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212 results for “parallel evolution”
Compiling forty years of guppy research to investigate the factors contributing to (non)parallel evolution
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Data from: On measurements of phenotypic parallel evolution
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Adding the third dimension to studies of parallel evolution of morphology and function: an exploration based on parapatric lake-stream stickleback
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Functional characterization of luciferase in a brittle star indicates parallel evolution influenced by genomic availability of haloalkane dehalogenase
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Datasets and scripts from: Sensory-based quantification of male colour patterns in Trinidadian guppies reveals no support for parallel phenotypic evolution in multivariate trait space
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Parallel and divergent morphological adaptations underlying the evolution of jumping ability in ants
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Data from: Parallel molecular evolution in pathways, genes, and sites in high-elevation hummingbirds revealed by comparative transcriptomics
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Niche conservatism and sympatric parallel evolution may help to maintain eight nascent tree taxa along a sharp elevation gradient
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Parallel evolution of phenological isolation across the speciation continuum in serpentine-adapted annual wildflowers
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Data from: Devonian tetrapod-like fish reveals substantial parallelism in stem tetrapod evolution
The fossils assigned to the tetrapod stem group document the evolution of terrestrial vertebrates from lobe-finned fishes. During the past 18 years the phylogenetic structure of this stem group has remained remarkably stable, even when accommodating new discoveries such as the earliest known stem tetrapod Tungsenia and the elpistostegid (fish–tetrapod intermediate) Tiktaalik. Here we present a large lobe-finned fish from the Late Devonian period of China that disrupts this stability. It combines characteristics of rhizodont fishes (supposedly a basal branch in the stem group, distant from tetrapods) with derived elpistostegid-like and tetrapod-like characters. This mélange of characters may reflect either detailed convergence between rhizodonts and elpistostegids plus tetrapods, under a phylogenetic scenario deduced from Bayesian inference analysis, or a previously unrecognized close relationship between these groups, as supported by maximum parsimony analysis. In either case, the overall result reveals a substantial increase in homoplasy in the tetrapod stem group. It also suggests that ecological diversity and biogeographical provinciality in the tetrapod stem group have been underestimated.
Excessive parallelism in protein evolution of Lake Baikal amphipod species flock
Repeated emergence of similar adaptations is often explained by parallel evolution of underlying genes. However, evidence of parallel evolution at amino acid level is limited. When the analyzed species are highly divergent, this can be due to epistasic interactions underlying the dynamic nature of the amino acid preferences: the same amino acid substitution may have different phenotypic effects on different genetic backgrounds. Distantly related species also often inhabit radically different environments, which makes the emergence of parallel adaptations less likely. Here, we hypothesize that parallel molecular adaptations are more prevalent between closely related species. We analyze the rate of parallel evolution in genome-size sets of orthologous genes in three groups of species with widely ranging levels of divergence: 47 species of the relatively recent lake Baikal amphipod radiation, a species flock of very closely related cichlids, and a set of significantly more divergent vertebrates. In genes of amphipods, the rate of parallel substitutions at nonsynonymous sites exceeded that at synonymous sites, suggesting rampant selection driving parallel adaptation. By contrast, in cichlids, the rate of nonsynonymous parallel evolution nearly equalled that at synonymous sites, while in vertebrates, this rate was lower than that at synonymous sites, indicating the role of drift in fixation of parallel substitutions. Further data is needed to clarify the cause of the excessive parallelism observed in gammarids.
Data from: Parallel evolution of local adaptation and reproductive isolation in the face of gene flow
Parallel evolution of similar phenotypes provides strong evidence for the operation of natural selection. Where these phenotypes contribute to reproductive isolation, they further support a role for divergent, habitat-associated selection in speciation. However, the observation of pairs of divergent ecotypes currently occupying contrasting habitats in distinct geographical regions is not sufficient to infer parallel origins. Here we show striking parallel phenotypic divergence between populations of the rocky-shore gastropod, Littorina saxatilis, occupying contrasting habitats exposed to either wave action or crab predation. This divergence is associated with barriers to gene exchange but, nevertheless, genetic variation is more strongly structured by geography than by ecotype. Using approximate Bayesian analysis of sequence data and AFLP markers, we show that the ecotypes are likely to have arisen in the face of continuous gene flow and that the demographic separation of ecotypes has occurred in parallel at both regional and local scales. Parameter estimates suggest a long delay between colonisation of a locality and ecotype formation, perhaps because the postglacial spread of crab populations was slower than the spread of snails. Adaptive differentiation may not be fully genetically independent despite being demographically parallel. These results provide new insight into a major model of ecologically-driven speciation.
