cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.n1506
title: Data from: Genetic and phenotypic divergence in an island bird: isolation by distance, by colonisation or by adaptation?

description: Discerning the relative roles of adaptive and non-adaptive processes in
 generating differences among populations and species, as well as how these
 processes interact, are fundamental aims in biology. Both genetic and
 phenotypic divergence across populations can be the product of limited
 dispersal and gradual genetic drift across populations (isolation by
 distance), of colonisation history and founder effects (isolation by
 colonisation) or of adaptation to different environments preventing
 migration between populations (isolation by adaptation). Here we attempt
 to differentiate between these processes using island populations of
 Berthelot's pipit (Anthus berthelotii), a passerine bird endemic to
 three Atlantic archipelagos. Using microsatellite markers and approximate
 Bayesian computation, we reveal that the northwards colonisation of this
 species ca 8,500 years ago resulted in genetic bottlenecks in the
 colonised archipelagos. We then show that high levels of genetic structure
 exist across archipelagos, and that these are consistent with a pattern of
 isolation by colonisation, but not with isolation by distance or
 adaptation. Finally, we show that substantial morphological divergence
 also exists and that this is strongly concordant with patterns of genetic
 structure and bottleneck history, but not with environmental differences
 or geographic distance. Overall our data suggest that founder effects are
 responsible for both genetic and phenotypic changes across archipelagos.
 Our findings provide a rare example of how founder effects can persist
 over evolutionary timescales, and suggest that they may play an important
 role in the early stages of speciation.
description: Microsatellite
 dataMicrosatellite genotypes
 for 371 individuals and 27 loci. Island abbreviations as in the
 manuscript.Morphometric
 dataMorphometric traits for
 all Berthelot's pipits from 2005/2006. Individual codes as in the
 microsatellite file. Island codes as in the manuscript.Climate
 dataClimate data for 13
 Berthelot's pipits populations, used to make geographical and
 ecological distance matrices.
DOI: 10.5061/dryad.6c7v5
title: Data from: Clinal variation in colony breeding structure and level of inbreeding in the subterranean termites Reticulitermes flavipes and R. grassei

description: Social insects exhibit remarkable variation in their colony breeding
 structures, both within and among species. Ecological factors are believed
 to be important in shaping reproductive traits of social insect colonies,
 yet there is little information linking specific environmental variables
 with differences in breeding structure. Subterranean termites
 (Rhinotermitidae) show exceptional variation in colony breeding structure,
 differing in the number of reproductives and degree of inbreeding;
 colonies can be simple families headed by a single pair of monogamous
 reproductives (king and queen) or they can be extended families headed by
 multiple inbreeding neotenic reproductives (wingless individuals). Using
 microsatellite markers, we characterized colony breeding structure and
 levels of inbreeding in populations over large parts of the range of the
 subterranean termites Reticulitermes flavipes in the USA and R. grassei in
 Europe. Combining these new data with previous results on populations of
 both species, we found that latitude had a strong effect on the proportion
 of extended-family colonies in R. flavipes and on levels of inbreeding in
 both species. We examined the effect of several environmental variables
 that vary latitudinally; while the degree of inbreeding was greatest in
 cool, moist habitats in both species, seasonality affected the species
 differently. Inbreeding in R. flavipes was most strongly associated with
 climatic variables (mean annual temperature and seasonality), whereas
 nonclimatic variables, including the availability of wood substrate and
 soil composition, were important predictors of inbreeding in R. grassei.
 These results are the first showing that termite breeding structure is
 shaped by local environmental factors and that species can vary in their
 responses to these factors.
description: Reticulitermes_flavipes_microsatellite_genotypesMicrosatellite genotypes of Reticulitermes flavipes colonies from 6 populations in the eastern U.S.Reticulitermes_grassei_microsatellite_genotypesMicrosatellite genotypes of Reticulitermes grassei colonies from three population in SpainRegression_analysis_spreadsheetData used in the regression analysis of the effects of bioclimatic variables on colony breeding structure and levels of inbreeding in Reticulitermes flavipes and R. grassei
DOI: 10.5061/dryad.dj51c
title: Data from: Identification and analysis of novel salt responsive candidate gene based SSRs (cgSSRs) from rice (Oryza sativa L.)

