cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.db322
title: Data from: Resource quality affects weapon and testis size and the ability of these traits to respond to selection in the leaf-footed cactus bug, Narnia femorata

description: The size of weapons and testes can be central to male reproductive
 success. Yet, the expression of these traits is often extremely variable.
 Studies are needed that take a more complete organism perspective,
 investigating the sources of variation in both traits simultaneously and
 using developmental conditions that mimic those in nature. In this study,
 we investigated the components of variation in weapon and testis sizes
 using the leaf-footed cactus bug, Narnia femorata (Hemiptera: Coreidae) on
 three natural developmental diets. We show that the developmental diet has
 profound effects on both weapon and testis expression and scaling.
 Intriguingly, males in the medium-quality diet express large weapons but
 have relatively tiny testes, suggesting complex allocation decisions. We
 also find that heritability, evolvability, and additive genetic variation
 are highest in the high-quality diet for testis and body mass. This result
 suggests that these traits may have an enhanced ability to respond to
 selection during a small window of time each year when this diet is
 available. Taken together, these results illustrate that normal, seasonal
 fluctuations in the nutritional environment may play a large role in the
 expression of sexually selected traits and the ability of these traits to
 respond to selection.
description: Sasson et al. 2016
 dataContains bug
 identification and morphometric data.
DOI: 10.5061/dryad.103h8
title: Data from: Lack of evolution in a leaf beetle that lives on two contrasting host plants

description: The interactions between plant-eating insects and their hosts have shaped
 both the insects and the plants, driving evolution of plant defenses and
 insect specialization. The leaf beetle Trirhabda eriodictyonis
 (Chrysomelidae) lives on two shrubs with differing defenses: Eriodictyon
 crassifolium has hairy leaves, whereas E. trichocalyx has resinous leaves.
 We tested whether these beetles have differentiated onto the two host
 plants, and if not, whether the beetles prefer the better host plant and
 prefer mates who are from that host plant. In feeding tests, adult beetles
 strongly preferred eating E. trichocalyx regardless of which host they
 came from. In addition, females laid more eggs if they ate E. trichocalyx
 than E. crassifolium. So, E. trichocalyx is generally the better host.
 However, beetle mate preference was not in line with food choice. Males
 did not prefer to mate with females from E. trichocalyx. Females from E.
 crassifolium did prefer males from E. trichocalyx over males from E.
 crassifolium, but did not lay more eggs as a result of these matings. We
 conclude that the beetle populations we studied have not differentiated
 based on their host plants and may not have even adapted to the better
 host. Although to humans these host plant defenses differ dramatically,
 signs that they have caused evolution in the beetles are lacking. The case
 of T. eriodictyonis stands counter to many other studies that have seen
 the differentiation of ecotypes and/or adaptive coordination of an
 herbivore's life cycle based on host plant differences.
description: Feeding, mating, and
 fecundity data and analysis for T. eriodictyonisOriginal data collected
 by Katherine Gould. Excel 2013 file (.xlsx). Clarifying notes can be found
 withing the spreadsheets. In general, Et refers to Eriodictyon trichocalyx
 and Ec refers to Eriodictyon crassifolium. Mating treatments (e.g. Et-Ec)
 use male's plant then female's plant code.GouldWilson-beetledata-2013-14.xlsx
DOI: 10.5061/dryad.7r24c
title: Data from: Sex-specific mitonuclear epistasis and the evolution of mitochondrial bioenergetics, ageing and life history in seed beetles

description: The role of mitochondrial DNA for the evolution of life history traits
 remains debated. We examined mitonuclear effects on the activity of the
 multi-subunit complex of the electron transport chain (ETC) involved in
 oxidative phosphorylation (OXPHOS) across lines of the seed beetle
 Acanthoscelides obtectus, selected for a short (E) or a long (L) life for
 more than &gt;160 generations. We constructed and phenotyped
 mitonuclear introgression lines, which allowed us to assess the
 independent effects of the evolutionary history of the nuclear and the
 mitochondrial genome. The nuclear genome was responsible for the largest
 share of divergence seen in ageing. However, the mitochondrial genome also
 had sizeable effects, which were sex-specific and expressed primarily as
 epistatic interactions with the nuclear genome. The effects of mitonuclear
 disruption were largely consistent with mitonuclear coadaptation.
 Variation in ETC activity explained a large proportion of variance in
 ageing and life history traits and this multivariate relationship differed
 somewhat between the sexes. In conclusion, mitonuclear epistasis has
 played an important role in the laboratory evolution of ETC complex
 activity, ageing and life histories and these are closely associated. The
 mitonuclear architecture of evolved differences in life history traits and
 mitochondrial bioenergetics was sex-specific.
description: ETC file for
 DryadRaw data for life span
 and ETC activity
DOI: 10.5061/dryad.h9022
title: Data from: Local adaptation (mostly) remains local: reassessing environmental associations of climate-related candidate SNPs in Arabidopsis halleri

