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Data from: New ways to acquire resistance – Imperfect convergence in insect adaptations to a potent plant toxin
Evolution of insensitivity to the toxic effects of cardiac glycosides has become a model in the study of convergent evolution, as five taxonomic orders of insects use the same few similar amino acid substitutions in the otherwise highly conserved Na,K-ATPase α. We here show that insensitivity in pyrgomorphid grasshoppers evolved along a slightly divergent path. As in other lineages, duplication of the Na,K-ATPase α gene paved the way for subfunctionalization: one copy maintains the ancestral, sensitive state while the other copy is resistant. Nonetheless, in contrast to all other investigated insects, the grasshoppers' resistant copy shows length variation by two amino acids in the first extracellular loop, the main part of the cardiac glycoside binding pocket. RT-qPCR analyses confirmed this copy is predominantly expressed in tissues exposed to the toxins, while the ancestral copy predominates in the nervous tissue. Functional tests with genetically engineered Drosophila Na,K-ATPases bearing the first extracellular loop of the pyrgomorphid genes showed the derived form to be highly resistant, while the ancestral state is sensitive. Thus, we report convergence in gene duplication and in the gene targets for toxin insensitivity, however the means to the phenotypic end have been novel in pyrgomorphid grasshoppers.
Data from: Application of benchmark concentration (BMC) analysis on zebrafish data – a new perspective for quantifying toxicity in alternative animal models
Over the past decade, the zebrafish is increasingly being used as a model to screen for chemical-mediated toxicities including developmental toxicity (DT) and neurotoxicity (NT). One of the major challenges is lack of harmonization in data analysis approaches, thereby posing difficulty in comparing findings across laboratories. To address this, we sought to establish a unified data analysis strategy for both DT and NT data, by adopting the benchmark concentration (BMC) analysis. There are two critical aspects in the BMC analysis: having a toxicity endpoint amenable for BMC and selecting a proper benchmark response (BMR) for the endpoint. For the former, in addition to the typical endpoints in NT assay (e.g., hyper/hypo- response quantified by distance moved), we also used endpoints that assess the differences in movement patterns between chemical-treated embryos and control embryos. For the latter, we standardized the selection of BMR, which is analogous to minimum activity threshold, based on intrinsic response variations in the endpoint. When comparing our BMC results with a traditionally used LOAEL method (Lowest-Observed-Adverse-Effect Level), we found high active compound concordance (100% for DT vs 74% for NT); generally, the BMC was more sensitive than LOAEL (# of BMC more sensitive/# of concordant active compounds, 43/50 for DT vs 16/26 for NT). Using the BMC with standardized toxicity endpoints and an appropriate BMR, we may now have a unified data-analysis approach to comparing results across different zebrafish datasets, for a better understanding of strengths and challenges when using the zebrafish as a screening tool.
Data from: New Crystal Forms and Amorphous Phase of Sophoricoside: X-Ray Structures and Characterization
Sophoricoside, which is an isoflavone glycoside found in many plant species, has recently attracted attention because of its anti-fertility activity. One solvent-free form, two solvatomorphs and an amorphous phase of sophoricoside are reported for the first time. X-ray diffractometry, differential scanning calorimetry, thermal gravimetric analysis and Fourier-transform infrared spectroscopy were used to characterize the different forms. The results show that factors such as crystal symmetry, intermolecular arrangement, conformational flexibility, hydrogen-bonding interactions and solvent incorporation lead to different solid-state forms. An investigation of the transformations of the four forms showed that they can interconvert with each other under certain conditions. Amorphous phase and solvatomorphism were unstable but can improve the solubility of sophoricoside in water.
Data from: Loss of olfaction in sea snakes provides new perspectives on the aquatic adaptation of amniotes
Marine amniotes, a polyphyletic group, provide an excellent opportunity for studying convergent evolution. Their sense of smell tends to degenerate, but this process has not been explored by comparing fully-aquatic species with their amphibious relatives in an evolutionary context. Here, we sequenced the genomes of fully-aquatic and amphibious sea snakes, and identified repertoires of chemosensory receptor genes involved in olfaction. Snakes possess large numbers of the olfactory receptor (OR) genes and the type-2 vomeronasal receptor (V2R) genes, and expression profiling in the olfactory tissues suggests that snakes use the ORs in the main olfactory system (MOS) and the V2Rs in the vomeronasal system (VNS). The number of OR genes has decreased in sea snakes, and fully-aquatic species lost the MOS which is responsible for detecting airborne odors. In contrast, sea snakes including fully-aquatic species retain a number of V2R genes and a well-developed VNS for smelling underwater. This study suggests that the sense of smell also degenerated in sea snakes, particularly in fully-aquatic species, but their residual olfactory capability is distinct from that of other fully-aquatic amniotes. Amphibious species show an intermediate status between terrestrial and fully-aquatic snakes, implying their importance in understanding the process of aquatic adaptation.
