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Fig. 5 in Parallel evolution of leaf morphology in gnetophytes
Fig. 5 Nodal portion of a shoot of Ephedra multinervia. a The swollen node and the lengthy strap leaf. b The multiple dichotomizing parallel veins. c Connections of veins. l leaf, v vein, n node
Fig. 2 in Parallel evolution of leaf morphology in gnetophytes
Fig. 2 Leaf venation of the modern gnetophytes. a–b Ephedra (from Foster 1971). c Gnetum (from Rodin 1967). d Welwitschia (from Martens 1971)
Fig. 1 in Parallel evolution of leaf morphology in gnetophytes
Fig. 1 Phylogeny of the modern gnetophytes indicating the diversified morphology of leaves and female cones
Fig. 4 in Phylogeographical and Morphological Analyses of Triplophysa stenura (Cypriniformes: Nemacheilidae) from the Three Parallel Rivers Region, China
Fig. 4. The haplotype network constructed by median-joining method. Haplotypes are named as in table 1. Red dots are median vectors, which are hypothesized sequences to connect existing sequences within the network under maximum parsimony. The yellow circles are haplotypes from the Jinsha River drainage, blue circles are haplotypes from the Lancang River drainage, and green circles represent haplotypes from the Nu River drainage. The size of the circles is proportional to haplotype frequency.
Fig. 3 in Phylogeographical and Morphological Analyses of Triplophysa stenura (Cypriniformes: Nemacheilidae) from the Three Parallel Rivers Region, China
Fig. 3. Phylogenetic relationships within Triplophysa stenura as inferred by Bayesian analysis of combined Cytochrome b and D-Loop sequences. (Posterior probabilities are shown on nodes). © 2018 Academia Sinica, Taiwan
Fig. 2 in Phylogeographical and Morphological Analyses of Triplophysa stenura (Cypriniformes: Nemacheilidae) from the Three Parallel Rivers Region, China
Fig. 2. Lateral views of Triplophysa stenura individuals from different localities. (A) Changdu, Tibet. KIZ 20100045 138 mm SL; (B) Batang, Sichuan KIZ 2009003584 113 mm SL; (C) Baiyu, Sichuan KIZ 2006009508 121 mm SL; (D) Shigu, Yunnan KIZ 201100003 86.6 mm SL; (E) Gongshan, Yunnan KIZ 20007198 78.4 mm SL; (F) Tuotuohe, Qinghai KIZ 2004002141 68.9 mm SL; (G) Anduoqu, Tibet KIZ 2004002201 79.9 mm SL; (H) Yangbi,Yunnan KIZ 1974000595 60.1 mm SL. Scale bar = 1 cm.
Fig. 1 in Phylogeographical and Morphological Analyses of Triplophysa stenura (Cypriniformes: Nemacheilidae) from the Three Parallel Rivers Region, China
Fig. 1. Map showing the collection localities of Triplophysa stenura in this study (numbers correspond to name of localities in Table 1). © 2018 Academia Sinica, Taiwan
Fig. 5 in Phylogeographical and Morphological Analyses of Triplophysa stenura (Cypriniformes: Nemacheilidae) from the Three Parallel Rivers Region, China
Fig. 5. Scatter plots of the first two principal components for Triplophysa stenura individuals from three drainages (A) and populations within three drainages respectively (B: Jinsha R. Drainage; C: Lancang R. Drainage; D: Nu R. Drainage). The locality abbreviations are shown in table 1.
