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opencc-by-4.0Jan 2021View details →

Distortions of Visual Time Induced by Motor Adaptation

For details please read the file readme.txt. For more details contact the authors.

opencc-zeroDec 2011View details →

Data from: Genetic basis of local adaptation and flowering time variation in Arabidopsis lyrata

Understanding how genetic variation at individual loci contributes to adaptation of populations to different local environments is an important topic in modern evolutionary biology. To date, most evidence has pointed to conditionally neutral quantitative trait loci (QTL) showing fitness effects only in some environments, while there has been less evidence for single-locus fitness trade-offs. At QTL underlying local adaptation, alleles from the local population are expected to show a fitness advantage. Cytoplasmic genomes also can have a role in local adaptation, but the role of cytonuclear interactions in adaptive differentiation has remained largely unknown. We mapped genomic regions underlying adaptive differentiation in multiple fitness components and flowering time in diverged populations of a perennial plant Arabidopsis lyrata. Experimental hybrids for this purpose were grown in natural field conditions of the parental populations in Norway and North Carolina (NC), USA and in the greenhouse. We found QTL where high fitness and early flowering were associated with local alleles, indicating a role of different selection pressures in phenotypic differentiation. At two QTL regions, a fitness component showing local adaptation between the parental populations also showed signs of putative fitness trade-offs. Beneficial dominance effects of conditionally neutral QTL for different fitness components resulted in hybrid vigor at the Norwegian site in the F2 hybrids. We also found that cytoplasmic genomes contributed to local adaptation and hybrid vigor by interacting with nuclear QTL, but these interactions did not show evidence for cytonuclear coadaptation (high fitness of local alleles combined with the local cytoplasm).

opencc-zeroDec 2016View details →

Data from: Adaptive developmental plasticity in a butterfly: mechanisms for size and time at pupation differ between diapause and direct development

Diapause (overwintering) and direct development are alternative developmental pathways in temperate insects. Diapause necessitates physiological preparations for dormancy, while direct development is associated with strong time constraints, resulting in selection for fast development under the direct development pathway. Physiological and behavioural preparations for pupation contribute to development time, so divergent selection in them is expected between the alternative developmental pathways. Critical mass for pupation induction is a central physiological parameter for the pupation process. Here, we compare the critical masses and the characteristics of the wandering stage – wandering taking place after the cessation of growth and before pupation – between diapausing and directly developing larvae in the butterfly Pieris napi. Critical mass estimation succeeded only for diapausing individuals, among which it was lower in females than in males, indicating an inter-pathway difference in the physiology of critical mass. Directly developing individuals wandered for a shorter time and distance and lost less mass before pupation than diapausing individuals. These physiological and behavioural differences represent adaptive phenotypic plasticity and contribute to fast development under direct development. Thus, the observed developmental plasticity in physiology offers a mechanistic explanation for adaptive life-history variation between alternative developmental pathways and sexual dimorphism.

Data from: Diversity and disparity through time in the adaptive radiation of Antarctic notothenioid fishes

According to theory, adaptive radiation is triggered by ecological opportunity that can arise through the colonization of new habitats, the extinction of antagonists or the origin of key innovations. In the course of an adaptive radiation, diversification and morphological evolution are expected to slow down after an initial phase of rapid adaptation to vacant ecological niches, followed by speciation. Such 'early bursts' of diversification are thought to occur because niche space becomes increasingly filled over time. The diversification of Antarctic notothenioid fishes into over 120 species has become one of the prime examples of adaptive radiation in the marine realm and has likely been triggered by an evolutionary key innovation in the form of the emergence of antifreeze glycoproteins. Here, we test, using a novel time-calibrated phylogeny of 49 species and five traits that characterize notothenioid body size and shape as well as buoyancy adaptations and habitat preferences, whether the notothenioid adaptive radiation is compatible with an early burst scenario. Extensive Bayesian model comparison shows that phylogenetic age estimates are highly dependent on model choice and that models with unlinked gene trees are generally better supported and result in younger age estimates. We find strong evidence for elevated diversification rates in Antarctic notothenioids compared to outgroups, yet no sign of rate heterogeneity in the course of the radiation, except that the notothenioid family Artedidraconidae appears to show secondarily elevated diversification rates. We further observe an early burst in trophic morphology, suggesting that the notothenioid radiation proceeds in stages similar to other prominent examples of adaptive radiation.