Data from: Conflicting evolutionary histories of the mitochondrial and nuclear genomes in New World Myotis bats
The rapid diversification of Myotis bats into more than 100 species is one of the most extensive mammalian radiations available for study. Efforts to understand relationships within Myotis have primarily utilized mitochondrial markers and trees inferred from nuclear markers lacked resolution. Our current understanding of relationships within Myotis is therefore biased towards a set of phylogenetic markers that may not reflect the history of the nuclear genome. To resolve this, we sequenced the full mitochondrial genomes of 37 representative Myotis, primarily from the New World, in conjunction with targeted sequencing of 3,648 ultraconserved elements (UCEs). We inferred the phylogeny and explored the effects of concatenation and summary phylogenetic methods, as well as combinations of markers based on informativeness or levels of missing data, on our results. Of the 294 phylogenies generated from the nuclear UCE data, all are significantly different from phylogenies inferred using mitochondrial genomes. Even within the nuclear data, quartet frequencies indicate that around half of all UCE loci conflict with the estimated species tree. Several factors can drive such conflict, including incomplete lineage sorting, introgressive hybridization, or even phylogenetic error. Despite the degree of discordance between nuclear UCE loci and the mitochondrial genome and among UCE loci themselves, the most common nuclear topology is recovered in one quarter of all analyses with strong nodal support. Based on these results, we re-examine the evolutionary history of Myotis to better understand the phenomena driving their unique nuclear, mitochondrial, and biogeographic histories.
Data from: Has snake fang evolution lost its bite? New insights from a structural mechanics viewpoint
Venomous snakes—the pinnacle of snake evolution—are characterized by their possession of venom-conducting fangs ranging from grooved phenotypes characterizing multiple lineages of rear-fanged taxa to tubular phenotypes present in elapids, viperids and atractaspidines. Despite extensive research, controversy still exists on the selective pressures involved in fang phenotype diversification. Here, we test the hypothesis that larger fangs and consequently a shift to an anterior position in the maxilla evolved to compensate for the costs of structural changes, i.e. higher stress upon impact in tubular fangs compared to grooved fangs. Direct voxel-based stress simulations conducted on high-resolution µCT scans, analysed within a phylogenetic framework, showed no differences in stress distribution between the three fang phenotypes, despite differences in (relative) fang length. These findings suggest that additional compensatory mechanisms are responsible for the biomechanical optimization and that fang length might instead be related to differential striking behaviour strategies.
Data from: Sequence analysis of European maize inbred line F2 provides new insights into molecular and chromosomal characteristics of presence/absence variants
Maize is well known for its exceptional structural diversity, including copy number variants (CNVs) and presence/absence variants (PAVs), and there is growing evidence for the role of structural variation in maize adaptation. While PAVs have been described in this important crop species, the extent of presence/absence variation and the relative position of inbred-specific regions remain to be elucidated. De novo genome sequencing of the F2 maize inbred line which played a key role in European breeding programs over the past 50 years revealed thousands of novel genomic regions, making up 88Mb of DNA, that are present in the F2 but not in B73. Comparison of B73 and F2 PAV localization revealed contrasted chromosomal distributions between the two inbreds and specific evolutionary dynamics of PAVs as compared to SNPs. Detailed sequence and functional annotation of F2 PAV sequences revealed hundreds of new genes with transcriptional support, but also a large fraction of repetitive sequences. Detailed analysis of sequence breakpoint highlights the role of double strand break repair, but also transposon insertion in PAV generation. Typing of the B73 and F2 PAVs in maize temperate inbreds revealed that some PAVs are found only in European Flint material, thus pinpointing structural features that may be at the origin of adaptive traits involved in the success of this material. Linkage disequilibrium (LD) analysis revealed that LD is strong within PAVs, as expected by the absence of recombination in crosses where PAV is missing in one of the parents.
