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4,391 results for “cryptic”
Data from: From cryptic to colourful: evolutionary decoupling of larval and adult colour in butterflies
<p><span><span><span><span><span><span><span><span><span><span><span>Many animals undergo complete metamorphosis, where larval forms change abruptly in adulthood. Colour change during ontogeny is common, but there is little understanding of evolutionary patterns in these changes. Here we use data on larval and adult colour for 246 butterfly species (61% of all species in Australia) to test whether the evolution of colour is coupled between life stages. We show that adults are more variable in colour across species than caterpillars and that male adult colour has lower phylogenetic signal. These results suggest that sexual selection is driving colour diversity in male adult butterflies at a broad scale. Moreover, colour similarities between species at the larval stage do not predict colour similarities at the adult stage, indicating that colour evolution is decoupled between young and adult forms. Most species transition from cryptic coloration as caterpillars to conspicuous colouration as adults, but even species with conspicuous caterpillars change to different conspicuous colours as adults. The use of high-contrast coloration is correlated with body size in caterpillars but not adults. Taken together, our results suggest a change in the relative importance of different selective pressures at different life stages, resulting in the evolutionary decoupling of coloration through ontogeny. </span></span></span></span></span></span></span></span></span></span></span></p>
Data from: A worldwide molecular phylogeny provides new insight on cryptic diversity within the moonworts (Botrychium s. s., Ophioglossaceae)
The moonwort genus, Botrychium s. s., includes diploid and polyploid taxa that occur primarily in the northern hemisphere. Their evolutionary history, morphologically cryptic taxa and deep divergence of the family in the phylogeny of ferns has long fascinated pteridologists. Previous molecular studies did not include a complete taxonomic sampling of the taxa in the genus, nor multiple specimens from throughout the known geographical range of each taxon. Therefore, to investigate evolutionary relationships of the major clades of Botrychium s. s., we increased both taxonomic representativeness (multiple accessions per taxa), as well as phylogenetic resolution by including additional new chloroplast markers. To confirm identification and provide evidence from both maternal and paternal parentage of allopolyploids, we also included specimens that have been characterized by allozyme profiles determined by electrophoretic analysis of 20 nuclear enzyme loci for each taxon. We analyzed four chloroplast regions (matK intron, trnHGUG —psbA, andtrnLUAA —trnFGAA intergenic spacers, and rpL16 intron region) of 365 specimens fromAsia, Europe, North America, Oceania, and South America, sampling the geographical range of 34 of 35 accepted Botrychium s. s. taxa and thirteen putatively new taxa. We conducted a phylogenetic analysis of maternal lineages based on 2,385 aligned nucleotides using maximum likelihood and Bayesian inference to explore genetic diversity and phylogenetic relationships among taxa. We found strong support for themonophyly of three major clades: Lanceolatum, Lunaria, and Simplex-Campestre, and resolved 15 subclades. Our results suggest multiple origins for at least four polyploid taxa (B. boreale, B. michiganense, B. yaaxudakeit, and B. watertonense). The Simplex-Campestre clade had the largest number of species, despite having a similar total number of haplotypes as the Lunaria clade (62 and 59, respectively), which has the broadest worldwide distribution. In total, our new molecular phylogeny comprises 47 taxa, of which thirteen are discussed for possible taxonomic recognition.
