Journal articles: 'Cryptic variation'

1

Gibson, Greg, and Laura K. Reed. "Cryptic genetic variation." Current Biology 18, no. 21 (November 2008): R989—R990. http://dx.doi.org/10.1016/j.cub.2008.08.011.

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Gibson, Greg, and Ian Dworkin. "Uncovering cryptic genetic variation." Nature Reviews Genetics 5, no. 9 (September 2004): 681–90. http://dx.doi.org/10.1038/nrg1426.

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Burgess, Darren J. "An eye for cryptic variation." Nature Reviews Genetics 15, no. 2 (December 24, 2013): 64. http://dx.doi.org/10.1038/nrg3660.

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Zheng, Jia, Joshua L. Payne, and Andreas Wagner. "Cryptic genetic variation accelerates evolution by opening access to diverse adaptive peaks." Science 365, no. 6451 (July 25, 2019): 347–53. http://dx.doi.org/10.1126/science.aax1837.

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Cryptic genetic variation can facilitate adaptation in evolving populations. To elucidate the underlying genetic mechanisms, we used directed evolution in Escherichia coli to accumulate variation in populations of yellow fluorescent proteins and then evolved these proteins toward the new phenotype of green fluorescence. Populations with cryptic variation evolved adaptive genotypes with greater diversity and higher fitness than populations without cryptic variation, which converged on similar genotypes. Populations with cryptic variation accumulated neutral or deleterious mutations that break the constraints on the order in which adaptive mutations arise. In doing so, cryptic variation opens paths to adaptive genotypes, creates historical contingency, and reduces the predictability of evolution by allowing different replicate populations to climb different adaptive peaks and explore otherwise-inaccessible regions of an adaptive landscape.

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McGuigan, Katrina, and Carla M. Sgrò. "Evolutionary consequences of cryptic genetic variation." Trends in Ecology & Evolution 24, no. 6 (June 2009): 305–11. http://dx.doi.org/10.1016/j.tree.2009.02.001.

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Paaby, Annalise B., and Matthew V. Rockman. "Cryptic genetic variation: evolution's hidden substrate." Nature Reviews Genetics 15, no. 4 (March 11, 2014): 247–58. http://dx.doi.org/10.1038/nrg3688.

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Paaby, Annalise, and Greg Gibson. "Cryptic Genetic Variation in Evolutionary Developmental Genetics." Biology 5, no. 2 (June 13, 2016): 28. http://dx.doi.org/10.3390/biology5020028.

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Omland, Kevin E., Cheryl L. Tarr, William I. Boarman, John M. Marzluff, and Robert C. Fleischer. "Cryptic genetic variation and paraphyly in ravens." Proceedings of the Royal Society of London. Series B: Biological Sciences 267, no. 1461 (December 22, 2000): 2475–82. http://dx.doi.org/10.1098/rspb.2000.1308.

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Hodgkinson, Alan, Emmanuel Ladoukakis, and Adam Eyre-Walker. "Cryptic Variation in the Human Mutation Rate." PLoS Biology 7, no. 2 (February 3, 2009): e1000027. http://dx.doi.org/10.1371/journal.pbio.1000027.

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Titus, Robert. "Cryptic variation and its manifestation in the Lower Trentonian Rafinesquina lineage (Ordovician, New York State)." Paleontological Society Special Publications 6 (1992): 292. http://dx.doi.org/10.1017/s2475262200008522.

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Species populations commonly carry a great deal of genetic variation which is not expressed in individual phenotypes. Cryptic variation can be carried in recessive alleles, in cases of heterosis, or where modifier genes inhibit expression of the hidden trait. Other genetic and ecological factors also allow cryptic variation. Stabilizing selection prevents the expression of hidden traits; normalizing selection weeds out the deviants and canalizing selection suppresses their traits. Together the two keep the species near the top of the adaptive peak. Cryptic variation balances a species' need to be well-adapted to its environment and also for it to maintain a reserve of variation for potential environmental change. Expression of cryptic traits is rare and is usually associated with times of greatly reduced natural selection and rapid population growth, when the lower slopes of the adaptive peak are exposed.A possible example of the manifestation of cryptic traits occurs within the lower Trentonian Rafinesquina lineage of New York State. The two most commonly reported species of the genus have been reappraised in terms of cryptic variation. Extensive collections of Rafinesquina “lennoxensis” reveal far more intergrading morphotypes than had hitherto been recognized. The form which Salmon (1942) described is broadly U-shaped with sulcate margins. It grades into very convex forms as well as sharply-defined or convexly geniculate types. Of great importance, all forms grade into the flat, U-shaped, alate R. trentonensis, which is, by far, the most common and widespread lower Trentonian member of the genus. The R. “lennoxensis” assemblage has a very narrow biostratigraphy, being confined to a few locations in the upper Napanee Limestone. This places it in a quiet, protected, low stress, lagoonal setting behind the barrier shoal facies of the Kings Falls Limestone.The R. “lennoxensis” assemblage does not constitute a natural biologic species; it is reinterpreted as an assemblage of phenodeviants occupying a low stress, low natural selection lagoon facies. All such forms should be included within R. trentonensis. Given the evolutionary plasticity of this genus, extensive cryptic variation is not surprising.

