
title: Data from: Differential introgression and the maintenance of species boundaries in an advanced generation avian hybrid zone

description: Background: Evolutionary processes, including selection and differential
 fitness, shape the introgression of genetic material across a hybrid zone,
 resulting in the exchange of some genes but not others. Differential
 introgression of molecular or phenotypic markers can thus provide insight
 into factors contributing to reproductive isolation. We characterized
 patterns of genetic variation across a hybrid zone between two tidal marsh
 birds, Saltmarsh (Ammodramus caudacutus) and Nelson’s (A. nelsoni)
 sparrows (n = 286), and compared patterns of introgression among multiple
 genetic markers and phenotypic traits. Results: Geographic and genomic
 cline analyses revealed variable patterns of introgression among marker
 types. Most markers exhibited gradual clines and indicated that
 introgression exceeds the spatial extent of the previously documented
 hybrid zone. We found steeper clines, indicating strong selection for loci
 associated with traits related to tidal marsh adaptations, including for a
 marker linked to a gene region associated with metabolic functions,
 including an osmotic regulatory pathway, as well as for a marker related
 to melanin-based pigmentation, supporting an adaptive role of darker
 plumage (salt marsh melanism) in tidal marshes. Narrow clines at
 mitochondrial and sex-linked markers also offer support for Haldane’s
 rule. We detected patterns of asymmetrical introgression toward A.
 caudacutus, which may be driven by differences in mating strategy or
 differences in population density between the two species. Conclusions:
 Our findings offer insight into the dynamics of a hybrid zone traversing a
 unique environmental gradient and provide evidence for a role of
 ecological divergence in the maintenance of pure species boundaries
 despite ongoing gene flow.
description: Sparrow
 Genotypes/HaplotypesGenotypes at 24
 microsatellite loci and haplotype information at 5 genes for 292
 Ammodramus caudacutus and A. nelsoni. Sparrows were sampled from 34 sites
 along a geographic transect, including allopatric and sympatric
 populations.Walsh et al. Transect Data
 2016.xlsx
DOI: 10.5061/dryad.n2d7d
title: Data from: Testing for homologies in the axial skeleton of primitive echinoderms

description: The extraxial axial theory is used to investigate homology of ambulacral
 and oral plating because it predicts terminal branching and terminal
 addition of plates in the axial skeleton, although exceptions to the
 former may occur in some Paleozoic echinoderms. The variety of
 morphological designs and anomalous individuals also provide tests of
 plate homology. Homology of ambulacra is generally accepted, with the
 hydropore and/or single gonopore in Carpenter’s CD interray. In the 2-1-2
 ambulacral pattern the unbranched ambulacrum is always in Carpenter’s A
 ray. All ambulacral morphology requires just three instructions: ‘grow,’
 ‘branch,’ and ‘stop.’ The range of variation in echinoderms with fewer
 than five ambulacra implies that both the ‘branch’ and ‘stop’ instructions
 acted independently in all five rays. Numbers of ambulacra may or may not
 correlate with numbers of orals. Two basic patterns of ‘cystoid’ oral
 plating occur; with a single radial (circum-oral, CO) plate from each
 ambulacrum plus a sixth in the CD interray, and with all six interradial
 peri-oral (PO) plates, with two in the CD interambulacrum. Five ‘orals’
 may involve loss of PO3 or PO6. Erect ambulacral structures are lost first
 in taphonomy and so poorly known. All ambulacral skeletal elements bear
 the same topological relationship to ambulacral soft tissues. Where
 branched ambulacra occur, the trunk or flooring plates are often modified
 first brachiolars or pinnulars. Both brachioles and pinnules may arise
 from facets developed on one or two flooring plates. Terminal addition of
 plates, spacing of brachioles/pinnules, and lack of musculature to open
 cover plates all suggest that ‘cystoids’ had extensions of the water
 vascular system in their ambulacra.
description: Supplementary
 referencesA text file in UTF-8
 format that includes additional references not mentioned in the main text,
 but referred to in the supplementary data tablesSupplementary_references.txtTable1An MS Excel file listing ambulacral patterns found in early echinoderm genera with five ambulacra.Table2An MS Excel table of ambulacral patterns found in early echinoderms with fewer than 5 ambulacra.Table3An MS Excel table listing ambulacral structures (arms, pinnules, brachioles) present in various early echinoderm groups.
DOI: 10.5061/dryad.b43jn
title: Data from: Female brain size affects the assessment of male attractiveness during mate choice

