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opencc-by-4.0Mar 2012View details →

Towards deciphering dynamic changes and evolutionary mechanisms involved in the adaptation to low salinities in Ectocarpus (brown algae) - test dataset

Objectives : Examine salinity tolerance and adaptations to low salinities in a freshwater strain of Ectocarpuson physiological and molecular levels. Cohort : Two clonal strains of Ectocarpus sp. (Ectocarpales, Phaeophyceae), the genome-sequenced marine strain (MS) (accession CCAP 1310/4, origin San Juan de Marcona, Peru) and a freshwater strain (FWS, accession CCAP 1310/196, origin Hopkins River Falls, Victoria, Australia) were used. Mass spectrometer : Gas chromatography-mass spectrometry (GC-MS) as described by Ritteret al.(2008) : samples were analysed with a Hewlett-Packard 5873 Mass Selective Detector interfaced to a Hewlett-Packard 6890 Series+ gas chromatograph (Agilent, Les Ullis, France).

opencc-zeroSep 2021View details →

Tool for genomic selection and breeding to evolutionary adaptation: Development of a 100K single nucleotide polymorphism array for the honey bee

High-throughput high density genotyping arrays continue to be a fast, accurate, and cost-effective method for genotyping thousands of polymorphisms in high numbers of individuals. Here we have developed a new high-density SNP genotyping array (103 270 SNPs) for honey bees, one of the most ecologically and economically important pollinators worldwide. SNPs were detected by conducting whole genome resequencing of 61 honey bee drones (haploid males) from throughout Europe. Selection of SNPs for the chip was done in multiple steps using several criteria. The majority of SNPs were selected based on their location within known candidate regions or genes underlying a range of honey bee traits, including hygienic behaviour against pathogens, foraging and subspecies. Additionally, markers from a GWAS of hygienic behaviour against the major honey bee parasite Varroa destructor, were brought over. The chip also includes SNPs associated with each of three major breeding objectives - honey yield, gentleness and Varroa resistance. We validated the chip and make recommendations for its use by determining error rates in repeat genotypings, examining the genotyping performance of different tissues, and by testing how well different sample types represent the queen's genotype. The latter is a key test because it is highly beneficial to be able to determine the queen's genotype by non-lethal means. The array is now publicly available and we suggest it will be a useful tool in genomic selection and honey bee breeding, as well as for GWAS of different traits, and for population genomic, adaptation and conservation questions.

opencc-zeroDec 2016View details →

Data from: Evolutionary online behaviour learning and adaptation in real robots

Online evolution of behavioural control on real robots is an open-ended approach to autonomous learning and adaptation: robots have the potential to automatically learn new tasks and to adapt to changes in environmental conditions, or to failures in sensors and/or actuators. However, studies have so far almost exclusively been carried out in simulation because evolution in real hardware has required several days or weeks to produce capable robots. In this article, we successfully evolve neural network-based controllers in real robotic hardware to solve two single-robot tasks and one collective robotics task. Controllers are evolved either from random solutions or from solutions pre-evolved in simulation. In all cases, capable solutions are found in a timely manner (1 h or less). Results show that more accurate simulations may lead to higher-performing controllers, and that completing the optimization process in real robots is meaningful, even if solutions found in simulation differ from solutions in reality. We furthermore demonstrate for the first time the adaptive capabilities of online evolution in real robotic hardware, including robots able to overcome faults injected in the motors of multiple units simultaneously, and to modify their behaviour in response to changes in the task requirements. We conclude by assessing the contribution of each algorithmic component on the performance of the underlying evolutionary algorithm.

opencc-zeroDec 2016View details →

Data from: Phylogenetic evidence from freshwater crayfishes that cave adaptation is not an evolutionary dead-end

