cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.67cn1
title: Data from: Genetic signs of multiple colonization events in Baltic ciscoes with radiation into sympatric spring and autumn-spawners confined to early post-glacial arrival

description: Presence of sympatric populations may reflect local diversification or
 secondary contact of already distinct forms. The Baltic cisco (Coregonus
 albula) normally spawns in late autumn, but in a few lakes in Northern
 Europe sympatric autumn and spring- or winter-spawners have been
 described. So far, the evolutionary relationships and taxonomic status of
 these main life history forms have remained largely unclear. With
 microsatellites and mtDNA sequences, we analyzed extant and extinct
 spring- and autumn-spawners from a total of 23 Swedish localities,
 including sympatric populations. Published sequences from Baltic ciscoes
 in Germany and Finland, and Coregonus sardinella from North America were
 also included together with novel mtDNA sequences from Siberian C.
 sardinella. A clear genetic structure within Sweden was found that
 included two population assemblages markedly differentiated at
 microsatellites and apparently fixed for mtDNA haplotypes from two
 distinct clades. All sympatric Swedish populations belonged to the same
 assemblage, suggesting parallel evolution of spring-spawning rather than
 secondary contact. The pattern observed further suggests that postglacial
 immigration to Northern Europe occurred from at least two different
 refugia. Previous results showing that mtDNA in Baltic cisco is
 paraphyletic with respect to North American C. sardinella were confirmed.
 However, the inclusion of Siberian C. sardinella revealed a more
 complicated pattern, as these novel haplotypes were found within one of
 the two main C. albula clades and were clearly distinct from those in
 North American C. sardinella. The evolutionary history of Northern
 Hemisphere ciscoes thus seems to be more complex than previously
 recognized.
description: Delling et al
 2014_Coregonus albula_microsatellite dataMicrosatellite genotypes
 (9 loci) for 698 Coregonus albula individuals. See read me file for
 further details.
DOI: 10.5061/dryad.77249
title: Data from: Ejaculate characteristics depend on social environment in the horse (Equus caballus)

description: Sperm competition theory predicts semen characteristics to be affected by
 the social environment. We used the polygamous horse (Equus caballus) to
 experimentally study within-subject plasticity in response to different
 social environments. Stallions were sequentially exposed, over a period of
 8 weeks each, to other stallions and then singly to mares, or vice versa
 (in adjacent boxes separated by grills). Ejaculates were collected to
 determine semen characteristics. Highest sperm numbers were found in
 stallions that were first exposed to other stallions and then to mares,
 while lowest sperm numbers were observed in stallions that had been
 exposed to mares but not yet to other stallions. One of three sperm
 velocity measures (curvilinear velocity) was consistently elevated in
 stallions that were first exposed to stallions and then to mares. Sperm
 number after exposure to mares and curvilinear sperm velocity after
 exposure to stallions were both positively correlated to average blood
 testosterone levels during the corresponding period of exposure. We
 conclude that ejaculate characteristics are plastic traits affected by the
 social environment in horses.
description: Data
 BurgerDolivoWedekind PLOS ONE 2015Ejaculate
 characteristics and peripheral testosterone plasma concentration in 12
 stallion horses after exposure to different social
 environments
DOI: 10.5061/dryad.4c6bd
title: Data from: Cockroaches that exchange respiratory gases discontinuously survive food and water restriction

description: Metabolic rate and respiratory gas exchange patterns vary significantly
 both between and within species, even after a number of biotic and abiotic
 factors are taken into account. This suggests that such variation is of
 evolutionary importance, but the life history implications of this
 variation remain relatively poorly characterised. In the present study we
 examine the effect of metabolic variation on starvation and desiccation
 resistance in the speckled cockroach Nauphoeta cinerea. We also compare
 the starvation and desiccation resistance of individuals that exchange
 respiratory gases continuously with those that breathe discontinuously. We
 show that metabolic rate has no effect on survival during food and water
 restriction, but cockroaches exhibiting discontinuous gas exchange cycles
 (DGCs) live longer than those that do not and those provisioned with water
 lived longer than those that were not. This finding represents the first
 demonstration that DGCs confer a fitness benefit, and supports the oldest
 hypothesis for the evolution of DGCs (which suggests that DGCs arose or
 are maintained to reduce respiratory water loss) as we also reveal reduced
 water loss (both respiratory and total) in cockroaches exhibiting
 discontinuous gas exchange.
description: Dryad Data Archiving
 Natalie Schimpf EvolutionAll data collected in
 the laboratory and worked in Excel.
DOI: 10.5061/dryad.26031
title: Data from: Effects of multi-generational stress exposure and offspring environment on the expression and persistence of transgenerational effects in Arabidopsis thaliana

