cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5c8n1
title: Data from: Adaptive differentiation in floral traits in the presence of high gene flow in scarlet gilia (Ipomopsis aggregata)

description: Plant-pollinator interactions are thought to be major drivers of floral
 trait diversity. However, the relative importance of divergent
 pollinator-mediated selection versus neutral processes in floral character
 evolution has rarely been explored. We tested for adaptive floral trait
 evolution by comparing differentiation at neutral genetic loci to
 differentiation at quantitative floral traits in a putative Ipomopsis
 aggregata hybrid zone. Typical I. aggregata subsp. candida displays
 slender white tubular flowers that are typical of flowers pollinated by
 hawkmoths and subsp. collina displays robust red tubular flowers typical
 of flowers pollinated by hummingbirds; yet hybrid flower morphs are
 abundant across the East Slope of the Colorado Rockies. We estimated
 genetic differentiation (FST) for nuclear and chloroplast microsatellite
 loci and used a half-sib design to calculate quantitative trait divergence
 (QST) from collection sites across the morphological hybrid zone. We found
 little evidence for population structure and estimated mean FST to be
 0.032. QST values for several floral traits including corolla tube length
 and width, color, and nectar volume were large and significantly greater
 than mean FST. We performed multivariate comparisons of neutral loci to
 genetic correlations within and between populations and found a strong
 signal for divergent selection, suggesting that specific combinations of
 floral display and reward traits may be the targets of selection. Our
 results show little support for historical subspecies categories, yet
 floral traits are more diverged than expected due to drift alone.
 Non-neutral divergence for multivariate quantitative traits suggests that
 selection by pollinators is maintaining a correlation between display and
 reward traits.
description: qst_dataExcel file with three datasheets. Phenotype contains the data used to calculate Qst for each floral trait. Pedigree contain half-sib family information. Genotype contains microsatellite data used to calculate Fst.
DOI: 10.5061/dryad.244b8
title: Data from: Genetic variation and structure in the neotropical tree, Manilkara zapota (L) P. Royen (Sapotaceae) used by the ancient Maya

description: Manilkara zapota is a tropical tree species that was used by the ancient
 Maya in construction of their temples and as a source for fruit. Although
 this has been supported by ethnographic and paleoethnobotanical data, we
 used genetic approaches to estimate variation and structure in modern
 populations of this neotropical tree species to discern if genetic
 patterns were consistent with earlier influences of ancient Maya
 management or if they could be explained by the natural history of the
 species. Nine microsatellite markers, consisting of seven novel markers
 and two markers identified in a related species, were used to characterize
 the genetic diversity and population genetic structure in three
 populations of M. zapota collected from reforested, historically urbanized
 ancient Maya ceremonial centers in Guatemala and Belize, from home gardens
 in Guatemala, and from a number of cultivars. Levels of genetic variation
 were slightly higher in forest populations (H O = 0.447) than in gardens
 (0.430) and cultivated varieties of M. zapota (0.351). We observed low but
 significant population substructuring (θ = 0.01) between sites 90 km
 apart, and minimal evidence of inbreeding. Substantial levels of genetic
 diversity with minimal genetic structure in M. zapota are consistent with
 movement of the ancient Maya as they possibly carried fruits and seedlings
 during immigration, but they may more likely reflect natural processes
 such as seed and pollen being dispersed widely throughout the tropical
 forest.
description: M_zapota_Data_GenAlExThis is the microsatellite allele information in GenAlEx format for all populations and individuals for Manilkara zapota.geographic coordinates for GenAlexThis is an Excel file formatting for GenAlEx that contains all the geographic coordinate information for each individual represented in the microsatellite file.
DOI: 10.5061/dryad.984b0528
title: Data from: Superiority of extra-pair offspring: maternal but not genetic effects as revealed by a mixed cross-fostering design

description: Extra-pair copulations (EPC) are a rule rather than an exception in
 socially monogamous birds. Despite widespread occurrences, the benefits of
 female infidelity remain illusive. Most attention has been paid to the
 possibility that females gain genetic benefits from EPC. Fitness
 comparison between maternal half-siblings is considered to be a defining
 test of this hypothesis. Recently it was shown that these comparisons may
 be confounded by within-brood maternal effects. One such effect may be the
 distribution of half-siblings in the laying order. This possibility is
 difficult to study since it would be necessary to detect from which egg
 the chick hatched. Here we used a new approach for egg-chick assignment.
 We cross-fostered eggs on an individual basis among a set of nests of the
 collared flycatcher Ficedula albicollis. After hatching, chicks were
 ascribed to mothers and therefore to individual eggs by molecular-genetic
 methods. Extra-pair young predominated early in the laying order. Under
 natural conditions, this should give them a competitive advantage over
 their half-siblings mediated by hatching asynchrony. However, we
 experimentally synchronized hatching. After this treatment extra-pair
 young did not outperform within-pair young in any studied trait including
 survival up to recruitment and several indicators of reproductive success
 and attractiveness. We obtained only modest sample size for the last two
 traits and did not test for extra-pair success of male offspring. Thus we
 cannot exclude the possibility of slight advantages of EPY during their
 adult phase of life. However, our data tentatively suggest that more
 likely reason for females’ EPCs is the insurance against the infertility
 of a social mate.
description: dataset
DOI: 10.5061/dryad.vb073
title: Data from: Social chromosome variants differentially affect queen determination and the survival of workers in the fire ant Solenopsis invicta