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Masel, Joanna. "Cryptic Genetic Variation Is Enriched for Potential Adaptations." Genetics 172, no. 3 (December 30, 2005): 1985–91. http://dx.doi.org/10.1534/genetics.105.051649.

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Schlichting, Carl D. "Hidden Reaction Norms, Cryptic Genetic Variation, and Evolvability." Annals of the New York Academy of Sciences 1133, no. 1 (June 2008): 187–203. http://dx.doi.org/10.1196/annals.1438.010.

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Renner, Matt A. M., Elizabeth A. Brown, and Glenda M. Wardle. "Averaging v. outlier removal. Decrypting variance among cryptic Lejeunea species (Lejeuneaceae: Jungermanniopsida) using geometric morphometrics." Australian Systematic Botany 26, no. 1 (2013): 13. http://dx.doi.org/10.1071/sb12016.

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Molecular data have revealed many morphologically cryptic species. More surprising than lack of difference, however, is that morphological variation and complex patterns of overlapping features can mask cryptic species. We employ geometric morphometric methods (GMM) to explore patterns of variation within four liverwort species, three of which were previously attributed to Lejeunea tumida Mitt. Each species exhibited considerable variation within, and overlap among, species in size and shape, independent of degree of relatedness. Most variation was expressed within individuals, suggesting that the observed breadth of variation was within the developmental capacity of single genotypes. Size and shape variation within, and consequently overlap among, individuals resulted primarily from variance in growth of shoots. Inter-specific differences were swamped by intra- and inter-individual variation. We coupled GMM with multivariate methods for outlier removal, and simple averaging of individuals to explore whether intra-individual variation could be reconciled to maximise the inter-species difference, facilitating resolution of cryptic species despite extensive morphological continuity and overlap. Unfortunately, outlier removal did not achieve separation among species, because removing extremes failed to eliminate overlap resulting from within-species variation. Individual averaging was partially successful in extracting L. tumida as a discrete entity but did not segregate the remaining three species. Although the challenges for morphology-based identification of cryptic species are significant, GMM provide one of the best sets of methods for identifying and communicating any subtle morphological differences that may exist.

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Mcgovern, Tamara M., and Michael E. Hellberg. "Cryptic species, cryptic endosymbionts, and geographical variation in chemical defences in the bryozoan Bugula neritina." Molecular Ecology 12, no. 5 (April 14, 2003): 1207–15. http://dx.doi.org/10.1046/j.1365-294x.2003.01758.x.

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Alam, MM Mahbub, Kristen M. Westfall, and Snaebjörn Pálsson. "Mitochondrial DNA variation reveals cryptic species in Fenneropenaeus indicus." Bulletin of Marine Science 91, no. 1 (January 1, 2014): 15–31. http://dx.doi.org/10.5343/bms.2014.1036.

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Rabbani, Mohamad, Brigette Zacharczenko, and David M. Green. "Color Pattern Variation in a Cryptic Amphibian,Anaxyrus fowleri." Journal of Herpetology 49, no. 4 (December 2015): 649–54. http://dx.doi.org/10.1670/14-114.

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Kingswood, S. C., A. T. Kumamoto, S. J. Charter, and M. L. Jones. "Cryptic chromosomal variation in suni Neotragus moschatus (Artiodactyla, Bovidae)." Animal Conservation 1, no. 2 (May 1998): 95–100. http://dx.doi.org/10.1111/j.1469-1795.1998.tb00016.x.

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Ledon-Rettig, C. C., D. W. Pfennig, A. J. Chunco, and I. Dworkin. "Cryptic Genetic Variation in Natural Populations: A Predictive Framework." Integrative and Comparative Biology 54, no. 5 (June 17, 2014): 783–93. http://dx.doi.org/10.1093/icb/icu077.