description: Plant phenotypes can be affected by environments experienced by their
 parents. Parental environmental effects are reported for the first
 offspring generation and some studies showed persisting environmental
 effects in second and further offspring generations. However, the
 expression of these transgenerational effects proved context-dependent and
 their reproducibility can be low. Here we study the context-dependency of
 transgenerational effects by evaluating parental and transgenerational
 effects under a range of parental induction and offspring evaluation
 conditions. We systematically evaluated two factors that can influence the
 expression of transgenerational effects: single- versus
 multiple-generation exposure and offspring environment. For this purpose,
 we exposed a single homozygous Arabidopsis thaliana Col-0 line to salt
 stress for up to three generations and evaluated offspring performance
 under control and salt conditions in a climate chamber and in a natural
 environment. Parental as well as transgenerational effects were observed
 in almost all traits and all environments and traced back as far as
 great-grandparental environments. The length of exposure exerted strong
 effects; multiple-generation exposure often reduced the expression of the
 parental effect compared to single-generation exposure. Furthermore, the
 expression of transgenerational effects strongly depended on offspring
 environment for rosette diameter and flowering time, with opposite effects
 observed in field and greenhouse evaluation environments. Our results
 provide important new insights into the occurrence of transgenerational
 effects and contribute to a better understanding of the context-dependency
 of these effects.
description: DataFieldandClimatechamberPhenotype data of A. thaliana plants grown in either a field environment or in a climate chamber environment. In the climate chamber environment plants were grown under control conditions or salt stress.
DOI: 10.5061/dryad.77tm17st
title: Data from: Genetic structure in a fragmented Northern Hemisphere rainforest: large effective sizes and high connectivity among populations of the epiphytic lichen Lobaria pulmonaria

description: An extraordinary diversity of epiphytic lichens is found in the boreal
 rainforest of central Norway, the highest-latitude rainforest in the
 world. These rainforest relicts are located in ravine systems, and clear
 cutting has increased the distance between remaining patches. We
 hypothesized that the relatively small lichen populations in the remaining
 forest stands have suffered a depletion of genetic diversity through
 bottlenecks and founder events. In order to test this hypothesis we
 assessed genetic diversity and structure in populations of the tripartite
 lichen Lobaria pulmonaria using eight SSR loci. We sampled thalli growing
 on Picea abies branches and propagules deposited in snow at three
 localities. Contrary to expectations, we found high genetic diversity in
 lichen and snow samples, and high effective sizes of the studied
 populations. Also, limited genetic differentiation between populations,
 high historical migration rates, and a high proportion of first generation
 immigrants were estimated, implying high connectivity across distances
 &lt;30 km. Almost all genetic variation was due to variation within
 sites; spatial genetic structures within populations were absent or
 appeared on small scales (5–10 m). The high genetic diversity in the
 remaining old boreal rainforests shows that even relict forest patches
 might be suitable for conservation of genetic diversity.
description: Lobaria_raw data file
 for DryadThis file present the
 results of genetic analyses of Lobaria pulmonaria sampled in three
 different localities in boreal rainforests of central
 Norway.
DOI: 10.5061/dryad.cv6n5
title: Data from: Like a pig out of water: seaborne spread of domestic pigs in Southern Italy and Sardinia during the Bronze and Iron Ages