Data from: A new method to scan genomes for introgression in a secondary contact model
Secondary contact between divergent populations or incipient species may result in the exchange and introgression of genomic material. We develop a simple DNA sequence measure, called Gmin, which is designed to identify genomic regions experiencing introgression in a secondary contact model. Gmin is defined as the ratio of the minimum between-population number of nucleotide differences in a genomic window to the average number of between-population differences. Although it is conceptually simple, one advantage of Gmin is that it is computationally inexpensive relative to model-based methods for detecting gene flow and it scales easily to the level of whole-genome analysis. We compare the sensitivity and specificity of Gmin to those of the widely used index of population differentiation, FST, and suggest a simple statistical test for identifying genomic outliers. Extensive computer simulations demonstrate that Gmin has both greater sensitivity and specificity for detecting recent introgression than does FST. Furthermore, we find that the sensitivity of Gmin is robust with respect to both the population mutation and recombination rates. Finally, a scan of Gmin across the X chromosome of Drosophila melanogaster identifies candidate regions of introgression between sub-Saharan African and cosmopolitan populations that were previously missed by other methods. These results show that Gmin is a biologically straightforward, yet powerful, alternative to FST, as well as to more computationally intensive model-based methods for detecting gene flow.
Data from: Under the snow: a new camera trap opens the white box of subnivean ecology
Snow covers the ground over large parts of the world for a substantial portion of the year. Yet very few methods are available to quantify biotic variables below the snow, with most studies of subnivean ecological processes relying on comparisons of data before and after the snow cover season. We developed a camera trap prototype to quantify subnivean small mammal activity. The trap consists of a camera that is attached facing downward from the ceiling of a box, which is designed to function as a snow-free tunnel. We tested it by placing nine traps with passive infrared sensors in a subarctic habitat where snow cover lasted for about 6 months. The traps were functional for the whole winter, permitting continuous data collection of site-specific presence and temporal activity patterns of all three small mammal species present (the insectivorous common shrew, Sorex araneus, the herbivorous tundra vole, Microtus oeconomus, and the carnivorous stoat, Mustela erminea) as well as abiotic conditions (presence/absence of snow cover and subnivean temperature). Based on their successful functioning (only 6% of the photographs appeared empty or were of poor quality, whereas ca 80% were of small mammals and the remaining of birds and invertebrates), we discuss how the new camera trap can enable subnivean studies of small mammal communities. This greatly increases the temporal resolution and extent of data collection and thereby provides unpreceded opportunities to understand population and food web dynamics in ecosystems with snow cover.
Data from: Molecular phylogeny of unikonts: new insights into the position of apusomonads and ancyromonads and the internal relationships of Opisthokontsí
The eukaryotic supergroup known as the Opisthokonta includes animals (Metazoa), fungi, choanoflagellates, as well as some poorly-studied unicellular eukaryotes, such as the Nucleariidea, Fonticula alba, the Ichthyosporea, the Filasterea and Corallochytrium limacisporum. Whereas the evolutionary positions of the well-known opisthokont lineages are mostly resolved, the specific phylogenetic relationships among those neglected opisthokont lineages is unsettled. Moreover, it remains unclear whether Amoebozoa or Apusozoa are the sister group to opisthokonts. Aiming at elucidating the evolutionary tree of the opisthokonts, we have produced a dataset with a large sampling of both organisms and number of genes, including representatives from all known opisthokont lineages. Moreover, we have generated new molecular data from an additional ichthyosporean (Creolimax fragrantissima) and a choanoflagellate (Codosiga botrytis). Our analyses show the Apusozoa as a paraphyletic assemblage with the Apusomonadida as sister group to Opisthokonta. Within the the Holozoa, the Ichthyosporea are shown as the first splitting group, followed by C. limacisporum, the Filasterea, the Choanoflagellata, and the Metazoa. With this taxon-rich opisthokont tree, it is possible to pinpoint the origin and evolution of morphological characters. As an example, we discuss cilia evolution under the evolutionary scenario here presented.
Data from: Angelica muliense sp. nov. (Apiaceae), a new species from Sichuan, Southwest China
Angelica muliensis (Apiaceae), a new species from Sichuan Province, southwest China, is described and illustrated. The new species resembles A. biserrata, but is mainly differed by the shapes of leaflets and sheaths, umbel number and size, especially mericarp features. The distinguishing characters of these two species are presented and compared.
Data from: A new method for estimating locomotion type in large ground birds
Estimating the locomotion type of fossil ground birds is necessary for a better understanding of their ecology. Until now, only one method has allowed us to estimate the locomotion of fossil ground birds, but its application is complicated in the majority of fossil cases because it requires data from the three bones from the same hindlimb of one individual. Here, we propose a new method using only the maximum length and minimum width of the tarsometatarsus to estimate the locomotion of these fossil birds. This method is easy to apply and better distinguishes the intermediate cases between graviportal (walking) and cursorial (running) birds. This study shows that the species of large ground birds of the families Gastornithidae and Brontornithidae were all graviportal, probably because of their large body mass. More unexpectedly, it also shows that some Phorusrhacidae (e.g. Paraphysornis), usually described as cursorial birds, were in fact graviportal, probably because of their considerable body mass. All these new data about locomotion provide a better understanding of the ecology of fossil ground birds.