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Hughes, Tulloss, and Petersen. "Intragenomic nuclear RNA variation in a cryptic Amanita taxon." Mycologia 110, no. 1 (January 2, 2018): 93–103. http://dx.doi.org/10.1080/00275514.2018.1427402.

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Amanita cf. lavendula collections in eastern North America, Mexico, and Costa Rica were found to consist of four cryptic taxa, one of which exhibited consistently unreadable nuclear rDNA ITS1-5.8S-ITS2 (fungal barcode) sequences after ITS1 base 130. This taxon is designated here as Amanita cf. lavendula taxon 1. ITS sequences from dikaryotic basidiomata were cloned, but sequences recovered from cloning did not segregate into distinct haplotypes. Rather, there was a mix of haplotypes that varied among themselves predominantly at 28 ITS positions. Analysis of each of these 28 variable bases showed predominantly two alternate bases at each position. Based on these findings and additional sequence data from the nuclear rDNA 28S, RNA polymerase II subunit 2 (RPB2) and mitochondrial rDNA small subunit (SSU) and 23S genes, we speculate that taxon 1 represents an initial hybridization event between two divergent taxa followed by failure of the ribosomal repeat to homogenize. Homogenization failure may be a result of repeated hybridization between divergent internal transcribed spacer (ITS) types with inadequate time for concerted evolution of the ribosomal repeat or, alternately, a complete failure of the ribosomal homogenization process. To our knowledge, this finding represents the first report of a geographically widespread taxon (Canada, eastern USA, Costa Rica) with apparent homogenization failure across all collections. Findings such as these have implications for fungal barcoding efforts and the application of fungal barcodes in identifying environmental sequences.

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Bijl, Wouter, and Judith E. Mank. "Widespread cryptic variation in genetic architecture between the sexes." Evolution Letters 5, no. 4 (July 3, 2021): 359–69. http://dx.doi.org/10.1002/evl3.245.

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Iizuka, M. "A model to estimate the increase of genetic variability due to electrophoretically cryptic alleles." Genetics 118, no. 2 (February 1, 1988): 365–69. http://dx.doi.org/10.1093/genetics/118.2.365.

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Abstract To consider the problem of the increase of genetic variability due to electrophoretically cryptic alleles, the equally degenerate electromorph model is proposed. Mutation, random sampling drift and selection can be incorporated in this model. Simple formulas are obtained to show how genetic variability increases when cryptic alleles are distinguished. This model is extended to a two-population system to see the effect of cryptic allele variation on genetic differentiation.

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Niu, Yang, Zhe Chen, Martin Stevens, and Hang Sun. "Divergence in cryptic leaf colour provides local camouflage in an alpine plant." Proceedings of the Royal Society B: Biological Sciences 284, no. 1864 (October 4, 2017): 20171654. http://dx.doi.org/10.1098/rspb.2017.1654.

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The efficacy of camouflage through background matching is highly environment-dependent, often resulting in intraspecific colour divergence in animals to optimize crypsis in different visual environments. This phenomenon is largely unexplored in plants, although several lines of evidence suggest they do use crypsis to avoid damage by herbivores. Using Corydalis hemidicentra, an alpine plant with cryptic leaf colour, we quantified background matching between leaves and surrounding rocks in five populations based on an approximate model of their butterfly enemy's colour perception. We also investigated the pigment basis of leaf colour variation and the association between feeding risk and camouflage efficacy. We show that plants exhibit remarkable colour divergence between populations, consistent with differences in rock appearances. Leaf colour varies because of a different quantitative combination of two basic pigments—chlorophyll and anthocyanin—plus different air spaces. As expected, leaf colours are better matched against their native backgrounds than against foreign ones in the eyes of the butterfly. Furthermore, improved crypsis tends to be associated with a higher level of feeding risk. These results suggest that divergent cryptic leaf colour may have evolved to optimize local camouflage in various visual environments, extending our understanding of colour evolution and intraspecific phenotype diversity in plants.

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Lee, Jonathan T., Alessandro L. V. Coradini, Amy Shen, and Ian M. Ehrenreich. "Layers of Cryptic Genetic Variation Underlie a Yeast Complex Trait." Genetics 211, no. 4 (February 20, 2019): 1469–82. http://dx.doi.org/10.1534/genetics.119.301907.

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Tubaro, Pablo L., Dario A. Lijtmaer, and Stephen C. Lougheed. "CRYPTIC DICHROMATISM AND SEASONAL COLOR VARIATION IN THE DIADEMED TANAGER." Condor 107, no. 3 (2005): 648. http://dx.doi.org/10.1650/0010-5422(2005)107[0648:cdascv]2.0.co;2.

