cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tm8d0
title: Data from: Loci under selection during multiple range expansions of an invasive plant are mostly population-specific, but patterns are associated with climate

description: Identifying the genes underlying rapid evolutionary changes, describing
 their function and ascertaining the environmental pressures that determine
 fitness are the central elements needed for understanding of evolutionary
 processes and phenotypic changes that improve the fitness of populations.
 It has been hypothesized that rapid adaptive changes in new environments
 may contribute to the rapid spread and success of invasive plants and
 animals. As yet, studies of adaptation during invasion are scarce, as is
 knowledge of the genes underlying adaptation, especially in multiple
 replicated invasions. Here, we quantified how genotype frequencies change
 during invasions, resulting in rapid evolution of naturalized populations.
 We used six fully replicated common garden experiments in Brazil where
 Pinus taeda (loblolly pine) was introduced at the same time, in the same
 numbers, from the same seed sources, and has formed naturalized
 populations expanding outward from the plantations. We used a combination
 of nonparametric, population genetics and multivariate statistics to
 detect changes in genotype frequencies along each of the six
 naturalization gradients and their association with climate as well as
 shifts in allele frequencies compared to the source populations. Results
 show 25 genes with significant shifts in genotype frequencies. Six genes
 had shifts in more than one population. Climate explained 25% of the
 variation in the groups of genes under selection across all locations, but
 specific genes under strong selection during invasions did not show
 climate-related convergence. In conclusion, we detected rapid evolutionary
 changes during invasive range expansions, but the particular gene-level
 patterns of evolution may be population specific.
description: Data and R
 code## snp_D.R -&gt;
 contains the annotated code for reading and preparing the data, and the
 custom code for the K-W tests. ## prov_inv_snp_D.csv -&gt; contain the raw
 data for the K-W tests ## RDA_SNPxLocationxClimate.R -&gt; Annotated R
 code for the redundancy analysis (RDA) and for Figure 7 ## BRsites_bioclim
 -&gt; climate data for RDA ## SNPcommunity_table.csv -&gt; SNP
 "community"matrix for RDA ## sorted_12_pops.csv -&gt; lositan
 results. This is the list of loci, with heterozygosity and Fst, ordered by
 p value.Archive.zip
DOI: 10.5061/dryad.t3b51
title: Data from: The relationship between microhabitat use, allometry, and functional variation in the eyes of Hawaiian Megalagrion damselflies

description: The evolution of visual systems is guided by visual requirements imposed
 by the environment, the size of the animal's eyes, and physical
 limitations imposed by the resolution-sensitivity trade-off. Given a
 particular eye surface area, resolution and sensitivity cannot be
 simultaneously maximized: gains in resolution, the ability of the eye to
 detect detail, will come at the cost of sensitivity, the ability to
 capture photons, and vice versa, without an increase to eye size. How this
 constraint interacts with ecology and whether it allows the fine-tuning of
 the visual system to smaller scale habitat heterogeneity remains an
 understudied question in visual ecology. Here, we use closely-related
 species of damselflies in the Hawaiian genus Megalagrion which differ in
 ecology to test whether variation in the resolution-sensitivity trade-off
 is the evolutionary result of scaling or differences in microhabitat use.
 We use regression analyses and phylogenetic comparative methods to examine
 the effects of size and microhabitat use on traits related to light
 sensitivity and visual resolution. We find that eye size is tightly
 associated with body size in these damselflies, but other visual
 morphology traits related to light sensitivity and resolution are
 associated with microhabitat type. Furthermore, size and morphology
 relationships vary across microhabitats, and performance related to
 resolution tends to be more conserved than to variation in light
 sensitivity. Additionally, smaller species in visually challenging
 microhabitats have more regionalized eyes than species with larger eyes in
 open, well-lit areas. Thus, regionalization of the eye allows a decoupling
 of size and morphology/performance so that even small insect species can
 exploit visually challenging habitats. These results suggest that
 variation in visual performance results from changes in eye geometry as
 well as size. These morphological changes are likely adaptive to
 differences in microhabitat, indicating that variation in microhabitat
 use, even at small scales, can play an important role in the evolution of
 visual systems.
description: Raw Eye and body size
 data for Megalagrion speciesA spreadsheet of Eye
 size data (eye height) and body size data (thorax length) for 13 species
 of Megalagrion damselflies.Raw_eyeandbodysize.csvFacet diameter dataA spreadsheet of facet diameters along a vertical transect of the eye for 13 species of Megalagrion damselflies. Species codes are included.Raw_facet_diameters.csvRaw interommatidial anglesA spreadsheet of interommatidial angles along a vertical transect of the eye for 13 species of Megalagrion damselflies. Species codes are included.Raw_IO_angles.csv
DOI: 10.5061/dryad.3ng2s
title: Data from: Movement of a hybrid zone between lineages of the Australian glass shrimp (Paratya australiensis)