description: Background: Majority of the Asian people depend on rice for nutritional
 energy. Rice cultivation and yield are severely affected by soil salinity
 stress worldwide. Marker assisted breeding is a rapid and efficient way to
 develop improved variety for salinity stress tolerance. Genomic
 microsatellite markers are an elite group of markers, but there is
 possible uncertainty of linkage with the important genes. In contrast,
 there are better possibilities of linkage detection with important genes
 if SSRs are developed from candidate genes. To the best of our knowledge,
 there is no such report on SSR markers development from candidate gene
 sequences in rice. So the present study was aimed to identify and analyse
 SSRs from salt responsive candidate genes of rice. Results: In the present
 study, based on the comprehensive literature survey, we selected 220
 different salt responsive genes of rice. Out of them, 106 genes were found
 to contain 180 microsatellite loci with, tri-nucleotide motifs (56%) being
 most abundant, followed by di-(41%) and tetra nucleotide (2.8%) motifs.
 Maximum loci were found in the coding sequences (37.2%), followed by in
 5′UTR (26%), intron (21.6%) and 3′UTR (15%). For validation, 19 primer
 sets were evaluated to detect polymorphism in diversity analysis among the
 two panels consisting of 17 salt tolerant and 17 susceptible rice
 genotypes. Except one, all primer sets exhibited polymorphic nature with
 an average of 21.8 alleles/primer and with a mean PIC value of 0.28.
 Calculated genetic similarity among genotypes was ranged from 19%-89%. The
 generated dendrogram showed 3 clusters of which one contained entire 17
 susceptible genotypes and another two clusters contained all tolerant
 genotypes. Conclusion: The present study represents the potential of salt
 responsive candidate gene based SSR (cgSSR) markers to be utilized as
 novel and remarkable candidate for diversity analysis among rice genotypes
 differing in salinity response.
description: Fig 4Figure-4: Dendrogram
 generated from an unweighted pair group method analysis (UPGMA) cluster
 analysis s based on salt responsive cgSSR markers. First two clusters
 showing all tolerant genotypes, whereas third cluster showing all
 susceptible genotypes.
DOI: 10.5061/dryad.kc33b
title: Data from: Within-population Y-linked genetic variation for lifespan in Drosophila melanogaster

description: The view that the Y chromosome is of little importance for phenotypic
 evolution stems from early studies of Drosophila melanogaster. This
 species’ Y chromosome contains only 13 protein coding genes, is almost
 entirely heterochromatic, and is not necessary for male viability.
 Population genetic theory further suggests that non-neutral variation can
 only be maintained at the Y chromosome under special circumstances. Yet,
 recent studies suggest that the D. melanogaster Y chromosome
 trans-regulates hundreds to thousands of X and autosomal genes. This
 finding suggests that the Y chromosome may play a far more active role in
 adaptive evolution than has previously been assumed. To evaluate the
 potential for the Y chromosome to contribute to phenotypic evolution from
 standing genetic variation, we test for Y-linked variation in lifespan
 within a population of D. melanogaster. Assessing variation for lifespan
 provides a powerful test because lifespan i) shows sexual dimorphism,
 which the Y is primarily predicted to contribute to, ii) is influenced by
 many genes, which provides the Y with many potential regulatory targets,
 and iii) is sensitive to heterochromatin remodelling, a mechanism through
 which the Y chromosome is believed to regulate gene expression. Our
 results show a small but significant effect of the Y chromosome, and thus
 suggest that the Y chromosome has the potential to respond to selection
 from standing genetic variation. Despite its small effect size, Y-linked
 variation may still be important, in particular when evolution of sexual
 dimorphism is genetically constrained elsewhere in the genome.
description: Lifespan Data for
 Y-lines from Griffin et al 2015Data contains lifespan
 (variable: Age) data for 33 Y chromosome substitution lines (variable:
 Line), measured in 13560 flies, across three experimental blocks
 (variable: Block) and 456 vials (variable: Vial).Final.txt
DOI: 10.5061/dryad.n62dm
title: Data from: Anthropogenic hybridization between endangered migratory and commercially harvested stationary whitefish taxa (Coregonus spp.)