Caves are perceived as isolated, extreme habitats with a set of uniquely specialized biota, which long ago led to the idea that caves are 'evolutionary dead-ends.' This suggests that cave-adapted taxa may be doomed for extinction before they can diversify or transition to a more stable state. However, this hypothesis has not been explicitly tested in a phylogenetic framework with multiple independent cave-dwelling groups. Here we use the freshwater crayfish, a group with dozens of cave-dwelling species in multiple lineages, as a system to test this hypothesis. We consider historical patterns of lineage diversification and habitat transition as well as current patterns of geographic range size. We find that while cave-dwelling lineages have small relative range sizes and rarely transition back to the surface, they exhibit remarkably similar diversification patterns to those of other habitat types and appear to be able to maintain a diversity of lineages through time. This suggests that cave-adaptation is not a 'dead-end' for freshwater crayfish, which has positive implications for our understanding of biodiversity and conservation in cave habitats.

opencc-zeroDec 2017View details →

Data from: Evolutionary dynamics of quantitative variation in an adaptive trait at the regional scale: the case of zinc hyperaccumulation in Arabidopsis halleri

Metal hyperaccumulation in plants is an ecological trait whose biological significance remains debated, in particular because the selective pressures that govern its evolutionary dynamics are complex. One of the possible causes of quantitative variation in hyperaccumulation may be local adaptation to metalliferous soils. Here we explored the population genetic structure of Arabidopsis halleri at fourteen metalliferous and non-metalliferous sampling sites in Southern Poland. The results were integrated with a quantitative assessment of variation in zinc hyperaccumulation to trace local adaptation. We identified a clear hierarchical structure with two distinct genetic groups at the upper level of clustering. Interestingly, these groups corresponded to different geographic sub-regions, rather than to ecological types (i.e. metallicolous vs non-metallicolous). Also, approximate Bayesian computation analyses suggested that the current distribution of A. halleri in Southern Poland could be relictual as a result of habitat fragmentation caused by climatic shifts during the Holocene, rather than due to recent colonization of industrially polluted sites. In addition, we find evidence that some non-metallicolous lowland populations may have actually derived from metallicolous populations. Meanwhile, the distribution of quantitative variation in zinc hyperaccumulation did separate metallicolous and non-metallicolous accessions, indicating more recent adaptive evolution and diversifying selection between metalliferous and non-metalliferous habitats. This suggests that zinc hyperaccumulation evolves both ways – towards higher levels at non-metalliferous sites and lower levels at metalliferous sites. Our results open a new perspective on possible evolutionary relationships between A. halleri edaphic types that may inspire future genetic studies of quantitative variation in metal hyperaccumulation.

opencc-zeroDec 2014View details →

Data from: Experimental evidence for an eco-evolutionary coupling between local adaptation and intraspecific competition

Determining how adaptive evolution can be coupled to ecological processes is key for developing a more integrative understanding of the demographic factors that regulate populations. Intraspecific competition is an especially important ecological process because it generates negative density dependence in demographic rates. Although ecological factors are most often investigated to determine the strength of density dependence, evolutionary processes such as local adaptation could also feed back to shape variation in the strength of density dependence among populations. Using an experimental approach with damselflies, a predaceous aquatic insect, we find evidence that both density-dependent intraspecific competition and local adaptation can reduce per capita growth rates. In some cases, the effects of local adaptation on reducing per capita growth rates exceeded the ecological competitive effects of a doubling of density. However, we also found that these ecological and evolutionary properties of populations are coupled, and we offer two interpretations of the causes underlying this pattern: (1) the strength of density-dependent competition depends on the extent of local adaptation, or (2) the extent of local adaptation is shaped by the strength of density-dependent competition. Regardless of the underlying causal pathway, these results show how eco-evolutionary dynamics can affect a key demographic process regulating populations.

opencc-zeroFeb 2020View details →

Evolutionary constraints and adaptation shape the size and colour of rain forest fruits and flowers at continental scale