description: In 1993, a population of freshwater glass shrimp (Paratya australiensis)
 was translocated from Kilcoy Creek to Branch Creek in the Conondale Range,
 Queensland. Subsequent genetic analysis revealed that the translocated and
 resident shrimp belonged to different mitochondrial DNA lineages (mtDNA)
 that were capable of hybridising. Monitoring of the pools along Branch
 Creek up until 2002 suggested that the translocated lineage had an
 advantage in upstream pools, and the resident lineage dominated
 downstream. Differential temperature tolerance and hybridisation barriers
 such as hybrid inviability and mate selection were factors proposed to
 explain hybrid zone structure. The major objective of this study was to
 combine nuclear and mtDNA markers to identify the structure of the hybrid
 zone in 2013 and identify any changes that had occurred since 2002.
 Specifically, we used genetic data to test for evidence of hybrid zone
 movement, and used FIS values to investigate whether mating was random in
 the contact zone; where hybridisation barriers could be present. The
 results revealed that the hybrid zone centre has shifted 510m downstream
 since 2002. Increased rainfall in the region since 2010 could have
 facilitated this. Secondly, mating appears significantly non-random in the
 pools where both lineages occur; supporting the occurrence of
 hybridisation barriers which appear to prevent the co-occurrence of the
 two lineages in the same pool. This study reveals a complex and dynamic
 hybrid zone, and exemplifies why multiple temporal studies are necessary
 to understand hybrid zone structure.
description: Raw data for
 "Movement of an Australian Glass Shrimp Hybrid
 Zone"Sheet 1: Raw data from
 the first analysis stage in which 32 shrimp from each of 11 pools (9 along
 Branch Creek and 2 control pools) were genotyped for 3 microsatellite
 loci. Sheet 2: Raw data from the second analysis stage in which 96 shrimp
 from Pool -3 and 96 from Pool -3.5 were genotyped for 3 microsatellite
 loci and 3 allozyme loci.2016_JeremyWilson_ParatyaHybridZone_rawdata.xlsx
DOI: 10.5061/dryad.qn5q7
title: Data from: Divergence of gastropod life history in contrasting thermal environments in a geothermal lake