Data for "Parallel-Field Hall effect in ZrTe5"
<p>Here we upload the raw data for the manuscript entitled “Parallel-Field Hall effect in ZrTe5”</p>
Data set and simulation code for "Static workspace computation for underactuated cable-driven parallel robots"
<p>See the attached readme file</p>
Data from: Investigating genomic and phenotypic parallelism between piscivorous and planktivorous lake trout (Salvelinus namaycush) ecotypes by means of RADseq and morphometrics analyses
Repeated adaptive ecological diversification has commonly been reported in fish and has often been associated with trophic niche diversity. The main goal of this study was to investigate the extent of parallelism in the genomic and phenotypic divergence between piscivorous and planktivorous lake trout ecotypes from Laurentian Shield lakes, Canada. This was achieved by documenting the extent of morphological differentiation using geometric morphometrics and linear measurements as well as the pattern of genomic divergence by means of RADseq genotyping (3925 filtered SNPs) in 12 lakes. Our results indicate that the two ecotypes evolved distinct body shape and several linear measurements in parallel. Neutral genetic differentiation was pronounced between all isolated populations (Mean FST = 0.433), indicating no or very limited migration and pronounced genetic drift. Significant genetic differentiation also suggested partial reproductive isolation between ecotypes in the two lakes where they are found in sympatry. Combining different outlier detection methods, we identified 48 SNPs putatively under divergent selection between ecotypes, among which 10 could be annotated and related to functions such as developmental processes and ionic regulation. Finally, our results indicate that parallel morphological divergence is accompanied by both parallel and nonparallel genomic divergence, which is associated with the use of different trophic niches between ecotypes. The results are also discussed in the context of management and conservation of this highly exploited species throughout northern North America.
Data from: Parallel evolution of jugal structures in Devonian athyridide brachiopods
Here, we describe Sinathyris crassa gen. et sp. nov., a new early Emsian (Early Devonian) athyridide brachiopod with a double spiralium from the Guangxi Province of southern China. Unlike the majority of genera of the subfamily Helenathyridinae, which possess accessory spiral lamellae developed directly from the jugal branches, the form described here shows these lamellae arising from a distally bifurcating jugal stem. These differences suggest that the double spiralium in S. crassa might have appeared independently from the double spiralium of the helenathyridins. To test the subfamily assignment of Sinathyris gen. nov., we carried out phylogenetic analyses, which indicate that the new genus is more appropriately referred to the Didymothyridinae. The cladistic analyses of the athyridides indicate that double spiralia have developed independently among these brachiopods at least five times during their evolutionary history.
Data from: Do North Atlantic Eels show parallel patterns of spatially varying selection?
Background: The two North Atlantic eel species, the European and the American eel, represent an ideal system in which to study parallel selection patterns due to their sister species status and the presence of ongoing gene flow. A panel of 80 coding-gene SNPs previously analyzed in American eel was used to genotype European eel individuals (glass eels) from 8 sampling locations across the species distribution. We tested for single-generation signatures of spatially varying selection in European eel by searching for elevated genetic differentiation using FST-based outlier tests and by testing for significant associations between allele frequencies and environmental variables. Results: We found signatures of possible selection at a total of 11 coding-gene SNPs. Candidate genes for local selection constituted mainly genes with a major role in metabolism as well as defense genes. Contrary to what has been found for American eel, only 2 SNPs in our study correlated with differences in temperature, which suggests that other explanatory variables may play a role. None of the genes found to be associated with explanatory variables in European eel showed any correlations with environmental factors in the previous study in American eel. Conclusions: The different signatures of selection between species could be due to distinct selective pressures associated with the much longer larval migration for European eel relative to American eel. The lack of parallel selection in North Atlantic eels could also be due to most phenotypic traits being polygenic, thus reducing the likelihood of selection acting on the same genes in both species.
Data from: Do the same genes underlie parallel phenotypic divergence in different Littorina saxatilis populations?