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CHAN, LAUREN M. "Seasonality, microhabitat and cryptic variation in tropical salamander reproductive cycles." Biological Journal of the Linnean Society 78, no. 4 (April 1, 2003): 489–96. http://dx.doi.org/10.1046/j.0024-4066.2002.00157.x.

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McGuigan, Katrina, Nicole Nishimura, Mark Currey, Dan Hurwit, and William A. Cresko. "CRYPTIC GENETIC VARIATION AND BODY SIZE EVOLUTION IN THREESPINE STICKLEBACK." Evolution 65, no. 4 (December 22, 2010): 1203–11. http://dx.doi.org/10.1111/j.1558-5646.2010.01195.x.

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Tubaro, Pablo L., Dario A. Lijtmaer, and Stephen C. Lougheed. "Cryptic Dichromatism and Seasonal Color Variation in the Diademed Tanager." Condor 107, no. 3 (August 1, 2005): 648–56. http://dx.doi.org/10.1093/condor/107.3.648.

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Abstract We studied the patterns of sexual dichromatism and seasonal variation in plumage color in the Diademed Tanager (Stephanophorus diadematus), a species previously considered devoid of variation in adult plumage. The general coloration of this species is dark blue-violet, with a white-blue and red crown. Plumage reflectance of seven body regions from 33 study skins belonging to adults of both sexes was measured. Reflectance values were used in a principal components analysis (PCA) and hue, short-wave chroma, and UV chroma were also measured directly on the spectra. Both PCA factor scores and these latter variables were subjected to two-way ANCOVAs with sex and season as main factors and the year of capture as a covariate. We found that crowns of males were significantly brighter than those of females. In addition, the nape, chest, and belly showed significant differences in spectral shape, with relatively greater short-wave reflectance and less long-wave reflectance in males than in females. Although sexes were alike in hue, they differed in chroma in almost all body regions. Brightness also differed between seasons, and contrary to our expectation nonbreeding birds were brighter than breeding ones. This result may be a consequence of the particular molt program of tanagers that includes only a complete post-reproductive molt. Despite finding seasonal differences in spectral shape in various body regions, no significant changes in hue, short-wave chroma, or UV chroma were evident. To our knowledge, this is the first report of variation in adult plumage color for the Diademed Tanager, and we suggest that dichromatism in tanagers may be even more pervasive than is currently recognized. Dicromatismo Críptico y Variación Estacional de Color en Stephanophorus diadematus Resumen. Estudiamos los patrones de dicromatismo sexual y variación estacional en la coloración del plumaje de Stephanophorus diadematus, una especie previamente considerada carente de variación en la coloración del plumaje adulto. La coloración general de esta especie es azul violáceo oscuro, con una corona blanca azulada y roja. Se midió la reflectancia de siete regiones corporales en 33 pieles de estudio pertenecientes a adultos de ambos sexos. Los valores de reflectancia se utilizaron en un análisis de componentes principales, y además se midieron el tono (hue), la intensidad del color de onda corta y la intensidad del color de UV directamente sobre los espectros. Tanto los factores del análisis de componentes principales como las variables mencionadas fueron sujetos a ANCOVAs de dos factores, considerando el sexo y la estación como factores principales, y el año de captura como covariable. Estos análisis mostraron que la corona de los machos es significativamente más brillante que la de las hembras. Además, la nuca, el pecho y el vientre mostraron diferencias significativas en la forma espectral, presentando los machos mayor reflectancia en la zona de onda corta y menor en la zona de onda larga que las hembras. Si bien el tono no difirió entre sexos, la intensidad del color difirió en la mayoría de las regiones corporales entre machos y hembras. El brillo también difirió entre temporadas y, contrariamente a nuestra expectativa, los individuos capturados en la temporada no reproductiva fueron más brillantes que aquellos capturados en la temporada reproductiva. Este resultado podría deberse al programa de muda particular presente en Thraupidae, que incluye una única muda post-reproductiva completa. Si bien encontramos diferencias entre estaciones en la forma espectral en varias regiones corporales, no se detectaron diferencias en el tono, la intensidad del color de onda corta ni la intensidad del color de UV. Este es, de acuerdo a nuestro conocimiento, el primer estudio que muestra variación en la coloración del plumaje adulto de S. diadematus. Sugerimos que el dicromatismo en Thraupidae podría ser más común de lo que actualmente se piensa.