Data from: DNA barcoding identifies cryptic animal tool materials
<p>Some animals fashion tools and other constructions out of plant materials to aid foraging, reproduction, self-maintenance, and protection. The choice of raw materials can affect the structure and mechanical properties of the resulting artefacts, with significant fitness consequences. Documenting animals' material preferences is challenging, however, as manufacture behaviour is often difficult to observe directly, and materials may be processed so heavily that they lack identifying features. Here, we use DNA barcoding techniques to identify, from just a few recovered tool specimens, the plant species New Caledonian crows (<em>Corvus moneduloides</em>) use for crafting elaborate hooked stick tools in one of our long-term study populations. The method succeeded where extensive fieldwork using conventional approaches had failed, including targeted observations, radio-tracking, bird-mounted video-cameras, and behavioural experiments with wild and temporarily captive subjects. We believe that DNA barcoding will prove useful for investigating many other tool and construction behaviours, helping to unlock significant research potential across a wide range of study systems.</p>
Taxonomic Uncertainty on Range Size and Niche Estimation in a Southern Ocean Cryptic Species Complex
<p>R code and data related to assessing the effect of taxonomic uncertainty on range size and environmental niche estimates for a Southern Ocean invertebrate. </p> <p>Clarke, D.A., Wilson, N.G. and McGeoch, M.A. (2025) ‘Effects of Taxonomic Uncertainty on Range Size and Niche Estimation in a Southern Ocean Cryptic Species Complex’, Journal of Biogeography, n/a(n/a), p. e15182. Available at: https://doi.org/10.1111/jbi.15182.</p>
Cryptic Magma Chamber in the Deccan Traps imaged using receiver functions and Surface wave dispersion
<p>This is a Dataset for the article titled "Cryptic Magma Chamber in the Deccan Traps imaged using receiver functions and Surface wave dispersion" by Saha et. al. (2023). For more information about the data, contact <a href="mailto:kumarsahagokul123@gmail.com">kumarsahagokul123@gmail.com.</a></p>
Pinellia discolor: A new cryptic species distinguished from P. cordata in Mainland China
<p><em>Pinellia cordata</em> (Araceae) is a perennial herb species distributed in China and Japan. Several studies have shown that there are two types of this species, and chromosome counts have shown irregular variation among populations. In this study, we investigated the morphological characteristics, established the chromosome number in root tips, reconstructed phylogenetic relationship based on whole chloroplast genomes, and elucidated biogeographic patterns based on data collected from the Chinese Virtual Herbarium (CVH) and the Plant Photo Bank of China (PPBC) for the two types of <em>P. cordata</em>, including type I (greenish leaf blade) and type II (colored leaf blade). We found stable significant differences in morphometric characteristics (color of the leaf blade abaxially, petiole, spathe, and appendix) and the number of chromosomes. The results of the phylogenetic analysis showed that types I and II were located in different places in the evolutionary tree compared to the group. The distribution regions of these types of <em>P. cordata</em> were also slightly different in Mainland China. These findings suggested that <em>P. cordata</em> should be divided into <em>P. cordata </em>(Type I) and <em>P. discolor</em> (Type II, a cryptic species), and the latter is here described as a new species.</p>
Data from: Multi-generation genetic contributions of immigrants reveal cryptic elevated and sex-biased effective gene flow within a natural meta-population
<p>Impacts of immigration on micro-evolution and population dynamics fundamentally depend on net rates and forms of resulting gene flow into recipient populations. Yet, the degrees to which observed rates and sex ratios of physical immigration translate into multi-generational genetic legacies have not been explicitly quantified in natural meta-populations, precluding inference on how movements translate into effective gene flow and eco-evolutionary outcomes. Our analyses of three decades of complete song sparrow (<em>Melospiza melodia</em>) pedigree data show that multi-generational genetic contributions from regular natural immigrants substantially exceeded those from contemporary natives, consistent with heterosis-enhanced introgression. Further, while contributions from female immigrants exceeded those from female natives by up to three-fold, male immigrants' lineages typically went locally extinct soon after arriving. Both the overall magnitude, and the degree of female bias, of effective gene flow therefore greatly exceeded those which would be inferred from observed physical arrivals, reshaping the eco-evolutionary implications of immigration.</p>