Parallel patterns of adaptive divergence and speciation are cited as powerful evidence for the role of selection driving these processes. However, it is often not clear whether parallel phenotypic divergence is underlain by parallel genetic changes. Here, we asked about the genetic basis of parallel divergence in the marine snail Littorina saxatilis, which has repeatedly evolved coexisting ecotypes adapted to either crab predation or wave action. We sequenced the transcriptome of snails of both ecotypes from three distant geographical locations (Spain, Sweden and United Kingdom) and mapped the reads to the L. saxatilis reference genome. We identified genomic regions potentially under divergent selection between ecotypes within each country, using an outlier approach based on FST values calculated per locus. In line with previous studies indicating that gene reuse is generally common, we expected to find extensive sharing of outlier loci due to recent shared ancestry and gene flow between at least two of the locations in our study system. Contrary to our expectations, we found that most outliers were country specific, suggesting that much of the genetic basis of divergence is not shared among locations. However, we did find that more outliers were shared than expected by chance and that differentiation of shared outliers is often generated by the same SNPs. We discuss two mechanisms potentially explaining the limited amount of sharing we observed. First, a polygenic basis of divergent traits might allow for multiple distinct molecular mechanisms generating the same phenotypic patterns. Second, additional, location-specific axes of selection that we did not focus on in this study may produce distinct patterns of genetic divergence within each site.
Data from: Parallel signatures of selection in temporally-isolated lineages of pink salmon
Studying the effect of similar environments on diverse genetic backgrounds has long been a goal of evolutionary biologists with studies typically relying on experimental approaches. Pink salmon, a highly-abundant and widely-ranging salmonid, provide a naturally-occurring opportunity to study the effects of similar environments on divergent genetic backgrounds due to a strict two-year semelparous life-history. The species is composed of two reproductively-isolated lineages with overlapping ranges that share the same spawning and rearing environments in alternate years. We used restriction site-associated DNA (RAD) sequencing to discover and genotype approximately 8,000 SNP loci in three population pairs of even- and odd-year pink salmon along a latitudinal gradient in North America. We found greater differentiation within the odd-year than the even-year lineage and greater differentiation in the southern pair from Puget Sound than in the northern Alaskan population pairs. We identified 15 SNPs reflecting signatures of parallel selection using both a differentiation-based method (BAYESCAN) and an environmental correlation method (BAYENV). These SNPs represent genomic regions that may be particularly informative in understanding adaptive evolution in pink salmon and exploring how differing genetic backgrounds within a species respond to selection from the same natural environment.
Data from: Parsing parallel evolution: ecological divergence and differential gene expression in the adaptive radiations of thick-lipped Midas cichlid fishes from Nicaragua
The study of parallel evolution facilitates the discovery of common rules of diversification. Here, we examine the repeated evolution of thick lips in Midas cichlid fishes (the Amphilophus citrinellus species complex)—from two Great Lakes and two crater lakes in Nicaragua—to assess whether similar changes in ecology, phenotypic trophic traits and gene expression accompany parallel trait evolution. Using next-generation sequencing technology, we characterize transcriptome-wide differential gene expression in the lips of wild-caught sympatric thick- and thin-lipped cichlids from all four instances of repeated thick-lip evolution. Six genes (apolipoprotein D, myelin-associated glycoprotein precursor, four-and-a-half LIM domain protein 2, calpain-9, GTPase IMAP family member 8-like and one hypothetical protein) are significantly underexpressed in the thick-lipped morph across all four lakes. However, other aspects of lips' gene expression in sympatric morphs differ in a lake-specific pattern, including the magnitude of differentially expressed genes (97-510). Generally, fewer genes are differentially expressed among morphs in the younger crater lakes than in those from the older Great Lakes. Body shape, lower pharyngeal jaw size and shape, and stable isotopes (δ13C and δ15N) differ between all sympatric morphs, with the greatest differentiation in the Great Lake Nicaragua. Some ecological traits evolve in parallel (those related to foraging ecology; e.g. lip size, body and head shape) but others, somewhat surprisingly, do not (those related to diet and food processing; e.g. jaw size and shape, stable isotopes). Taken together, this case of parallelism among thick- and thin-lipped cichlids shows a mosaic pattern of parallel and nonparallel evolution.
