cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k1s2n
title: Data from: Generation of a neutral FST baseline for testing local adaptation on gill-raker number within and between European whitefish ecotypes in the Baltic Sea basin

description: Divergent selection at ecologically important traits is thought to be a
 major factor driving phenotypic differentiation between populations. To
 elucidate the role of different evolutionary processes shaping the
 variation in gill-raker number of European whitefish (Coregonus lavaretus
 sensu lato) in the Baltic Sea basin, we assessed the relationships between
 genetic and phenotypic variation among and within three whitefish ecotypes
 (sea-, river and lake-spawners). To generate expected neutral distribution
 of FST and to evaluate whether highly variable microsatellite loci
 resulted in deflated FST estimates compared to less variable markers we
 performed population genetic simulations under finite island and
 hierarchical island models. The genetic divergence observed among
 (FCT=0.010) and within (FST=0.014–0.041) ecotypes was rather low. The
 divergence in gill-raker number, however, was substantially higher between
 sea- and river-spawners compared to observed microsatellite data and
 simulated neutral baseline (PCT&gt;FCT). This suggests that the
 differences in gill-raker number between sea- and river-spawners are
 likely driven by divergent natural selection. We also found strong support
 for divergent selection on gill-raker number among different populations
 of sea-spawners (PST&gt;FST), most likely caused by highly variable
 habitat use and diverse diet. The putative role of divergent selection
 within lake-spawners initially inferred from empirical microsatellite
 data, was not supported by simulated FST distributions. This work provides
 a first formal test of divergent selection on gill-raker number in Baltic
 whitefish, and demonstrates the usefulness of population genetic
 simulations to generate informative neutral baselines for PST–FST analyses
 helping to disentangle the effects of stochastic evolutionary processes
 from natural selection.
description: Ozerov_et_al_2015_Whitefish_PST-FSTGill-raker number and microsatellite genotypesOzerov_et_al_2015_WF_PST_FST_Dryad.xlsx
DOI: 10.5061/dryad.9vv1vb6
title: Data from: Maternal presence facilitates plasticity in offspring behavior: insights into the evolution of parental care

description: Fundamental to the definition of parental care is that care confers
 benefits to the offspring. However, the mechanisms resulting in these
 benefits remain poorly understood, particularly in species where postnatal
 care is not obligatory. Here, we address this shortcoming using a lizard,
 Liopholis whitii, in which family life is facultative and relatively
 simple – extending to prolonged associations between parents and offspring
 within the parental territory. Using a split-clutch design, we housed
 offspring either with their mother or alone during the first eight weeks
 of postnatal life and examined whether maternal presence affected (i) the
 expression of key functional behaviors, and (ii) learning ability in a
 biologically relevant anti-predatory task. We found that offspring housed
 with their mothers expressed heightened levels of activity, boldness and
 exploration compared to offspring who were housed alone. Furthermore, we
 show that associating with mothers during early postnatal periods led to
 improved offspring performance in the anti-predation learning task.
 Together these results suggest that even relatively simple forms of
 enhanced parent-offspring association can have significant impacts on
 offspring traits. We argue that such effects may help refine and stabilize
 parent-offspring associations early in their evolution, potentially
 setting the stage for the elaboration of both parent and offspring
 behaviors.
description: Behaviour
 DataAll data used to
 generate the results for the behavioural component of the
 studyBehaviour.csvLearning DataAll data used to generate the results for the learning component of the studyLearning.csv
DOI: 10.5061/dryad.r6624
title: Data from: Male pregnancy and bi-parental immune priming