description: Experiments using natural populations have provided mixed support for
 thermal adaptation models, probably because the conditions are often
 confounded with additional environmental factors like seasonality. The
 contrasting geothermal environments within Lake Mývatn, northern Iceland,
 provide a unique opportunity to evaluate thermal adaptation models using
 closely located natural populations. We conducted laboratory common garden
 and field reciprocal transplant experiments to investigate how thermal
 origin influences the life history of Radix balthica snails originating
 from stable cold (6 °C), stable warm (23 °C) thermal environments or from
 areas with seasonal temperature variation. Supporting thermal optimality
 models, warm origin snails survived poorly at 6 °C in the common garden
 experiment and better than cold origin and seasonal snails in the warm
 habitat in the reciprocal transplant experiment. Contrary to thermal
 adaptation models, growth rate in both experiments was highest in the warm
 populations irrespective of temperature, indicating cogradient variation.
 The optimal temperatures for growth and reproduction were similar
 irrespective of origin, but cold origin snails always had the lowest
 performance, and seasonal origin snails often performed at an intermediate
 level compared to snails originating in either stable environment. Our
 results indicate that central life-history traits can differ in their mode
 of evolution, with survival following the predictions of thermal
 optimality models, whereas ecological constraints have shaped the
 evolution of growth rates in local populations.
description: Divergence of gastropod
 life historyData from a common
 garden experiment conducted on Radix balthica sampled from thermal
 environments on Iceland.
DOI: 10.5061/dryad.41pr0
title: Data from: Aggressive behaviours, food deprivation and the foraging gene

description: A pleiotropic gene governs multiple traits, which might constrain the
 evolution of complexity due to conflicting selection on these traits.
 However, if the pleiotropic effect is modular, then this can facilitate
 synergistic responses to selection on functionally related traits, thereby
 leveraging the evolution of complexity. To understand the evolutionary
 consequence of pleiotropy, the relation among functionally different
 traits governed by the same gene is key. We examined a pleiotropic
 function of the foraging (for) gene with its rover and sitter allelic
 variants in fruit fly, Drosophila melanogaster. We measured for's
 effect on adult male aggressive behaviours and whether this effect was
 shaped by for's known role in food-related traits. Rover exhibited
 higher levels of offensive behaviour than sitters and s2, a sitter-like
 mutant on rover genetic background. With a Markov chain model, we
 estimated the rate of aggression escalation, and found that the rover
 pattern of aggressive escalation more rapidly intensified fights.
 Subsequent analysis revealed that this was not caused by for's effect
 on food-related traits, suggesting that for might directly regulate
 aggressive behaviours. Food deprivation did not elevate aggression, but
 reduced intermediate-level aggressive behaviours. Aggression and other
 foraging-related behaviour might comprise a synergistic trait module
 underlaid by this pleiotropic gene.
description: 24hours_fooddep_experiment_freqBehavior frequency of each treatment and strain.24hours_fooddep_weightDry weight of flies in each treatment and strainBehavior_transition_networksRaw behavior transition matrices used to calculate escalation rate from approach to head-to-head-interaction.
DOI: 10.5061/dryad.sh1611tm
title: Data from: Are there indirect fitness benefits of female extra-pair reproduction? Lifetime reproductive success of within-pair and extra-pair offspring

description: The forces driving extra-pair reproduction by socially monogamous females,
 and the resulting genetic polyandry, remain unclear. A testable prediction
 of the hypothesis that extra-pair reproduction partly reflects indirect
 selection on females is that extra-pair young (EPY) will be fitter than
 their within-pair young (WPY) maternal half-siblings. This prediction has
 not been comprehensively tested in a wild population, requiring data on
 the lifetime reproductive success (LRS) of maternal half-sib EPY and WPY.
 We used 17 years of genetic parentage data from song sparrows, Melospiza
 melodia, to compare the LRS of hatched EPY and WPY maternal half-siblings
 measured as their lifetime number of hatched offspring, recruited
 offspring and hatched grandoffspring. EPY hatchlings were not
 significantly fitter than WPY hatchlings for any of three measures of LRS.
 Furthermore, opposite to prediction, EPY hatchlings tended to have lower
 LRS than their maternal half-sibling WPY hatchlings on average. EPY also
 tended to be less likely to survive to hatch than their maternal
 half-sibling WPY. Taken together, these results fail to support one key
 hypothesis explaining the evolution of genetic polyandry by socially
 monogamous females and suggest there may be weak indirect selection
 against female extra-pair reproduction in song sparrows.
description: SOSP LRS
 data
DOI: 10.5061/dryad.7gs71
title: Data from: An investigation for population maintenance mechanism in a miniature garden: genetic connectivity or independence of small islet populations of the Ryukyu five-lined skink