Data from: A new resource for the development of SSR markers: millions of loci from a thousand plant transcriptomes
Premise of the study: The One Thousand Plant Transcriptomes Project (1KP, 1000+ assembled plant transcriptomes) provides an enormous resource for developing microsatellite loci across the plant tree of life. We developed loci from these transcriptomes and tested their utility. Methods and Results: Using software packages and custom scripts, we identified microsatellite loci in 1KP transcriptomes. We assessed the potential for cross-amplification and whether loci were biased toward exons, as compared to markers derived from genomic DNA. We characterized over 5.7 million simple sequence repeat (SSR) loci from 1334 plant transcriptomes. Eighteen percent of loci substantially overlapped with open reading frames (ORFs), and electronic PCR revealed that over half the loci would amplify successfully in conspecific taxa. Transcriptomic SSRs were approximately three times more likely to map to translated regions than genomic SSRs. Conclusions: We believe microsatellites still have a place in the genomic age—they remain effective and cost-efficient markers. The loci presented here are a valuable resource for researchers.
Data from: New quantitative approaches reveal the spatial preference of nuclear compartments in mammalian fibroblasts
The nuclei of higher eukaryotic cells display compartmentalization and certain nuclear compartments have been shown to follow a degree of spatial organization. To date, the study of nuclear organization has often involved simple quantitative procedures that struggle with both the irregularity of the nuclear boundary and the problem of handling replicate images. Such studies typically focus on inter-object distance, rather than spatial location within the nucleus. The concern of this paper is the spatial preference of nuclear compartments, for which we have developed statistical tools to quantitatively study and explore nuclear organization. These tools combine replicate images to generate 'aggregate maps' which represent the spatial preferences of nuclear compartments. We present two examples of different compartments in mammalian fibroblasts (WI-38 and MRC-5) that demonstrate new knowledge of spatial preference within the cell nucleus. Specifically, the spatial preference of RNA polymerase II is preserved across normal and immortalized cells, whereas PML nuclear bodies exhibit a change in spatial preference from avoiding the centre in normal cells to exhibiting a preference for the centre in immortalized cells. In addition, we show that SC35 splicing speckles are excluded from the nuclear boundary and localize throughout the nucleoplasm and in the interchromatin space in non-transformed WI-38 cells. This new methodology is thus able to reveal the effect of large-scale perturbation on spatial architecture and preferences that would not be obvious from single cell imaging.
Data from: Additional molecular support for the new chordate phylogeny
Recent phylogenomic analyses have suggested tunicates instead of cephalochordates as the closest living relatives of vertebrates. In direct contradiction with the long accepted view of Euchordates, this new phylogenetic hypothesis for chordate evolution has been the object of some skepticism. We assembled an expanded phylogenomic dataset focused on deuterostomes. Maximum-likelihood using standard models and Bayesian phylogenetic analyses using the CAT site-heterogeneous mixture model of amino-acid replacement both provided unequivocal support for the sister-group relationship between tunicates and vertebrates (Olfactores). Chordates were recovered as monophyletic with cephalochordates as the most basal lineage. These results were robust to both gene sampling and missing data. New analyses of ribosomal rRNA also recovered Olfactores when compositional bias was alleviated. Despite the inclusion of 25 taxa representing all major lineages, the monophyly of deuterostomes remained poorly supported. The implications of these phylogenetic results for interpreting chordate evolution are discussed in light of recent advances from evolutionary developmental biology and genomics.
Data from: Nest shape explains variation in sexual dichromatism in New World blackbirds
Following Charles Darwin, research on sexual dichromatism has long focused on sexual selection driving ornamentation in males. However, Alfred Russel Wallace proposed another explanation – that dichromatism evolves as a result of selection favoring crypsis in incubating females. Many recent studies suggest that evolutionary changes in sexual dichromatism often result from changes in female, in addition to male, plumage, yet the evolutionary mechanisms driving changes in female plumage remain largely unexplained. To test Wallace's hypothesis, we examined variation in sexual dichromatism and nest shape, a proxy for predation risk, among New World blackbirds (Aves: Icteridae). Phylogenetic models reveal an evolutionary correlation between sexual dichromatism and nest exposure. Specifically, we found that transitions in monochromatic lineages with exposed nests toward either concealed nests or dichromatism were common. Although this evidence supports Wallace's hypothesis that female incubation leads to selection for crypsis or concealment, we also found that transitions to monomorphism were common, even in lineages with exposed nests – a result suggestive of a role for positive selection on female ornamentation. These patterns of plumage evolution support a growing body of work emphasizing the importance of developing and testing hypotheses to explain evolutionary changes in female, as well as male, ornamentation.