Data from: Cryptic diversity of cellulose-degrading gut bacteria in industrialized humans
<p>Humans, like all mammals, depend on the gut microbiome for digestion of cellulose, the main component of plant fiber, but evidence for cellulose fermentation in the human gut is scarce. We have identified ruminococcal species in the gut microbiota of human populations that assemble functional multi-enzymatic cellulosome systems capable of degrading plant cell wall polysaccharides. One of these species, which is strongly associated with humans, likely originated in the ruminant gut and was subsequently transferred to the human gut potentially during domestication, where it underwent diversification and diet-related adaptation through the acquisition of genes from other gut microbes. Collectively, these species are abundant and widespread among ancient humans, hunter-gatherers, and rural populations, but are extremely rare in populations from industrialized societies, suggesting potential disappearance in response to the westernized lifestyle.</p>
Discovering cryptic pocket opening and binding of a stimulant derivative in a vestibular site of the 5-HT3A receptor
<p>Raw MD simulation data of 4-Bromoamphetamine-5HT3A complex in two different forceeild, AMBER and CHARMM.</p> <p>Original paper title: "Discovering cryptic pocket opening and binding of a stimulant derivative in a vestibular site of the 5-HT3A receptor"</p> <p>Author list: <span>Nandan Haloi</span><span>,</span> <span>Emelia Karlsson</span><span>,</span> <span>Marc Delarue, </span><span>Rebecca J. Howard</span><span>,</span> <span>Erik Lindahl</span></p>
Data from: A winged relative of ice crawlers in amber bridges the cryptic extant Xenonomia and a rich fossil record
<p>Until the advent of phylogenomics, the atypical morphology of extant representatives of the insect orders <em>Grylloblattodea</em> (ice crawlers) and <em>Mantophasmatodea </em>(gladiators) had confounding effects on efforts to resolve their placement within Polyneoptera. This recent research has unequivocally shown that these species‐poor groups are closely related and form the clade Xenonomia. Nonetheless, divergence dates of these groups remain poorly constrained, and their evolutionary history debated, as the few well‐identified fossils, characterized by a suite of morphological features similar to that of extant forms, are comparatively young. Notably, the extant forms of both groups are wingless, whereas most of the pre‐Cretaceous insect fossil record is composed of winged insects, which represents a major shortcoming of the taxonomy. Here, we present new specimens embedded in Early Cretaceous amber from Myanmar and belonging to the recently described species <em>Aristovia daniili</em>. The abundant material and pristine preservation allowed a detailed documentation of the morphology of the species, including critical head features. Combined with a morphological data set encompassing all Polyneoptera, these new data unequivocally demonstrate that <em>A. daniili</em> is a winged stem <em>Grylloblattodea</em>. This discovery demonstrates that winglessness was acquired independently in <em>Grylloblattodea </em>and <em>Mantophasmatodea</em>. Concurrently, wing apomorphic traits shared by the new fossil and earlier fossils demonstrate that a large subset of the former "Protorthoptera" assemblage, representing a third of all known insect species in some Permian localities, are genuine representatives of Xenonomia. Data from the fossil record depict a distinctive evolutionary trajectory, with the group being both highly diverse and abundant during the Permian but experiencing a severe decline from the Triassic onwards.</p>
Data and code for: Does the definition of a novel environment affect the ability to detect cryptic genetic variation?