description: Natural hybridization plays a key role in the process of speciation.
 However, anthropogenic (human induced) hybridization of historically
 isolated taxa raises conservation issues. Due to weak barriers to gene
 flow and the presence of endangered taxa, the whitefish species complex is
 an excellent study system to investigate the consequences of hybridization
 in conservation. We focused on three naturally reproductively isolated
 whitefish taxa in Germany: the endangered, anadromous North Sea houting
 (NSH) and Baltic houting (BH), which were reintroduced after local
 extinction, and the commercially stocked European whitefish (EW). To
 evaluate the genetic integrity of each taxon, source and reintroduced
 populations of NSH and BH, and EW populations were characterized based on
 two mitochondrial and 17 microsatellite loci. Additionally, we
 investigated gill raker counts as an adaptive phenotypic trait. Even
 though clear genetic and phenotypic differentiation confirmed the houtings
 as separate evolutionarily significant units, admixture analyses revealed
 an extensive hybrid zone. Hybridizations were introgressive, positively
 correlated with genetic diversity, and were reflected in the gill raker
 counts. The BH distribution range showed higher heterogeneity and stronger
 admixture than the NSH range. Erroneous stocking with non-native genotypes
 best explained these patterns, which pose challenges for the conservation
 of the endangered NSH and BH.
description: Dierking et al
 Evolutionary Applications Microsat dataThis file contains the
 microsatellite data used for the analyses in the
 manuscript.Dierking et al
 Evolutionary Applications mtDNA dataThis file contains the
 mtDNA data used for the analyses in the manuscript.Dierking et al
 Evolutionary Applications gill raker countsThis file contains the
 data on gill raker counts used for analyses in the
 manuscript.
DOI: 10.5061/dryad.9bb60
title: Data from: Avoidance, tolerance, and resistance to ectoparasites in nestling and adult tree swallows

description: We examined avoidance, tolerance, and resistance strategies of nestling
 and adult tree swallows Tachycineta bicolor in response to ectoparasitic
 blowflies Protocalliphora sialia. Tree swallows avoided settling in
 north-facing nest boxes early in the breeding season. These boxes were
 more likely to be parasitized later in the season, suggesting that box
 selection may facilitate blowfly avoidance. After experimentally
 manipulating blowfly intensity, we found that nestlings were generally
 tolerant of parasitism. Parasites significantly reduced nestling blood
 hemoglobin but had no effect on nestling body mass, primary feather
 growth, age at fledging, or fledging success. Parents of parasitized
 nestlings did not increase their food provisioning rate to promote
 nestling tolerance. Adult female tree swallows demonstrated both tolerance
 and resistance: blowfly parasitism had no effect on adult hemoglobin and
 body mass, and those with higher P. sialia-binding antibody levels had
 fewer blowfly larvae in their nests. Nestling antibodies were unrelated to
 blowfly intensity. Despite considerable variation among years, our results
 suggest that the costs of blowfly parasitism to nestling and adult tree
 swallows are modest, and limited to blood loss in nestlings. Future work
 should examine the effects of reduced blood hemoglobin on fledgling
 survival and the importance of parasite-specific antibodies.
description: DeSimone et al dataset
 2014-2016 grouped by nestThese are data on tree
 swallows and their associated blowfly parasites, in which each row
 represents one nest. One sheet includes the data, the other sheet includes
 the descriptions of variables.DeSimone et al dataset
 2014-2016 grouped by nestlingThese are data on tree
 swallows and their associated blowfly parasites, in which each row
 represents one nestling. One sheet includes the data, the other sheet
 includes the descriptions of variables.
DOI: 10.5061/dryad.75940
title: Data from: Nutritional control of body size through FoxO-Ultraspiracle mediated ecdysone biosynthesis