Data from: Avian malaria: a new lease of life for an old experimental model to study the evolutionary ecology of Plasmodium
Avian malaria has historically played an important role as a model in the study of human malaria, being a stimulus for the development of medical parasitology. Avian malaria has recently come back to the research scene as a unique animal model to understand the ecology and evolution of the disease, both in the field and in the laboratory. Avian malaria is highly prevalent in birds and mosquitoes around the world and is amenable to laboratory experimentation at each stage of the parasite's life cycle. Here, we take stock of 5 years of experimental laboratory research carried out using Plasmodium relictum SGS1, the most prevalent avian malaria lineage in Europe, and its natural vector, the mosquito Culex pipiens. For this purpose, we compile and analyse data obtained in our laboratory in 14 different experiments. We provide statistical relationships between different infection-related parameters, including parasitaemia, gametocytaemia, host morbidity (anaemia) and transmission rates to mosquitoes. This analysis provides a wide-ranging picture of the within-host and between-host parameters that may bear on malaria transmission and epidemiology.
Data from: Interspecific competition counteracts negative effects of dispersal on adaptation of an arthropod herbivore to a new host
Dispersal and competition have both been suggested to drive variation in adaptability to a new environment, either positively or negatively. A simultaneous experimental test of both mechanisms is however lacking. Here, we experimentally investigate how population dynamics and local adaptation to a new host plant in a model species, the two-spotted spider mite (Tetranychus urticae), are affected by dispersal from a stock population (no-adapted) and competition with an already adapted spider mite species (Tetranychus evansi). For the population dynamics, we find that competition generally reduces population size and increases the risk of population extinction. However, these negative effects are counteracted by dispersal. For local adaptation, the roles of competition and dispersal are reversed. Without competition, dispersal exerts a negative effect on adaptation (measured as fecundity) to a novel host and females receiving the highest number of immigrants performed similarly to the stock population females. By contrast, with competition, adding more immigrants did not result in a lower fecundity. Females from populations with competition receiving the highest number of immigrants had a significantly higher fecundity than females from populations without competition (same dispersal treatment) and than the stock population females. We suggest that by exerting a stronger selection on the adapting populations, competition can counteract the migration load effect of dispersal. Interestingly, adaptation to the new host does not significantly reduce performance on the ancestral host, regardless of dispersal rate or competition. Our results highlight that assessments of how species can adapt to changing conditions need to jointly consider connectivity and the community context.
Data from: Functional MRI in the Nile crocodile: a new avenue for evolutionary neurobiology
Crocodilians are important for understanding the evolutionary history of amniote neural systems as they are the nearest extant relatives of modern birds and share a stem amniote ancestor with mammals. Although the crocodilian brain has been investigated anatomically, functional studies are rare. Here we employed fMRI, never tested in poikilotherms, to investigate crocodilian telencephalic sensory processing. Juvenile Crocodylus niloticus were placed in a 7T MRI scanner to record BOLD signal changes during presentation of visual as well as auditory stimuli. Visual stimulation increased BOLD signals in rostral to mid-caudal portions of the dorso-lateral anterior dorsal ventricular ridge (ADVR). Simple auditory stimuli led to signal increase in the rostromedial and caudocentral ADVR. These activation patterns are in line with previously described projection fields of diencephalic sensory fibers. Furthermore, complex auditory stimuli activated additional regions of the caudomedial ADVR. The recruitment of these additional, presumably higher-order, sensory areas reflect observations made in birds and mammals. Our results indicate that structural and functional aspects of sensory processing have been likely conserved during the evolution of sauropsids. In addition, our study shows that fMRI can be utilized to investigate neural processing in poikilotherms, providing a new avenue for neurobiological research in these critical species.
Data from: New evidence from linguistic phylogenetics identifies limits to punctuational change
Since the early 1970s, biologists have debated whether evolution is punctuated by speciation events with bursts of cladogenetic changes, or whether evolution tends to be of a more gradual, anagenetic nature. A similar discussion among linguists has barely begun, but the present results suggest that there is also room for controversy over this issue in linguistics. The only previous study correlated the number of nodes in linguistic phylogenies with branch lengths and found support for punctuated equilibrium. We replicate this result for branch lengths, but find no support for punctuated equilibrium using a different, automated measure of linguistic divergence and a much larger data set. With the automated measure, segments of trees containing more nodes show no greater divergence from an outgroup than segments containing fewer nodes.
ScienceDex guides
Understand access before you commit
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.