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4,391 results for “cryptic”
Fig. 3 in Comparative Analysis Of Karyotypes Of Two Cryptic Species Of Pelobatid Frogs (Amphibia, Anura) Of Ukraine
Fig. 3. Absolute length of chromosomes in spadefoots (Pelobates) of Ukraine. nm.
Cryptic species in a colorful genus: integrative taxonomy of the bush robins (Aves, Muscicapidae, Tarsiger) suggests two overlooked species
<p>Several cryptic avian species ha<span>ve been validated</span><span> </span>by recent integrative taxonomic efforts in the Sino-Himalayan mountains, indicating that avian diversity in this global biodiversity hotspot may be underestimated. In the present study<span>,</span>we investigated species limits in the genus <em>Tarsiger</em>, the bush robins, a group of montane forest specialists with high species richness in the Sino-Himalayan region. Based on comprehensive sampling of all 11 subspecies of the six currently recognized species, we applied an integrative taxonomic approach by combining multilocus, acoustic, plumage and morphometric analyses. Our results reveal that the isolated north-central Chinese populations of<em> Tarsiger cyanurus</em>, described as the subspecies <em>albocoeruleus</em> but usually considered invalid, is distinctive in genetics and vocalisation, but only marginally differentiated in morphology. We also found the Taiwan endemic <em>T. indicus formosanus</em> to be distinctive in genetics, song and morphology from <em>T. i. indicus</em> and <em>T. i. yunnanensis</em> of the Sino-Himalayan mountains. Moreover, Bayesian species delimitation using BPP suggests that both <em>albocoeruleus</em> and <em>formosanus</em> merit full species status. We propose their treatment as 'Qi<span>lian</span><span> </span>Bluetail' <em>T.</em> <em>albocoeruleus</em> and 'Taiwan Bush Robin' <em>T. formosanus</em>, respectively.</p>
Systematics of the New World bats Eptesicus and Histiotus suggest trans-marine dispersal followed by Neotropical cryptic diversification
<p>Biodiversity can be boosted by colonization of new habitats, such as different continents and remote islands. Molecular studies have suggested that recently evolved organisms probably colonized already separated continents by dispersal, either via land bridge connections or crossing the ocean. Here we test the on-land and trans-marine dispersal hypotheses by evaluating possibilities of colonization routes over Bering land bridge and across the Atlantic Ocean in the cosmopolitan bat genus <em>Eptesicus</em> (Chiroptera, Vespertilionidae). Previous molecular studies have found New World <em>Eptesicus</em> more closely related to <em>Histiotus</em>, a Neotropical endemic lineage with enlarged ears, than to Old World <em>Eptesicus</em>. However, phylogenetic relationships within the New World group remained unresolved and their evolutionary history was unclear. Here we studied the systematics of New World <em>Eptesicus</em> and <em>Histiotus</em> using extensive taxonomic and geographic sampling, and genomic data from thousands of ultra-conserved elements (UCEs). We estimated phylogenetic trees using concatenation and multispecies coalescent. All analyses supported four major New World clades and a novel topology where <em>E. fuscus</em> and <em>Histiotus</em> are sister clades that together diverged from two sister clades of Neotropical <em>Eptesicus</em>. Intra-clade divergence suggested cryptic diversity that has been concealed by morphological features, especially in the Neotropics where taxonomic re-evaluations are warranted. Molecular dating estimated that Old World and New World clades diverged around 17 million years ago followed by radiation of major New World clades in the mid-Miocene, when climatic changes might have facilitated global dispersal and radiation events. Biogeographic ancestral reconstruction supported the Neotropical origin of the New World clades, suggesting a trans-Atlantic colonization route from North Africa to the northern Neotropics. We highlight that trans-marine dispersal may be more prevalent than currently acknowledged and may be an important first step to global biodiversification.</p>
The generality of cryptic dietary niche differences in diverse large-herbivore assemblages