description: Numerous landscape genomic studies have identified single-nucleotide
 polymorphisms (SNPs) and genes potentially involved in local adaptation.
 Rarely, it has been explicitly evaluated whether these environmental
 associations also hold true beyond the populations studied. We tested
 whether putatively adaptive SNPs in Arabidopsis halleri (Brassicaceae),
 characterized in a previous study investigating local adaptation to a
 highly heterogeneous environment, show the same environmental associations
 in an independent, geographically enlarged set of 18 populations. We
 analysed new SNP data of 444 plants with the same methodology (partial
 Mantel tests, PMTs) as in the original study and additionally with a
 latent factor mixed model (LFMM) approach. Of the 74 candidate SNPs, 41%
 (PMTs) and 51% (LFMM) were associated with environmental factors in the
 independent data set. However, only 5% (PMTs) and 15% (LFMM) of the
 associations showed the same environment–allele relationships as in the
 original study. In total, we found 11 genes (31%) containing the same
 association in the original and independent data set. These can be
 considered prime candidate genes for environmental adaptation at a broader
 geographical scale. Our results suggest that selection pressures in highly
 heterogeneous alpine environments vary locally and signatures of selection
 are likely to be population-specific. Thus, genotype-by-environment
 interactions underlying adaptation are more heterogeneous and complex than
 is often assumed, which might represent a problem when testing for
 adaptation at specific loci.
description: nSSR and SNP
 genotypesnSSR and SNP
 genotypesrellstab_raw_data.xlsx
DOI: 10.5061/dryad.52fh7
title: Data from: Glutamatergic drive along the septo-temporal axis of hippocampus boosts prelimbic oscillations in the neonatal mouse

description: The long-range coupling within prefrontal-hippocampal networks that
 account for cognitive performance emerges early in life. The discontinuous
 hippocampal theta bursts have been proposed to drive the generation of
 neonatal prefrontal oscillations, yet the cellular substrate of these
 early interactions is still unresolved. Here, we selectively target
 optogenetic manipulation of glutamatergic projection neurons in the CA1
 area of either dorsal or intermediate/ventral hippocampus at neonatal age
 to elucidate their contribution to the emergence of prefrontal oscillatory
 entrainment. We show that despite stronger theta and ripples power in
 dorsal hippocampus, the prefrontal cortex is mainly coupled with
 intermediate/ventral hippocampus by phase-locking of neuronal firing via
 dense direct axonal projections. Theta band-confined activation by light
 of pyramidal neurons in intermediate/ventral but not dorsal CA1 that were
 transfected by in utero electroporation with high-efficiency
 channelrhodopsin boosts prefrontal oscillations. Our data causally
 elucidates the cellular origin of the long-range coupling in the
 developing brain.
description: Figure
 1BRaw
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 1DRaw
 data for figure 1DFigure
 1FRaw
 data for figure 1FFigure
 1HRaw
 data for figure 1HFigure
 1JRaw
 data for figure 1JFigure
 2B(ii)Raw data for figure
 2B(ii)Figure
 2CRaw
 data for figure 2CFigure
 3CRaw
 data for figure 3CFigure
 4ARaw
 data for figure 4AFigure
 5D(ii)Raw data for figure
 5D(ii)Figure
 6B(ii)Raw data for figure
 6B(ii)Figure
 6Cii)Raw data for figure
 6C(ii)
DOI: 10.5061/dryad.4fq25
title: Data from: Population differentiation in common walnut (Juglans regia L.) across major parts of its native range - insights from molecular and morphometric data

description: Juglans regia is an economically highly important species for fruit and
 wood production in the warm temperate and subtropical zones of the
 Northern Hemisphere. Besides the natural influence of climatic and
 geomorphological barriers, its genetic structure has been strongly
 modified by humans and the population history is still unclear. For this
 reason, we investigated mainly natural walnut populations across the
 Eurasian continent on a molecular (44 populations, 581 trees) and
 morphometric level (23 populations, 1391 ripe nuts). Population genetic
 diversity and differentiation were examined by using 7 microsatellite
 loci. Morphometric characteristics of the nuts (mainly roundness index and
 nut density) were used to estimate trait variation and population
 differentiation. Highest allelic richness Rs12 = 7.05 was observed in a
 Pakistani and the lowest value Rs12 = 3.04 in a Kyrgyz population. The
 genetic differentiation among populations was high (FST = 0.217; RST =
 0.530) indicating a strong phylogeographic pattern. While variation of the
 roundness index within single populations was high, this trait neither
 differentiated geographical regions nor was it associated to genetic
 clusters. Approximated QST based on this trait equalled FST, while
 approximated QST based on nut density considerably exceeded FST,
 indicating selection. Nut density was moderately correlated with altitude,
 latitude, and longitude, and differentiated populations according to their
 origin. Pakistani and Indian populations showed highest nut densities.
 These South Asian populations contain putatively ancestral nut forms,
 which probably have been lost in other populations as a consequence of
 human selection.
description: Juglans_genotypes_DRYADSheet genotypes: Individual-ID, Population-ID, SSR genotypes for 7 loci; sheet quanttraits: Individual-ID, Population-ID, morphometric data for 7 traitsJuglans_genotypes_quanttrais_DRYAD.xlsx
DOI: 10.5061/dryad.2pk34
title: Data from: Genetic population structure of the round whitefish (Prosopium cylindraceum) in North America: multiple markers reveal glacial refugia and regional subdivision.