Data from: Targeted resequencing reveals geographical patterns of differentiation for loci implicated in parallel evolution
Parallel divergence and speciation provide evidence for the role of divergent selection in generating biological diversity. Recent studies indicate that parallel phenotypic divergence may not have the same genetic basis in different geographical locations - "outlier loci" (loci potentially affected by divergent selection) are often not shared among parallel instances of phenotypic divergence. However, limited sharing may be due, in part, to technical issues if false positive outliers occur. Here, we test this idea in the marine snail Littorina saxatilis, which has evolved two partly isolated ecotypes (adapted to crab predation vs. wave action) in multiple locations independently. We argue that if the low extent of sharing observed in earlier studies in this system is due to sampling effects, we expect outliers not to show elevated FST when sequenced in new samples from the original locations, and also not to follow predictable geographical patterns of elevated FST. Following a hierarchical sampling design (within vs. between country), we applied capture sequencing, targeting outliers from earlier studies and control loci. We found that outliers again showed elevated levels of FST in their original location, suggesting they were not generated by sampling effects. Outliers were also likely to show increased FST in geographically close locations, which may be explained by higher levels of gene flow or shared ancestral genetic variation compared to more distant locations. However, in contrast to earlier findings, we also found some outlier types to show elevated FST in geographically distant locations. We discuss possible explanations for this unexpected result.
Parallel evolution of ancient, pleiotropic enhancers underlies butterfly wing pattern mimicry
Color pattern mimicry in Heliconius butterflies is a classic case study of complex trait adaptation via selection on a few large effect genes. Association studies have linked color pattern variation to a handful of noncoding regions, yet the presumptive cis-regulatory elements (CREs) that control color patterning remain unknown. Here we combine chromatin assays, DNA sequence associations, and genome editing to functionally characterize 5 cis-regulatory elements of the color pattern gene optix. We were surprised to find that the cis-regulatory architecture of optix is characterized by pleiotropy and regulatory fragility, where deletion of individual cis-regulatory elements has broad effects on both color pattern and wing vein development. Remarkably, we found orthologous cis-regulatory elements associate with wing pattern convergence of distantly related comimics, suggesting that parallel coevolution of ancestral elements facilitated pattern mimicry. Our results support a model of color pattern evolution in Heliconius where changes to ancient, multifunctional cis-regulatory elements underlie adaptive radiation.
Data from: Genomics of rapid ecological divergence and parallel adaptation in four tidal marsh sparrows
Theory suggests that different taxa having colonized a similar, challenging environment will show parallel or lineage-specific adaptations to shared selection pressures, but empirical examples of parallel evolution in independent taxa are exceedingly rare. We employed comparative genomics to identify parallel and lineage-specific responses to selection within and among four species of North American sparrows that represent four independent, post-Pleistocene colonization events by an ancestral, upland subspecies and a derived salt marsh specialist. We identified multiple cases of parallel adaptation in these independent comparisons following salt marsh colonization, including selection on twelve candidate genes linked to osmoregulation. In addition to detecting shared genetic targets of selection across multiple comparisons, we found many novel, species-specific signatures of selection, including evidence of selection on loci associated with both physiological and behavioral mechanisms of osmoregulation. Demographic reconstructions of all four species highlighted their recent divergence and small effective population sizes, as expected given their rapid radiation into saline environments. Our results highlight the interplay of both shared and lineage-specific selection pressures in the colonization of a biotically and abiotically challenging habitat and confirm theoretical expectations that steep environmental clines can drive repeated and rapid evolutionary diversification in birds.
Efficient parallelization of tensor network contractions for simulating quantum computation
<p> In this paper, we demonstrate a classical simulation framework for quantum computation by contracting tensor networks of sizes previously deemed out of reach. The main contribution of this work is a parallelization scheme called <em>index slicing</em> that breaks down an infeasibly large tensor network contraction task into smaller subtasks that can be executed fully in parallel, without interdependencies or intermediate communications. As a benchmarking example, we show that our algorithm can reduce the simulation of the Sycamore random circuit sampling task to less than 20 days, achieving an acceleration of over five orders of magnitude compared to the original proposal. We then showcase the capabilities of the simulation framework via investigations of near-term quantum algorithms and quantum error correction. Given the ubiquity of tensor networks in quantum information science, we believe that our simulation framework will be a valuable tool in the era of quantum information technology.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.