description: Intraspecific variation in social organization is common, yet the
 underlying causes are rarely known. An exception is the fire ant
 Solenopsis invicta in which the existence of two distinct forms of social
 colony organization is under the control of the two variants of a pair of
 social chromosomes, SB and Sb. Colonies containing exclusively SB/SB
 workers accept only one single queen and she must be SB/SB. By contrast,
 when colonies contain more than 10% of SB/Sb workers, they accept several
 queens but only SB/Sb queens. The variants of the social chromosome are
 associated with several additional important phenotypic differences,
 including the size, fecundity and dispersal strategies of queens,
 aggressiveness of workers, and sperm count in males. However, little is
 known about whether social chromosome variants affect fitness in other
 life stages. Here we perform experiments to determine whether differential
 selection occurs during development, and in adult workers. We find
 evidence that the Sb variant of the social chromosome increases the
 likelihood of female brood to develop into queens and that adult SB/Sb
 workers, the workers that cull SB/SB queens, are overrepresented in
 comparison to SB/SB workers. This demonstrates that supergenes such as the
 social chromosome can have complex effects on phenotypes at various stages
 of development.
description: Dryad_buechel et
 al
DOI: 10.5061/dryad.54n1q
title: Data from: Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary

description: Dromedaries have been fundamental to the development of human societies in
 arid landscapes and for long-distance trade across hostile hot terrains
 for 3,000 y. Today they continue to be an important livestock resource in
 marginal agro-ecological zones. However, the history of dromedary
 domestication and the influence of ancient trading networks on their
 genetic structure have remained elusive. We combined ancient DNA sequences
 of wild and early-domesticated dromedary samples from arid regions with
 nuclear microsatellite and mitochondrial genotype information from 1,083
 extant animals collected across the species’ range. We observe little
 phylogeographic signal in the modern population, indicative of extensive
 gene flow and virtually affecting all regions except East Africa, where
 dromedary populations have remained relatively isolated. In agreement with
 archaeological findings, we identify wild dromedaries from the southeast
 Arabian Peninsula among the founders of the domestic dromedary gene pool.
 Approximate Bayesian computations further support the “restocking from the
 wild” hypothesis, with an initial domestication followed by introgression
 from individuals from wild, now-extinct populations. Compared with other
 livestock, which show a long history of gene flow with their wild
 ancestors, we find a high initial diversity relative to the native
 distribution of the wild ancestor on the Arabian Peninsula and to the
 brief coexistence of early-domesticated and wild individuals. This study
 also demonstrates the potential to retrieve ancient DNA sequences from
 osseous remains excavated in hot and dry desert environments.
description: Drom970_17msatThis data matrix contains the raw data of 17 microsatellite loci genotyped in 970 dromedaries from 36 populations worldwide.Drom36pop_ind_Dryad.txt
DOI: 10.5061/dryad.fk5k3vs
title: Data from: Influence of haemosporidian infection status on structural and carotenoid‐based colouration in the blue tit (Cyanistes caeruleus)