<p>Ecological niche differences are necessary for stable species coexistence but are often difficult to discern. Models of dietary niche differentiation in large mammalian herbivores invoke the quality, quantity, and spatiotemporal distribution of plant tissues and growth-forms but are agnostic towards food-plant species identity. Empirical support for these models is variable, suggesting that additional mechanisms of resource partitioning may be important in sustaining large-herbivore diversity in African savannas. We used DNA metabarcoding to conduct a taxonomically explicit analysis of large-herbivore diets across southeastern Africa, analyzing ~4,000 fecal samples of 30 species from 10 sites in 7 countries over 6 years. We detected 893 food-plant taxa from 124 families, but just two families—grasses and legumes—accounted for the majority of herbivore diets. Nonetheless, herbivore species almost invariably partitioned food-plant taxa; diet composition differed significantly in 97% of pairwise comparisons between sympatric species, and dissimilarity was pronounced even between the strictest grazers (grass eaters), strictest browsers (non-grass eaters), and closest relatives at each site. Niche differentiation was weakest in an ecosystem recovering from catastrophic defaunation, indicating that food-plant partitioning is driven by species interactions, and stronger at low rainfall, as expected if interspecific competition is a predominant driver. Diets differed more between browsers than grazers, which predictably shaped community organization: grazer-dominated trophic networks had higher nestedness and lower modularity. That dietary differentiation is structured along taxonomic lines complements prior work on how herbivores partition plant parts and patches and suggests that common mechanisms govern herbivore coexistence and community assembly in savannas.</p>
Data and supplementary materials from: Large genetic divergence underpins cryptic local adaptation across ecological and evolutionary gradients
<p><span>Environmentally covarying local adaptation is a form of cryptic local adaptation in which the covariance of the genetic and environmental effects on a phenotype obscures the divergence between locally adapted genotypes. Here, we systematically document the magnitude and drivers of the genetic effect (V<sub>G</sub>) for two forms of environmentally covarying local adaptation: counter- and cogradient variation. Using a hierarchical Bayesian meta-analysis, we calculated the overall effect size of V<sub>G</sub> as 1.05 and 2.13 for populations exhibiting countergradient or cogradient variation, respectively. These results indicate that the genetic contribution to phenotypic variation represents a 1.05 to 2.13 standard deviation change in trait value between the most disparate populations depending on if populations are expressing counter- or cogradient variation. We also found that while there was substantial variance among abiotic and biotic covariates, the covariates with the largest mean effects were temperature (2.41) and gamete size (2.81). Our results demonstrate the pervasiveness and large genetic effects underlying environmentally covarying local adaptation in wild populations and highlights the importance of accounting for these effects in future studies.</span></p>
The emergence of a cryptic lineage and cytonuclear discordance through past hybridization in the Japanese fire-bellied newt, Cynops pyrrhogaster (Amphibia: Urodela)
<p> Discrepancies in geographic variation patterns between nuclear DNA and mitochondrial DNA (mtDNA) are the result of the complicated differentiation processes in organisms and the key to understanding their true evolutionary process. The genetic differentiation of the northern and southern Izu lineages of the Japanese newt <em>Cynops pyrrhogaster</em> was investigated <span>through their single nucleotide polymorphism</span> variations by multiplexed ISSR genotyping by sequencing (MIG-seq). We found three genetic groups (Tohoku, N-Kanto, and S-Kanto) those not detected by mtDNA in the northern lineage. N-Kanto has intermediate genetic characteristics between Tohoku and S-Kanto. The western populations of N-Kanto are close to S-Kanto, whereas the eastern populations of N-Kanto are close to Tohoku. Tohoku, N-Kanto, and S-Kanto are now moderately isolated from each other and have unique genetic characteristics. An estimation of the evolutionary history by t<span>he </span><span>Approximate Bayesian Computation </span>approach suggested that Tohoku diverged from the common ancestor of S-Kanto and S-Izu. Then, S-Kanto and S-Izu split and the recent hybridization between Tohoku and S-Kanto gave rise to N-Kanto. The origin of N-Kanto through the hybridization is relatively young and seems to be related to changes in the distributions of Tohoku and S-Kanto as a result of the climatic oscillation in the Pleistocene. We concluded that the mitochondrial genome of S-Kanto was captured into Tohoku and the past original mitochondrial genome of Tohoku was entirely swept out from Tohoku through the hybridization. </p>