description: In vertebrates, maternal transfer of immunity via the eggs or the placenta
 provides offspring with crucial information on prevailing pathogens and
 parasites. Males contribute little to such trans-generational immune
 priming, either because they do not share the environment and parasite
 pressure of the offspring, or because sperm are suggested to be too small
 for transfer of immunity. In the teleost group of Syngnathids (pipefish,
 seahorses and sea dragons) males brood female eggs in a placenta-like
 structure. Such sex-role-reversed species provide a unique opportunity to
 test for adaptive plasticity in immune transfer. Here males in addition to
 females should influence offspring immunity. We experimentally tested
 paternal effects on offspring immunity by examining immune cell
 proliferation and immune gene expression. Maternal and paternal bacterial
 exposure induced the offspring's immune defence five weeks after
 hatching, and this effect persisted in four-month-old offspring. For
 several offspring immune traits double parental exposure (maternal and
 paternal) enhanced the response, while for another group of immune traits,
 the trans-generational induction already took place if only one parent was
 exposed. Our study shows that sex-role reversal in connection with male
 pregnancy opens the door for bi-parental influences on offspring immunity,
 and may represent one additional advantage for the evolution of male
 pregnancy.
description: direct_immune_parameters_four_month_offspringMeasurements of direct immune parameter analyses in four month old offspring.gene_expression_five_weeks_old_offspringGene expression measurements of five week old offspring.gene_expression_fluidigm_four_month_old_offspringGene expression measurements of four-month-old offspring using the fluidigm method.gene_expresssion_qpcr_four_month_offspringGene expression measurement of four-month-old offspring using quantitative PCR method.
DOI: 10.15468/dl.2r8dhc
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Jaborosa volkmannii",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 9 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000931-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.j2q14vn5
title: Data from: Drift and selection influence geographic variation at immune loci of prairie-chickens

description: Previous studies of immunity in wild populations have focused primarily on
 genes of the major histocompatibility complex (MHC); however, studies of
 model species have identified additional immune-related genes that also
 affect fitness. In this study, we sequenced five non-MHC immune genes in
 six greater prairie-chicken (Tympanuchus cupido) populations that have
 experienced varying degrees of genetic drift as a consequence of
 population bottlenecks and fragmentation. We compared patterns of
 geographic variation at the immune genes with six neutral microsatellite
 markers to investigate the relative effects of selection and genetic
 drift. Global FST outlier tests identified positive selection on just one
 of five immune genes (IAP-1) in one population. In contrast, at other
 immune genes, standardized G′ST-values were lower than those at
 microsatellites for a majority of pairwise population comparisons,
 consistent with balancing selection or with species-wide positive or
 purifying selection resulting in similar haplotype frequencies across
 populations. The effects of genetic drift were also evident as summary
 statistics (e.g., Tajima’s D) did not differ from neutrality for the
 majority of cases, and immune gene diversity (number of haplotypes per
 gene) was correlated positively with population size. In summary, we found
 that both genetic drift and selection shaped variation at the five immune
 genes, and the strength and type of selection varied among genes. Our
 results caution that neutral forces, such as drift, can make it difficult
 to detect current selection on genes.
description: Immune Gene
 AlignmentsAlignments of sequences
 from five immune genes in six greater prairie-chicken populations. The
 five immune genes are chicken B-cell marker 6 (ChB6), interleukin-2 (IL2),
 transforming growth hormone beta 3 (TGFB3), inhibitor of apoptosis
 protein-1 (IAP), and tumor necrosis factor-related apoptosis inducing
 ligand-like protein (TRAIL).Microsat
 genotypesMicrosatellite genotypes
 at six loci for greater prairie-chickens from six
 populations.SNP
 haplotypesSNP haplotypes at five
 immune genes for six greater prairie-chicken
 populations.22 individual SNP
 lociSNP genotypes at five
 immune genes for greater prairie-chickens from six
 populations.
DOI: 10.15468/dl.d3ekx9
title: Occurrence Download

description: A dataset containing 129 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Artocarpus sericicarpus"
 ]
}

