Evolutionary Biology

eLife assessment

This fundamental study uses a creative experimental system to directly test Ohno's hypothesis, which describes how and why new genes might evolve by duplication of existing ones. In agreement with existing criticism of Ohno's original idea, the authors present compelling evidence that having two gene copies does not speed up the evolution of a new function as posited by Ohno, but instead leads to the rapid inactivation of one of the copies through the accumulation of mostly deleterious mutations. These findings will be of broad interest to evolutionary biologists and geneticists.

eLife assessment

The authors examined whether the frequency of alternative splicing across entire genomes correlates with measures of complexities across prokaryotes and eukaryotes. Although the question is very interesting and important for our general understanding of the evolution of life forms, the work is inadequate: the methods, data, and analyses do not support the primary claims. The measure of alternative splicing frequency used by the authors is problematic; the method is inappropriate; the observed correlations may also be explained by known population genetics principles; and parts of the manuscript are difficult to understand.

eLife assessment

This important study presents a significant methodological advance by leveraging previously discarded, unmapped DNA sequence reads to estimate pest infestation loads across plant accessions, and map variation in these apparent pest loads to defense genes. While the bioinformatics approach is convincing, the study appears incomplete because actual pest infestation was not systematically quantified, and thus loads inferred from sequencing reads are not validated. The results could have broad implications for phenotype-genotype prediction, especially regarding the use of unmapped reads for GWAS.

eLife assessment

The authors present a critique of current usage of principal component analysis in geometric morphometrics, making a convincing case with benchmark data that standard techniques perform poorly. The work is an important contribution to the field and will hopefully lead to a reassessment of the methodology most scientists in morphometrics currently use. The authors also present a new Python package that uses machine learning to provide better-supported results than principal component analysis. While the package is in the title of the manuscript, it is not its main focus.

eLife assessment

This useful study describes expression profiling by scRNA-seq of thousands of cells of recombinant yeast genotypes from a system that models natural genetic variation. The rigorous new method presented here holds promise for improving the efficiency of genotype-to-phenotype mapping in yeast, providing convincing evidence for its efficacy. This manuscript focuses on overcoming technical challenges with this approach. It currently offers somewhat limited new biological insights to place the work within the broader context of the field. Doing so would broaden the interest of the work for all geneticists and evolutionary biologists.

eLife assessment

This study provides valuable new insights into the trade-offs associated with the evolution of drug resistance. The authors use a solid approach to evolve and phenotype hundreds of independent strains. They identify distinct phenotypic clusters based on growth across defined conditions that suggest that tradeoffs are diverse but at the same time could be limited to a few classes based on the underlying resistance mechanisms. The methodologies used align with the current state-of-the-art, and the data and analysis are solid as they broadly support the claims, with only minor weaknesses. This work will interest molecular biologists working on the evolution of new phenotypes and microbiologists studying multi-drug therapy.

eLife assessment

The authors provide useful information, confirming previous observations that heterologous sequecnes affect crossing-over frequency. Surprisingly, they conclude that heterozygous introgressed regions, with greater levels of heterology, have greater noncrossover levels than non-introgressed regions with much lower levels of heterology. As the evidence for this conclusion is incomplete and potentially biased, the significance of these findings relative to previous knowledge in the field remains to be determined.

eLife assessment

This study presents valuable empirical work and simulations that are relevant for the evolution of genetic load linked to self-incompatibility alleles in Arabidopsis. The evidence supporting the findings is solid but could be improved by a more detailed quantitative assessment of the impacts of deleterious alleles and their dominance. The simulation results are somewhat incomplete, as details of the approach and code do not appear to be available, but this could be easily remedied. The work will be of relevance to geneticists interested in the evolution of allelic diversity in similar systems.

eLife assessment

Maestri et al report the absence of phylogenetic evidence supporting codiversification of mammalian coronaviruses and their hosts, leading to the important conclusion that the evolutionary history of the virus and its hosts are decoupled through frequent host switches. The evidence for frequent host switching, derived from a probabilistic model of co-evolution, appears convincing, but evidence for quantitative statements about the time of the last common ancestor of extant mammalian coronaviruses remains incomplete. The results would be strengthened by a reconstruction of the evolutionary timescale and further investigation of robustness to sampling biases and unsampled diversity.

eLife assessment

This study provides a fundamental advance in palaeontology by reporting the fossils of a new invertrebrate, Beretella spinosa, and inferring its relationship with already described species. The analysis placed the newly described species in the earliest branch of moulting invertebrates. The study, supported by convincing fossil observation, hypothesizes that early moulting invertebrate animals were not vermiform.

