C.-I. Wu

The Generalized Haldane (GH) model tracking population size changes and resolving paradoxes of genetic drift

The paper integrates the Wright-Fisher and Haldane models to resolve paradoxes in genetic drift by defining it through variance in transmission success rather than population size.

The paradox of extremely fast evolution driven by genetic drift in multi-copy gene systems

The paper uses the GH model to analyze genetic drift in mammalian rDNA genes, finding that fixation times are faster than expected, suggesting stronger drift or adaptive evolution.

Gene expression as phenotype - Many small-step changes leading to little long-term phenotypic evolution

The paper tests the Fishers Geometric Model postulate by analyzing gene expression data, showing that small-step evolution via miRNA regulation is common but does not lead to long-term phenotypic changes.

The runaway evolution of SARS-CoV-2 leading to the highly evolved Delta strain

This paper analyzes the evolution of SARS-CoV-2 through multiple strain waves, showing increasing mutations and suggesting a feedback loop between viral population size and mutation accumulation leading to the Delta strain.

Two decades of suspect evidence for adaptive molecular evolution - Negative selection confounding positive selection signals

This paper investigates the concordance between two methods for detecting positive selection and finds that they often disagree, suggesting negative selection variation may mislead positive selection inferences.

One viral sequence for each host? - The neglected within-host diversity as the main stage of SARS-CoV-2 evolution

The paper shows that SARS-CoV-2 exhibits substantial within-host genetic diversity, challenging the assumption of low diversity per infected individual and highlighting the importance of studying evolution within hosts.

Homo-harringtonine (HHT) - A highly effective drug against coronaviruses and the potential for large-scale clinical applications

The paper identifies Homo-harringtonine (HHT) as a potent antiviral drug against coronaviruses, effective in mouse models and safe in dogs, with potential for large-scale clinical use.

Many are called but few are chosen - Multiple clonal origins greatly elevate the functional heterogeneity of tumors

The paper shows that tumors can have multiple clonal origins, leading to high functional heterogeneity, with some tumors containing 13 independent clones and others having a dominant clone with minor patches.

Sex, fitness decline and recombination - Muller's ratchet vs. Ohta's ratchet

The paper compares Muller's ratchet and Ohta's ratchet, finding that recombination may not significantly slow fitness decline in most parameter spaces.

Two decades of suspect evidence for adaptive DNA-sequence evolution - Failure in consistent detection of positive selection

The paper re-examines evidence for adaptive DNA sequence evolution using MK and PAML tests on Drosophila and Arabidopsis data, finding little overlap and suggesting unreliable results.

Two decades of suspect evidence for adaptive DNA-sequence evolution - Less negative selection misconstrued as positive selection

The paper investigates whether apparent signals of positive selection in DNA sequences are actually due to relaxed negative selection, finding strong fluctuations in negative selection strength across species.

Variation in the life history strategy of cells underlies tumor’s functional diversity

This study applies r- and K-selection to HeLa cells to show how life history strategies influence tumor functional diversity through gene expression and ecological competition.

Mutations beget more mutations - The baseline mutation rate and runaway accumulation

This paper proposes a runaway mutation model explaining how mutator mutations can lead to escalating mutation rates in both germline and somatic tissues, affecting evolutionary strategies across species.

Molecular evolution in small steps under prevailing negative selection - A nearly-universal rule of codon substitution

The paper examines codon substitution rates across species and finds that evolutionary rates are strongly negatively correlated with amino acid distance under predominant negative selection.

Molecular evolution in large steps - Codon substitutions under positive selection

The paper shows that positive selection drives amino acid substitutions with large chemical property changes, while negative selection favors smaller changes, suggesting distinct evolutionary mechanisms.

Mechanisms of gene death in the Red Queen race revealed by the analysis of de novo microRNAs

The paper investigates how de novo microRNAs in Drosophila affect male fitness and reveals that adaptive de novo genes may die due to canceling fitness effects, suggesting quasi-neutrality and ongoing period-specific adaptations.

Speciation with gene flow via cycles of isolation and migration: Insights from multiple mangrove taxa

The paper investigates speciation mechanisms in mangroves, finding that cycles of isolation and gene flow (MIM) drive speciation between oceanic regions, challenging the traditional model of strict allopatry.

Genetic load and mutational meltdown in cancer cell populations

The paper studies mutational meltdown in HeLa cancer cell populations, finding high rates of deleterious copy number variations and significant fitness reduction per mutation.