Aim: Large-scale patterns in flower and fruit traits provide critical insights into selection processes and the evolutionary history of plant lineages. To isolate and identify the role of selective pressures including different plant-animal interactions, and the factors driving trait evolution, we investigate convergence and divergence between flower and fruit traits in shared environments. Location: Australia to Southeast Asia. Time period: Eocene (~45 My) to Present. Major taxa studied: Woody angiosperm rainforest species (2248 species, 133 families). Methods: Using a continental scale data set for all woody angiosperm species in the Australian rainforest (1816 free-standing and 432 climbing species) we compare the colour and size of fleshy fruits and flowers in relation to life form (trees/shrubs and vines), species biogeographic histories and origins (Sunda vs. Sahul), and bio-regional distributions. Results: Fleshy fruits in the Australian rainforest are mostly small, with a diversity of colours (<30mm; 81%), while flowers are mostly small (<10mm; 65%) and whitish (~80%). Compared to trees and shrubs, climbing species showed a higher proportion of red fleshy fruits, and large coloured flowers. Small whitish flowers were dominant across lineages from different biogeographic origins (Sunda-Sahul) and geographical regions, while both small and large fleshy fruits retained a range of disperser attractant colours. Main conclusions: Continental scale size and colour characteristics of flowers and fleshy fruits differed despite sharing environments with similar abiotic selective pressures through time. Plant-animal interactions including pollination and dispersal likely mediate different evolutionary outcomes for plant traits, and reflect both adaptation and evolutionary constraints.

opencc-zeroDec 2011View details →

Data from: Ecological and evolutionary determinants for the adaptive radiation of the Madagascan vangas

Adaptive radiation is the rapid diversification of a single lineage into many species that inhabit a variety of environments or use a variety of resources and differ in traits required to exploit these. Why some lineages undergo adaptive radiation is not well-understood, but filling unoccupied ecological space appears to be a common feature. We construct a complete, dated, species-level phylogeny of the endemic Vangidae of Madagascar. This passerine bird radiation represents a classic, but poorly known, avian adaptive radiation. Our results reveal an initial rapid increase in evolutionary lineages and diversification in morphospace after colonizing Madagascar in the late Oligocene some 25 Mya. A subsequent key innovation involving unique bill morphology was associated with a second increase in diversification rates about 10 Mya. The volume of morphospace occupied by contemporary Madagascan vangas is in many aspects as large (shape variation)—or even larger (size variation)—as that of other better-known avian adaptive radiations, including the much younger Galapagos Darwin's finches and Hawaiian honeycreepers. Morphological space bears a close relationship to diet, substrate use, and foraging movements, and thus our results demonstrate the great extent of the evolutionary diversification of the Madagascan vangas.

opencc-zeroDec 2011View details →

Data from: Proteomic evidence of a paedomorphic evolutionary process within a marine snail species: a strategy for adapting to extreme ecological conditions?

The exposed and sheltered ecotypes of the marine snail Littorina saxatilis from European rocky shores are considered a key model system to study adaptation and ecological speciation. Previous studies showed that two ecotypes (RB and SU) of this species in NW Spain have differently adapted to different shore levels and microhabitats. In order to understand how this divergent adaptive process has been accomplished, we followed a quantitative proteomic approach to investigate the proteome variation in a number of different biological factors, i.e. ecotype, ontogeny and their interactions. This approach allowed testing the hypothesis that one of the ecotypes has evolved by paedomorphosis, and also whether or not the molecular mechanisms related to ecotype differentiation are set up in early developmental stages. Additionally the identification of some candidate proteins by mass spectrometry provides some functional insights about these evolutionary processes. Results from this study provided evidence of higher ontogenetic differentiation at proteome level in the RB (metamorphic) than in SU (paedomorphic) ecotype that point to the possibility of juvenile stage retention in this latter ecotype. The level of protein expression (proteome) differences between ecotypes maintained nearly constant from late embryonic stages to adulthood, although some proteins involved in these changes considerably differed in embryonic compared to other ontogenetic stages. Paedomorphosis may be the evolutionary response of the SU ecotype of solving the trade-off during sexually immaturity that is caused by the evolution of small size arising from adaptation to the wave exposed habitat. Some potential candidate genes of adaptation related to energetic metabolism have been identified, providing a promising baseline for future functional analyses.