description: The Ryukyu five-lined skink (Plestiodon marginatus) is an island lizard
 that is even found in tiny islets with less than half a hectare of habitat
 area. We hypothesized that the island populations are maintained under
 frequent gene flow among the islands or independent of each other. To test
 our hypotheses, we investigated genetic structure of 21 populations from
 11 land-bridge islands that were connected during the latest glacial age,
 and four isolated islands. Analyses using mitochondrial cytochrome b gene
 sequence (n = 67) and 10 microsatellite loci (n = 235) revealed moderate
 to high levels of genetic differentiation, existence of many private
 alleles/haplotypes in most islands, little contemporary migration, a
 positive correlation between genetic variability and island area, and a
 negative correlation between relatedness and island area. These evidences
 suggest a strong effect of independent genetic drift as opposed to gene
 flow, favoring the isolation hypothesis even in tiny islet populations.
 Isolation-by-distance effect was demonstrated and it became more prominent
 when the four isolated islands were excluded, suggesting that the pattern
 is a remnant of the land-bridge age. In a few island populations, however,
 the possibility of occasional overwater dispersals was partially supported
 and therefore could not be ruled out.
description: Microsatellite genotype
 of Plestiodon marginatusThis file includes
 genotypes of 235 individuals of Plestiodon marginatus for 10
 microsatellite loci in GenAlEx format. The samples names indicate the
 number of the Zoological Collection of the Kyoto University Museum. The
 locality names correspond with numbers of Table 1 in the
 text.
DOI: 10.5061/dryad.2tj43
title: Data from: Host coevolution alters the adaptive landscape of a virus

description: The origin of new and complex structures and functions is fundamental for
 shaping the diversity of life. Such key innovations are rare because they
 require multiple interacting changes. We sought to understand how the
 adaptive landscape led to an innovation whereby bacteriophage λ evolved
 the new ability to exploit a receptor, OmpF, on Escherichia coli cells.
 Previous work showed that this ability evolved repeatedly, despite
 requiring four mutations in one virus gene. Here, we examine how this
 innovation evolved by studying six intermediate genotypes of λ isolated
 during independent transitions to exploit OmpF and comparing them to their
 ancestor. All six intermediates showed large increases in their adsorption
 rates on the ancestral host. Improvements in adsorption were offset, in
 large part, by the evolution of host resistance, which occurred by reduced
 expression of LamB, the usual receptor for λ. As a consequence of host
 coevolution, the adaptive landscape of the virus changed such that
 selection favouring four of the six virus intermediates became stronger
 after the host evolved resistance, thereby accelerating virus populations
 along the path to using the new OmpF receptor. This dependency of viral
 fitness on host genotype thus shows an important role for coevolution in
 the origin of the new viral function.
description: Burmeister_2016_Dryad_Data_Scripts
DOI: 10.5061/dryad.2s7s5
title: Data from: Temporal carry-over effects in sequential plant–soil feedbacks

description: Plant-soil feedbacks (PSF) strongly influence plant performance. However,
 to what extent these PSF effects are persistent in the soil and how they
 are altered by species that subsequently condition the soil is unclear.
 Here we test how conspecific and heterospecific soil-conditioning effects
 interact across different soil-conditioning phases. We conducted a fully
 factorial glasshouse experiment where six plant species conditioned soils
 in two consecutive phases and measured the performance of Jacobaea
 vulgaris. The species that conditioned the soil during the second
 conditioning phase strongly determined the performance of J. vulgaris, but
 also the order and combination of species that conditioned the soil in the
 two phases accounted for a large part of the variance. For shoot biomass
 this interaction was the dominant variance component. We show that soil
 conditioning legacies carry-over and interact with the conditioning
 effects of succeeding plants. In the field, species replacements at the
 patch level often appear to be unpredictable and we suggest that
 sequential feedbacks may explain these apparently unpredictable
 transitions.
description: Sequential plant-soil
 feedback plant biomass dataThe file contains the
 shoot (per plant) and root (total) biomass of all the plants in the test
 phase (phase 3) of the experiment of all experimental
 units.Temp
 PSF P3 biomass data Dryad.xlsx
DOI: 10.5061/dryad.35115
title: Data from: Effects of individual-based preferences for colour-banded mates on sex allocation in zebra finches