description: Despite their fundamental importance for body size regulation, the
 mechanisms that stop growth are poorly understood. In Drosophila
 melanogaster, growth ceases in response to a peak of the molting hormone
 ecdysone that coincides with a nutrition-dependent checkpoint, critical
 weight. Previous studies indicate that insulin/insulin-like growth factor
 signaling (IIS)/Target of Rapamycin (TOR) signaling in the prothoracic
 glands (PGs) regulates ecdysone biosynthesis and critical weight. Here we
 elucidate a mechanism through which this occurs. We show that Forkhead Box
 class O (FoxO), a negative regulator of IIS/TOR, directly interacts with
 Ultraspiracle (Usp), part of the ecdysone receptor. While overexpressing
 FoxO in the PGs delays ecdysone biosynthesis and critical weight,
 disrupting FoxO–Usp binding reduces these delays. Further, feeding
 ecdysone to larvae eliminates the effects of critical weight. Thus,
 nutrition controls ecdysone biosynthesis partially via FoxO–Usp prior to
 critical weight, ensuring that growth only stops once larvae have achieved
 a target nutritional status.
description: Real-Time PCR
 finalReal-Time PCR
 quantification of E74B, phm and dibEcdysone quantification
 finalEcdysone quantifications
 for P0206&gt;, &gt;FoxO, P0206&gt;FoxO and P0206&gt;FoxO NK. All genotypes
 are in a FoxO null background.Final weight
 allPharate adult weights
 for males and females in all genotypes examined.CWData&Scripts
DOI: 10.5061/dryad.q2b5cs2
title: Data from: Urbanization drives genetic differentiation in physiology and structures the evolution of pace-of-life syndromes in the water flea Daphnia magna

description: Natural and human-induced stressors elicit changes in energy metabolism
 and stress physiology in populations of a wide array of species. Cities
 are stressful environments that may lead to differential selection on
 stress-coping mechanisms. Given that city ponds are exposed to the urban
 heat island effect and receive polluted run-off, organisms inhabiting
 these ecosystems might show genetic differentiation for physiological
 traits enabling them to better cope with higher overall stress levels. A
 common garden study with 62 Daphnia magna genotypes from replicated urban
 and rural populations revealed that urban Daphnia have significantly
 higher concentrations of total body fat, proteins, and sugars. Baseline
 activity levels of the antioxidant defense enzymes superoxide dismutase
 (SOD) and glutathione-S-transferase (GST) were higher in rural compared to
 city populations, yet urban animals were equally well protected against
 lipid peroxidation. Our results add to the recent evidence of
 urbanisation-driven changes in stress physiology and energy metabolism in
 terrestrial organisms. Combining our results with data on urban life
 history evolution in Daphnia revealed that urban genotypes show a
 structured pace-of-life syndrome involving both life history and
 physiological traits, whereas this is absent in rural populations.
description: ProceedingsB_Brans_UrbanPOLS2018_datafileData contains raw life history traits + PCA ordinates and raw physiology data + PCA ordinates from the experiment as described.DATASET_lavaan_SEM_2017.csv
DOI: 10.5061/dryad.hm63867
title: Data from: City life on fast lanes: urbanization induces an evolutionary shift towards a faster life style in the water flea Daphnia