Genetic data from: Cryptic persistence and loss of local endemism in Lake Constance charr subject to anthropogenic disturbance
<p>Habitat restoration can help to protect and support endangered species. Following the restoration of Lake Constance to oligotrophic conditions, deep-water charr (originally described as <em>Salvelinus</em> <em>profundus</em> Schillinger, 1901) were rediscovered after more than 40 years of presumed extinction caused by eutrophication. Subsequent targeted surveys lead to the capture of a further 127 deep-water charr and 233 sympatric normal charr, <em>Salvelinus</em> cf. <em>umbla</em>. Given a history of intensive stocking in the lake and the possibility of introgressive hybridization, a discussion arose about the genetic status and future conservation strategies of both forms. The current study gathered life history traits and morphological and population genomic data for both extant forms, for comparison with 60–120 years' worth of historical data and museum specimens. The extant deep-water charr resembled historical specimens in terms of body shape, but significant differences between historical and extant normal charr included a decline in gill raker number over time and distinctly different body shapes and growth patterns. RAD-based population genomic analyses of the contemporary samples support these results, revealing the two extant forms to be highly divergent, albeit with a few putative hybrids. SNPs-based population assignment tests of historical and contemporary samples strongly suggest that deep-water charr persisted unaltered in Lake Constance during the eutrophic phase. Meanwhile, none of the historical genomic samples could be assigned to the extant normal <em>S</em>. cf. <em>umbla</em> population. Functional analyses of gill raker number and stocking intensity pointed to stocking with non-endemic charr as the most likely reason for the disappearance of the endemic normal form. These results show that interplay between different anthropogenic impacts, i.e. eutrophication and stocking can lead to irreversible but hard-to-detect impacts on endemic biodiversity. Understanding these impacts is a prerequisite for effective conservation of endangered populations of cryptic fish.</p>
Ecological divergence despite common mating sites: Genotypes and symbiotypes shed light on cryptic diversity in the black bean aphid species complex
<p>Different host plants represent ecologically dissimilar environments for phytophagous insects. The resulting divergent selection can promote the evolution of specialized host races, provided that gene flow is reduced between populations feeding on different plants. In black bean aphids belonging to the <em>Aphis fabae </em>complex, several morphologically cryptic taxa have been described based on their distinct host plant preferences. However, host choice and mate choice are largely decoupled in these insects: they are host-alternating and migrate between specific summer host plants and shared winter hosts, with mating occurring on the shared hosts. This provides a yearly opportunity for gene flow among aphids using different summer hosts, and raises the question if and to what extent the ecologically defined taxa are reproductively isolated. Here, we analyzed a geographically and temporally structured dataset of microsatellite genotypes from <em>A. fabae </em>that were mostly collected from their main winter host <em>Euonymus europaeus,</em> and additionally from another winter host and fourteen summer hosts. The data reveals multiple, strongly differentiated genetic clusters, which differ in their association with different summer and winter hosts. The clusters also differ in the frequency of infection with two heritable, facultative endosymbionts, separately hinting at reproductive isolation and divergent ecological selection. Furthermore, we found evidence for occasional hybridization among genetic clusters, with putative hybrids collected more frequently in spring than in autumn. This suggests that similar to host races in other phytophagous insects, both prezygotic and postzygotic barriers including selection against hybrids maintain genetic differentiation among <em>A. fabae </em>taxa, despite a common mating habitat.</p>
Fig. 6. ANSP 8138 in Cryptic multicolored lizards in the Polychrus marmoratus Group (Squamata: Sauria: Polychrotidae) and the status of Leiolepis auduboni Hallowell
Fig. 6. ANSP 8138. The holotype for Leiolepis auduboni Hallowell. Photo credit: Ned Gilmore.