 The dataset includes 129 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000932-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.3qk84
title: Data from: Evidence of functional divergence in MSP7 paralogous proteins: a molecular-evolutionary and phylogenetic analysis

description: Background: The merozoite surface protein 7 (MSP7) is a Plasmodium protein
 which is involved in parasite invasion; the gene encoding it belongs to a
 multigene family. It has been proposed that MSP7 paralogues seem to be
 functionally redundant; however, recent experiments have suggested that
 they could have different roles. Results: The msp7 multigene family has
 been described in newly available Plasmodium genomes; phylogenetic
 relationships were established in 12 species by using different molecular
 evolutionary approaches for assessing functional divergence amongst MSP7
 members. Gene expansion and contraction rule msp7 family evolution;
 however, some members could have had concerted evolution. Molecular
 evolutionary analysis showed that relaxed and/or intensified selection
 modulated Plasmodium msp7 paralogous evolution. Furthermore, episodic
 diversifying selection and changes in evolutionary rates suggested that
 some paralogous proteins have diverged functionally. Conclusions: Even
 though msp7 has mainly evolved in line with a birth-and-death evolutionary
 model, gene conversion has taken place between some paralogous genes
 allowing them to maintain their functional redundancy. On the other hand,
 the evolutionary rate of some MSP7 paralogs has become altered, as well as
 undergoing relaxed or intensified (positive) selection, suggesting
 functional divergence. This could mean that some MSP7s can form different
 parasite protein complexes and/or recognise different host receptors
 during parasite invasion. These results highlight the importance of this
 gene family in the Plasmodium genus.
description: Garzón-Ospina et al.,-
 2016 - BMC Evolutionary Biology, sequences and
 alignmentsMSP7 sequences and
 alignments used in Evidence of functional divergence in MSP7 paralogous
 proteins: a molecular-evolutionary and phylogenetic
 analysisGarzón-Ospina et al.,- 2016 -
 BMC Evolutionary Biology.zip
DOI: 10.5061/dryad.sd3b0
title: Data from: Evidence that implicit assumptions of ‘no evolution’ of disease vectors in changing environments can be violated on a rapid timescale

description: Projected impacts of climate change on vector-borne disease dynamics must
 consider many variables relevant to hosts, vectors and pathogens,
 including how altered environmental characteristics might affect the
 spatial distributions of vector species. However, many predictive models
 for vector distributions consider their habitat requirements to be fixed
 over relevant time-scales, when they may actually be capable of rapid
 evolutionary change and even adaptation. We examine the genetic signature
 of a spatial expansion by an invasive vector into locations with novel
 temperature conditions compared to its native range as a proxy for how
 existing vector populations may respond to temporally changing habitat.
 Specifically, we compare invasions into different climate ranges and
 characterize the importance of selection from the invaded habitat. We
 demonstrate that vector species can exhibit evolutionary responses
 (altered allelic frequencies) to a temperature gradient in as little as
 7–10 years even in the presence of high gene flow, and further, that this
 response varies depending on the strength of selection. We interpret these
 findings in the context of climate change predictions for vector
 populations and emphasize the importance of incorporating vector evolution
 into models of future vector-borne disease dynamics.
description: Hawaiian Ae. j.
 japonicusMicrosatellite genotypes
 from the mosquito Aedes japonicus japonicus collected in Hawaii, USA in
 2010-2011Hawaiian_Dryad.csvVirginia Ae. j. japonicusMicrosatellite genotypes from the mosquito Aedes japonicus japonicus collected in Virginia, USA in 2011Virginia_Dryad.csvKyoto and Tokyo Ae. j. japonicusMicrosatellite genotypes from the mosquito Aedes japonicus japonicus collected in Kyoto and TokyoJapan_Dryad.csv
DOI: 10.5061/dryad.rc1p0
title: Data from: Individual marking of soft-bodied subtidal invertebrates in situ - a novel staining technique applied to the giant plumose anemone Metridium farcimen (Tilesius, 1809)