<p>Anthropogenic change exposes populations to environments that have been rare or entirely absent from their evolutionary past. Such novel environments are hypothesised to release cryptic genetic variation, a hidden store of variance that can fuel evolution. However, support for this hypothesis is mixed. One possible reason is a lack of clarity in what is meant by 'novel environment', an umbrella term encompassing conditions with potentially contrasting effects on the exposure or concealment of cryptic variation. Here, we use a meta-analysis approach to investigate changes in the total genetic variance of multivariate traits in ancestral versus novel environments. To determine whether the definition of a novel environment could explain the mixed support for a release of cryptic genetic variation, we compared absolute novel environments, those not represented in a population's evolutionary past, to extreme novel environments, those involving frequency or magnitude changes to environments present in a population's ancestry. Despite sufficient statistical power, we detected no broadscale pattern of increased genetic variance in novel environments, finding the type of novel environment did not explain any significant variation in effect sizes. When effect sizes were partitioned by experimental design, we found increased genetic variation in studies based on broad-sense measures of variance, and decreased variation in narrow-sense studies, in support of previous research. Therefore, the source of genetic variance, not the definition of a novel environment, was key to understanding environment-dependant genetic variation, highlighting non-additive genetic variance as an important component of cryptic genetic variation and avenue for future research.</p>
Trophic resource partitioning drives fine-scale coexistence in cryptic bat species
Understanding the processes that enable species coexistence has important implications for assessing how ecological systems will respond to global change. Morphology and functional similarity increase the potential for competition, and therefore, co-occurring morphologically similar but genetically unique species are a good model system for testing coexistence mechanisms. We used DNA metabarcoding and High Throughput Sequencing to characterise for the first time the trophic ecology of two recently-described cryptic bat species with parapatric ranges, Myotis escalerai and Myotis crypticus. We collected faecal samples from allopatric and sympatric regions and from syntopic and allotopic locations within the sympatric region to describe the diets both taxonomically and functionally and compare prey consumption with prey availability. The two bat species had highly similar diets characterised by high arthropod diversity, particularly Lepidoptera, Diptera and Araneae, and a high proportion of prey that is not volant at night, which points to extensive use of gleaning. Diet overlap at the prey-item level was lower in syntopic populations, supporting trophic shift under fine-scale co-occurrence. Furthermore, the diet of M. escalerai had a marginally lower proportion of not nocturnally volant prey in syntopic populations, suggesting that the shift in diet may be driven by a change in foraging mode. Our findings suggest that fine-scale coexistence mechanisms can have implications for maintaining broad-scale diversity patterns. This study highlights the importance of including both allopatric and sympatric populations and choosing meaningful spatial scales for detecting ecological patterns. We conclude that a combination of high taxonomic resolution with a functional approach helps identify patterns of niche shift.
Supplementary dataset for Correlational networking guides the discovery of cryptic natural product biosynthetic enzymes
<p>Supplementary files for the paper: Correlational networking guides the discovery of cryptic natural product biosynthetic enzymes</p> <p>23777967_protease.fasta.xz:<br> A fasta file (compressed by xz) containing 23777967 protease sequences obtained from 161954 bacterial genomes<br> 23777967_protease_cluster.csv.xz:<br> A csv file (compressed by xz) containing MMseqs2 cluster information of 23777967 proteases<br> This csv file has 5 columns: rep (representative sequence name), mem (member sequence name), number of members in cluster, cluster No.<br> Fig1C_cytoscape.zip:<br> Cytoscape file corresponding to Fig.1C, as well as its node and edge tables<br> Fig2C_cytoscape.zip:<br> Cytoscape file corresponding to Fig.2C, as well as its node and edge tables<br> FigS2_cytoscape.zip:<br> Cytoscape file corresponding to Supplementary Fig.2, as well as its node and edge tables. Size was differently scaled for very large nodes containing more than 1000 precursors/proteases</p>
Decrypting cryptic crosswords: Semantically complex wordplay puzzles as a target for NLP
