scholarly journals Cryptic genetic variation accelerates evolution by opening access to diverse adaptive peaks

Science ◽  
2019 ◽  
Vol 365 (6451) ◽  
pp. 347-353 ◽  
Author(s):  
Jia Zheng ◽  
Joshua L. Payne ◽  
Andreas Wagner
Keyword(s):  
Genetic Variation ◽  
Fluorescent Proteins ◽  
Adaptive Landscape ◽  
Deleterious Mutations ◽  
Historical Contingency ◽  
Green Fluorescence ◽  
Cryptic Genetic Variation ◽  
Adaptive Mutations ◽  
Cryptic Variation ◽  
Genetic Mechanisms

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.

scholarly journals Amitosis confers benefits of sex in the absence of sex to Tetrahymena

2019 ◽  
Author(s):  
Hao Zhang ◽  
Joe A. West ◽  
Rebecca A. Zufall ◽  
Ricardo B. R. Azevedo
Keyword(s):  
Genetic Variation ◽  
Copy Number ◽  
Environmental Changes ◽  
Nuclear Division ◽  
Biotic Interactions ◽  
Deleterious Mutations ◽  
Mutation Load ◽  
Low Expectations ◽  
Genetic Mechanisms

Sex appears to be the most successful reproductive strategy in eukaryotes despite its many costs1–3. While a complete explanation for sex’s success remains elusive, several evolutionary benefits of sex have been identified4, 5, such as, the purging of deleterious mutations6, 7, the accumulation of beneficial mutations8, 9, and an advantage in biotic interactions3, 10, 11. It is predicted that, by forgoing these benefits, asexual lineages are evolutionary dead-ends2, 12 due to genetic deterioration and/or an inability to adapt to environmental changes. Consistent with this prediction, many asexual lineages show signs of accelerated accumulation of deleterious mutations compared to their sexual relatives13–18. Despite these low expectations, some asexual eukaryotic lineages appear to be successful, including the ciliate Tetrahymena19. Here, we show that the mechanism of somatic nuclear division in Tetrahymena, termed amitosis, provides benefits similar to sex, allowing for the long-term success of asexual lineages. We found that, when compared to mitosis, amitosis with chromosome copy number control reduces mutation load deterministically, slows the accumulation of deleterious mutations under genetic drift, and accelerates adaptation. These benefits arise because, like sex, amitosis can generate substantial genetic variation in fitness among (asexual) progeny. Our results indicate that the ability of Tetrahymena to persist in the absence of sex may depend on non-sexual genetic mechanisms conferring benefits typically provided by sex, as has been found in other asexual lineages20–23.

scholarly journals Cryptic genetic variation in a heat shock protein modifies the outcome of a mutation affecting epidermal stem cell development in C. elegans

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sneha L. Koneru ◽  
Mark Hintze ◽  
Dimitris Katsanos ◽  
Michalis Barkoulas
Keyword(s):  
Genetic Variation ◽  
Stem Cell ◽  
Heat Shock ◽  
Heat Shock Protein ◽  
Cell Fate ◽  
Cell Development ◽  
Wnt Signalling ◽  
Single Amino Acid ◽  
Cryptic Genetic Variation ◽  
Seam Cell

AbstractA fundamental question in medical genetics is how the genetic background modifies the phenotypic outcome of mutations. We address this question by focusing on the seam cells, which display stem cell properties in the epidermis of Caenorhabditis elegans. We demonstrate that a putative null mutation in the GATA transcription factor egl-18, which is involved in seam cell fate maintenance, is more tolerated in the CB4856 isolate from Hawaii than the lab reference strain N2 from Bristol. We identify multiple quantitative trait loci (QTLs) underlying the difference in phenotype expressivity between the two isolates. These QTLs reveal cryptic genetic variation that reinforces seam cell fate through potentiating Wnt signalling. Within one QTL region, a single amino acid deletion in the heat shock protein HSP-110 in CB4856 is sufficient to modify Wnt signalling and seam cell development, highlighting that natural variation in conserved heat shock proteins can shape phenotype expressivity.

scholarly journals Characterization of Deleterious Mutations in Outcrossing Populations

Genetics ◽  
1998 ◽  
Vol 150 (2) ◽  
pp. 945-956 ◽  
Author(s):  
Hong-Wen Deng
Keyword(s):  
Genetic Variation ◽  
Genetic Variance ◽  
Estimation Bias ◽  
Deleterious Mutations ◽  
Environmental Variance ◽  
Higher Power ◽  
Sib Mating ◽  
The Mean ◽  
Simulation Results

Abstract Deng and Lynch recently proposed estimating the rate and effects of deleterious genomic mutations from changes in the mean and genetic variance of fitness upon selfing/outcrossing in outcrossing/highly selfing populations. The utility of our original estimation approach is limited in outcrossing populations, since selfing may not always be feasible. Here we extend the approach to any form of inbreeding in outcrossing populations. By simulations, the statistical properties of the estimation under a common form of inbreeding (sib mating) are investigated under a range of biologically plausible situations. The efficiencies of different degrees of inbreeding and two different experimental designs of estimation are also investigated. We found that estimation using the total genetic variation in the inbred generation is generally more efficient than employing the genetic variation among the mean of inbred families, and that higher degree of inbreeding employed in experiments yields higher power for estimation. The simulation results of the magnitude and direction of estimation bias under variable or epistatic mutation effects may provide a basis for accurate inferences of deleterious mutations. Simulations accounting for environmental variance of fitness suggest that, under full-sib mating, our extension can achieve reasonably well an estimation with sample sizes of only ∼2000-3000.

scholarly journals Cryptic variation and its manifestation in the Lower Trentonian Rafinesquina lineage (Ordovician, New York State)