description: The ability to recognize individuals and track growth over time is crucial
 to population dynamics research as well as studies of animal behavior.
 Invertebrates are particularly difficult to track as they often molt, have
 regenerative capabilities, or lack hard parts to attach markers. We
 tested, in laboratory and field studies, a new way of marking sea anemones
 (order Actiniaria) by injection of three vital stains (i.e., neutral red,
 methylene blue, and fluorescein). Neutral red and methylene blue did not
 affect growth or survival, but fluorescein was lethal at high
 concentrations. Marked individuals could be identified up to seven months
 after injection with neutral red, six weeks with methylene blue, and three
 days with low concentrations of fluorescein. Neutral red could be used for
 long-term monitoring of growth and survival in the field, and in
 combination with methylene blue could be used to mark individuals in
 distinguishable patterns for short-term studies such as examining
 predator-prey interactions, movement of individuals, and recruitment
 survival.
description: S1
 AppendixRaw data from the
 laboratory experiment.S2
 AppendixRaw data from the field
 experiment.
DOI: 10.5061/dryad.f25c87j
title: Data from: Thirdhand smoke uptake to aerosol particles in the indoor environment

description: Aerosol composition measurements made in an indoor classroom indicate the
 uptake of thirdhand smoke (THS) species to indoor particles, a novel
 exposure route for THS to humans indoors. Chemical speciation of the
 organic aerosol fraction using mass spectrometric data and factor analysis
 identified a reduced nitrogen component, predominantly found in the indoor
 environment, contributing 29% of the indoor submicron aerosol mass. We
 identify this factor as THS compounds partitioning from interior surfaces
 to gas phase and then aerosol phase. Partitioning of THS vapors to
 aerosols requires an aqueous phase for reactive uptake of the reduced
 nitrogen species (RdNS), leading to seasonal differences in THS
 concentration indoors. RdNS protonate under the acidic conditions expected
 for indoor aerosols of outdoor origin. Controlled laboratory measurements
 performed using cigarette smoke deposited into a Pyrex vessel showed a
 similar partitioning behavior to aerosol of outdoor origin and mass
 spectral features comparable to the measured indoor THS factor after 1
 week of residence time in the closed vessel. This study reports a new,
 potentially large THS exposure route from partitioning of surface volatile
 organic compounds into the aerosol phase and subsequent dispersion in a
 mechanically ventilated building.
description: Data from: Thirdhand
 smoke uptake to aerosol particle in the indoor
 environmentThis file includes data
 used to produce Figures 1, 2, 3, SI1, SI2, SI3 for the
 manuscript.SA_8368_data.zip
DOI: 10.5061/dryad.f6r10
title: Data from: Ocean acidification impacts spine integrity but not regenerative capacity of spines and tube feet in adult sea urchins

description: Increasing atmospheric carbon dioxide (CO2) has resulted in a change in
 seawater chemistry and lowering of pH, referred to as ocean acidification.
 Understanding how different organisms and processes respond to ocean
 acidification is vital to predict how marine ecosystems will be altered
 under future scenarios of continued environmental change. Regenerative
 processes involving biomineralization in marine calcifiers such as sea
 urchins are predicted to be especially vulnerable. In this study, the
 effect of ocean acidification on regeneration of external appendages
 (spines and tube feet) was investigated in the sea urchin Lytechinus
 variegatus exposed to ambient (546 µatm), intermediate (1027 µatm) and
 high (1841 µatm) partial pressure of CO2 (pCO2) for eight weeks. The rate
 of regeneration was maintained in spines and tube feet throughout two
 periods of amputation and regrowth under conditions of elevated pCO2.
 Increased expression of several biomineralization-related genes indicated
 molecular compensatory mechanisms; however, the structural integrity of
 both regenerating and homeostatic spines was compromised in high pCO2
 conditions. Indicators of physiological fitness (righting response, growth
 rate, coelomocyte concentration and composition) were not affected by
 increasing pCO2, but compromised spine integrity is likely to have
 negative consequences for defence capabilities and therefore survival of
 these ecologically and economically important organisms.
description: Emerson et al Raw
 DataRaw data for "Ocean
 acidification impacts spine integrity but not regenerative capacity of
 spines and tube feet in adult sea urchins"Emerson et al RawData
 v4.docx
DOI: 10.5061/dryad.vt968
title: Data from: Are sympatrically speciating Midas cichlid fish special? Patterns of morphological and genetic variation in the closely related species Archocentrus centrarchus