<p>Cryptic crosswords, the dominant crossword variety in the UK, are a promising target for advancing NLP systems that seek to process semantically complex, highly compositional language. Cryptic clues read like fluent natural language but are adversarially composed of two parts: a definition and a wordplay cipher requiring character-level manipulations. Expert humans use creative intelligence to solve cryptics, flexibly combining linguistic, world, and domain knowledge. In this paper, we make two main contributions. First, we present a dataset of cryptic clues as a challenging new benchmark for NLP systems that seek to process compositional language in more creative, human-like ways. After showing that three non-neural approaches and T5, a state-of-the-art neural language model, do not achieve good performance, we make our second main contribution: a novel curriculum approach, in which the model is first fine-tuned on related tasks such as unscrambling words. We also introduce a challenging data split, examine the meta-linguistic capabilities of subword-tokenized models, and investigate model systematicity by perturbing the wordplay part of clues, showing that T5 exhibits behavior partially consistent with human solving strategies. Although our curricular approach considerably improves on the T5 baseline, our best-performing model still fails to generalize to the extent that humans can. Thus, cryptic crosswords remain an unsolved challenge for NLP systems and a potential source of future innovation.</p>
Unexpected cryptic species among streptophyte algae most distant to land plants
<p>Streptophytes are one of the major groups of the green lineage (Chloroplastida or Viridiplantae). During one-billion-years of evolution, streptophytes have radiated into an astounding diversity of uni- and multicellular green algae as well as land plants. Most divergent from land plants is a clade formed by Mesostigmatophyceae, Spirotaenia spp., and Chlorokybophyceae. All three lineages are species-poor and the Chlorokybophyceae consist of a single described species, Chlorokybus atmophyticus. In this study, we used phylogenomic analyses to shed light into the diversity within Chlorokybus using a sampling of isolates across its known distribution. We uncovered a consistent deep genetic structure within the Chlorokybus isolates, which prompted us to formally extend the Chlorokybophyceae by describing four new species. Gene expression differences among Chlorokybus species suggest certain constitutive variability that might influence their response to environmental factors. Failure to account for this diversity can hamper comparative genomic studies aiming to understand the evolution of stress response across streptophytes. Our data highlight that future studies on the evolution of plant form and function can tap into an unknown diversity at key deep branches of the streptophytes.</p>
Specimens from Brand et al. 2021, "Large-scale phylogenomics of the genus Macrostomum (Platyhelminthes) reveals cryptic diversity and novel sexual traits"
<p>The deposited folders contain image and video material of free-living flatworm specimens that were documented in vivo. These data support the following publication:</p> <p>Jeremias N. Brand, Gudrun Viktorin, R. Axel W. Wiberg, Christian Beisel, Lukas Schärer.<br> Large-scale phylogenomics of the genus<em> Macrostomum</em> (Platyhelminthes) reveals cryptic diversity and novel sexual traits.<br> Molecular Phylogenetics and Evolution. Volume 166. 2022. <a href="https://doi.org/10.1016/j.ympev.2021.107296">https://doi.org/10.1016/j.ympev.2021.107296</a></p> <p>For more information about these specimens see also http://macrostomorpha.info.</p>
Data sets and analyses for genomics of cryptic speciation in Catharus thrushes
<p>Cryptic speciation may occur when reproductive isolation is recent or the accumulation of morphological differences between sister lineages is slowed by stabilizing selection preventing phenotypic differentiation. In North America, Bicknell's Thrush (<i>Catharus bicknelli</i>) and its sister species, the Gray-cheeked Thrush (<i>Catharus minimus</i>), are parapatrically breeding migratory songbirds, distinguishable in nature only by subtle differences in song and coloration, and were recognized as distinct species only in the 1990s. Previous molecular studies have estimated that the species diverged ~120 - 420 thousand YBP and found very low levels of introgression despite their similarity and sympatry in the spring (prebreeding) migration. To further clarify the history, genetic divergence, genomic structure and adaptive processes in <i>C. bicknelli</i> and <i>C</i>. <i>minimus</i>, we sequenced and assembled high-coverage reference genomes of both species and re-sequenced genomes from population samples of <i>C. bicknelli</i>, <i>C. minimus</i>, and two individuals of the Swainson's Thrush (<i>C. ustulatus</i>). The genome of <i>C. bicknelli</i> exhibits markedly higher abundances of transposable elements compared to other <i>Catharus</i> and chicken. Demographic and admixture analyses confirm moderate genome-wide differentiation (<i>F</i><sub>st</sub> <i>≈</i> 0.10) and limited gene flow between <i>C. bicknelli</i> and C. <i>minimus,</i> but suggest a more recent divergence than estimates based on mtDNA. We find evidence of rapid evolution of the Z-chromosome and elevated divergence consistent with natural selection on genomic regions near genes involved with neuronal processes in <i>C. bicknelli.</i> These genomes are a useful resource for future investigations of speciation, migration, and adaptation in <i>Catharus </i>thrushes.</p>