Data from: Phylogeography of the prickly sculpin (Cottus asper) in north-western North America reveals parallel phenotypic evolution across multiple coastal–inland colonizations
Aim: Glacial cycles during the Pleistocene may have frequently contributed to parallel evolution of phenotypes across independently evolving genetic lineages associated with separate glacial refugia. Previous studies based on morphology suggested that the prickly sculpin (Cottus asper) survived the Last Glacial Maximum (LGM) in southern coastal and inland refugia, favouring allopatric divergence between coastal and inland prickling phenotypes, which vary in the degree to which spine-like scales cover the body of the fish. Herein, we aimed to test whether parallel evolution across multiple genetic lineages rather than a single-lineage origin of highly prickled inland sculpins could serve as an explanation for the biogeographical distribution of prickling phenotypes. Location: North-western North America, Southeast Alaska and Canada (British Columbia). Methods: We used data from mitochondrial haplotypes and 19 microsatellite loci to identify distinct genetic lineages as a basis to interpret patterns of phenotypic evolution. Results: The occurrence of multiple mtDNA groups suggests that highly prickled inland phenotypes comprise more than one genetic lineage. Both mtDNA and microsatellite data are consistent with post-glacial dispersal along the coast and repeated coastal to inland colonization events, as opposed to inland dispersal of a single lineage from a southern refugium to northern regions. Main conclusions: Our results suggest that highly prickled inland phenotypes evolved repeatedly following multiple inland colonization events, probably via coastal rivers. The prickly sculpin therefore provides an example of recent (post-glacial) parallel evolution, potentially facilitated by standing genetic variation already present in the ancestral coastal populations.
Data from: Evolution of thermal tolerance and its fitness consequences: parallel and non-parallel responses to urban heat islands across three cities
The question of parallel evolution—what causes it, and how common it is—has long captured the interest of evolutionary biologists. Widespread urban development over the last century has driven rapid evolutionary responses on contemporary timescales, presenting a unique opportunity to test the predictability and parallelism of evolutionary change. Here we examine rapid urban evolution in an acorn-dwelling ant species, focusing on the urban heat island signal and the ant's tolerance of these altered urban temperature regimes. Using a common-garden experimental design with acorn ant colonies collected from urban and rural populations in three cities and reared under five temperature treatments in the laboratory, we assessed plastic and evolutionary shifts in the heat and cold tolerance of F1 offspring worker ants. In two of three cities, we found evolved losses of cold tolerance, and compression of thermal tolerance breadth. Results for heat tolerance were more complex: in one city, we found evidence of simple evolved shifts in heat tolerance in urban populations, though in another, the difference in urban and rural population heat tolerance depended on laboratory rearing temperature, and only became weakly apparent at the warmest rearing temperatures. The shifts in tolerance appeared to be adaptive, as our analysis of the fitness consequences of warming revealed that while urban populations produced more sexual reproductives under warmer laboratory rearing temperatures, rural populations produced fewer. Patterns of natural selection on thermal tolerances supported our findings of fitness tradeoffs and local adaptation across urban and rural acorn ant populations, as selection on thermal tolerance acted in opposite directions between the warmest and coldest rearing temperatures. Our study provides mixed support for parallel evolution of thermal tolerance under urban temperature rise.
Data from: Genomic clustering of adaptive loci during parallel evolution of an Australian wildflower
The buildup of the phenotypic differences that distinguish species has long intrigued biologists. These differences are often inherited as stable polymorphisms that allow the co-segregation of adaptive variation within species, and facilitate the differentiation of complex phenotypes between species. It has been suggested that the clustering of adaptive loci could facilitate this process but evidence is still scarce. Here we used QTL analysis to study the genetic basis of phenotypic differentiation between coastal populations of the Australian wildflower Senecio lautus. We found that a genomic region consistently governs variation in several of the traits that distinguish these contrasting forms. Additionally, some of the taxon specific traits controlled by this QTL cluster have evolved repeatedly during the adaptation to the same habitats, suggesting that it could mediate divergence between locally adapted forms. This cluster contains footprints of divergent natural selection across the range of S. lautus, which suggests that it could have been instrumental for the rapid diversification of this species.
Data from: Parallel evolution and adaptation to environmental factors in a marine flatfish: implications for fisheries and aquaculture management of the turbot (Scophthalmus maximus)
Unraveling adaptive genetic variation represents, in addition to the estimate of population demographic parameters, a cornerstone for the management of aquatic natural living resources, which in turn, represent the raw material for breeding programs. The turbot (Scophthalmus maximus) is a marine flatfish of high commercial value living on the European continental shelf. While wild populations are declining, aquaculture is flourishing in Southern Europe. We evaluated the genetic structure of turbot throughout its natural distribution range (672 individuals; 20 populations) by analyzing allele frequency data from 755 Single Nucleotide Polymorphism discovered and genotyped by Double Digest RAD Sequencing. The species was structured into four main regions: Baltic Sea, Atlantic Ocean, Adriatic Sea and Black Sea, with subtle differentiation apparent at the distribution margins of the Atlantic region. Genetic diversity and effective population size estimates were highest in the Atlantic populations, the area of greatest occurrence, while turbot from other regions showed lower levels, reflecting geographical isolation and reduced abundance. Divergent selection was detected within and between the Atlantic Ocean and Baltic Sea regions, and also when comparing these two regions with the Black Sea. Evidence of parallel evolution was detected between the two low salinity regions, the Baltic and Black seas. Correlation between genetic and environmental variation indicated that temperature and salinity were probably the main environmental drivers of selection. Mining around the four genomic regions consistently inferred to be under selection identified candidate genes related to osmoregulation, growth and resistance to diseases. The new insights are useful for the management of turbot fisheries and aquaculture by providing the baseline for evaluating the consequences of turbot releases from restocking and farming.