Data from: How much can history constrain adaptive evolution? A real time evolutionary approach of inversion polymorphisms in Drosophila subobscura

Chromosomal inversions are present in a wide range of animals and plants, having an important role in adaptation and speciation. Although empirical evidence of their adaptive value is abundant, the role of different processes underlying evolution of chromosomal polymorphisms is not fully understood. History and selection are likely to shape inversion polymorphism variation to an extent yet largely unknown. Here, we perform a real-time evolution study addressing the role of historical constraints and selection in the evolution of these polymorphisms. We founded laboratory populations of Drosophila subobscura derived from three locations along the European cline and followed the evolutionary dynamics of inversion polymorphisms throughout the first 40 generations. At the beginning, populations were highly differentiated and remained so throughout generations. We report evidence of positive selection for some inversions, variable between foundations. Signs of negative selection were more frequent, in particular for most cold-climate standard inversions across the three foundations. We found that previously observed convergence at the phenotypic level in these populations was not associated with convergence in inversion frequencies. In conclusion, our study shows that selection has shaped the evolutionary dynamics of inversion frequencies, but doing so within the constraints imposed by previous history. Both history and selection are therefore fundamental to predict the evolutionary potential of different populations to respond to global environmental changes.

Data from: The relative roles of cultural drift and acoustic adaptation in shaping syllable repertoires of island bird populations change with time since colonization

In birds, song divergence often precedes and facilitates divergence of other traits. We assessed the relative roles of cultural drift, innovation and acoustic adaptation in divergence of island bird dialects, using silvereyes (Zosterops lateralis). In recently colonized populations, syllable diversity was not significantly lower than source populations, shared syllables between populations decreased with increasing number of founder events and dialect variation displayed contributions from both habitat features and drift. The breadth of multivariate space occupied by recently colonized Z. l. lateralis populations was comparable to evolutionarily old forms that have diverged over thousands to hundreds of thousands of years. In evolutionarily old subspecies, syllable diversity was comparable to the mainland and the amount of variation in syllable composition explained by habitat features increased by two- to three-fold compared to recently colonized populations. Together these results suggest that cultural drift influences syllable repertoires in recently colonized populations, but innovation likely counters syllable loss from colonization. In evolutionarily older populations, the influence of acoustic adaptation increases, possibly favoring a high diversity of syllables. These results suggest that the relative importance of cultural drift and acoustic adaptation changes with time since colonization in island bird populations, highlighting the value of considering multiple mechanisms and timescale of divergence when investigating island song divergence.

opencc-zeroDec 2023View details →

Dataset from: Parapatric and sympatric adaptation of Setaria viridis populations in Japan to heterogeneous coastal habitats via trait divergence of plant form, salt spray tolerance and flowering time

This study aimed to determine how coastal variants of plants arise from local populations under natural selection by studying variations in phenotypic variations and survival of Setaria viridis populations inhabiting mosaic environments of two seashores in Japan. S.viridis populations comprised five coastal variants showing significantly higher salt spray tolerance than the inland variant: ST, short and tolerant (common variant); TM, tall and mid-tolerant (Inland Sea); TT, tall and tolerant; PT, prostrate and tolerant; L, extremely late flowering; I, inland and susceptible variants. These variations imply that maritime plants first acquired salt spray tolerance for survival, after which compact plants evolved in habitats where strong winds caused damage from salt spray. Results indicate that diverse intensities of salt spray and winds as well as summer drought generated various coastal variations in parapatry and sympatry.

opencc-by-4.0Jul 2024View details →

Run-time Performance Measurements to "Instanced Rendering of Parameterized 3D Glyphs with Adaptive Level-of-Detail using three.js"

Open the record for dataset details and reuse information.

opencc-zeroDec 2016View details →

Data from: Effects of gene action, marker density, and time since selection on the performance of landscape genomic scans of local adaptation