1992 ◽  
Vol 6 ◽  
pp. 292-292
Author(s):  
Robert Titus
Keyword(s):  
New York ◽  
Genetic Variation ◽  
Natural Selection ◽  
New York State ◽  
Ecological Factors ◽  
Stabilizing Selection ◽  
Rapid Population Growth ◽  
York State ◽  
Cryptic Variation ◽  
Adaptive Peak

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.

scholarly journals Contribution of trans regulatory eQTL to cryptic genetic variation in C. elegans

BMC Genomics ◽  
2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Basten L. Snoek ◽  
Mark G. Sterken ◽  
Roel P. J. Bevers ◽  
Rita J. M. Volkers ◽  
Arjen van’t Hof ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Cryptic Genetic Variation ◽  
C Elegans

scholarly journals Recessive deleterious variation has a limited impact on signals of adaptive introgression in human populations

2020 ◽  
Author(s):  
Xinjun Zhang ◽  
Bernard Kim ◽  
Kirk E. Lohmueller ◽  
Emilia Huerta-Sánchez
Keyword(s):  
False Positive ◽  
False Positive Rate ◽  
Genomic Variation ◽  
Human Populations ◽  
Deleterious Mutations ◽  
Modern Humans ◽  
Recombination Rates ◽  
Limited Impact ◽  
Adaptive Mutations ◽  
Adaptive Introgression

AbstractAdmixture with archaic hominins has altered the landscape of genomic variation in modern human populations. Several gene regions have been previously identified as candidates of adaptive introgression (AI) that facilitated human adaptation to specific environments. However, simulation-based studies have suggested that population genetics processes other than adaptive mutations, such as heterosis from recessive deleterious variants private to populations before admixture, can also lead to patterns in genomic data that resemble adaptive introgression. The extent to which the presence of deleterious variants affect the false-positive rate and the power of current methods to detect AI has not been fully assessed. Here, we used extensive simulations to show that recessive deleterious mutations can increase the false positive rates of tests for AI compared to models without deleterious variants. We further examined candidates of AI in modern humans identified from previous studies and show that, although deleterious variants may hinder the performance of AI detection in modern humans, most signals remained robust when deleterious variants are included in the null model. While deleterious variants may have a limited impact on detecting signals of adaptive introgression in humans, we found that at least two AI candidate genes, HYAL2 and HLA, are particularly susceptible to high false positive rates due to the recessive deleterious mutations. By quantifying parameters that affect heterosis, we show that the high false positives are largely attributed to the high exon densities together with low recombination rates in the genomic regions, which can further be exaggerated by the population growth in recent human evolution. Although the combination of such parameters is rare in the human genome, caution is still warranted in other species with different genomic composition and demographic histories.

scholarly journals Layers of Cryptic Genetic Variation Underlie a Yeast Complex Trait

Genetics ◽  
2019 ◽  
Vol 211 (4) ◽  
pp. 1469-1482 ◽  
Author(s):  
Jonathan T. Lee ◽  
Alessandro L. V. Coradini ◽  
Amy Shen ◽  
Ian M. Ehrenreich
Keyword(s):  
Genetic Variation ◽  
Complex Trait ◽  
Cryptic Genetic Variation

scholarly journals Green Fluorescence Patterns in Closely Related Symbiotic Species of Zanclea (Hydrozoa, Capitata)

Diversity ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 78 ◽  
Author(s):  
Davide Maggioni ◽  
Luca Saponari ◽  
Davide Seveso ◽  
Paolo Galli ◽  
Andrea Schiavo ◽  
...  
Keyword(s):  
Cryptic Species ◽  
Genetic Divergence ◽  
Large Scale ◽  
Marine Invertebrates ◽  
Fluorescent Proteins ◽  
Green Fluorescent Proteins ◽  
Green Fluorescence ◽  
Promising Tool ◽  
Species Specific ◽  
Green Fluorescent

Green fluorescence is a common phenomenon in marine invertebrates and is caused by green fluorescent proteins. Many hydrozoan species display fluorescence in their polyps and/or medusa stages, and in a few cases patterns of green fluorescence have been demonstrated to differ between closely related species. Hydrozoans are often characterized by the presence of cryptic species, due to the paucity of available morphological diagnostic characters. Zanclea species are not an exception, showing high genetic divergence compared to a uniform morphology. In this work, the presence of green fluorescence and the morpho-molecular diversity of six coral- and bryozoan-associated Zanclea species from the Maldivian coral reefs were investigated. Specifically, the presence of green fluorescence in polyps and newly released medusae was explored, the general morphology, as well as the cnidome and the interaction with the hosts, were characterized, and the 16S rRNA region was sequenced and analyzed. Overall, Zanclea species showed a similar morphology, with little differences in the general morphological features and in the cnidome. Three of the analyzed species did not show any fluorescence in both life stages. Three other Zanclea species, including two coral-associated cryptic species, were distinguished by species-specific fluorescence patterns in the medusae. Altogether, the results confirmed the morphological similarity despite high genetic divergence in Zanclea species and indicated that fluorescence patterns may be a promising tool in further discriminating closely related and cryptic species. Therefore, the assessment of fluorescence at a large scale in the whole Zancleidae family may be useful to shed light on the diversity of this enigmatic taxon.

scholarly journals Species delimitation in the African tree genus Lophira (Ochnaceae) reveals cryptic genetic variation

2020 ◽  
Vol 21 (3) ◽  
pp. 501-514 ◽  
Author(s):  
Eben-Ezer Baba Kayode Ewédjè ◽  
Simon Jansen ◽  
Guillaume Kouame Koffi ◽  
Adrien Staquet ◽  
Rosalia Piñeiro ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Species Delimitation ◽  
Cryptic Genetic Variation
Sign in / Sign up

Export Citation Format

Share Document