Transient mutation bias increases the predictability of evolution on an empirical genotype-phenotype landscape

Predicting how a population will likely navigate a genotype-phenotype landscape requires consideration of selection in combination with mutation bias, which can skew the likelihood of following a particular trajectory. Strong and persistent directional selection can drive populations to ascend toward a peak. However, with a greater number of peaks and more routes to reach them, adaptation inevitably becomes less predictable. Transient mutation bias, which operates only on one mutational step, can influence landscape navigability by biasing the mutational trajectory early in the adaptive walk. This sets an evolving population upon a particular path, constraining the number of accessible routes and making certain peaks and routes more likely to be realized than others. In this work, we employ a model system to investigate whether such transient mutation bias can reliably and predictably place populations on a mutational trajectory to the strongest selective phenotype or usher populations to realize inferior phenotypic outcomes. For this we use motile mutants evolved from ancestrally non-motile variants of the microbe Pseudomonas fluorescens SBW25, of which one trajectory exhibits significant mutation bias. Using this system, we elucidate an empirical genotype-phenotype landscape, where the hill-climbing process represents increasing strength of the motility phenotype, to reveal that transient mutation bias can facilitate rapid and predictable ascension to the strongest observed phenotype in place of equivalent and inferior trajectories. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.</p

Genome-Wide Association Study Identifies Candidate Loci Underlying Agronomic Traits in a Middle American Diversity Panel of Common Bean

Common bean (Phaseolus vulgaris L.) breeding programs aim to improve both agronomic and seed characteristics traits. However, the genetic architecture of the many traits that affect common bean production are not completely understood. Genome-wide association studies (GWAS) provide an experimental approach to identify genomic regions where important candidate genes are located. A panel of 280 modern bean genotypes from race Mesoamerica, referred to as the Middle American Diversity Panel (MDP), were grown in four US locations, and a GWAS using \u3e150,000 single-nucleotide polymorphisms (SNPs) (minor allele frequency [MAF] ≥ 5%) was conducted for six agronomic traits. The degree of inter- and intrachromosomal linkage disequilibrium (LD) was estimated after accounting for population structure and relatedness. The LD varied between chromosomes for the entire MDP and among race Mesoamerica and Durango–Jalisco genotypes within the panel. The LD patterns reflected the breeding history of common bean. Genome-wide association studies led to the discovery of new and known genomic regions affecting the agronomic traits at the entire population, race, and location levels. We observed strong colocalized signals in a narrow genomic interval for three interrelated traits: growth habit, lodging, and canopy height. Overall, this study detected ~30 candidate genes based on a priori and candidate gene search strategies centered on the 100-kb region surrounding a significant SNP. These results provide a framework from which further research can begin to understand the actual genes controlling important agronomic production traits in common bean

An Algal Nucleus-encoded Subunit of Mitochondrial ATP Synthase Rescues a Defect in the Analogous Human Mitochondrial-encoded Subunit

Unlike most organisms, the mitochondrial DNA (mtDNA) of Chlamydomonas reinhardtii, a green alga, does not encode subunit 6 of F(0)F(1)-ATP synthase. We hypothesized that C. reinhardtii ATPase 6 is nucleus encoded and identified cDNAs and a single-copy nuclear gene specifying this subunit (CrATP6, with eight exons, four of which encode a mitochondrial targeting signal). Although the algal and human ATP6 genes are in different subcellular compartments and the encoded polypeptides are highly diverged, their secondary structures are remarkably similar. When CrATP6 was expressed in human cells, a significant amount of the precursor polypeptide was targeted to mitochondria, the mitochondrial targeting signal was cleaved within the organelle, and the mature polypeptide was assembled into human ATP synthase. In spite of the evolutionary distance between algae and mammals, C. reinhardtii ATPase 6 functioned in human cells, because deficiencies in both cell viability and ATP synthesis in transmitochondrial cell lines harboring a pathogenic mutation in the human mtDNA-encoded ATP6 gene were overcome by expression of CrATP6. The ability to express a nucleus-encoded version of a mammalian mtDNA-encoded protein may provide a way to import other highly hydrophobic proteins into mitochondria and could serve as the basis for a gene therapy approach to treat human mitochondrial diseases