description: Hypotheses postulating parasite-mediated mate choice intrinsically assume
 that parasitic infections deteriorate the quality of male ornamentation.
 Although this assumption has often been studied in the context of
 carotenoid-based colouration, only few studies investigated this with
 reference to structural feather colouration, which in many species plays a
 vital role in sexual selection. Here, using a three-years dataset from a
 wild blue tit (Cyanistes caeruleus) population, we examined the
 relationship between the haemosporidian infection status and the
 structural as well as the carotenoid-based colouration of adult birds.
 Furthermore, we investigated potential differences in the impact on
 feather colouration between two examined parasite genera: Plasmodium and
 Haemoproteus. For analysis of the feathers spectral reflectance we used
 both the tristimulus model and the avian tetrahedral colour space model,
 incorporating visual phenotype of the blue tit. Contrary to expectations
 we found that infected birds showed higher brightness, in both the
 structural and the carotenoid-based colours. We also found no differences
 in the feather colouration between birds infected with Plasmodium and
 Haemoproteus. Observed pattern might be best explained by the
 parasite-mediated selection hypothesis, as only individuals of superior
 quality should be able to survive the acute stage of infection and
 therefore they could produce more elaborate ornamental colouration.
description: Crown
 colourationData set on crown
 colouration and infection status of blue tits (Cyanistes caeruleus) from
 the nest-box population on the island of Gotland (Sweden; 57°01'N
 18°16'E). The table contain details on identity, sex, age, mass,
 tarsus length, status of parasitic infection and six colour metrics. All
 colour metrics were calculated using package pavo, in R
 software.Breast
 colourationData set on breast
 colouration and infection status of blue tits (Cyanistes caeruleus) from
 the nest-box population on the island of Gotland (Sweden; 57°01'N
 18°16'E). The table contain details on identity, sex, age, status of
 parasitic infection and six colour metrics. All colour metrics were
 calculated using package pavo, in R software.
DOI: 10.5061/dryad.7m644
title: Data from: Gene expression changes in male accessory glands during ageing are accompanied by reproductive decline in Drosophila melanogaster

description: Senescence is accompanied by loss of reproductive functions. Here we
 studied reproductive ageing in Drosophila melanogaster males and asked
 whether the expected decline in male reproductive success is due to
 diminished functionality of the male accessory gland. The male accessory
 gland produces the majority of seminal fluid proteins (SFPs) transferred
 to the female at mating. SFPs induce female post-mating changes and are
 key to male reproductive success. We measured age-dependent gene
 expression changes for five representative SFP genes in males from four
 different age groups ranging from one to six weeks after eclosion.
 Simultaneously, we also measured male reproductive success in post-mating
 traits mediated by transfer of these five SFPs. We found a decrease in
 male SFP gene expression with advancing age and an accompanying decline in
 male post-mating success. Hence, male reproductive senescence is
 associated with a decline in functionality of the male accessory gland.
 While overall individual SFP genes decrease in expression our results
 point towards the idea that the composition of an ejaculate might change
 with male age as the rate of change was variable for those five genes.
description: Cp values from the gene
 expression assayRaw_Cp_Values.xlsxBehavioural data on mating behaviourBehavioural_Data_Mating.txtBehavioural data on remating behaviourBehavioural_Data_Remating.txtData on male reproductive successBehavioural_Data_Reproduction.txtData on accessory gland protein replenishmentProtein_Data.txt
DOI: 10.5061/dryad.837d96j
title: Data from: Competition for mates and the improvement of nonsexual fitness

description: Competition for mates can be a major source of selection, not just on
 secondary sexual traits but across the genome. Mate competition
 strengthens selection on males via sexual selection, which typically
 favours healthy, vigorous individuals and, thus, all genetic variants that
 increase overall quality. However, recent studies suggest another major
 effect of mate competition that could influence genome-wide selection:
 sexual harassment by males can drastically weaken selection on quality in
 females. Because of these conflicting effects, the net effect of mate
 competition is uncertain, though perhaps not entirely unpredictable. We
 propose that the environment in which mate competition occurs mediates the
 importance of sexual selection relative to sexual conflict, and hence the
 net effect of mate competition on nonsexual fitness. To test this, we
 performed experimental evolution with 63 fruit fly populations adapting to
 novel larval conditions where each population was maintained with or
 without mate competition. In half the populations with mate competition,
 adults interacted in simple, high-density environments. In the remainder,
 adults interacted in more spatially complex environments in which
 male-induced harm is reduced. Populations evolving with mate competition
 in the complex environment adapted faster to novel larval environments
 than did populations evolving without mate competition or with mate
 competition in the simple environment. Moreover, mate competition in the
 complex environment caused a substantial reduction in inbreeding
 depression in egg-to-adult viability relative to the other two mating
 treatments. These results demonstrate that the mating environment has a
 substantial and predictable effect on nonsexual fitness through adaptation
 and purging.
description: inbreeding_dryadData from inbreeding depression assayviability_dryadData from adaptation assay
DOI: 10.5061/dryad.1847s
title: Data from: Variation in harbour porpoise activity in response to seismic survey noise

