Evolutionary Biology

RETRACTED: Biases of Principal Component Analysis (PCA) in Physical Anthropology Studies Require a Reevaluation of Evolutionary Insights

1. Nima Mohseni
2. Eran Elhaik

• Curated by eLife

  eLife Assessment

  The authors present a critique of current usage of principal component analysis in geometric morphometrics, making a compelling 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. This work challenges a very commonly used analytical approach and is bound to raise some controversy in the community, but the authors' critique is based on a well-founded and well-thought out analysis.

Reviewed by eLife

A generalist microbial predator shows innate attraction to more profitable prey, but does not learn from experience

1. P. M. Shreenidhi
2. Rachel I. McCabe
3. Heng Liang
4. Margaret I. Steele
5. David C. Queller
6. Joan E. Strassmann

Reviewed by Arcadia Science

Genetic Predisposition Toward Multicellularity in Chlamydomonas reinhardtii

1. I Chen Kimberly Chen
2. Shania Khatri
3. Matthew D Herron
4. Frank Rosenzweig

Reviewed by Arcadia Science

A suite of selective pressures supports the maintenance of alleles of a Drosophila immune peptide

1. Sarah R Mullinax
2. Andrea M Darby
3. Anjali Gupta
4. Patrick Chan
5. Brittny R Smith
6. Robert L Unckless

• Curated by eLife

  eLife Assessment

  This valuable study investigates evolutionary aspects around a single amino acid polymorphism, known to be under long-term balancing selection, in an immune peptide of Drosophila melanogaster. Using alleles with different substitutions, the investigators demonstrate that while one allele provides better survival after systemic infections by a bacterial pathogen, the alternative allele endows its carriers with a longer lifespan under certain conditions. The authors suggest that these contrasting fitness effects of the two alleles contribute to balancing their long-term evolutionary fate. While the work is very interesting, the strength of the provided evidence is still incomplete, and the study would benefit from more rigorous approaches.

Reviewed by eLife

Characterization of cancer-driving nucleotides (CDNs) across genes, cancer types, and patients

1. Lingjie Zhang
2. Tong Deng
3. Zhongqi Liufu
4. Xiangnyu Chen
5. Shijie Wu
6. Xueyu Liu
7. Changhao Shi
8. Bingjie Chen
9. Zheng Hu
10. Qichun Cai
11. Chenli Liu
12. Mengfeng Li
13. Miles E Tracy
14. Xuemei Lu
15. Chung-I Wu
16. Hai-Jun Wen

• Curated by eLife

  eLife Assessment

  This valuable study is a companion to a paper introducing a theoretical framework and methodology for identifying Cancer Driving Nucleotides (CDNs). The evidence that recurrent SNVs or CDNs are common in true cancer driver genes is convincing, with more limited evidence that many more undiscovered cancer driver mutations will have CDNs, and that this approach could identify these undiscovered driver genes with about 100,000 samples.

Reviewed by eLife

The theory of massively repeated evolution and full identifications of cancer-driving nucleotides (CDNs)

1. Lingjie Zhang
2. Tong Deng
3. Zhongqi Liufu
4. Xueyu Liu
5. Bingjie Chen
6. Zheng Hu
7. Chenli Liu
8. Miles E Tracy
9. Xuemei Lu
10. Hai-Jun Wen
11. Chung-I Wu

• Curated by eLife

  eLife Assessment

  This important paper introduces a theoretical framework and methodology for identifying Cancer Driving Nucleotides (CDNs), primarily based on single nucleotide variant (SNV) frequencies. A variety of solid approaches indicate that a mutation recurring three or more times is more likely to reflect selection rather than being the consequence of a mutation hotspot. The method is rigorously quantitative, though the requirement for larger datasets to fully identify all CDNs remains a noted limitation. The work will be of broad interest to cancer geneticists and evolutionary biologists.

Reviewed by eLife

Discarded sequencing reads uncover natural variation in pest resistance in Thlaspi arvense

1. Dario Galanti
2. Jun Hee Jung
3. Caroline Müller
4. Oliver Bossdorf

• Curated by eLife

  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. The bioinformatics approach is compelling, and the results should bear broad implications for phenotype-genotype prediction, especially regarding the use of unmapped reads for GWAS.

Reviewed by eLife

Archaic introgression contributed to shape the adaptive modulation of angiogenesis and cardiovascular traits in human high-altitude populations from the Himalayas

1. Giulia Ferraretti
2. Paolo Abondio
3. Marta Alberti
4. Agnese Dezi
5. Phurba T Sherpa
6. Paolo Cocco
7. Massimiliano Tiriticco
8. Marco Di Marcello
9. Guido Alberto Gnecchi-Ruscone
10. Luca Natali
11. Angela Corcelli
12. Giorgio Marinelli
13. Davide Peluzzi
14. Stefania Sarno
15. Marco Sazzini

• Curated by eLife

  eLife Assessment

  This study presents valuable findings on what networks of genes were impacted by introgression from Denisovans, to identify the biological functions involved in high-altitude adaptation in Tibet. This study applies solid and previously validated methodology to identify genes with signatures of both introgression and positive selection. This paper would be of interest to population geneticists, anthropologists, and scientists studying the genetic basis underlying high-altitude adaptation.

Reviewed by eLife

The recombination landscape of introgression in yeast

1. Enrique J. Schwarzkopf
2. Nathan Brandt
3. Caiti Smukowski Heil

• Curated by eLife

  eLife Assessment

  This study aims to analyse the effect of polymorphism on meiotic recombination in subspecies of Saccharomyces. The detection of reciprocal and non-reciprocal events is based on sequencing the haploid products of meiosis, and frequencies are compared between strains having introgressed genomic segments and strains lacking such segments. Unfortunately, the method used are inadequate for quantifying the non-reciprocal events.

Reviewed by eLife

Population genomics reveals strong impacts of genetic drift without purging and guides conservation of bull and giant kelp

1. Jordan B. Bemmels
2. Samuel Starko
3. Brooke L. Weigel
4. Kaede Hirabayashi
5. Alex Pinch
6. Cassandra Elphinstone
7. Megan N. Dethier
8. Loren H. Rieseberg
9. Jonathan E. Page
10. Christopher J. Neufeld
11. Gregory L. Owens

Reviewed by Arcadia Science