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145 results for “cryptic lineage”
Cryptic lineages respond differently to coral bleaching
<p>Coral cover is decreasing worldwide largely as a result of a rise in seawater temperatures that triggers coral bleaching and induces coral mortality. How coral reefs will respond to climate change will be a function of genetic variation and how it is partitioned within and among species. A critical initial step is to accurately delineate species and quantify their physiological potential to cope with heat stress. Cryptic species are morphologically similar but genetically distinct and may respond physiologically different to climate change. A dominant Caribbean reef builder severely affected by climate change is the mountainous star coral, <em>Orbicella faveolata</em>. Recently, Dziedzic <em>et al</em>. (2019) reported quantitative genetic variation in the physiological response to thermal stress in a single population of this species, suggesting that variation within populations will allow these corals to adapt to rising ocean temperatures. We reanalyzed their data and found multiple cryptic lineages rather than a single panmictic population, with one of the lineages being not heat-tolerant. While different cryptic lineages co-occur in certain locations, there is at least one lineage that occurs only in a single location. Our finding of hidden lineages within a threatened species highlights the varying extinction risks faced by these independently evolving groups, especially when the prospects of survival under warmer oceans seem favorable for some of them only.</p>
Data from: Cryptic divergent lineages of Pultenaea pauciflora M.B. Scott (Fabaceae, Mirbelieae) exhibit different evolutionary history
Genetic structure among disjunct population groups of Pultenaea pauciflora was assessed to determine the evolutionary history of this species as a basis for conservation management strategies. Analysis of individuals from all extant populations using 1737 amplified length polymorphism markers revealed two highly divergent genetic entities with strong geographical structuring. Populations located at Narrogin and Brookton clustered together in Bayesian assignment analysis with every individual optimally placed in a single cluster with complete membership. Genetic differentiation between populations in these two areas was very low. Populations at Boddington were highly divergent from those located at Narrogin and Brookton. All individuals from Boddington populations were optimally placed into a second cluster with complete membership. Populations located at Boddington maintain lower levels of allelic diversity, yet greater levels of mean heterozygosity than populations located at Narrogin and Brookton. The degree of genetic differentiation and different patterns of genetic diversity strongly suggest historical divergence and separate evolutionary influences on the two lineages that occur in different ecological habitat. These Evolutionary Significant Units are likely to represent two cryptic sister taxa in the extant populations currently recognized as P. pauciflora, and the reassessment of taxonomic and conservation status of both lineages is required.
Data from: Genetics, morphology and ecology reveal a cryptic pika lineage in the Sikkim Himalaya
Asian pika species are morphologically ∼similar and have overlapping ranges. This leads to uncertainty and species misidentification in the field. Phylogenetic analyses of such misidentified samples leads to taxonomic ambiguity. The ecology of many pika species remains understudied, particularly in the Himalaya, where sympatric species could be separated by elevation and/or substrate. We sampled, measured, and acquired genetic data from pikas in the Sikkim Himalaya. Our analyses revealed a cryptic lineage, Ochotona sikimaria, previously reported as a subspecies of O. thibetana. The results support the elevation of this lineage to the species level, as it is genetically divergent from O. thibetana, as well as sister species, O. cansus (endemic to central China) and O. curzoniae (endemic to the Tibetan plateau). The Sikkim lineage diverged from its sister species' about 1.7–0.8 myr ago, coincident with uplift events in the Himalaya. Our results add to the recent spate of cryptic diversity identified from the eastern Himalaya and highlight the need for further study within the Ochotonidae.