description: Round whitefish (Prosopium cylindraceum) have a broad, disjunct range
 across northern North America and Eurasia, and little is known about their
 genetic population structure. We performed genetic analyses of round
 whitefish from 17 sites across its range using nine microsatellites, two
 mitochondrial DNA (mtDNA) loci, and 4918 to 8835 single-nucleotide
 polymorphism (SNP) loci. Our analyses identified deep phylogenetic
 division between eastern and western portions of the range, likely
 indicative of origins from at least two separate Pleistocene glacial
 refugia. Regionally, microsatellites and SNPs identified congruent
 patterns in subdivision, and population structure was consistent with
 expectations based on hydrologic connectivity. Within the Laurentian Great
 Lakes, Lake Huron and Lake Ontario were identified as key areas of
 interest. Lake Huron appears to be a contemporary source population for
 several other Great Lakes, and Lake Ontario contains a genetically
 discrete group of round whitefish. In all cases, multiple genetic markers
 yielded similar patterns, but SNPs offered substantially enhanced
 resolution. We conclude that round whitefish have population subdivision
 on several scales important for understanding their evolutionary history
 and conservation planning.
description: Genepop 9 loci all
 sitesRound whitefish
 genotypes for 9 microsatellite loci from Morgan et al.
 2017Morgan et al. 2017 -
 Location dataPopulation data for
 round whitefish samplesMorgan et al. 2017 - Population
 information.xlsxSNP046_round_whitefish_192_indexes_HS100NEXTRAD run 1 (part 1 of 2)NEXTRAD run 1 - 1of2.zipNEXTRAD run 1 (part 2 of 2)NEXTRAD run 1 - 2of2.zipNEXTRAD run 2 (part 1 of 2)NEXTRAD run 2 - 1of2.zipNEXTRAD run 2 (part 2 of 2)NEXTRAD run 2 - 2of2.zip
DOI: 10.5061/dryad.39np8rd7
title: Data from: Experimental tests of sex allocation theory with two species of simultaneously hermaphroditic acorn barnacles

description: Sex allocation theory for simultaneous hermaphrodites predicts increases
 in relative allocation to male-specific function as competition for
 fertilizations increases. Theoretical models developed specifically for
 competing acorn barnacles predict that the proportional allocation to male
 function increases towards an asymptote of 50% as the number of
 competitors for fertilizations increases. Experimental manipulations were
 used to investigate how mate competition affected both relative and
 absolute allocation to the sex functions for two species of acorn
 barnacle: Semibalanus balanoides and Balanus glandula. The ratio of male
 to female allocation did not increase with the number of competitors for
 either species. However, both species showed increased allocation to male
 function (estimated as total mass of sex-specific tissues) with increased
 crowding. Allocation to female function seemed to be limited by other
 factors and did not vary with mating group size as predicted. Allocation
 to male and female function were both positively related to body size, but
 a trade-off between male and female function, a key assumption of prior
 models, was not observed.
description: Archive-DataExcel file containing data from Semibalanus balanoides collected from Long Island, NY and Balanus glandula collected from San Juan Island, WA. Data includes Block ID, Block number, site name, number treatment, density treatment, overall treatment, test volume, egg mass (F), teste mass, penis mass, total male mass (M), the relative proportion of male mass (Q), and transformed values of numerical data.
DOI: 10.5061/dryad.30r6p
title: Data from: A recently transferred cluster of bacterial genes in Trichomonas vaginalis –lateral gene transfer and the fate of acquired genes.