Data from: Juvenile experience with male cues triggers cryptic choice mechanisms in adult female redback spiders
<p>Female choice may be linked to population density if expected encounter rates with potential mates affects choosiness (energy and risk engaged to express mate preferences). Choosiness should covary with male availability, which could be assessed using social cues available during development. We tested whether exposure of juvenile females to cues of male density affected mechanisms of choosiness of adult <i>Latrodectus hasselti</i> spiders in two experiments simulating natural contexts. Juvenile females were exposed to (1) volatile chemicals from two densities of adult males (airborne cues), and (2) tactile, vibrational, and chemical cues from adult males or other females (cohabitation cues). As adults, females mated readily, regardless of treatment, but there was strong evidence for post-copulatory mechanisms of choosiness in females exposed to cues of high male availability. These included abbreviated matings (both experiments), cannibalism of males before mating was complete (cohabitation), and, remarkably, a reduction in the successful placement of internal sperm plugs (cohabitation). These shifts decrease the likelihood that the first mate would monopolize paternity if the female chose to mate again. We conclude that female choosiness may impose strong selection on males despite high mating rates, and these effects can hinge on cues of male availability detected by juveniles.</p>
Ecological traits drive genetic structuring in two open-habitat birds from the morphologically cryptic genus Elaenia (Aves: Tyrannidae)
<p>Understanding the relative contributions of the many factors that shape population genetic structuring is a central theme in evolutionary and conservation biology. Historically, abiotic or extrinsic factors (such as geographic barriers or climatic shifts) have received greater attention than biotic or intrinsic factors (such as dispersal or migration). This focus stems in part from the logistical difficulties in taking a comparative phylogeographic approach that contrasts species that have experienced similar abiotic conditions during their evolution yet differ in the intrinsic attributes that might shape their genetic structure. To explore the effects of intratropical migration on the genetic structuring of Neotropical birds, we chose two congeneric species, the Lesser Elaenia (<em>Elaenia chiriquensis</em>) and the Plain-crested Elaenia (<em>E. cristata</em>), that are largely sympatric, and which have similar plumage, habitat preferences, and breeding phenology. Despite these many commonalities, they differ in migratory behavior: <em>E. chiriquensis</em> is an intratropical migratory species while <em>E. cristata</em> is sedentary. We used a reduced representation genomic approach to test whether migratory behavior is associated with increased gene flow and therefore lower genetic population structure. As predicted, we found notably stronger genetic structuring in the sedentary species than in the migratory ones. <em>E. cristata</em> comprises genetic clusters with geographic correspondence throughout its distribution, while there are no geographic groups within Brazil for <em>E. chiriquensis</em>. This comparison adds to the growing evidence about how intrinsic traits like migration can shape the genetic structuring of birds, and advances our understanding of the diversification patterns of the understudied, open habitat species from South America.</p>
Supporting trees and alignments for the publication: Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome
<div class="page"> <div class="layoutArea"> <div class="column"> <p>Whereas DNA viruses are known to be abundant, diverse, and commonly key ecosystem players, RNA viruses are relatively understudied outside disease settings. Here, we analyzed ≈28 terabases of Global Ocean RNA sequences to expand Earth's RNA virus catalogues and their taxonomy, investigate their evolutionary origins, and assess their marine biogeography from pole to pole. Using new approaches to optimize discovery and classification, we identified RNA viruses that necessitate substantive revisions of taxonomy (doubling phyla and adding >50% new classes) and evolutionary understanding. "Species"-rank abundance determination revealed that viruses of new phyla<span> </span><em>"Taraviricota"</em><span>, </span>a missing link in early RNA virus evolution, and<span> </span><em>"Arctiviricota"</em><span> </span>are widespread and dominant in the oceans. These efforts provide foundational knowledge critical to integrating RNA viruses into ecological and epidemiological models.</p> </div> </div> </div>
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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.
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