Population genetics: past, present, and future

Okazaki, Atsuyuki; Yamazaki, Satoru; Inoue, Ituro; Ott, Jürg

doi:10.1007/s00439-020-02208-5

Cited by 7 publications

(5 citation statements)

References 91 publications

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“…Population genetics is the study of gene distribution, gene frequency and genotype frequency maintenance, and change in a population ( Okazaki et al, 2021 ). Population genetics reveals the genetic relationship between gene and genotype frequencies of a random mating population by the Hardy–Weinberg Principle, but gene frequency is affected by various factors in practice, such as mutation, natural selection, genetic drift, in-migration, and out-migration ( Salanti et al, 2005 ).…”

Section: Introductionmentioning

confidence: 99%

SLC44A2 Frequency, a New TaqMan Real-Time Polymerase Chain Reaction Method for HNA-3A/3B Genotyping, and a New Application of Droplet Digital PCR

Wang

Chen

et al. 2022

Front. Genet.

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Background: Human neutrophil antigen-3A (HNA-3A) and human neutrophil antigen-3B (HNA-3B) are generated by a single-nucleotide polymorphism (rs2288904, c.461G > A) in exon 7 of the choline transporter-like protein-2 gene (CTL2, also known as SLC44A2). Antibodies to HNA-3 can be generated following blood transfusion or other factors resulting in exposure to HNA-3 antigens. These antibodies can cause transfusion-related acute lung injury (TRALI) or neonatal alloimmune neutropenia (NAIN). This study describes a sensitive and specific TaqMan real-time polymerase chain reaction (PCR) method to screen for the HNA-3 genotype using specific primers and probes designed to detect allelic polymorphisms. Considering the high sensitivity and accuracy of droplet digital PCR (ddPCR) in the identification of the rare SLC44A2*2 allele, we used this technique to identify blood donors with the rare HNA-3B antigen and calculate the allele frequency of SLC44A2 in mixed populations with different proportions.Methods: DNA samples purified from 208 donors in northwest China were subjected to TaqMan real-time PCR to detect allelic polymorphisms in SLC44A2. The results were confirmed by Sanger sequencing. The rare HNA-3B antigen was detected by ddPCR. SLC44A2 frequency was determined by two-channel ddPCR.Results: The genotypes of all DNA samples were detected by the TaqMan real-time PCR using specific probes for HNA-3, and the results were consistent with the Sanger sequencing results in respect to the HNA-3A and HNA-3B polymorphisms. The allele frequencies of SLC44A2*1 and SLC44A2*2 in the 208 donors in northwest China were 64.9% (95% confidence interval [CI], 59%–70.8%) and 35.1% (95% CI, 29.2%–41%), respectively. The ratio of SLC44A2*2 alleles was accurately detected in all blood pools by ddPCR but not by TaqMan real-time PCR. This allowed for the SLC44A2 frequency in the population to be accurately inferred.Conclusion: This new method of detecting SLC44A2 alleles was highly sensitive and specific, as confirmed by Sanger sequencing. ddPCR using the designed probes resulted in successful detection of the rare HNA-3B antigen. Furthermore, we successfully detected the rare HNA-3B antigen and inferred the SLC44A2 frequency by ddPCR using the probes that we designed.

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Section: Introductionmentioning

confidence: 99%

SLC44A2 Frequency, a New TaqMan Real-Time Polymerase Chain Reaction Method for HNA-3A/3B Genotyping, and a New Application of Droplet Digital PCR

Wang

Chen

et al. 2022

Front. Genet.

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“…In this context it is worth noting that the founders of the neutral theory, despite often considering the entire genome, did not believe that the neutral hypothesis stands or falls by the proportion of mutations in non‐functional DNA (Kimura, 1991 a ). Although King & Jukes (1969) did discuss the presence of non‐coding DNA, they did so merely as a correction to Kimura's ‘cost of selection’ calculations (Okazaki et al ., 2021). In a subsequent study, Ohta & Kimura (1971 c , p. 24) wrote: ‘ We are quite sure that the adaptive gene substitutions constitute a small fraction of the total substitutions.…”

Section: In Which Measurement Unit Is the Neutral Hypothesis Defined?mentioning

confidence: 99%

Moderating the neutralist–selectionist debate: exactly which propositions are we debating, and which arguments are valid?