description: Multiple species show significant trait shifts in response to
 urbanization. Yet, the impact of anthropogenic warming linked to the urban
 heat island effect is remarkably understudied. Additionally the relative
 contributions of phenotypic plasticity and genetic change underlying trait
 shifts in response to urbanization are poorly known. A common garden study
 with the water flea Daphnia magna revealed that both genetic
 differentiation in response to urbanization and phenotypic plasticity in
 response to higher rearing temperature (24 °C) induced significant
 parallel multivariate shifts in life history strategy along the slow-fast
 pace-of-life axis. Urban animals and animals reared at higher temperatures
 are characterized by fast maturation, early release of progeny, a smaller
 size at maturity, increased fecundity, and higher performance (given by
 maximal population growth rate r) compared to genotypes isolated from
 rural ponds and animals reared at lower temperatures respectively.
 Evolution in response to urbanization accounted for 30% of the total
 observed shift in life history and caused a significant change in mean
 trait values, while plasticity responses to experimental warming were
 unaltered between urban and rural populations. The total trait change
 achieved through both plasticity and evolution ranged from 8 to 56%
 depending on the trait. Our results provide clear evidence for evolution
 underlying an increase in pace-of-life of populations in response to
 urbanization. Given the pivotal role of Daphnia in aquatic ecosystems,
 this shift potentially feeds back to population structure, top-down
 control of algae, and food web dynamics in urban freshwater ecosystems.
 Additionally, we argue that adaptation to urban heat islands might render
 these populations pre-adapted in a context of future climate change.
description: BransDeMeester_FE_data_UrbanizationPaceOfLifeData include life history data and physiological data reported in Brans et al., 2018, Functional Ecology (City life on fast lanes: urbanization induces an evolutionary shift towards a faster life style in the water flea Daphnia), as wel as Brans et al., 2018, Proceedings B (Urbanization drives genetic differentiation in physiology and structures the evolution of pace-of-life syndromes in the water flea Daphnia magna).DATASET_lavaan_SEM_2017.csv
DOI: 10.5061/dryad.5646b
title: Data from: Conservation value of low-productive forests measured as the amount and diversity of dead wood and saproxylic beetles

description: In many managed landscapes, low-productive land comprises most of the
 remaining relatively untouched areas, and is often over-represented within
 protected areas. The relationship between the productivity and
 conservational value of a site is poorly known; however, it has been
 hypothesized that biodiversity increases with productivity due to higher
 resource abundance or heterogeneity, and that the species communities of
 low-productive land are a nested sub-set of communities from more
 productive land. We tested these hypotheses for dead wood-dependent
 beetles by comparing their species richness and composition, as well as
 the amount and diversity of dead wood, between low-productive (potential
 forest growth &lt; 1 m3 ha-1 year-1) and productive Scots
 pine-dominated stands in Sweden. We included four stand types: stands
 situated on (i) thin soils and (ii) mires (both low-productive), (iii)
 managed stands, and (iv) unmanaged stands set aside for conservation
 purposes (both productive). Beetle species richness and number of
 red-listed species were highest in the productive set-asides. Species
 richness was positively correlated with the volume and diversity of dead
 wood, but volume appeared to be a better predictor than diversity for the
 higher species richness in set-asides. Beetle species composition was
 similar among stand types, and the assemblages in low-productive stands
 were largely subsets of those in productive set-asides. However, 11% of
 all species and 40% of red-listed species only occurred in productive
 stands, while no species were unique to low-productive stands. We conclude
 that low-productive forests are less valuable for conservation than
 productive forest land. Given the generally similar species composition
 among stand types, a comparable conservational effect could be obtained by
 setting aside a larger area of low-productive forest in comparison to the
 productive. In terms of dead wood volumes, 1.8–3.6 ha of low-productive
 forest has the same value as 1 ha of unmanaged productive forest. This
 figure can be used to estimate the conservation value of low productive
 forests; however, as productive forests harbored some unique species, they
 are not completely exchangeable.
description: saproxylic_beetle_data_hamalainen_et_alOccurrence of saproxylic beetles, given as the number of observations per stand for each species. The studied stands are arranged in blocked design, with “BlockID” referring to the number of the block and “StandID” to the number of the stand within this block.deadwood_data_hamalainen_et_alAmount and characteristics of dead wood of Scots pine. "BlockID" and "StandID" as above. On each stand sampling was carried out in eight study plots (“PlotID”). “DeadwoodID” refers to the measured individual deadwood items.living_tree_data_hamalainen_et_alCharacteristics of living Scots pines, and stand basal area (including all living trees).