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Rosas, Ulises, Nick H. Barton, Lucy Copsey, Pierre Barbier de Reuille, and Enrico Coen. "Cryptic Variation between Species and the Basis of Hybrid Performance." PLoS Biology 8, no. 7 (July 20, 2010): e1000429. http://dx.doi.org/10.1371/journal.pbio.1000429.

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Lemos, B., L. O. Araripe, and D. L. Hartl. "Polymorphic Y Chromosomes Harbor Cryptic Variation with Manifold Functional Consequences." Science 319, no. 5859 (January 4, 2008): 91–93. http://dx.doi.org/10.1126/science.1148861.

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Lebedev, Vladimir, Alexey Bogdanov, Oleg Brandler, Marina Melnikova, Undrakhbayar Enkhbat, Andrey Tukhbatullin, Alexei Abramov, Alexey Surov, Irina Bakloushinskaya, and Anna Bannikova. "Cryptic variation in mole voles Ellobius (Arvicolinae, Rodentia) of Mongolia." Zoologica Scripta 49, no. 5 (August 19, 2020): 535–48. http://dx.doi.org/10.1111/zsc.12440.

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Brochu, Christopher A., and Colin D. Sumrall. "Modern cryptic species and crocodylian diversity in the fossil record." Zoological Journal of the Linnean Society 189, no. 2 (May 13, 2020): 700–711. http://dx.doi.org/10.1093/zoolinnean/zlaa039.

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Abstract Advances in molecular biology and genetics are revealing that many recognized crocodylian species are complexes of two or more cryptic species. These discoveries will have a profound impact on interpretation of the crocodyliform fossil record. Our understanding of ranges of intraspecific variation in modern crocodylian morphology may be based on multiple species and thus express both intraspecific and interspecific variation. This raises questions about our ability to recognize modern species in the fossil record, and it also indicates that specimens from disparate localities or horizons may represent not single widespread species, but multiple related species. Ranges of variation in modern species require a thorough re-evaluation, and we may have to revisit previous perceptions of past crocodyliform diversity, rates of evolution or anagenetic lineages in stratigraphic succession. These challenges will not be unique to those studying crocodyliforms and will require sophisticated approaches to variation among modern and fossil specimens.

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Ewe, Chee Kiang, Yamila N. Torres Cleuren, Sagen E. Flowers, Geneva Alok, Russell G. Snell, and Joel H. Rothman. "Natural cryptic variation in epigenetic modulation of an embryonic gene regulatory network." Proceedings of the National Academy of Sciences 117, no. 24 (June 1, 2020): 13637–46. http://dx.doi.org/10.1073/pnas.1920343117.

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Gene regulatory networks (GRNs) that direct animal embryogenesis must respond to varying environmental and physiological conditions to ensure robust construction of organ systems. While GRNs are evolutionarily modified by natural genomic variation, the roles of epigenetic processes in shaping plasticity of GRN architecture are not well understood. The endoderm GRN inCaenorhabditis elegansis initiated by the maternally supplied SKN-1/Nrf2 bZIP transcription factor; however, the requirement for SKN-1 in endoderm specification varies widely among distinctC. eleganswild isotypes, owing to rapid developmental system drift driven by accumulation of cryptic genetic variants. We report here that heritable epigenetic factors that are stimulated by transient developmental diapause also underlie cryptic variation in the requirement for SKN-1 in endoderm development. This epigenetic memory is inherited from the maternal germline, apparently through a nuclear, rather than cytoplasmic, signal, resulting in a parent-of-origin effect (POE), in which the phenotype of the progeny resembles that of the maternal founder. The occurrence and persistence of POE varies between different parental pairs, perduring for at least 10 generations in one pair. This long-perduring POE requires piwi-interacting RNA (piRNA) function and the germline nuclear RNA interference (RNAi) pathway, as well as MET-2 and SET-32, which direct histone H3K9 trimethylation and drive heritable epigenetic modification. Such nongenetic cryptic variation may provide a resource of additional phenotypic diversity through which adaptation may facilitate evolutionary changes and shape developmental regulatory systems.

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Kim, Jeongho, Jaehyun Kim, Wonchoel Lee, and Ivana Karanovic. "The First Insight into the Patterns of Size and Shape Variation of a Microcerberid Isopod." Water 13, no. 4 (February 17, 2021): 515. http://dx.doi.org/10.3390/w13040515.