description: Southern Italy has a long history of human occupation and passage of
 different cultures since the Early Holocene. Repeated, ancient
 introductions of pigs in several geographic areas in Europe make it
 difficult to understand pig translocation and domestication in Italy. The
 archeozoological record may provide fundamental information on this, hence
 shedding light on peopling and on trading among different ancient cultures
 in the Mediterranean. Yet, because of the scanty nature of the fossil
 record, ancient remains from human-associated animals are somewhat rare.
 Fortunately, ancient DNA analysis as applied to domestic species proved to
 be a powerful tool in revealing human migrations. Herein, we analyzed
 80-bp fragment of mitochondrial DNA control region from 27 Sus scrofa
 ancient samples retrieved from Southern Italian and Sardinian
 archeological sites, spanning in age from the Mesolithic to the Roman
 period. Our results surprisingly indicate the presence of the Near Eastern
 haplotype Y1 on both Italy’s major islands (Sardinia and Sicily) during
 the Bronze Age, suggesting the seaborne transportation of domestic pigs by
 humans at least during 1600–1300 BC. The presence of the Italian E2 clade
 in domestic contexts shows that the indigenous wild boar was effectively
 domesticated or incorporated into domestic stocks in Southern Italy during
 the Bronze Age, although the E2 haplotype has never been found in modern
 domestic breeds. Pigs belonging to the endemic E2 clade were thus traded
 between the Peninsula and Sardinia by the end of the second millennium BC
 and this genetic signature is still detected in Sardinian feral pigs.
description: Supporting
 InformationGENBANK accession
 numbers and sequences, measurements of individual
 specimens
DOI: 10.5061/dryad.n6sk3
title: Data from: Pheromone diversification and age-dependent behavioural plasticity decrease interspecific mating costs in Nasonia

description: Interspecific mating can cause severe fitness costs due to the fact that
 hybrids are often non-viable or less fit. Thus, theory predicts the
 selection of traits that lessen reproductive interactions between closely
 related sympatric species. Males of the parasitic wasp Nasonia vitripennis
 differ from all other Nasonia species by an additional sex pheromone
 component, but the ecological selective forces underlying this pheromone
 diversification are unknown. Here we present data from lab experiments
 suggesting that costly interspecific sexual interactions with the
 sympatric species N. giraulti might have been responsible for the
 pheromone evolution and some courtship-related behavioural adaptations in
 N. vitripennis. Most N. giraulti females are inseminated already within
 the host, but N. giraulti males still invest in costly sex pheromones
 after emergence. Furthermore, they do not discriminate between N.
 vitripennis females and conspecifics during courtship. Therefore, N.
 vitripennis females, most of which emerge as virgins, face the risk of
 mating with N. giraulti resulting in costly all-male broods due to
 Wolbachia-induced cytoplasmic incompatibility. As a counter adaptation,
 young N. vitripennis females discriminate against N. giraulti males using
 the more complex conspecific sex pheromone and reject most of them during
 courtship. With increasing age, however, N. vitripennis females become
 less choosy, but often compensate mating errors by re-mating with a
 conspecific. By doing so, they can principally avoid suboptimal offspring
 sex ratios, but a microcosm experiment suggests that under more natural
 conditions N. vitripennis females cannot completely avoid fitness costs
 due to heterospecific mating. Our study provides support for the
 hypothesis that communication interference of closely related sympatric
 species using similar sexual signals can generate selective pressures that
 lead to their divergence.
description: Experimental
 dataThe file contains all
 data used for statistical analysis and to produce Figures 1-6 and Figures
 S2-S3 of the paper.Raw data Plos
 One.xlsx
DOI: 10.5061/dryad.km3qd
title: Data from: Immune-challenged fish up-regulate their metabolic scope to support locomotion