Aligned DNA sequence matrix for phylogenetic analyses in the article "Systematics of Huicundomantis, a new subgenus of Pristimantis (Anura, Strabomantidae) with extraordinary cryptic diversity and eleven new species"
<p>Aligned DNA sequence matrix for phylogenetic analyses of the article "Systematics of Huicundomantis, a new subgenus of Pristimantis (Anura, Strabomantidae) with extraordinary cryptic diversity and eleven new species"</p> <p>The matrix is in NEXUS format. Genes are arranged as follows:</p> <p>16S RNA, tRNA-Leu = 1–1408<br> ND1 codon position 1 = 1409–2369\3;<br> ND1 codon position 2 = 1410–2367\3;<br> ND1 codon position 3 = 1411–2368\3;<br> tRNA-Ile, tRNA-Gln, rRNA-Met = 2370–2544; <br> RAG1 codon position 3 = 2545–3199\3;<br> RAG1 codon position 1 = 2546–3197\3<br> RAG1 codon position 2 = 2547–3198\3;</p>
Bayesian consensus phylogram from the article "Systematics of Huicundomantis, a new subgenus of Pristimantis (Anura, Strabomantidae) with extraordinary cryptic diversity and eleven new species"
<p>Bayesian consensus phylogram depicting relationships within <em>Pristimantis</em> (<em>Huicundomantis</em>). Museum catalog numbers are shown before the species name. Posterior probabilities resulting from Bayesian Markov chain Monte Carlo searches appear next to the branches.</p>
Dataset 1. Validated natural and cryptic mRNA splicing mutations
<p>Source data computed by the Shannon pipeline and Veridical, displayed on the ValidSpliceMut (<a href="https://validsplicemut.cytognomix.com/">https://validsplicemut.cytognomix.com/</a>) website.</p>
Fig. 6 in Evidence for cryptic diversity in the Neotropical water snake, Helicops angulatus (Linnaeus, 1758) (Dipsadidae, Hydropsini), with comments on its ecology, facultative reproductive mode, and conservation
Fig. 6. The lectotype of Natrix asper Wagler. Photos by Michael Franzen.
Fig. 7 in Evidence for cryptic diversity in the Neotropical water snake, Helicops angulatus (Linnaeus, 1758) (Dipsadidae, Hydropsini), with comments on its ecology, facultative reproductive mode, and conservation
Fig. 7. The holotype of Helicops fumigatus Cope, 1868. Photo by Ned Gilmore.
Fig. 4. NRM 17 in Evidence for cryptic diversity in the Neotropical water snake, Helicops angulatus (Linnaeus, 1758) (Dipsadidae, Hydropsini), with comments on its ecology, facultative reproductive mode, and conservation
Fig. 4. NRM 17, the holotype for Helicops angulatus. Photo courtesy of NRM.
Fig. 8 in A new cryptic species of Cnemaspis Strauch, 1887 (Squamata: Gekkonidae), in the C. littoralis complex, from Anakkal, Palakkad, Kerala, India
Fig. 8. Habitat of Cnemaspis palakkadensis sp. nov. Photos by Amit Sayyed.