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Cryptic species are a biological phenomenon only recently recognized due to progress in molecular studies. They pose a significant challenge to conventional taxonomic work since these species manifest low morphological differences, but considerable genetic disparity. New taxonomic methods are in development but have yet to be tested for many animal groups. Isopods belonging to the suborder Microcerberidea are one such group. The Asian microcerberid isopod, Coxicerberus fukudai (Ito, 1974), is a major component of marine interstitial fauna with suspected cryptic species inhabiting Japan and Korea. We chose six Korean populations with high molecular interpopulations divergence and applied 2D landmark-based geometric morphometrics to cephalic sensilla, pleonal points, and male pleopod II. This quantitative approach allowed us to study interpopulation size and shape variations, morphospace structure, and whether the morphological pattern mirrored the genetic species. We determined that a high degree of interpopulation size variation significantly influences shape changes. Once we removed the allometric effect, the size-corrected male pleopod II shape variations yielded a new species, C. jangsaensis sp. nov. At the same time, we were able to resolve the C. fukadai species complex.

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Hodgson, N. A., and M. J. Le Bas. "The geochemistry and cryptic zonation of pyrochlore from San Vicente, Cape Verde Islands." Mineralogical Magazine 56, no. 383 (June 1992): 201–14. http://dx.doi.org/10.1180/minmag.1992.056.383.06.

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AbstractZr-rich pyrochlore crystals in carbonatite from San Vicente (Cape Verdes Islands) show cryptic, concentric and rhythmic chemical zonation with Ca increasing and Ti, U and Zr decreasing towards the rims. In one carbonatite, taken from the Camile dyke, previously undocumented cryptic sector zonation of Ti, U and Zr is also observed in these crystals. The chemical variation is investigated by wavelength-dispersive electron microprobe, with both single spot and crystal map analyses.The concentric and rhythmic zonation, marked by element substitution, was generated by magma heterogeneity and/or element diffusion kinetics, but it is suggested that the sector zonation, marked by differential site substitution, was governed by protosite variation between octahedral and cubic faces.

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Holmes, NJ, VJ Harriott, and SA Banks. "Latitudinal variation in patterns of colonisation of cryptic calcareous marine organisms." Marine Ecology Progress Series 155 (1997): 103–13. http://dx.doi.org/10.3354/meps155103.

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Ji, Lexiang, Drexel A. Neumann, and Robert J. Schmitz. "Crop Epigenomics: Identifying, Unlocking, and Harnessing Cryptic Variation in Crop Genomes." Molecular Plant 8, no. 6 (June 2015): 860–70. http://dx.doi.org/10.1016/j.molp.2015.01.021.

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Grimbert, Stéphanie, and Christian Braendle. "Cryptic genetic variation uncovers evolution of environmentally sensitive parameters inCaenorhabditisvulval development." Evolution & Development 16, no. 5 (August 20, 2014): 278–91. http://dx.doi.org/10.1111/ede.12091.

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Barata, Mafalda, Ana Perera, and D. James Harris. "Cryptic variation in the Moroccan high altitude lizardAtlantolacerta andreanskyi(Squamata: Lacertidae)." African Journal of Herpetology 64, no. 1 (January 2, 2015): 1–17. http://dx.doi.org/10.1080/21564574.2014.967815.

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OLIVER, JEFFREY C., and ARTHUR M. SHAPIRO. "Genetic isolation and cryptic variation within theLycaena xanthoidesspecies group (Lepidoptera: Lycaenidae)." Molecular Ecology 16, no. 20 (October 2007): 4308–20. http://dx.doi.org/10.1111/j.1365-294x.2007.03494.x.

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Hayden, Eric J., Evandro Ferrada, and Andreas Wagner. "Cryptic genetic variation promotes rapid evolutionary adaptation in an RNA enzyme." Nature 474, no. 7349 (June 2011): 92–95. http://dx.doi.org/10.1038/nature10083.

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Wilke, Thomas, Markus Pfenninger, and George M. Davis. "Anatomical variation in cryptic mudsnail species: Statistical discrimination and evolutionary significance." Proceedings of the Academy of Natural Sciences of Philadelphia 152, no. 1 (October 2002): 45–66. http://dx.doi.org/10.1635/0097-3157(2002)152[0045:avicms]2.0.co;2.

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Murray, Christopher, Allison Litmer, Matthew Grisnik, Mackenzie L. Sconyers, and Craig Guyer. "Head shape variation among cryptic populations of ground skinks ( Scincella lateralis )." Journal of Zoological Systematics and Evolutionary Research 57, no. 4 (November 2019): 877–83. http://dx.doi.org/10.1111/jzs.12314.