eLife assessment

The manuscript explores the ways in which the genetic code evolves, specifically how stop codons are reassigned to become sense codons. The authors present phylogenetic data showing that mutations at position 67 of the termination factor are present in organisms that nevertheless use the UGA codon as a stop codon, thereby questioning the importance of this position in the reassignment of stop codons. Alternative models on the role of eRF1 would reflect a more balanced view of the data. Overall, the data are solid and these findings will be valuable to the genomic/evolution fields.

eLife assessment

This valuable study describes an investigation of the properties of two heterologously-expressed Nav1.4 channels, with mutations close to the selectivity filter found in tetrodotoxin(TTX)-resistant snakes. The authors studied these mutants by electrophysiological methods, assessed the muscle properties of two types of snakes bearing these mutations, and built homology models of the channels to hypothesize a molecular explanation of the altered channel properties. The methods employed and the results are generally solid, although some aspects would benefit from additional experiments and a more nuanced discussion.

eLife assessment

This manuscript provides important information on the calcification process, especially the properties and formation of freshly formed tests (the foraminiferan shells), in the miliolid foraminiferan species Pseudolachlanella eburnea. The evidence from the high-quality SEM images is solid, but the evidence is incomplete when it comes to the specificity of the auto-fluorescent signals for calcified structures, or the presence of photosynthetic (living) symbionts, which are not verified experimentally. The conclusions based on fluorescent imagery therefore do not have strong support.

eLife assessment

Drawing on a human population genomic data set, this valuable study seeks to show that potentially advantageous alleles are on average older than neutral alleles, invoking the action of balancing selection as the underlying explanation. Currently it is unfortunately unclear how robust the estimates of allele ages are, and the evidence for the authors' proposal is therefore at this stage incomplete. If confirmed, the conclusions would be of interest to population genomicists, especially those studying humans.

eLife assessment

This is an important study of the recovery of genome-reduced bacterial cells in laboratory evolution experiments, to understand how they regain their fitness. Through the analysis of gene expression and a series of tests, the authors present convincing evidence indicating distinct molecular changes in the evolved bacterial strains, although the precise mechanisms remain uncharacterized. These findings imply that diverse mechanisms are employed to offset the effects of a reduced genome, offering intriguing insights into genome evolution.

eLife assessment

This fundamental study evaluates the evolutionary significance of variations in the accuracy of the intron-splicing process across vertebrates and insects. Using a powerful combination of comparative and population genomics approaches, the authors present convincing evidence that higher rates of alternative splicing tend to be observed in species with lower effective population size, a key prediction of the drift-barrier hypothesis. The analysis is carefully conducted and has broad implications beyond the studied species. As such, it will strongly appeal to anyone interested in the evolution of genome architecture and the optimisation of genetic systems.

eLife assessment

This study provides a valuable theoretical exploration of non-enzymatic sustained replication of RNA systems, in the parabolic growth regime of the evolution of putative primordial replicators. It provides convincing evidence that parabolic growth mitigates the error threshold catastrophe, thus demonstrating another way in which this regime contributes to the maintenance of genetic diversity. The findings shed light on relevant evolutionary regimes of primordial replicators, with potential applicability to our understanding of the origin of life.

eLife assessment

This valuable study introduces a new simulation model to explain the wide-spread occurrence of genetic inversions in fruit-fly genomes, based on sexually antagonistic alleles and a trade-off between male reproduction and survival. The evidence supporting the conclusions is currently incomplete, but it might be possible to address this with additional simulations and experiments as well as more rigorous analysis of the model and the data. The work will be of interest to population geneticists beyond the fruit-fly system.

eLife assessment

Through a theoretical approach, this study makes important contributions to our understanding of the evolutionary causes of the ageing process. Using a simple individual-based model and computational simulations, the authors provide convincing evidence that ageing can be a trait under natural selection, opening the door for further discussion in the context of lifespan extension research.

eLife assessment

This useful study applies solid and previously validated methodology to identify archaically introgressed genes involved in high altitude adaptation. However, to test the robustness of the approach, this study would benefit from using at least one other method to detect adaptive introgression, and clarification on how the authors scored the networks in the signet analysis. With these parts strengthened, this paper would be of interest to population geneticists, anthropologists, and scientists interested in the genetic basis underlying high-altitude adaptation in Tibet.