Data from: Cryptic lineages in the Wolf Cardinalfish living in sympatry on remote coral atolls
Coral reef health and biodiversity is under threat worldwide due to rapid climate change. However, much of the inter- and intra-specific diversity of coral reefs are undescribed even in well studied taxa such as fish. Delimiting previously unrecognised diversity is important for understanding the processes that generate and sustain biodiversity in coral reef ecosystems and informing strategies for their conservation and management. Many taxa that inhabit geographically isolated coral reefs rely on self-recruitment for population persistence, providing the opportunity for the evolution of unique genetic lineages through divergent selection and reproductive isolation. Many such lineages in corals and fish are morphologically similar or indistinguishable. Here, we report the discovery and characterisation of cryptic lineages of the Wolf Cardinalfish, Cheilodipterus artus, from the coral atolls of northwest Australia using multiple molecular markers from mitochondrial (CO1 and D-loop) and nuclear (microsatellites) DNA. Concordant results from all markers identified two highly divergent lineages that are morphologically cryptic and reproductively isolated. These lineages co-occurred at daytime resting sites, but the relative abundance of each lineage was strongly correlated with wave exposure. It appears, therefore, that fish from each lineage are better adapted to different microhabitats. Such cryptic and ecologically based diversity appears to be common in these atolls and may well aid resilience of these systems. Our results also highlight that underwater surveys based on visual identification clearly underestimate biodiversity, and that a taxonomic revision of the Cheilodipterus genus is necessary.
Data from: Strong selection against hybrids maintains a narrow contact zone between morphologically cryptic lineages in a rainforest lizard
Phenotypically cryptic lineages comprise an important yet understudied part of biodiversity; in particular, we have much to learn about how these lineages are formed and maintained. To better understand the evolutionary significance of such lineages, we studied a hybrid zone between two morphologically-cryptic phylogeographic lineages in the rainforest lizard, Lampropholis coggeri. Analyzing a multilocus genetic dataset through cline inference, individual-based methods and population measures of disequilibrium and using simulations to explore our genetic results in context of theoretical expectations, we inferred the processes maintaining this hybrid zone. We find that these lineages meet in a hybrid zone that is narrow (~400 m) relative to inferred dispersal rate. Further, the hybrid zone exhibits substantial genetic disequilibrium and sharply coincident and largely concordant clines. Based on our knowledge about the region's biogeography, the species' natural history, and our simulation results, we suggest that strong selection against hybrids structures this system. As all clines show a relatively narrow range of introgression, we posit that this hybrid zone might not yet be in equilibrium. Nonetheless, our results clearly show that phylogeographic lineages can evolve substantial reproductive isolation without concomitant morphological diversification, suggesting that such lineages can constitute a significant component of evolutionary diversity.
Data from: Phylogeographic pattern of range expansion provides evidence for cryptic species lineages in Silene nutans in Western Europe
As a result of recent or past evolutionary processes, a single species might consist of distinct Evolutionary Significant Units (ESUs), even corresponding to cryptic species. Determining the underlying mechanisms of range shifts and the processes at work in the build-up of divergent ESUs requires elucidating the factors that contribute to population genetic divergence across a species' range. We investigated the large-scale patterns of genetic structure in the perennial herbaceous plant species Silene nutans (Caryophyllaceae) in Western Europe. We sampled and genotyped 111 populations using 13 nuclear microsatellite loci and 6 plastid single-nucleotide polymorphisms. Broad-scale spatial population genetic structure was examined using Bayesian clustering, spatial multivariate analyses and measures of hierarchical genetic differentiation. The genotypic structure of S. nutans was typical of a predominantly allogamous mating system. We also identified plastid lineages with no intra-population polymorphism, mirroring two genetically differentiated nuclear lineages. No evidence of admixture was found. Spatial trends in genetic diversity further suggested independent leading-edge expansion associated with founding events and subsequent genetic erosion. Overall, our findings suggested speciation processes in S. nutans and highlighted striking patterns of distinct stepwise recolonisation of Western Europe shaped by Quaternary climate oscillations. Two main potential ESUs can be defined in Western Europe, corresponding to Eastern and Western nuclear-plastid lineages. In situ preservation of populations and genetic rescue implying ex situ conservation techniques should take the lineage identity into account. This is particularly true in Great Britain, northern France and Belgium, where S. nutans is rare and where distinct lineages co-occur in close contact.
Fig. 5 in Integrated morphometrics reveals conservatism in the cryptic yellowstripe scad (Perciformes: Carangidae) lineages from the Tropical Western Pacific
Fig. 5. (A–F) Scatterplots of the scores from PC1 to PC4 and (G–H) coordinate plots according to the first two discriminant functions of the studied lineages of S. leptolepis through geometric morphometrics.