description: Energy-based trade-offs occur when investment in one fitness-related trait
 diverts energy away from other traits. The extent to which such trade-offs
 are shaped by limits on the rate of conversion of energy ingested in food
 (e.g. carbohydrates) into chemical energy (ATP) by oxidative metabolism
 rather than by the amount of food ingested in the first place is, however,
 unclear. Here we tested whether the ATP required for mounting an immune
 response will lead to a trade-off with ATP available for physical activity
 in mosquitofish (Gambusia holbrooki). To this end, we challenged fish
 either with lipopolysaccharide (LPS) from E. coli or with Sheep Red Blood
 Cells (SRBC), and measured oxygen consumption at rest and during swimming
 at maximum speed 24h, 48h and 7 days post-challenge in order to estimate
 metabolic rates. Relative to saline-injected controls, only LPS-injected
 fish showed a significantly greater resting metabolic rate two days
 post-challenge and significantly higher maximal metabolic rates two and
 seven days post-challenge. This resulted in a significantly greater
 metabolic scope two days post-challenge, with LPS-fish transiently
 overcompensating by increasing maximal ATP production more than would be
 required for swimming in the absence of an immune challenge.
 LPS-challenged fish therefore increased their production of ATP to
 compensate physiologically for the energetic requirements of immune
 functioning. This response would avoid ATP shortages and allow fish to
 engage in an aerobically-challenging activity (swimming) even when
 simultaneously mounting an immune response. Nevertheless, relative to
 controls, both LPS- and SRBC-fish displayed reduced body mass gain one
 week post-injection, and LPS-fish actually lost mass. The concomitant
 increase in metabolic scope and reduced body mass gain of LPS-challenged
 fish indicates that immune-associated trade-offs are not likely to be
 shaped by limited oxidative metabolic capacities, but may instead result
 from limitations in the acquisition, assimilation or efficient use of
 resources.
description: PONE-D-16-04036R2Resting and maximal metabolic rates, and metabolic scope of LPS, SRBC, PBS-challenged mosquitofish
DOI: 10.5061/dryad.6bn74m7
title: Data from: Maternal immunization increases nestling energy expenditure, immune function, and fledging success in a passerine bird

description: Female birds transfer maternally-derived antibodies (matAb) to their
 nestlings, via the egg yolk. These antibodies are thought to provide
 passive protection, and allow nestlings to avoid the costs associated with
 mounting an innate immune response. To test whether there is an energetic
 benefit to nestlings of receiving matAb, we challenged adult female tree
 swallows (Tachycineta bicolor) prior to clutch initiation with either
 lipopolysaccharide (LPS) or saline (Control). Following hatching, one half
 of each females nestlings were immunized on day 8 post-hatch with LPS or
 saline, and for 4-hrs post immunization nestling metabolic rate (MR) was
 measured. There was no difference in either LPS-reactive antibodies or
 total Ig levels between offspring of immunized and non-immunized mothers
 on day 6 or 14 post-hatch, possibly reflecting a relatively short
 half-life of matAbs in altricial birds. Additionally, we found no evidence
 that nestlings from LPS-immunized mothers could avoid the
 growth-suppression that may result from activation of an inflammatory
 response. Unexpectedly, we found that control-nestlings from LPS-mothers
 had higher resting MR than control-nestlings of control-mothers. We
 attribute the increased MR to the costs associated with a general
 nonspecific enhancement of immune function in nestlings from LPS-immunized
 mothers. Consistent with enhanced immune function, nestlings of immunized
 mothers had a more robust inflammatory response to phytohaemagglutinin,
 and higher fledging success. Our results suggest maternal antigen exposure
 pre-laying can result in increased fitness for both mothers and offspring,
 depending on food availability.
description: Tree swallow maternal
 immunization dataTree swallow maternal
 immunization hatching success dataTree swallow maternal
 immunization fledging success data
DOI: 10.5061/dryad.504g588
title: Data from: Reconstruction of the regional summer ground surface temperature in the permafrost region of Northeast China from 1587 to 2008

description: To extend the historical temperature record in the permafrost region of
 northeast China, we reconstructed the regional ground surface temperature
 (GST) for the past four centuries based on a network of Dahurian larch
 (Larix gmelinii Rupr.) tree ring width chronologies. Seven standard tree
 ring chronologies, which correlated well with each other, were averaged to
 create a regional mean chronology. The GST was the major limiting factor
 for tree growth in this region. The optimum range of GSTs was from 30 May
 to 26 August (summer GST), identified by combining the days on which tree
 growth was strongly influenced by the daily GST data. The summer GST was
 significantly correlated with the regional mean chronology (r=0.704,
 p&lt;0.001) over the common period 1971–2008 and was reconstructed for
 the period 1587–2008. The reconstructed GST accounted for 49.4% of the
 actual variance in the GST over the period 1971–2008 and captured four
 warm periods (1597–1603, 1716–1723, 1781–1788, and 1925–1929) and three
 cold periods (1639–1647, 1686–1711, and 1799–1805). The reconstructed GST
 was consistent with the northern hemisphere temperature in the Little Ice
 Age, and the warming rate from 1857 to 2008 was similar to a previously
 reported temperature reconstruction in the Xiao Xing’an Mountains. The low
 frequency of the reconstructed GST was well matched with that of the
 permafrost thawing depth. The reconstructed GST represents the longest
 temperature record in this study region and may be used as a reference for
 the permafrost thawing depth.
description: Zhang et al. 2018 GST
 reconstrcution for past four centuriesReconstructed summer
 ground surface temperature for the northeast China from 1587 to 2008 (430
 years).
DOI: 10.5061/dryad.33553
title: Data from: Differences in larval nutritional requirements and female oviposition preference reflect the order of fruit colonization of Zaprionus indianus and Drosophila simulans