Genomic "scans" to identify loci that contribute to local adaptation are becoming increasingly common. Many methods used for such studies have assumed that local adaptation is created by loci experiencing antagonistic pleiotropy and that the selected locus itself is assayed, and few consider how signals of selection change through time. However, most empirical data sets have marker density too low to assume that a selected locus itself is assayed, researchers seldom know when selection was first imposed, and many locally adapted loci likely experience not antagonistic pleiotropy but conditional neutrality. We simulated data to evaluate how these factors affect the performance of tests for genotype-environment association. We found that three types of regression-based analyses (linear models, mixed linear models, and latent factor mixed models) and an implementation of BayEnv all performed well, with high rates of true positives and low rates of false positives, when the selected locus experienced antagonistic pleiotropy, and when the selected locus was assayed directly. However, all tests had reduced power to detect loci experiencing conditional neutrality, and the probability of detecting associations was sharply reduced when physically linked rather than causative loci were sampled. Antagonistic pleiotropy also maintained detectable genotype-environment associations much longer than conditional neutrality. Our analyses suggest that if local adaptation is often driven by loci experiencing conditional neutrality, genome-scan methods will have limited capacity to find loci responsible for local adaptation.

Data from: Using a 'time machine' to test for local adaptation of aquatic microbes to temporal and spatial environmental variation

Local adaptation occurs when different environments are dominated by different specialist genotypes, each of which is relatively fit in its local conditions and relatively unfit under other conditions. Analogously, ecological species sorting occurs when different environments are dominated by different competing species, each of which is relatively fit in its local conditions. The simplest theory predicts that spatial, but not temporal, environmental variation selects for local adaptation (or generates species sorting), but this prediction is difficult to test. Although organisms can be reciprocally transplanted among sites, doing so among times seems implausible. Here we describe a reciprocal transplant experiment testing for local adaptation or species sorting of lake bacteria in response to both temporal and spatial variation in water chemistry. The experiment used a −80 °C freezer as a 'time machine'. Bacterial isolates and water samples were frozen for later use, allowing transplantation of older isolates 'forward in time' and newer isolates 'backward in time'. Surprisingly, local maladaptation predominated over local adaptation in both space and time. Such local maladaptation may indicate that adaptation, or the analogous species sorting process, fails to keep pace with temporal fluctuations in water chemistry. This hypothesis could be tested with more finely-resolved temporal data.

opencc-zeroJun 2021View details →

Data for: Sex-specific ornament evolution is a consistent feature of climatic adaptation across space and time in dragonflies

Adaptation to different climates fuels the origins and maintenance of biodiversity. Detailing how organisms optimize fitness for their local climate is therefore an essential goal in biology. Although we increasingly understand how survival-related traits evolve as organisms adapt to climatic conditions, it is unclear if organisms also optimize traits that coordinate mating between the sexes. Here, we show that dragonflies consistently adapt to warmer climates across space and time by evolving less male melanin ornamentation—a mating-related trait that also absorbs solar radiation and heats individuals above ambient temperatures. Continent-wide macroevolutionary analyses reveal that species inhabiting warmer climates evolve less male ornamentation. Community-science observations across ten species indicate that populations adapt to warmer parts of species' ranges through microevolution of smaller male ornaments. Observations from 2005-2019 detail that contemporary selective pressures oppose male ornaments in warmer years; and our climate-warming projections predict further decreases by 2070. Conversely, our analyses show that female ornamentation responds idiosyncratically to temperature across space and time, indicating the sexes evolve in different ways to meet the demands of the local climate. Overall, these macro- and microevolutionary findings demonstrate that organisms predictably optimize their mating-related traits for the climate just as they do their survival-related traits.

opencc-by-4.0Aug 2021View details →

IQRM: real-time adaptive RFI masking for radio transient and pulsar searches

This is repository of the data that were used for the analysis and results presented in "IQRM: real-time adaptive RFI masking for radio transient and pulsar searches" submitted to the Monthly Notices for the Royal Astronomical Society for publication. The readme file along with the data contains all the necessary information one would need to process the data. The data will be made available to everyone once the paper has been accepted for publication. If you are using data from this repository, please do not forget to cite the following paper: "IQRM: real-time adaptive RFI masking for radio transient and pulsar searches", V M Morello, K M Rajwade and B W Stappers, 2021, Monthly Notices of the Royal Astronomical Society, in press.