Data from: Recurrent selection explains parallel evolution of genomic regions of high relative but low absolute differentiation in a ring species
Recent technological developments allow investigation of the repeatability of evolution at the genomic level. Such investigation is particularly powerful when applied to a ring species, in which spatial variation represents changes during the evolution of two species from one. We examined genomic variation among three subspecies of the greenish warbler ring species, using genotypes at 13 013 950 nucleotide sites along a new greenish warbler consensus genome assembly. Genomic regions of low within-group variation are remarkably consistent between the three populations. These regions show high relative differentiation but low absolute differentiation between populations. Comparisons with outgroup species show the locations of these peaks of relative differentiation are not well explained by phylogenetically conserved variation in recombination rates or selection. These patterns are consistent with a model in which selection in an ancestral form has reduced variation at some parts of the genome, and those same regions experience recurrent selection that subsequently reduces variation within each subspecies. The degree of heterogeneity in nucleotide diversity is greater than explained by models of background selection, but is consistent with selective sweeps. Given the evidence that greenish warblers have had both population differentiation for a long period of time and periods of gene flow between those populations, we propose that some genomic regions underwent selective sweeps over a broad geographic area followed by within-population selection-induced reductions in variation. An important implication of this 'sweep-before-differentiation' model is that genomic regions of high relative differentiation may have moved among populations more recently than other genomic regions.
Data from: A single interacting species leads to widespread parallel evolution of the stickleback genome
Biotic interactions are potent, widespread causes of natural selection and divergent phenotypic evolution, and can lead to genetic differentiation with gene flow among wild populations ("isolation by ecology") [1-4]. Biotic selection has been predicted to act on more genes than abiotic selection thereby driving greater adaptation [5]. However, difficulties in isolating the genome-wide effect of single biotic agents of selection have limited our ability to identify and quantify the number and type of specific genetic regions responding to biotic selection [6-9]. We identified geographically interspersed lakes in which threespine stickleback fish (Gasterosteus aculeatus) have repeatedly adapted to the presence/absence of a single member of the ecological community, prickly sculpin (Cottus asper), a fish species that is both competitor and predator of stickleback [10]. Whole genome sequencing revealed that sculpin presence/absence accounted for the majority of genetic divergence among populations, more so than geography. The major axis of stickleback genomic variation within and between the two lake types was correlated with multiple traits, indicating parallel natural selection across a gradient of biotic environments. A large proportion of the genome - about 1.8%, encompassing more than 600 genes – differentiated stickleback from the two biotic environments. Divergence occurred in 141 discrete genomic clumps located mainly in regions of low recombination within the stickleback genome, suggesting that genes brought to lakes by the colonizing ancestral population often evolved together in linked blocks. Strong selection and a wealth of standing genetic variation explain how a single member of the biotic community can have such a rapid and profound evolutionary impact.
Data from: Pumping ions: rapid parallel evolution of ionic regulation following habitat invasions
Marine to freshwater colonizations constitute among the most dramatic evolutionary transitions in the history of life. This study examined evolution of ionic regulation following saline-to-freshwater transitions in an invasive species. In recent years, the copepod Eurytemora affinis has invaded freshwater habitats multiple times independently. We found parallel evolutionary shifts in ion-motive enzyme activity (V-type H+ ATPase, Na+/K+-ATPase) across independent invasions and in replicate laboratory selection experiments. Freshwater populations exhibited increased V-type H+ ATPase activity in fresh water (0 PSU) and declines at higher salinity (15 PSU) relative to saline populations. This shift represented marked evolutionary increases in plasticity. In contrast, freshwater populations displayed reduced Na+/K+-ATPase activity across all salinities. Most notably, modifying salinity alone during laboratory selection experiments recapitulated the evolutionary shifts in V-type H+ ATPase activity observed in nature. Maternal and embryonic acclimation could not account for the observed shifts in enzyme activity. V-type H+ ATPase function has been hypothesized to be critical for freshwater and terrestrial adaptations, but evolution of this enzyme function had not been previously demonstrated in the context of habitat transitions. Moreover, the speed of these evolutionary shifts was remarkable, within a few generations in the laboratory and a few decades in the wild.
FIGURES 9–13. 9 in A new species of Dexoris (Coleoptera: Lycidae) and parallel evolution of brachyptery in the soft-bodied elateroid beetles
FIGURES 9–13. 9 Omalisus fontisbellaquaei, general appearance; 10–12 Dexoris chome sp. nov., male genitalia; 13 ditto, terminal abdominal segments. Scale 1 mm (Fig. 9), 0.2 mm (Figs 10–13).
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.