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1,456 results for “parallelism”
Data from: Oxidative phosphorylation gene transcription in whitefish species pairs reveals patterns of parallel and non-parallel physiological divergence
Across multiple lakes in North America, lake whitefish (Coregonus clupeaformis) have independently evolved "dwarf" and "normal" sympatric species pairs that exhibit pronounced phenotypic and genetic divergence. In particular, traits associated with metabolism have been shown to be highly differentiated between whitefish species. Here, we examine the transcription of genes associated with all five mitochondrial and nuclear genome-encoded oxidative phosphorylation (OXPHOS) complexes, the primary physiological mechanism responsible for the production of ATP, in whitefish species pairs from Cliff Lake and Webster Lake in Maine, USA. We observed OXPHOS gene transcription divergence between dwarf and normal whitefish in each of the two lakes, with the former exhibiting transcription upregulation for genes associated with each of the OXPHOS complexes. We also observed a significant influence of lake on transcription levels for some of the genes, indicating that inter-lake ecological or genetic differences are contributing to variation in OXPHOS gene transcription levels. Together, our results support the hypothesis that metabolic divergence is a critical adaptation involved in whitefish speciation, and implicate OXPHOS gene upregulation as a factor involved in meeting the enhanced energetic demands of dwarf whitefish. Further examination of the links between this critical physiological pathway and ecological and genetic variation will provide insight into the fine-scale evolutionary dynamics at work in nature.
Data from: Contrasting genetic diversity and population structure among three sympatric Madagascan shorebirds: parallels with rarity, endemism, and dispersal
Understanding the relative contributions of intrinsic and extrinsic factors to population structure and genetic diversity is a central goal of conservation and evolutionary genetics. One way to achieve this is through comparative population genetic analysis of sympatric sister taxa, which allows evaluation of intrinsic factors such as population demography and life history while controlling for phylogenetic relatedness and geography. We used ten conserved microsatellites to explore the population structure and genetic diversity of three sympatric and closely related plover species in southwestern Madagascar: Kittlitz's plover (Charadrius pecuarius), white-fronted plover (C. marginatus), and Madagascar plover (C. thoracicus). Bayesian clustering revealed strong population structure in the rare and endemic Madagascar plover, intermediate population structure in the white-fronted plover, and no detectable population structure in the geographically widespread Kittlitz's plover. In contrast, allelic richness and heterozygosity were highest for the Kittlitz's plover, intermediate for the white-fronted plover and lowest for the Madagascar plover. No evidence was found in support of the "watershed mechanism" proposed to facilitate vicariant divergence of Madagascan lemurs and reptiles, which we attribute to the vagility of birds. However, we found a significant pattern of genetic isolation by distance among populations of the Madagascar plover, but not for the other two species. These findings suggest that interspecific variation in rarity, endemism, and dispersal propensity may influence genetic structure and diversity, even in highly vagile species.
Data from: Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform
Genetic information is a valuable component of biosystematics, especially specimen identification through the use of species-specific DNA barcodes. Although many genomics applications have shifted to High-Throughput Sequencing (HTS) or Next-Generation Sequencing (NGS) technologies, sample identification (e.g., via DNA barcoding) is still most often done with Sanger sequencing. Here, we present a scalable double dual-indexing approach using an Illumina Miseq platform to sequence DNA barcode markers. We achieved 97.3% success by using half of an Illumina Miseq flowcell to obtain 658 base pairs of the cytochrome c oxidase I DNA barcode in 1,010 specimens from eleven orders of arthropods. Our approach recovers a greater proportion of DNA barcode sequences from individuals than does conventional Sanger sequencing, while at the same time reducing both per specimen costs and labor time by nearly 80%. In addition, the use of HTS allows the recovery of multiple sequences per specimen, for deeper analysis of genetic variation in target gene regions.
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.
Data from: Demographic modelling with whole-genome data reveals parallel origin of similar Pundamilia cichlid species after hybridization
Modes and mechanisms of speciation are best studied in young species pairs. In older taxa, it is increasingly difficult to distinguish what happened during speciation from what happened after speciation. Lake Victoria cichlids in the genus Pundamilia encompass a complex of young species and polymorphic populations. One Pundamilia species pair, P. pundamilia and P. nyererei, is particularly well suited to study speciation because sympatric population pairs occur with different levels of phenotypic differentiation and reproductive isolation at different rocky islands within the lake. Genetic distances between allopatric island populations of the same nominal species often exceed those between the sympatric species. It thus remained unresolved whether speciation into P. nyererei and P. pundamilia occurred once, followed by geographical range expansion and interspecific gene flow in local sympatry, or if the species pair arose repeatedly by parallel speciation. Here, we use genomic data and demographic modelling to test these alternative evolutionary scenarios. We demonstrate that gene flow plays a strong role in shaping the observed patterns of genetic similarity, including both gene flow between sympatric species and gene flow between allopatric populations, as well as recent and early gene flow. The best supported model for the origin of P. pundamilia and P. nyererei population pairs at two different islands is one where speciation happened twice, whereby the second speciation event follows shortly after introgression from an allopatric P. nyererei population that arose earlier. Our findings support the hypothesis that very similar species may arise repeatedly, potentially facilitated by introgressed genetic variation.
Data from: Parallelism isn't perfect: could disease and flooding drive a life history anomaly in Trinidadian guppies?