Figure 1. Shells.A–J in Tracking parallel adaptation of shell morphology through geological times in the land snail genus Pupilla (Gastropoda: Stylommatophora: Pupillidae)

Figure 1. Shells.A–J, Pupilla alpicola (A–E, lowland populations"P.pratensis"; F–J, typical mountain populations).K–P, P.loessica. Q–T, P. muscorum. A, M_6001_3_1, Lake Galenbeck (Mecklenburg-Western Pomerania, Germany). B, SMNS-ZI0138340, type locality Dinkelscherben near Augsburg (Bavaria, Germany). C, M_846_1_2, Burgtonna (Thuringia, Germany), fossil from Early

Figure 6 in Tracking parallel adaptation of shell morphology through geological times in the land snail genus Pupilla (Gastropoda: Stylommatophora: Pupillidae)

Figure 6. Thin-plate splines illustrating (theoretical) transitions in shape, side view, exaggeration 5 times. A, fossil P. loessica → extant P. loessica. B, fossil P. pratensis (including P. m. densegyrata) → extant P. pratensis. C, fossil P. pratensis (including P. m. densegyrata) → extant P. alpicola. D, extant P. pratensis → P. alpicola. E, extant P. loessica→ P. alpicola. F, fossil P. muscorum → extant P. muscorum.

Figure 8 in Tracking parallel adaptation of shell morphology through geological times in the land snail genus Pupilla (Gastropoda: Stylommatophora: Pupillidae)

Figure 8. Phylogenetic tree based on COI. 50% majority rule consensus tree from Bayesian analysis with posterior probabilities/bootstrap support values (from maximum likelihood analysis). Sample abbreviations and groups of samples are given in Tables 1 and 3.

Figure 11 in Tracking parallel adaptation of shell morphology through geological times in the land snail genus Pupilla (Gastropoda: Stylommatophora: Pupillidae)

Figure 11. Pupa muscorum var. pratensis. Series of four shells from type locality Dinkelscherben near Augsburg (Germany) in frontal and lateral view. A, neotype SMNS-ZI0138339. B–D, SMNS-ZI0138341.

Figure 10 in Tracking parallel adaptation of shell morphology through geological times in the land snail genus Pupilla (Gastropoda: Stylommatophora: Pupillidae)

Figure 10. Pupilla loessica. Series of four shells from type locality Předmostí at Přerov (Czech Republic, fossil from Saalian loess) in frontal and lateral view. A is the designated neotype. All deposited at the National Museum of Prague.

Figure 7 in Tracking parallel adaptation of shell morphology through geological times in the land snail genus Pupilla (Gastropoda: Stylommatophora: Pupillidae)

Figure 7. Shell microsculpture (SEM micrographs). A–T, P. loessica. U–Z, P. alpicola. a–d, P. alpicola (morphogroup P. m. densegyrata). e–h, P. alpicola (lowland populations "P. pratensis"). i–j, P. muscorum. A–B, M_4559, Altai, Saylyugem (Russia). C–D, M_4575, Altai, Saylyugem (Russia). E–F, H_MC409, Altai, Dzhazator (Russia). G–H, M_3970, Khatgal, shore of Lake Khövsgöl Nuur (northern Mongolia). I–J, M_2523_2, Yelantsy near Lake Baikal (Russia). K–L, M_2523_1, Yelantsy near Lake Baikal (Russia). M–N, M_994, Karsdorf (Saxony Anhalt, Germany), fossil from Early Saalian. O–P, M_459, Zeuchfeld (Saxony

Figure 9 in Tracking parallel adaptation of shell morphology through geological times in the land snail genus Pupilla (Gastropoda: Stylommatophora: Pupillidae)

Figure 9. Phylogenetic tree based on ITS2. 50% majority rule consensus tree from Bayesian analysis with posterior probabilities/bootstrap support values (from maximum likelihood analysis). Sample abbreviations and groups of samples are given in Tables 1 and 3.