Fig. 4 in Integrated morphometrics reveals conservatism in the cryptic yellowstripe scad (Perciformes: Carangidae) lineages from the Tropical Western Pacific
Fig. 4. (A) Scatterplot of the scores from PC1 and PC2 and (B–C) coordinate plots according to the first two discriminant functions of the studied lineages of S. leptolepis through truss morphometrics.
Fig. 3 in Integrated morphometrics reveals conservatism in the cryptic yellowstripe scad (Perciformes: Carangidae) lineages from the Tropical Western Pacific
Fig. 3. (A–F) Scatterplots of the scores from PC1 to PC4 and (G–H) coordinate plots according to the first two discriminant functions of the studied lineages of S. leptolepis through lineal morphometrics.
Fig. 1 in Integrated morphometrics reveals conservatism in the cryptic yellowstripe scad (Perciformes: Carangidae) lineages from the Tropical Western Pacific
Fig. 1. Map showing the collection sites of S. leptolepis across the Tropical Western Pacific. The corresponds to ASIA locations and for AUST (Map generated in Ocean Data View).
Fig. 2 in Integrated morphometrics reveals conservatism in the cryptic yellowstripe scad (Perciformes: Carangidae) lineages from the Tropical Western Pacific
Fig. 2. Overview of the different lineal morphometrics and location of the anatomical landmarks () on S. leptolepis. Landmarks refer to (1) tip of snout, (2) occiput/ posterior end of the cranium, (3) anterior insertion of 1st dorsal fin, (4) anterior insertion of 2nd dorsal fin, (5) upper base of caudal fin, (6) end of caudal peduncle, (7) lower base of caudal fin, (8) anterior base of anal fin, (9) anterior base of pelvic fin, (10) mid-base of the pectoral fin (11) ventral edge of the operculum, (12) posterior point of operculum (13) mid-point of the eye. See Table 2 for additional code definitions (Specimen on photo: KAUM-I16948, SL 114.72 mm).
Luciferase readout: Raw neutralization results for neutralization assays from pseudoparticles containing the SARS-CoV-2 receptor binding domain from a cryptic lineage
<div> <div> <div> <p>Deep sequencing of wastewater to detect SARS-CoV-2 has been used during the COVID- 19 pandemic to monitor viral variants as they appear and circulate in communities. SARS- CoV-2 lineages of an unknown source that have not been detected in clinical samples, referred to as cryptic lineages, are sometimes repeatedly detected from specific locations. We have continued to detect one such lineage previously seen in a Missouri site. This cryptic lineage has continued to evolve, indicating continued selective pressure similar to that observed in Omicron lineages.</p> </div> </div> </div> <p>This file contains the raw neutralization data using pseudoparticles containing a SARS-CoV-2 Spike protein with the RBD from the cryptic lineage detected in Missouri wastewater.</p>
Phylogeography of a widely distributed plant species reveals cryptic genetic lineages with parallel phenotypic responses to warming and drought conditions
<p>To predict how widely distributed species will perform under future climate change it is crucial to understand and reveal their underlying phylogenetics. However, detailed information about plant adaptation and its genetic basis and history remains scarce and especially widely distributed species receive little attention despite their putatively high adaptability. To examine the adaptation potential of a widely distributed species, we sampled the model plant <em>Silene vulgaris</em> across Europe. In a greenhouse experiment, we exposed the offspring of these populations to a climate-change scenario for central Europe and revealed the population structure through whole genome sequencing. Plants were grown under two temperature (18°C, 21°C) and three precipitation regimes (65 mm, 75 mm, 90 mm) to measure their response in biomass and fecundity related traits. To reveal the population genetic structure, ddRAD sequencing was employed for a whole genome approach. We found three major genetic clusters in <em>S. vulgaris</em> from Europe: one cluster comprising Southern European populations, one cluster of Western European populations and another cluster containing Central European populations. Population genetic diversity decreased with increasing latitude and a Mantel test revealed significant correlations between FST and geographic distances as well as between genetic and environmental distances. Our trait analysis showed that the genetic clusters significantly differed in biomass-related traits and in the days to flowering. However, half of the traits showed parallel response patterns to the experimental climate change scenario. Due to the differentiated but parallel response patterns, we assume that phenotypic plasticity plays an important role for the adaptation of the widely distributed species <em>S. vulgaris</em> and its intraspecific genetic lineages.</p>
Figure 3 in Cryptic lineages, cryptic barriers: historical seascapes and oceanic fronts drive genetic diversity in supralittoral rockpool beetles (Coleoptera: Hydraenidae)
Figure 3. Haplotype networks for COI and wingless for Ochthebius (Ochthebius) quadricollis. Colours represent the main geographic areas indicated in the legend.