description: Sex allocation theory predicts that females mated to attractive males
 produce more sons than females mated to unattractive males. However,
 previous tests of this hypothesis have obtained mixed results. We suggest
 that females differ in the traits they find attractive. To test this
 proposition, we assessed female zebra finches’ preferences for males
 banded with red or green plastic leg bands and then tested the sex
 allocation pattern of females paired with preferred and non-preferred
 males. Although most females preferred red-banded males, 34% of females
 consistently preferred green-banded males. The sex ratio at laying and
 hatching was not influenced by paternal preferred status. However, the
 fledging sex ratios differed between females paired with preferred and
 non-preferred males due to sex-biased chick mortality; sons of females
 paired with preferred males were born heavier and were more likely to
 survive than daughters. Our results indicate that female zebra finches
 show individual variation in their preferences for colour banded males,
 although females do not seem to adjust the offspring sex ratio in response
 to their mate’s band colour. However, the differential post-hatch
 mortality suggests females may differentially allocate resources into male
 and female eggs according to their individual mate preferences.
description: zebra finch sex
 ratio－paperThe brood sex ratio,
 brood size and other brood level data at zebra finch reproduction in this
 study.zebra finch selection
 originalFemale zebra
 finches' preference on red- or green-bands male, and the consistence
 of this behaviourzebra finch all
 chicksNestlings'
 condition at female zebra finch reproduction in this
 study
DOI: 10.5061/dryad.4bd12
title: Data from: Is diversification in male reproductive traits driven by evolutionary trade-offs between weapons and nuptial gifts?

description: Many male animals have evolved exaggerated traits that they use in combat
 with rival males to gain access to females and secure their reproductive
 success. But some male animals invest in nuptial gifts that gains them
 access to females. Both these reproductive strategies are costly in that
 resources are needed to produce the weapon or nuptial gift. In closely
 related species where both weapons and nuptial gifts are present, little
 is known about the potential evolutionary trade-off faced by males that
 have these traits. In this study, we use dobsonflies (order Megaloptera,
 family Corydalidae, subfamily Corydalinae) to examine the presence and
 absence of enlarged male weapons versus nuptial gifts within and among
 species. Many dobsonfly species are sexually dimorphic, and males possess
 extremely enlarged mandibles that they use in battles, whereas in other
 species, males produce large nuptial gifts that increase female fecundity.
 In our study, we show that male accessory gland size strongly correlates
 with nuptial gift size and that when male weapons are large, nuptial gifts
 are small and vice versa. We mapped weapons and nuptial gifts onto a
 phylogeny we constructed of 57 species of dobsonflies. Our among-species
 comparison shows that large nuptial gift production evolved in many
 species of dobsonfly but is absent from those with exaggerated weapons.
 This pattern supports the potential explanation that the trade-off in
 resource allocation between weapons and nuptial gifts is important in
 driving the diversity of male mating strategies seen in the dobsonflies,
 whereas reduced male–male competition in the species producing large
 spermatophores could be an alternative explanation on their loss of male
 weapons. Our results shed new light on the evolutionary interplay of
 multiple sexually selected traits in animals.
description: Dataset
 S1-2Dataset S1. Male and
 female traits by prothorax length (PTL): the log-log relationships between
 PTL and mandible length (ML) or flange length (FL), and those between PTL
 and wing length (WL). The male internal accessory gland size in weight is
 also shown; Dataset S2. Combined dataset for phylogenetic
 analysis.