description: Background: Lateral Gene Transfer (LGT) has recently gained recognition as
 an important contributor to some eukaryote proteomes, but the mechanisms
 of acquisition and fixation in eukaryotic genomes are still uncertain. A
 previously defined norm for LGTs in microbial eukaryotes states that the
 majority are genes involved in metabolism, the LGTs are typically
 localized one by one, surrounded by vertically inherited genes on the
 chromosome, and phylogenetics shows that a broad collection of bacterial
 lineages have contributed to the transferome. Results: A unique 34 kbp
 long fragment with 27 clustered genes (TvLF) of prokaryote origin was
 identified in the sequenced genome of the protozoan parasite Trichomonas
 vaginalis. Using a PCR based approach we confirmed the presence of the
 orthologous fragment in four additional T. vaginalis strains. Detailed
 sequence analyses unambiguously suggest that TvLF is the result of one
 single, recent LGT event. The proposed donor is a close relative to the
 firmicute bacterium Peptoniphilus harei. High nucleotide sequence
 similarity between T. vaginalis strains, as well as to P. harei, and the
 absence of homologs in other Trichomonas species, suggests that the
 transfer event took place after the radiation of the genus Trichomonas.
 Some genes have undergone pseudogenization and degradation, indicating
 that they may not be retained in the future. Functional annotations reveal
 that genes involved in informational processes are particularly prone to
 degradation. Conclusions: We conclude that, although the majority of
 eukaryote LGTs are single gene occurrences, they may be acquired in
 clusters of several genes that are subsequently cleansed of evolutionarily
 less advantageous genes.
description: TvLFphylogenetic_dataFiles underlying the phylogenetic trees shown in Additional File 2.
DOI: 10.5061/dryad.4gb6n541
title: Data from: Quantifying population divergence on short timescales

description: Quantifying the contribution of the various processes that influence
 population genetic structure is important, but difficult. One of the
 reasons is that no single measure appropriately quantifies all aspects of
 genetic structure. An increasing number of studies is analyzing population
 structure using the statistic D, which measures genetic differentiation,
 next to GST, which is the standardized variance in allele frequencies
 among populations. Few studies have evaluated which statistic is most
 appropriate in particular situations. In this study, we evaluated which
 index is more suitable in quantifying postglacial divergence between
 three-spined stickleback (Gasterosteus aculeatus) populations from Western
 Europe. Population structure on this short timescale (10, 000 generations)
 is likely shaped by colonization history, followed by migration and drift.
 Using microsatellite markers and anticipating that D and GST might have
 different capacities to reveal these processes, we evaluated population
 structure at two levels: 1) between lowland and upland populations, aiming
 to infer historical processes; and 2) among upland populations, aiming to
 quantify contemporary processes. In the first case, only D revealed clear
 clusters of populations, putatively indicative of population ancestry. In
 the second case, only GST was indicative for the balance between migration
 and drift. Simulations of colonization and subsequent divergence in a
 hierarchical stepping stone model confirmed this discrepancy, which
 becomes particularly strong for markers with moderate to high mutation
 rates. We conclude that on short timescales, and across strong clines in
 population size, D is useful to infer colonization history, whereas GST is
 sensitive for more recent demographic events.
description: Raeymaekers et
 al-MolEcol-2012 D vs GstSheet 1: microsatellite
 data (6 loci) of 28 lowland and upland samples collected in 2004. Sheet 2:
 microsatellite data (14 loci) of 18 lowland and upland samples collected
 in 2004. Sheet 3: microsatellite data (6 loci) of 21 upland samples
 collected in 2002.
DOI: 10.5061/dryad.k903r
title: Data from: Male mate choice in the Trinidadian guppy is influenced by the phenotype of audience sexual rivals

description: In populations with male mate-choice copying, males may mitigate their
 risk of sexual competition by reducing their preference for a particular
 female in the presence of sexual rivals (audience). Because of the cost of
 missed mating opportunities from such an audience effect, males should
 reduce their mating preference to a greater extent in the presence of more
 sexually competitive rivals compared with less competitive ones. We tested
 this hypothesis using the Trinidadian guppy (Poecilia reticulata). We
 compared a focal male’s baseline mating preference for either of 2
 stimulus females, which differed in overall body size, in the absence of
 any sexual rival to his preference for the same females in the presence of
 a sexual rival using dichotomous-choice tests. Focal and audience males
 differed in body length and proportion of their body covered in orange and
 black pigmentation. In the presence of a larger rival, focal males
 exhibited a greater reduction in preference for their initially preferred
 female compared to focal males in the presence of a smaller rival,
 irrespective of whether the latter male was more or less ornamented than
 the focal. The strength of the initial mating preference of focal males
 and the magnitude of the audience effect were significantly positively
 correlated when the audience male was larger than the focal male. Male
 guppies are thus sensitive to the phenotype of nearby males and alter
 their preference for a particular mate to a greater extent in the presence
 of relatively larger eavesdropping males compared to smaller ones.
description: Table 1
 dataExcel data file
 supporting the summary statistics shown in Table 1 of Auld et al.
 paperTable1
 data.xlsxFigure 2
 dataExcel data file
 supporting the results depicted in Figure 2 of Auld et al.
 paper.Figure 3
 dataExcel data file
 supporting the results depicted in Figure 3 of Auld et al.
 paper.Figure 4
 dataExcel data file
 supporting the results depicted in Figure 4 of Auld et al.
 paper.