Figure 2. Calibrated phylogenetic tree obtained with BEAST v.1.10.4 in Cryptic lineages, cryptic barriers: historical seascapes and oceanic fronts drive genetic diversity in supralittoral rockpool beetles (Coleoptera: Hydraenidae)
Figure 2. Calibrated phylogenetic tree obtained with BEAST v.1.10.4 of Ochthebius with focus on subgenus Cobalius (purple shade) and quadricollis species group (green shade) (former subgenus 'Calobius'). Numbers at nodes represent posterior probabilities, and 95% highest posterior density are given in blue horizontal rectangles. Calibrations points used in analysis are specified by grey dots.
Figure 5 in Cryptic lineages, cryptic barriers: historical seascapes and oceanic fronts drive genetic diversity in supralittoral rockpool beetles (Coleoptera: Hydraenidae)
Figure 5. Haplotype networks for COI and wingless for Ochthebius (Cobalius) lejolisii. Colours represent the main geographic areas indicated in the legend.
Figure 1 in Cryptic lineages, cryptic barriers: historical seascapes and oceanic fronts drive genetic diversity in supralittoral rockpool beetles (Coleoptera: Hydraenidae)
Figure 1. Distribution of sampling localities 1-57 (as listed in Table 1) and main surface marine currents and potential geographic barriers to dispersal (inset top-right).
Figure 4 in Cryptic lineages, cryptic barriers: historical seascapes and oceanic fronts drive genetic diversity in supralittoral rockpool beetles (Coleoptera: Hydraenidae)
Figure 4. Haplotype networks for COI and wingless for Ochthebius (Cobalius) subinteger. Colours represent the main geographic areas indicated in the legend.
Supplementary material 1 from: Wesener T, Voigtländer K, Decker P, Oeyen JF, Spelda J, Lindner N (2015) First results of the German Barcode of Life (GBOL) – Myriapoda project: Cryptic lineages in German Stenotaenia linearis (Koch, 1835) (Chilopoda, Geophilomorpha). In: Tuf IH, Tajovský K (Eds) Proceedings of the 16th International Congress of Myriapodology, Olomouc, Czech Republic. ZooKeys 510: 15-29. https://doi.org/10.3897/zookeys.510.8852
Table. Estimates of Evolutionary Divergence between Sequences: Explanation note: The number of base differences per site from between sequences are shown. The analysis involved 45 nucleotide sequences. Codon positions included were 1st+2nd+3rd+Noncoding. All ambiguous positions were removed for each sequence pair. There were a total of 658 positions in the final dataset. Evolutionary analyses were conducted in MEGA6.
FIGURE 13 in Taxonomizing a truly morphologically cryptic complex of dwarf geckos from Madagascar: molecular evidence for new species-level lineages within the Lygodactylus tolampyae complex
FIGURE 13. Habitat of species of the Lygodactylus tolampyae complex. A. Dry deciduous forest at Ampijoroa (Ankarafantsika) where L. morii sp. nov. occurs in high densities. B. View of remains of dry deciduous Ampondrabe forest (habitat of L. morii sp. nov. and L. herilalai sp. nov.) with large areas of forest destroyed by fire in the foreground. C, D. Transitional forest on Sahamalaza Peninsula, habitat of L. schwitzeri sp. nov. E. Forest in the Tsingy de Bemaraha, habitat of L. tolampyae. All photos by the authors except A by P. Galán.
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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.