Biology subjects

Petak, C.

Publications and source records attributed to Petak, C..

3 recordsLinked to original sources

bioRxiv2026

Evidence of Adaptation in Structural Variants among Wild Populations of the purple sea urchin, Strongylocentrotus purpuratus

Structural variants (SVs) are increasingly recognized as important components of genetic architecture, complementing and extending beyond traditionally studied single nucleotide polymorphisms. Though growing, our understanding of the evolutionary forces maintaining SVs in natural populations is limited. Chromosomal inversions in particular can facilitate local adaptation in populations with high gene flow, including many marine species. The purple sea urchin (Strongylocentrotus purpuratus) is a powerful system to study these dynamics due to its high gene flow, lack of population structure, and broad latitudinal range. We analyzed whole genome sequence data from 137 individuals from seven populations to identify structural variants using local PCA, linkage disequilibrium, and FST analyses. We integrated Bayesian selection scans and population genetic statistics to test for signatures of selection in putative inversions. We identified nine loci showing signatures consistent with inversion polymorphisms, including three-way genotype clustering, long range linkage, and the characteristic hanging-bridge pattern. These loci are polymorphic within sites and along the species range with three loci showing concordant signatures of selection based on enrichment of XTX outliers and distinct patterns of allelic age consistent with positive and balancing selection. In addition, these loci show enrichment for genes associated with biomineralization and development. Our results are the first instance of identifying putative inversions in the purple sea urchin, adding to the genomic repertoire of this model species. Our results add to the growing evidence that chromosomal inversions are a key component of standing genetic variation in natural populations with an important role in adaptation to heterogeneous environments. Significance statementChromosomal inversion polymorphisms are an important part of the repertoire of standing genetic variation in wild populations and can facilitate adaptation in the face of strong gene flow. The purple sea urchin, a widely studied marine species, exhibits high gene flow, large population sizes, and extensive genetic diversity across diverse environmental conditions, making it an ideal model for evolutionary genomics. We identified nine putative inversions, three with signatures of selection, adding echinoderms to the growing list of phyla with putatively adaptive inversions. These findings provide new insights into structural variation in a highly dispersive marine species and highlight potential evolutionary mechanisms maintaining these polymorphisms.

evolutionary biology↗

bioRxiv2025

The Variability of Evolvability: Properties of Dynamic Fitness Landscapes Determine How Phenotypic Variability Evolves

The magnitude and shape of phenotypic variation depends on properties of the genotype-to-phenotype (GP) map, which itself can evolve over time. The evolution of GP maps is particularly interesting in variable environments, as GP maps can evolve to bias variation in the direction of past selection, increasing the evolvability of the population over time. However, the degree and manner in which environmental variation shapes GP maps and influences evolutionary dynamics may depend on properties of the fitness landscape. To explore how evolutionary dynamics are affected by variable environments across a wide range of different pairs of fitness landscapes, we evolved GP maps to produce spatial-temporal gene expression patterns that matched two-dimensional patterns generated by different elementary cellular automata (CA) rules. We found remarkable variation in how populations evolved in variable environments. In some cases, changing the environment helped populations find higher fitness peaks; in others, it hindered them. The evolution of evolvability also depended on the fitness landscape pair. In some experiments, the ability to generate adaptive phenotypic variation upon environment change increased over time, while in some others, populations found shared areas between fitness landscapes. On the other hand, environmental variability consistently resulted in higher fitness landscape exploration, average fitness and mutational robustness compared to evolution in static environments, which we hypothesize are tightly connected. In conclusion, work presented here sheds light on important general consequences of environmental variability, while also demonstrating dependency on properties of fitness landscapes, which future research on the evolution of evolvability should consider. Significance statementThe speed and direction of evolution depend on the availability of phenotypic variation. Genotype-to-phenotype maps can over time bias phenotypic variability to more readily produce alternative adaptive phenotypes in fluctuating environments. However, because properties of the fitness landscapes influence evolutionary dynamics, it remains unclear which previously observed dynamics reflect general effects of environmental variability and which are specific to the pair of landscapes used. We found that the height of the fitness peaks discovered, and how the populations became more evolvable, significantly differed across landscape pairs. In contrast, environmental variability consistently increased average fitness and mutational robustness. Thus, future research investigating the inherent consequences of frequent environmental change should be done on a range of dynamic landscapes.

evolutionary biology↗

bioRxiv2025

The Population Genetics of Biological Noise

Information transmission is intrinsic to life, and noise is intrinsic to information transmission. Biological noise during development is essential for the flexibility and plasticity of individual organisms, but also underlies some diseases. Biological noise during reproduction is the fuel for evolution, including the evolution of therapy resistance in pathogenic microbes and in cancer. Recent technological advances in our ability to characterize many sources of biological noise have demonstrated that its amount is often heritable. Here, we frame the population genetics of loci that influence the amount of any source of biological noise. While analogous theory for heritable changes in mean trait values has been established for nearly a century, to our knowledge this is the first general approach for studying the evolution of heritable changes in their statistical distributions. This represents a critical theoretical contribution to an important and rapidly growing domain of intellectual inquiry. It also sheds light on the hypothesis that natural selection can increase evolvability, and generalizes modifier theory used in the tradition of Feldman and colleagues. Author summaryBiological noise is a fact of life. Genetically identical organisms reared in identical environments invariably exhibit random phenotypic differences. And siblings born of the same parent(s) in the same environment are endowed with inheritances that invariably differ at random. While the specific consequences of biological noise are unpredictable, extraordinary experimental advances now make clear that its amount can be influenced by an organisms genetics. For example, high- and low-noise promoter, and high- and low-noise DNA polymerase alleles are well known. This raises the question of when and how natural selection favors high- or low-noise alleles. While biological noise is on average deleterious, it can also occasionally induce high fitness phenotypes. Here, we solve a simple analytic model for the fitness difference between noise alleles that captures both these features. Our model predicts the existence of an evolutionary equilibrium in the amount of noise, whose location reflects just four features of an organisms biology. In light the clinical importance of biological noise, as well as its central role more broadly in both development and evolution, this work provides an urgently needed evolutionary framework for understanding its long-term determinants.

evolutionary biology↗