description: Established empirical cases of sympatric speciation are scarce, although
 there is an increasing consensus that sympatric speciation might be more
 common than previously thought. Midas cichlid fish are one of the few
 substantiated cases of sympatric speciation, and they formed repeated
 radiations in crater lakes. In contrast, in the same environment, such
 radiation patterns have not been observed in other species of cichlids and
 other families of fish. We analyze morphological and genetic variation in
 a cichlid species (Archocentrus centrarchus) that co-inhabits several
 crater lakes with the Midas species complex. In particular, we analyze
 variation in body and pharyngeal jaw shape (two ecologically important
 traits in sympatrically divergent Midas cichlids) and relate that to
 genetic variation in mitochondrial control region and microsatellites.
 Using these four datasets, we analyze variation between and within two
 Nicaraguan lakes: a crater lake where multiple Midas cichlids have been
 described and a lake where the source population lives. We do not observe
 any within-lake clustering consistent across morphological traits and
 genetic markers, suggesting the absence of sympatric divergence in A.
 centrarchus. Genetic differentiation between lakes was low and
 morphological divergence absent. Such morphological similarity between
 lakes is found not only in average morphology, but also when analyzing
 covariation between traits and degree of morphospace occupation. A
 combined analysis of the mitochondrial control region in A. centrarchus
 and Midas cichlids suggests that a difference between lineages in the
 timing of crater lake colonization cannot be invoked as an explanation for
 the difference in their levels of diversification. In light of our
 results, A. centrarchus represents the ideal candidate to study the
 genomic differences between these two lineages that might explain why some
 lineages are more likely to speciate and diverge in sympatry than others.
description: Body
 shapeRaw body shape data in
 TPS format. The data includes all landmarks, semilandmarks and
 "helper points" (please, see the paper for
 details).centrarchus2012BodyShape.tpsPharyngeal jaw shapeLower pharyngeal jaw shape data in TPS format. The data contains all landmarks and semilandmarks (prior to sliding). The dataset comprises missing landmark whose position has been reconstructed through reflection (please, see the paper for details).centrarchus2012PJshape.tpsMicrosatellitesMicrosatellite data. Numbers represent the different alleles. -9 stands for missing data.
DOI: 10.5061/dryad.5709n
title: Data from: Immune challenges decrease biliverdin concentration in the spleen of Northern Bobwhite Quail, Colinus virginianus

description: Most antioxidants have multiple functions; in addition to minimizing
 oxidative damage, many antioxidants have immune-modulating properties. For
 example, biliverdin is produced in the liver and spleen from the breakdown
 of heme, and has putative immune-suppressing and antioxidant properties.
 However, the majority of these properties have been investigated in vitro
 or in mammalian models, in which biliverdin reductase converts virtually
 all biliverdin to bilirubin. Thus, biliverdin’s physiological roles remain
 largely untested. Here, we investigated whether biliverdin has
 immunomodulating roles by injecting Northern Bobwhite quail (Colinus
 virginianus) with either a vehicle control, lysed and rinsed pig red blood
 cells (pRBC) that contain erythrocyte antigens but no heme, or intact pRBC
 that contain both erythrocyte antigens and hemoglobin, thus increasing the
 amount of heme that can be converted to biliverdin. We then quantified
 hemagglutination and hemolysis ability, and biliverdin concentration in
 the liver and spleen, on 3, 6, and 9 days post-injection. We found that
 hemagglutination was greater in individuals that received intact pRBC, but
 not in those injected with heme-removed pRBC, demonstrating that
 biliverdin does not suppress immune function at this dosage. Biliverdin
 levels of liver and spleen were correlated within individuals, suggesting
 organism-level variation in biliverdin production. Lastly, individuals
 injected with intact pRBC had a reduced biliverdin concentration in the
 spleen, suggesting that immune challenges may reduce biliverdin production
 or accumulation. This initial investigation demonstrated that biliverdin
 may have more nuanced physiological roles than previously reported,
 supporting the value of further investigations into the physiology of
 biliverdin.
description: DryadDataData used for analysis.