opencc-zeroDec 2013View details →

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.

opencc-zeroNov 2019View details →

Eco-evolutionary feedbacks link prey adaptation to predator performance

Eco-evolutionary feedbacks may determine the outcome of predator-prey interactions in nature, but little work has been done to quantify the feedback effect of short-term prey adaptation on predator performance. We tested the effects of prey availability and recent (< 100 years) prey adaptation on the feeding and growth rate of largemouth bass (Micropterus salmoides), foraging on western mosquitofish (Gambusia affinis). Field surveys showed higher densities and larger average body sizes of mosquitofish in recently introduced populations without bass. Over a six-week mesocosm experiment, bass were presented with either a high or low availability of mosquitofish prey from recently established populations either naïve or experienced with bass. Naïve mosquitofish were larger, less cryptic, and more vulnerable to bass predation compared to their experienced counterparts. Bass consumed more naïve prey, grew more quickly with naïve prey, and grew more quickly per unit biomass of naïve prey consumed. The effect of mosquitofish history with bass on bass growth was similar in magnitude to the effect of mosquitofish availability. In showing that recently-derived predation-related prey phenotypes strongly affect predator performance, this study supports the presence of reciprocal predator-prey trait feedbacks in nature.

opencc-zeroDec 2014View details →

Data from: Plastic and evolutionary gene expression responses are correlated in European grayling (Thymallus thymallus) sub-populations adapted to different thermal environments

Understanding how populations adapt to changing environmental conditions is a long-standing theme in evolutionary biology. Gene expression changes have been recognized as an important driver of local adaptation, but relatively little is known regarding the direction of change and in particular, about the interplay between plastic and evolutionary gene expression. We have previously shown that the gene expression profiles of European grayling (Thymallus thymallus) populations inhabiting different thermal environments include both plastic and evolutionary components. However, whether the plastic and evolutionary responses were in the same direction was not investigated in detail, nor was the identity of the specific genes involved. In this study, we show that the plastic changes in protein expression in response to different temperatures are highly correlated with the evolutionary response in grayling subpopulations adapted to different thermal environments. This finding provides preliminary evidence that the plastic response most likely facilitates adaptation during the early phases of colonization of thermal environments. The proteins that showed significant changes in expression level between warm and cold temperature treatments were mostly related to muscle development, which is consistent with earlier findings demonstrating muscle mass differentiation between cold and warm grayling populations.

opencc-zeroDec 2018View details →

Data from: A macroecological approach to evolutionary rescue and adaptation to climate change

Despite the widespread use of Ecological Niche Models (ENMs) for predicting the responses of species to climate change, these models do not explicitly incorporate any population-level mechanism. On the other hand, mechanistic models adding population processes (e.g., biotic interactions, dispersal and adaptive potential to abiotic constraints) are much more complex and difficult to parameterize, especially if the goal is to predict range shifts for many species simultaneously. In particular, the adaptive potential (based on genetic adaptations, phenotypic plasticity and behavioral adjustments for physiological responses) of local populations has been the less studied mechanism affecting species' responses to climatic change so far. Here, we discuss and apply an alternative macroecological framework to evaluate the potential role of evolutionary rescue under climate change based on ENMs. We begin by reviewing eco-evolutionary models that evaluate the maximum sustainable evolutionary rate under a scenario of environmental change, showing how they can be used to understand the impact of temperature change on a Neotropical anuran species, the Schneider's toad Rhinella diptycha. Then we show how to evaluate spatial patterns of species' geographic range shift using such models, by estimating evolutionary rates at the species' trailing edge distribution estimated by ENMs and by recalculating the relative amount of total range loss under climate change. We show how different models can reduce the expected range loss predicted for the studied species by potential ecophysiological adaptations in some regions of the trailing edge predicted by ENMs. For general applications, we believe that parameters for large numbers of species and populations can be obtained from macroecological generalizations (e.g. allometric equations and ecogeographical rules), so our framework coupling ENMs with eco-evolutionary models can be applied to achieve a more accurate picture of potential impacts from climate changes and other threats to biodiversity.