description: Animals exposed to anthropogenic disturbance make trade-offs between
 perceived risk and the cost of leaving disturbed areas. Impact assessments
 tend to focus on overt behavioural responses leading to displacement, but
 trade-offs may also impact individual energy budgets through reduced
 foraging performance. Previous studies found no evidence for broad-scale
 displacement of harbour porpoises exposed to impulse noise from a 10 day
 two-dimensional seismic survey. Here, we used an array of passive acoustic
 loggers coupled with calibrated noise measurements to test whether the
 seismic survey influenced the activity patterns of porpoises remaining in
 the area. We showed that the probability of recording a buzz declined by
 15% in the ensonified area and was positively related to distance from the
 source vessel. We also estimated received levels at the hydrophones and
 characterized the noise response curve. Our results demonstrate how
 environmental impact assessments can be developed to assess more subtle
 effects of noise disturbance on activity patterns and foraging efficiency.
description: Presence/absence of
 buzzes and associated covariatesdata_BACI.csv contains
 the data used for the analysis of buzz occurrence as a function of seismic
 period (before or during) and experimental block (control or impact).
 POD.no is the device number, to be used as a random effect; pres.buzzes
 indicates whether any buzz was detected in that hour. data_distance.csv
 contains the data used for the analysis of buzz occurrence as a function
 of distance from the source vessel. bootstrap_coef_sel.csv contains the
 bootstrapped coefficients of the relationship between SEL and the
 probability of buzz occurrence.data.zip
DOI: 10.5061/dryad.5dg56
title: Data from: Temporal genetic stability and high effective population size despite fisheries-induced life-history trait evolution in the North Sea sole.

description: Heavy fishing and other anthropogenic influences can have profound impact
 on a species’ resilience to harvesting. Besides the decrease of the census
 and effective population size, strong declines in mature adults and
 recruiting individuals may lead to almost irreversible genetic changes in
 life-history traits. Here, we investigated the evolution of genetic
 diversity and effective population size in the heavily exploited sole
 (Solea solea), through the analysis of historical DNA from a collection of
 1379 sole (Solea solea) otoliths dating back from 1957. Despite documented
 shifts in life-history traits, neutral genetic diversity inferred from 11
 microsatellite markers showed a remarkable stability over a period of 50
 years of heavy fishing. Using simulations and corrections for fisheries
 induced demographic variation, both point and temporal estimates of
 effective population size (Ne) were always higher than 1000, suggesting
 that despite the severe census size decrease over a 50 year period of
 harvesting, genetic drift is probably not strong enough to significantly
 decrease the neutral diversity of this species in the North Sea. However
 the ratio of effective population size to the census size (Ne/Nc) was very
 small (10-5), suggesting that overall only few adults contribute to the
 next generation. The high Ne level together with the low Ne/Nc ratio is
 most likely caused by a combination of an equalized reproductive output of
 younger cohorts, a decrease in generation time and a large variance in
 reproductive success typical for marine species. Because strong
 evolutionary changes in age and size at first maturation have been
 observed for sole, changes in adaptive genetic variation should be further
 monitored to detect the evolutionary consequences of human-induced
 selection.
description: OtolithGenotypes_bySamplingyear_11lociGenepop input: Otolith genotypes (11 loci) grouped by sampling year:1950s (‘NS50’; sampling years 1957-1959), 1960s (‘NS60’; sampling years 1966-1967),1970s (‘NS70’, sampling years 1971-1974), 1980s (NS80, sampling years 1984-1985-1987) and 1995 (NS95) (For details on age composition of the samples, see Supporting Information Table S2). In addition, contemporary samples were collected in 2007 during research surveys off the Thames (THA07), on the Norfolk Banks (NOR07) and off the Belgian Coast (BEL07)YEARFINAL_11LOC.popOtolithGenotypes_byCohorts_11lociGenepop input file. Otolith genotypes (11 loci),grouped by cohort (year-class). Pops are cohorts.Genotypes_BYCOHORTS.POP
DOI: 10.5061/dryad.37gr1
title: Data from: Cross–generational effects of sexual harassment on female fitness in the guppy

description: A large number of studies have identified several direct costs of sexual
 harassment, including energy expenditure and reduced foraging ability.
 However, the fitness consequences of sexual harassment over a longer
 time-scale have never been investigated. Here, we estimated the effects of
 male sexual harassment on female fitness in the guppy, Poecilia
 reticulata, a small tropical fish in which sexual conflict over mating
 rates is particularly pronounced. We compared the lifetime fecundity and
 survival of two groups of females exposed to different levels of sexual
 harassment. We further estimated the effect of sexual harassment on the
 fitness of the second generation by raising the offspring to maturity and
 measuring traits associated with fecundity in daughters and with pre- and
 post-copulatory competitiveness in sons. Although sexual harassment did
 not reduce mothers’ lifetime fecundity, it affected their timing of
 reproductive allocation. Interestingly, sexually harassed females produced
 daughters with smaller body size and sons that were less attractive to
 females and less successful in achieving coercive copulations than the
 sons of control females. This study provides compelling evidence that
 sexual harassment can have negative cross-generational fitness effects,
 suggesting that its consequences on female fitness may be more profound
 than currently thought.
description: sexual
 harassmentfemaleoffspringreadme