Nonparallel evolution, where independent populations occupy similar environments but show phenotypic differences, can uncover previously ignored selective factors. We investigated a nonparallelism in the life-history strategy of a Trinidadian guppy population, a system famous for parallel adaptation to differences in predation risk. We tested the hypothesis that high mortality drives an observed fast life-history pattern (i.e., earlier maturation and more frequent reproductive events) that is atypical for a low-predation environment. Using mark-recapture techniques, we compared neighboring low-predation populations, finding significantly higher mortality rates in the population with atypical life-history traits. Mortality was elevated during the wet season, when flooding was common. Moreover, individuals from the anomalous population were more likely to transition from healthy to infected disease states. Our results stand out against previous patterns observed in this system, indicating that higher mortality caused by disease and flooding may have selected for a faster life history. Thus, we highlight that even in systems famous for parallel adaptation, variation in selective pressures can result in nonparallel phenotypic evolution.
Data for: Increasing the Throughput of Pipe-and-Filter Architectures by Integrating the Task Farm Parallelization Pattern
<p>Data for the research paper "Increasing the Throughput of Pipe-and-Filter Architectures by Integrating the Task Farm Parallelization Pattern" in Proceedings of the CBSE, 2016</p>
FIGURE 3 in A phylogenetic reassessment of African fossorial skinks in the subfamily Acontinae (Squamata: Scincidae): evidence for parallelism and polyphyly
FIGURE 3. The revised acontine taxonomy. Dotted line shows placement of Acontias percivali based on analysis of the mitochondrial dataset.
FIGURE 2 in A phylogenetic reassessment of African fossorial skinks in the subfamily Acontinae (Squamata: Scincidae): evidence for parallelism and polyphyly
FIGURE 2. Majority rule consensus tree for Bayesian analysis of the combined dataset. Mean tree likelihood = -16416. Thickened branches indicate posterior probabilities ≥0.98; bootstrap values (≥70%) for ML and MP (italicized) analyses are placed at nodes. Note the polyphyletic status of the genus Typhlosaurus, whose branches are depicted in gray.
FIGURE 1 in A phylogenetic reassessment of African fossorial skinks in the subfamily Acontinae (Squamata: Scincidae): evidence for parallelism and polyphyly
FIGURE 1. Majority rule consensus trees for Bayesian analyses of the mitochondrial (Cytb, Co1, 16s) and nuclear (Rag1) datasets. Mean tree likelihoods are -10962 (mitochondrial) and -3634 (Rag1). Posterior probabilities ≥0.98 and ML bootstrap values ≥70% (italicized) are adjacent nodes. Topologies are rooted to the three outgroup taxa (not shown).
FIGURES 16–21 in On some species of Pandeleteius Schoenherr, 1834, in South America south of the tenth parallel (Coleoptera, Curculionidae: Entiminae: Tanymecini)
FIGURES 16–21. Pandeleteius sahlbergi Howden: 16–19: male genitalia, 16, lateral view; 17, enlarged lateral view (Brazil); 18, dorsal view genitalia; 19, tegmen. 20–21: female genitalia (allotype), 20, dorsal view; 21, ventral view.
FIGURES 10–15 in On some species of Pandeleteius Schoenherr, 1834, in South America south of the tenth parallel (Coleoptera, Curculionidae: Entiminae: Tanymecini)
FIGURES 10–15. Pandeleteius platensis (Brèthes): 10–12, male genitalia, aedeagus extruded (Argentina); 11, dorsal view genitalia (Brazil); 12, sternite 9 (Uruguay). 13–15, female: 13, genitalia (Argentina); 14, same but more mature; 15, sternite 8 (Argentina).
FIGURE 22 in On some species of Pandeleteius Schoenherr, 1834, in South America south of the tenth parallel (Coleoptera, Curculionidae: Entiminae: Tanymecini)
FIGURE 22. Map of collection localities for Pandeleteius griseus (black dots) and P. s a h l b e rg i (grey dots).
FIGURES 7–9 in On some species of Pandeleteius Schoenherr, 1834, in South America south of the tenth parallel (Coleoptera, Curculionidae: Entiminae: Tanymecini)
FIGURES 7–9. Pandeleteius griseus (Voss): 7, male, aedeagus, lateral view; 8, female, genitalia; 9, male, sternite 9.
FIGURE 3 in Linking operational clustered taxonomic units (OCTUs) from parallel ultra sequencing (PUS) to nematode species
FIGURE 3. Numbers of OCTUs formed at 99% within-OCTU similarity for each recovered nematode species. Brackets group species by the persistence (Always, Often, Never) of Head-Tail structure of OCTUs. Error bars indicate standard deviation across 7 metagenetic datasets.
FIGURE 5 in Linking operational clustered taxonomic units (OCTUs) from parallel ultra sequencing (PUS) to nematode species
FIGURE 5. Estimated (using the Head-Tail guidelines) number of nematode species from OCTUs generated at 99% within-OCTU similarity for sequencing reads recovered from soil, litter, and canopy habitats at La Selva Biological Station in Costa Rica.
FIGURE 2 in Linking operational clustered taxonomic units (OCTUs) from parallel ultra sequencing (PUS) to nematode species
FIGURE 2. Number of nematode species recovered using different levels of within-OCTU (operational clustered taxonomic units) similarity. Bars represent means across 7 metagenetic datasets. Error bars indicate standard deviation. Note: out of 41 used nematode species, three did not amplify (Porazinska et al. 2009a).
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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.