opencc-zeroDec 2017View details →

Data from: Can larvae of a marine fish adapt to ocean acidification? Evaluating the evolutionary potential of California Grunion (Leuresthes tenuis)

Ocean acidification can reduce the growth and survival of marine species during their larval stages. However, if populations have the genetic capacity to adapt and increase their tolerance of low pH and high pCO2 levels, this may offset the harmful effects of ocean acidification. By combining controlled breeding experiments with laboratory manipulations of seawater chemistry, we evaluated genetic variation in tolerance of ocean acidification conditions for a nearshore marine fish, the California Grunion (Leuresthes tenuis). Our results indicated that acidification conditions increased overall mortality rates of grunion larvae, but did not have a significant effect on growth. Groups of larvae varied widely with respect to mortality and growth rates in both ambient and acidified conditions. We demonstrate that the potential to evolve in response to ocean acidification is best described by considering additive genetic variation in fitness-related traits under both ambient and acidified conditions, and by evaluating the genetic correlation between traits expressed in these environments. We used a multivariate animal model to estimate additive genetic (co)variance in larval growth and mortality rates under both ambient and acidified conditions (low pH/high pCO2). Our results suggest appreciable genetic variation in larval mortality rates (h2Ambient = 0.120; h2Acidified = 0.183; rG = 0.460), but less genetic variation in growth (h2Ambient = 0.092; h2Acidified = 0.101; rG = 0.135). Maternal effects on larval mortality rates accounted for 26-36% of the variation in phenotypes, but maternal effects accounted for only 8% of the variation in growth. Collectively, our estimates of genetic variation and covariation suggest that populations of California Grunion have the capacity to adapt relatively quickly to long-term changes in ocean chemistry.

opencc-zeroDec 2014View details →

Data from: Unique evolutionary trajectories in repeated adaptation to hydrogen sulphide-toxic habitats of a neotropical fish (Poecilia mexicana)

Replicated ecological gradients are prime systems to study processes of molecular evolution underlying ecological divergence. Here, we investigated the repeated adaptation of the neotropical fish Poecilia mexicana to habitats containing toxic hydrogen sulphide (H2S) and compared two population pairs of sulphide-adapted and ancestral fish by sequencing population pools of >200 individuals (Pool-Seq). We inferred the evolutionary processes shaping divergence and tested the hypothesis of increase of parallelism from SNPs to molecular pathways. Coalescence analyses showed that the divergence occurred in the face of substantial bidirectional gene flow. Population divergence involved many short, widely dispersed regions across the genome. Analyses of allele frequency spectra suggest that differentiation at most loci was driven by divergent selection, followed by a selection-mediated reduction of gene flow. Reconstructing allelic state changes suggested that selection acted mainly upon de novo mutations in the sulphide-adapted populations. Using a corrected Jaccard index to quantify parallel evolution, we found a negligible proportion of statistically significant parallel evolution of Jcorr = 0.0032 at the level of SNPs, divergent genome regions (Jcorr = 0.0061) and genes therein (Jcorr = 0.0091). At the level of metabolic pathways, the overlap was Jcorr = 0.2545, indicating increasing parallelism with increasing level of biological integration. The majority of pathways contained positively selected genes in both sulphide populations. Hence, adaptation to sulphidic habitats necessitated adjustments throughout the genome. The largely unique evolutionary trajectories may be explained by a high proportion of de novo mutations driving the divergence. Our findings favour Gould's view that evolution is often the unrepeatable result of stochastic events with highly contingent effects.