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Tautz, Diethard, Martin Trick, and Gabriel A. Dover. "Cryptic simplicity in DNA is a major source of genetic variation." Nature 322, no. 6080 (August 1986): 652–56. http://dx.doi.org/10.1038/322652a0.

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Böhme, Manja U., Uwe Fritz, Tatiana Kotenko, Katarina Ljubisavljević, Nikolay Tzankov, and Thomas U. Berendonk. "Phylogeography and cryptic variation within the Lacerta viridis complex (Lacertidae, Reptilia)." Zoologica Scripta 36, no. 2 (March 2007): 119–31. http://dx.doi.org/10.1111/j.1463-6409.2006.00262.x.

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Brand, Harrison, Ryan L. Collins, Carrie Hanscom, Jill A. Rosenfeld, Vamsee Pillalamarri, Matthew R. Stone, Fontina Kelley, et al. "Paired-Duplication Signatures Mark Cryptic Inversions and Other Complex Structural Variation." American Journal of Human Genetics 97, no. 1 (July 2015): 170–76. http://dx.doi.org/10.1016/j.ajhg.2015.05.012.

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Couret, Jannelle, Danilo C. Moreira, Davin Bernier, Aria Mia Loberti, Ellen M. Dotson, and Marco Alvarez. "Delimiting cryptic morphological variation among human malaria vector species using convolutional neural networks." PLOS Neglected Tropical Diseases 14, no. 12 (December 17, 2020): e0008904. http://dx.doi.org/10.1371/journal.pntd.0008904.

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Deep learning is a powerful approach for distinguishing classes of images, and there is a growing interest in applying these methods to delimit species, particularly in the identification of mosquito vectors. Visual identification of mosquito species is the foundation of mosquito-borne disease surveillance and management, but can be hindered by cryptic morphological variation in mosquito vector species complexes such as the malaria-transmitting Anopheles gambiae complex. We sought to apply Convolutional Neural Networks (CNNs) to images of mosquitoes as a proof-of-concept to determine the feasibility of automatic classification of mosquito sex, genus, species, and strains using whole-body, 2D images of mosquitoes. We introduce a library of 1, 709 images of adult mosquitoes collected from 16 colonies of mosquito vector species and strains originating from five geographic regions, with 4 cryptic species not readily distinguishable morphologically even by trained medical entomologists. We present a methodology for image processing, data augmentation, and training and validation of a CNN. Our best CNN configuration achieved high prediction accuracies of 96.96% for species identification and 98.48% for sex. Our results demonstrate that CNNs can delimit species with cryptic morphological variation, 2 strains of a single species, and specimens from a single colony stored using two different methods. We present visualizations of the CNN feature space and predictions for interpretation of our results, and we further discuss applications of our findings for future applications in malaria mosquito surveillance.

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Frankino, W. Anthony, Eric Bakota, Ian Dworkin, Gerald S. Wilkinson, Jason B. Wolf, and Alexander W. Shingleton. "Individual Cryptic Scaling Relationships and the Evolution of Animal Form." Integrative and Comparative Biology 59, no. 5 (July 31, 2019): 1411–28. http://dx.doi.org/10.1093/icb/icz135.

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Abstract Artificial selection offers a powerful tool for the exploration of how selection and development shape the evolution of morphological scaling relationships. An emerging approach models the expression and evolution of morphological scaling relationships as a function of variation among individuals in the developmental mechanisms that regulate trait growth. These models posit the existence of genotype-specific morphological scaling relationships that are unseen or “cryptic.” Within-population allelic variation at growth-regulating loci determines how these individual cryptic scaling relationships are distributed, and exposure to environmental factors that affect growth determines the size phenotype expressed by each individual on their cryptic, genotype-specific scaling relationship. These models reveal that evolution of the intercept and slope of the population-level static allometry is determined, often in counterintuitive ways, largely by the shape of the distribution of these underlying individual-level scaling relationships. Here we review this modeling framework and present the wing-body size individual cryptic scaling relationships from a population of Drosophila melanogaster. To determine how these models might inform interpretation of published work on scaling relationship evolution, we review studies where artificial selection was applied to alter the parameters of population-level static allometries. Finally, motivated by our review, we outline areas in need of empirical work and describe a research program to address these topics; the approach includes describing the distribution of individual cryptic scaling relationships across populations and environments, empirical testing of the model’s predictions, and determining the effects of environmental heterogeneity on realized trait distributions and how this affects allometry evolution.