de Jong,

van Oosterhout,

Hoelzel

et al. 2023

Biological Reviews

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Half a century after its foundation, the neutral theory of molecular evolution continues to attract controversy. The debate has been hampered by the coexistence of different interpretations of the core proposition of the neutral theory, the ‘neutral mutation–random drift’ hypothesis. In this review, we trace the origins of these ambiguities and suggest potential solutions. We highlight the difference between the original, the revised and the nearly neutral hypothesis, and re‐emphasise that none of them equates to the null hypothesis of strict neutrality. We distinguish the neutral hypothesis of protein evolution, the main focus of the ongoing debate, from the neutral hypotheses of genomic and functional DNA evolution, which for many species are generally accepted. We advocate a further distinction between a narrow and an extended neutral hypothesis (of which the latter posits that random non‐conservative amino acid substitutions can cause non‐ecological phenotypic divergence), and we discuss the implications for evolutionary biology beyond the domain of molecular evolution. We furthermore point out that the debate has widened from its initial focus on point mutations, and also concerns the fitness effects of large‐scale mutations, which can alter the dosage of genes and regulatory sequences. We evaluate the validity of neutralist and selectionist arguments and find that the tested predictions, apart from being sensitive to violation of underlying assumptions, are often derived from the null hypothesis of strict neutrality, or equally consistent with the opposing selectionist hypothesis, except when assuming molecular panselectionism. Our review aims to facilitate a constructive neutralist–selectionist debate, and thereby to contribute to answering a key question of evolutionary biology: what proportions of amino acid and nucleotide substitutions and polymorphisms are adaptive?

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“…Population genetics is the sub-field of evolutionary biology addressing these questions and advances our understanding of evolutionary processes such as mutations, genetic drift, gene flow, and natural selection [34]. Its downstream applications include for example medical research [55,40,32,3], wildlife conservation [23,34,51,47], and -in conjunction with recent advances in ancient DNA sequencing technology [41,37,45,12] -studying human migration patterns in the past few thousand years [2,33,46,41]. Different, but correlated, trees each describe distinct regions of multiple aligned genomes.…”

Section: Introductionmentioning

confidence: 99%

Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests

Hübner,

Stamatakis

2024

Preprint

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The field of population genetics attempts to advance our understanding of evolutionary processes. It has applications, for example, in medical research, wildlife conservation, and - in conjunction with recent advances in ancient DNA sequencing technology - studying human migration patterns over the past few thousand years. The basic toolbox of population genetics includes genealogical tress, which describe the shared evolutionary history among individuals of the same species. They are calculated on the basis of genetic variations. However, in recombining organisms, a single tree is insufficient to describe the evolutionary history of the whole genome. Instead, a collection of correlated trees can be used, where each describes the evolutionary history of a consecutive region of the genome. The current corresponding state of-the-art data structure, tree sequences, compresses these genealogical trees via edit operations when moving from one tree to the next along the genome instead of storing the full, often redundant, description for each tree. We propose a new data structure, genealogical forests, which compresses the set of genealogical trees into a DAG. In this DAG identical subtrees that are shared across the input trees are encoded only once, thereby allowing for straight-forward memoization of intermediate results. Additionally, we provide a C++ implementation of our proposed data structure, called gfkit, which is 2.1 to 11.2 (median 4.0) times faster than the state-of-the-art tool on empirical and simulated datasets at computing important population genetics statistics such as the Allele Frequency Spectrum, Patterson's f, the Fixation Index, Tajima's D, pairwise Lowest Common Ancestors, and others. On Lowest Common Ancestor queries with more than two samples as input, gfkit scales asymptotically better than the state-of-the-art, and is thus up to 990 times faster. In conclusion, our proposed data structure compresses genealogical trees by storing shared subtrees only once, thereby enabling straight-forward memoization of intermediate results, yielding a substantial runtime reduction and a potentially more intuitive data representation over the state-of-the-art. Our improvements will boost the development of novel analyses and models in the field of population genetics and increases scalability to ever-growing genomic datasets.

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Population genetics: past, present, and future

Cited by 7 publications

References 91 publications

SLC44A2 Frequency, a New TaqMan Real-Time Polymerase Chain Reaction Method for HNA-3A/3B Genotyping, and a New Application of Droplet Digital PCR

SLC44A2 Frequency, a New TaqMan Real-Time Polymerase Chain Reaction Method for HNA-3A/3B Genotyping, and a New Application of Droplet Digital PCR

Moderating the neutralist–selectionist debate: exactly which propositions are we debating, and which arguments are valid?

Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests

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