FIGURE 3. A in Concentrated evolutionary novelties in the foot musculature of Odontophrynidae (Anura: Neobatrachia), with comments on adaptations for burrowing

FIGURE 3. A. Plantar view of the right foot of Odontophrynus carvalhoi (CFBH 23425). Note the portion of the FAD with origin from the common tendon of origin of lLBB IV and mLBB V (character 8). B. Plantar view of the left foot of Spea hammondii (CM 73782). Note the distal portion of the FAD with origin from the tendon of the mLBB V (the proximal portion of the mLBB V and its tendon of origin are exaggerated in the shading of the figure for clarity, since they are partly fused to the base of ABP V). Removed elements of Figure 3A, B: TS I–V, LBL III–V, LLG IV, LBB I–V (proximal end of lLBB IV and mLBB V not removed), distal portion of FBS, distal and lateral portion of APLA, distal and ventral portion of distal element of PH; additionally, in Figure 3B, the tendon of origin of the lLBB IV from the FBS was removed. Abbreviations as indicated in Material and Methods. Scale bars = 1 mm.

FIGURE 2 in Concentrated evolutionary novelties in the foot musculature of Odontophrynidae (Anura: Neobatrachia), with comments on adaptations for burrowing

FIGURE 2. Plantar view of the left foot of Odontophrynus americanus (MACN 48528). A. Original photograph of Figure 2B. B. sLBB II–IV are the supplementary slips (characters 6–8) of the LBB II–IV (medial slip) with a fleshy insertion on metatarsi II–IV. Removed elements: TS I–V, LBL III–V, LLG IV, LBB II, LBB III, mLBB IV, distal portion of FBS and laterodistal region of APLA (over the plantar cartilage, PC). C. Original photograph of Figure 2D. D. Note the LBB III (dissected at the insertion point and held with a forceps), and it associated supplementary slip with fleshy insertion on Metatarsus III (indicated as sLBB III). The LBB III and the sLBB III have a common origin from the APLA and diverge distally. The same morphology as shown in LBB III and the sLBB III is also present in the LBB II and mLBB IV and their associated sLBB II and IV respectively. Removed elements: TS I–V, LBL III–V, LLG IV, distal portion of FBS and laterodistal region of APLA (over PC). Note that in B and D only the distal region of the APLA is shaded (not proximally) for a better understanding of its relationship with the origin of the LBB II–IV. Finally, note that the origin of the LBB II is also from the APLA (not evident in the figure), as in LBB III and mLBB IV; since the mediodistal region of the APLA is covered by the PH, it gives the false impression of an origin from the PH. Abbreviations as indicated in Material and Methods. Scale bars = 1 mm.

FIGURE 1. Ancestral character-state reconstructions for Characters 1–9 in Concentrated evolutionary novelties in the foot musculature of Odontophrynidae (Anura: Neobatrachia), with comments on adaptations for burrowing

FIGURE 1. Ancestral character-state reconstructions for Characters 1–9. Ambiguities in Macrogenioglottus alipioi and Odontophrynus carvalhoi in Characters 5–7 are due to polymorphism.

FIGURE 4. A in Concentrated evolutionary novelties in the foot musculature of Odontophrynidae (Anura: Neobatrachia), with comments on adaptations for burrowing

FIGURE 4. A. Dorsal view of the left foot of Odontophrynus occidentalis (MACN 38689). Note the sEBS I, with a common insertion on PH with the EBS I. B. Dorsal view of the left foot of O. carvalhoi (MZUSP 98179), the EBS I with origin on the tibiale is absent in this species. C. Dorsal view of the right foot of Rhinophrynus dorsalis (MACN 39131). Note the presence of a well-developed EBM I from the tibiale. D. Dorsal view of the right foot of Uperodon systoma (KU 193677). The element indicated as "X" is an unidentified slip with origin from the tibiale and insertion on PH (in common with the EBS I). Abbreviations as indicated in Material and Methods. Scale bars = 1 mm.