description: Species coexist using the same nutritional resource by partitioning it
 either in space or time, but few studies explore how species-specific
 nutritional requirements allow partitioning. Zaprionus indianus and
 Drosophila simulans co-exist in figs by invading the fruit at different
 stages; Z. indianus colonizes ripe figs, whereas D. simulans oviposits in
 decaying fruit. Larvae feed on yeast growing on the fruit, which serves as
 their primary protein source. Because yeast populations increase as fruit
 decays, we find that ripe fruit has lower protein content than rotting
 fruit. Therefore, we hypothesized that Z. indianus and D. simulans larvae
 differ in their dietary requirements for protein. We used nutritional
 geometry to assess the effects of protein and carbohydrate concentration
 in the larval diet on life history characters in both species. Survival,
 development time, and ovariole number respond differently to the
 composition of the larval diet, with Z. indianus generally performing
 better across a wider range of protein concentrations. Correspondingly, we
 found that Z. indianus females preferred to lay eggs on low protein foods,
 while D. simulans females chose higher protein foods for oviposition when
 competing with Z. indianus. We propose the different nutritional
 requirements and oviposition preference of these two species allows them
 to temporally partition their habitat.
description: Data&ScriptsAll data sets and R scripts for 1) the change in the protein and sugar concentration of figs over time (FigData), 2) the response surfaces for survival, development time, and ovariole number according to the protein and carbohydrate content of the diet for Zaprionus indianus and Drosophila simulans (NutritionalGeometry), and 3) the oviposition preference for Zaprionus indianus and Drosophila simulans (Oviposition).
DOI: 10.5061/dryad.92h23
title: Data from: Clonality, genetic diversity, and support for the diversifying selection hypothesis, in natural populations of a flower-living yeast

description: Vast amounts of effort have been devoted to investigate patterns of
 genetic diversity and structuring in plants and animals, but similar
 information is scarce for organisms of other kingdoms. The study of the
 genetic structure of natural populations of wild yeasts can provide
 insights on the ecological and genetic correlates of clonality, and on the
 generality of recent hypotheses postulating that microbial populations
 lack the potential for genetic divergence and allopatric speciation.
 Ninety-one isolates of the flower-living yeast Metschnikowia gruessii from
 southeastern Spain were DNA fingerprinted using AFLP markers. Genetic
 diversity and structuring was investigated with band-based methods and
 model- and nonmodel-based clustering. Linkage disequilibrium tests were
 used to assess reproduction mode. Microsite-dependent, diversifying
 selection was tested by comparing genetic characteristics of isolates from
 bumble bee vectors and different floral microsites. AFLP polymorphism
 (91%) and genotypic diversity were very high. Genetic diversity was
 spatially structured, as shown by AMOVA (Φst = 0.155) and clustering. The
 null hypothesis of random mating was rejected, clonality seeming the
 prevailing reproductive mode in the populations studied. Genetic diversity
 of isolates declined from bumble bee mouthparths to floral microsites, and
 frequency of five AFLP markers varied significantly across floral
 microsites, thus supporting the hypothesis of diversifying selection on
 clonal lineages. Wild populations of clonal fungal microbes can exhibit
 levels of genetic diversity and spatial structuring that are not
 singularly different from those shown by sexually reproducing plants or
 animals. Microsite-dependent, divergent selection can maintain high local
 and regional genetic diversity in microbial populations despite extensive
 clonality.
description: Metschnikowia_gruessii_AFLP_fingerprintsAFLP profiles for 91 isolates of the flower-living yeast Metschnikowia gruessii from the Sierra de Cazorla, southeastern Spain. See Readme.txt file for the collection site, host plant and sampling microsite of each isolate.