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Brasier, Madeleine J., Helena Wiklund, Lenka Neal, Rachel Jeffreys, Katrin Linse, Henry Ruhl, and Adrian G. Glover. "DNA barcoding uncovers cryptic diversity in 50% of deep-sea Antarctic polychaetes." Royal Society Open Science 3, no. 11 (November 2016): 160432. http://dx.doi.org/10.1098/rsos.160432.

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The Antarctic marine environment is a diverse ecosystem currently experiencing some of the fastest rates of climatic change. The documentation and management of these changes requires accurate estimates of species diversity. Recently, there has been an increased recognition of the abundance and importance of cryptic species, i.e. those that are morphologically identical but genetically distinct. This article presents the largest genetic investigation into the prevalence of cryptic polychaete species within the deep Antarctic benthos to date. We uncover cryptic diversity in 50% of the 15 morphospecies targeted through the comparison of mitochondrial DNA sequences, as well as 10 previously overlooked morphospecies, increasing the total species richness in the sample by 233%. Our ability to describe universal rules for the detection of cryptic species within polychaetes, or normalization to expected number of species based on genetic data is prevented by taxon-specific differences in phylogenetic outputs and genetic variation between and within potential cryptic species. These data provide the foundation for biogeographic and functional analysis that will provide insight into the drivers of species diversity and its role in ecosystem function.

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Verrelli, Brian C., and Walter F. Eanes. "Clinal Variation for Amino Acid Polymorphisms at thePgmLocus inDrosophila melanogaster." Genetics 157, no. 4 (April 1, 2001): 1649–63. http://dx.doi.org/10.1093/genetics/157.4.1649.

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AbstractClinal variation is common for enzymes in the glycolytic pathway for Drosophila melanogaster and is generally accepted as an adaptive response to different climates. Although the enzyme phosphoglucomutase (PGM) possesses several allozyme polymorphisms, it is unique in that it had been reported to show no clinal variation. Our recent DNA sequence investigation of Pgm found extensive cryptic amino acid polymorphism segregating with the allozyme alleles. In this study, we characterize the geographic variation of Pgm amino acid polymorphisms at the nucleotide level along a latitudinal cline in the eastern United States. A survey of 15 SNPs across the Pgm gene finds significant clinal differentiation for the allozyme polymorphisms as well as for many of the cryptic amino acid polymorphisms. A test of independence shows that pervasive linkage disequilibrium across this gene region can explain many of the amino acid clines. A single Pgm haplotype defined by two amino acid polymorphisms shows the strongest correlation with latitude and the steepest change in allele frequency across the cline. We propose that clinal selection at Pgm may in part explain the extensive amino acid polymorphism at this locus and is consistent with a multilocus response to selection in the glycolytic pathway.

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Sweeney, Emma L., Cheryl Bletchly, Rita Gupta, and David M. Whiley. "False-negative Chlamydia polymerase chain reaction result caused by a cryptic plasmid-deficient Chlamydia trachomatis strain in Australia." Sexual Health 16, no. 4 (2019): 394. http://dx.doi.org/10.1071/sh18205.

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Background The 7.5-kb chlamydial cryptic plasmid remains a widely used sequence target for Chlamydia trachomatis nucleic acid amplification tests, but sequence variation in this plasmid, particularly a previously reported 377-bp deletion, can cause false-negative results. Here we report the presence in Australia of a C. trachomatis strain lacking the cryptic plasmid. Methods: A rectal swab from a male in his 50s provided a positive result for C. trachomatis using the Roche Cobas 4800 test, but a negative result in our confirmatory in-house polymerase chain reaction (PCR) method targeting the chlamydial cryptic plasmid. This result was unexpected given our in-house PCR assay targeted a region of sequence outside the recognised 377-bp deletion. To further investigate this discrepancy, the sample was retested using a second in-house PCR targeting a chromosomal (ompA) gene as well as six primer sets flanking various regions of the cryptic plasmid. Results: The sample provided positive results in the second in-house method, confirming the presence of C. trachomatis DNA. All other primer sets targeting the cryptic plasmid failed to amplify, indicating a lack of the chlamydial cryptic plasmid in this sample. Conclusions: The recognition of a plasmid-deficient strain of C. trachomatis within Australia highlights further limitations of using the chlamydial cryptic plasmid for C. trachomatis diagnostics and re-emphasises the benefits of using multitarget assays to avoid false-negative results.

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Journal articles on the topic 'Cryptic variation'

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