Cryptic diversity patterns of subterranean estuaries
<p>Data and results used in the analyses for the article:</p> <p>Calderón-Gutiérrez F, Labonté JM, Gonzalez B, Iliffe TM, Mejía‐Ortíz LM, Borda E. 2024. Cryptic diversity patterns of subterranean estuaries. Proceedings of the Royal Society B: Biological Sciences. (doi: 10.1098/rspb.2024.1483)</p>
Herbarium specimens reveal a cryptic invasion of polyploid Centaurea stoebe in Europe - ITS1 dataset
<h3>Description of the data and file structure</h3> <p>We genotyped the ITS1 locus of 178 herbarium specimens using protocol described in Suchan et al. (2018; https://doi.org/10.1111/1755-0998.12948) and processed using custom script. The specimens were chosen after morphological determination of their cytotypes (morphological determination accuracy: 97.8%). We choose this subsample (3.5% of the total number of specimens) to represent comparable distributional ranges and collection dates across both cytotypes, including specimens from both the native and expanded ranges of tetraploid <em>C. stoebe</em>. Genotyping of the ITS1 locus unambiguously identifies the cytotype, as all tetraploid samples exhibit a unique ribotype B, which has never been found in diploid samples (Mráz et al., 2012; https://doi.org/10.1016/j.ympev.2011.11.006).</p> <h4>Files and variables</h4> <p><strong>File: Centaurea_stoebe_ITS1_script.sh</strong></p> <p>Description: This file contains the script used for processing raw sequence data to obtain a table with the numbers of reads in each sample mapping to the obtained ITS1 variants. The software used was: PEAR v0.9.6, cutadapt v.3.2, vsearch v2.28.1</p> <p><strong>File: Centaurea_stoebe_sample_list.xlsx</strong></p> <p>Description: This file contains a list of analyzed herbarium specimens.</p> <p>Variables</p> <ul> <li>ID - sample ID</li> <li>Lab working no. - Identifier of the samples in the ITS1 analyses, specifically in the Centaurea_stoebe_ITS1_sequence_numbers.xlsx file</li> <li>Morphology-based estimation - ploidy of the sample estimated with morphology (2 - diploid, 4 - tetraploid)</li> <li>ITS seq based estimation - ploidy of the sample estimated using ITS1 sequencing (2 - diploid, 4 - tetraploid)</li> <li>Congruence(1)/mismatch(0) - congruence (1) or mismatch (0) between morphological and genetic policy estimation</li> <li>Country of origin</li> <li>Herbarium</li> <li>Herbarium coll. number</li> <li>Collector</li> <li>Collection year</li> <li>Locality</li> <li>Latitude</li> <li>Longitude</li> </ul> <p><strong>File: Centaurea_stoebe_ITS1_sequences.fasta</strong></p> <p>Description: This file contains sequences of the obtained ITS1 variants.</p> <p><strong>File: Centaurea_stoebe_ITS1_sequence_numbers.xlsx</strong></p> <p>Description: This file contains a table with the numbers of reads in each sample mapping to the obtained ITS1 variants.</p> <p>Variables</p> <ul> <li>OTU - ITS1 variant number</li> <li>size - number of sequences from the total data clustered to the variant</li> <li>next columns contain numbers of reads mapped to each ITS1 variant for each sample</li> </ul> <h3>Code/software</h3> <p>The code to process sequence data is included in Centaurea_stoebe_ITS1_script.sh file. The software used was: PEAR v0.9.6, cutadapt v.3.2, vsearch v2.28.</p>
Fig. 7 in Hiding in plain sight: Integrative analyses uncover a cryptic Salvia species in Europe
Fig. 7. Holotype of Salvia revelata Mátis & A.Z.Szabó. Photo: Attila Mátis.
Table 2 in Hiding in plain sight: Integrative analyses uncover a cryptic Salvia species in Europe
<p><b>Table 2.</b> Marginal likelihood estimates (lnMLE) and Bayes factors (2lnBF) for alternative delimitation hypotheses: grouping <i>Salvia austriaca</i> Jacq. and <i>Salvia</i> FDPD individuals into one species, <i>S. austriaca</i> s.l., or splitting them into two species.</p><table><tbody><tr><th>Repetition</th><th>Delimitation</th><th>lnMLE</th><th>2lnBF</th></tr></tbody><tbody><tr><th>1</th><td>1 species: <i>nemorosa</i>, <i>pratensis</i>, <i>nutans</i>, <i>austriaca</i> s.l.</td><td>–17,754.2</td><td>–</td></tr><tr><th>1</th><td>2 species: <i>nemorosa</i>, <i>pratensis</i>, <i>nutans</i>, <i>austriaca</i>, FDPD</td><td>–17,686.4</td><td>135.6</td></tr><tr><th>2</th><td>1 species: <i>nemorosa</i>, <i>pratensis</i>, <i>nutans</i>, <i>austriaca</i> s.l.</td><td>–17,968.3</td><td>–</td></tr><tr><th>2</th><td>2 species: <i>nemorosa</i>, <i>pratensis</i>, <i>nutans</i>, <i>austriaca</i>, FDPD</td><td>–17,687.5</td><td>561.7</td></tr></tbody></table><p>Both scenarios were run in two independent analyses (Repetitions 1 and 2).</p>
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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.