description: Mate choice decisions are central in sexual selection theory aimed to
 understand how sexual traits evolve and their role in evolutionary
 diversification. We test the hypothesis that brain size and cognitive
 ability are important for accurate assessment of partner quality and that
 variation in brain size and cognitive ability underlies variation in mate
 choice. We compared sexual preference in guppy female lines selected for
 divergence in relative brain size, which we have previously shown to have
 substantial differences in cognitive ability. In a dichotomous choice
 test, large-brained and wild-type females showed strong preference for
 males with color traits that predict attractiveness in this species. In
 contrast, small-brained females showed no preference for males with these
 traits. In-depth analysis of optomotor response to color cues and gene
 expression of key opsins in the eye revealed that the observed differences
 were not due to differences in visual perception of color, indicating that
 differences in the ability to process indicators of attractiveness are
 responsible. We thus provide the first experimental support that
 individual variation in brain size affects mate choice decisions and
 conclude that differences in cognitive ability may be an important
 underlying mechanism behind variation in female mate choice.
description: ColorPreferenceDataRaw and extracted data for female preference testsOpsinExpressionDataOpsin expression data of fish measured in preference testsOptomotorResponseDataData on optomotor response of fish
DOI: 10.5061/dryad.1v339
title: Data from: Evidence for long-term shift in plant community composition under decadal experimental warming

description: Summary: 1. Long-term, slow ecological processes such as changes in plant
 community structure and composition strongly regulate ecosystem responses
 to climate change. Shifts in plant community are expected in chronically
 altered environments under warming. However, experimental evidence for
 long-term shifts and the associated mechanisms is still scarce in
 temperate grasslands. 2. Here, we explore the long-term responses of a
 prairie plant community to 14-year (2000-2013) manipulations of climate
 warming and clipping in Oklahoma, USA. Infrared heaters were used to
 elevate soil temperature by about 2 ºC all year round and annual clipping
 was applied to mimic hay harvest. 3. Community composition was resistant
 to experimental warming in the first seven years, but started to show
 responses starting from the eighth year; clipping consistently affected
 community composition over the years. Compositional change under long-term
 warming was mainly due to one invasive species and three dominant species.
 The negative correlations in relative abundance between the invasive
 species and the dominant species suggest inter-specific competition.
 Community structure (i.e., richness, evenness and diversity) had no
 overall response to experimental warming. However, in 2007, the extreme
 wet year, warming reduced species richness by 30%. Clipping promoted
 species richness by 10% on average over the 14 years but decreased
 community evenness. Warming did not interact with clipping in influencing
 the plant community variables. 4. Synthesis: Our study provides
 experimental evidence for long-term shifts in plant community composition
 due to warming and revealed novel mechanisms (i.e., species invasion and
 associated biotic interactions) underlying the long-term shift. The
 results also suggest that climate extremes may elicit or advance community
 responses to climate warming. The findings highlight that long-term
 climate change experiments are essential to reveal potential shifts in
 community composition.
description: Relative abundance
 dataJEcol-Archived
 Data.xlsx
DOI: 10.5061/dryad.fk0b9
title: Data from: A multi-genome analysis approach enables tracking of the invasion of a single Russian wheat aphid (Diuraphis noxia) clone throughout the New World

description: This study investigated the population genetics, demographic history and
 pathway of invasion of the Russian wheat aphid (RWA) from its native range
 in Central Asia, the Middle East and Europe to South Africa and the
 Americas. We screened microsatellite markers, mitochondrial DNA, and
 endosymbiont genes in 504 RWA clones from nineteen populations worldwide.
 Following pathway analyses of microsatellite and endosymbiont data, we
 postulate that Turkey and Syria were the most likely sources of invasion
 to Kenya and South Africa, respectively. Furthermore, we found that one
 clone transferred between South Africa and the Americas was most likely
 responsible for the New World invasion. Finally, endosymbiont DNA was
 found to be a high resolution population genetic marker, extremely useful
 for studies of invasion over a relatively short evolutionary history
 timeframe. This study has provided valuable insights into the factors that
 may have facilitated the recent global invasion by this damaging pest.
description: RWA worldwide
 populations' microsatellite and sequences dataDryad
 upload.tar.gzDryad---microsatellite
 updateAdd haplotype number for
 each individualDryad---microsatellite.xlsx