scholarly journals Correction: Berner, D. Allele Frequency Difference AFD—An Intuitive Alternative to FST for Quantifying Genetic Population Differentiation. Genes 2019, 10, 308

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 810
Author(s):  
Berner
Keyword(s):  
Allele Frequency ◽  
Population Differentiation ◽  
Full Range ◽  
Allele Frequency Difference ◽  
Genetic Population ◽  
Count Range ◽  
Single Allele ◽  
Genetic Population Differentiation ◽  
Allele Count ◽  
The Continuum

This note is to correct an error in my paper, concerning the Shannon differentiation metric (DShannon) (Reference [43] in the paper). The paper states that DShannon is undefined mathematically whenever one or both populations are monomorphic, that is, fixed for a single allele. Accordingly, the DShannon curve in Figure 1a, showing population differentiation in relation to allele counts for the case in which the pooled minor allele frequency (MAF) is maximal, did not extend across the full range of allele counts; the rightmost data point reflecting complete population differentiation was missing. Moreover, DShannon was completely missing in Figure 1b visualizing the continuum of allele frequency differentiation when the MAF is minimal (one population monomorphic across the entire allele count range).

scholarly journals Allele Frequency Difference AFD–An Intuitive Alternative to FST for Quantifying Genetic Population Differentiation

Genes ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 308 ◽  
Author(s):  
Berner
Keyword(s):  
Allele Frequency ◽  
Population Differentiation ◽  
Genomic Analysis ◽  
Frequency Difference ◽  
General Definition ◽  
Allele Frequency Difference ◽  
Sample Sizes ◽  
Genetic Population ◽  
Genetic Population Differentiation ◽  
Low Sensitivity

Measuring the magnitude of differentiation between populations based on genetic markers is commonplace in ecology, evolution, and conservation biology. The predominant differentiation metric used for this purpose is FST. Based on a qualitative survey, numerical analyses, simulations, and empirical data, I here argue that FST does not express the relationship to allele frequency differentiation between populations generally considered interpretable and desirable by researchers. In particular, FST (1) has low sensitivity when population differentiation is weak, (2) is contingent on the minor allele frequency across the populations, (3) can be strongly affected by asymmetry in sample sizes, and (4) can differ greatly among the available estimators. Together, these features can complicate pattern recognition and interpretation in population genetic and genomic analysis, as illustrated by empirical examples, and overall compromise the comparability of population differentiation among markers and study systems. I argue that a simple differentiation metric displaying intuitive properties, the absolute allele frequency difference AFD, provides a valuable alternative to FST. I provide a general definition of AFD applicable to both bi- and multi-allelic markers and conclude by making recommendations on the sample sizes needed to achieve robust differentiation estimates using AFD.

scholarly journals Genetic population differentiation and connectivity among fragmented Moor frog (Rana arvalis) populations in The Netherlands

2007 ◽  
Vol 22 (10) ◽  
pp. 1489-1500 ◽  
Author(s):  
Paul Arens ◽  
Theo van der Sluis ◽  
Wendy P. C. van’t Westende ◽  
Ben Vosman ◽  
Claire C. Vos ◽  
...  
Keyword(s):  
The Netherlands ◽  
Population Differentiation ◽  
Rana Arvalis ◽  
Genetic Population ◽  
Genetic Population Differentiation ◽  
Moor Frog

scholarly journals Geographic and Genetic Population Differentiation of the Amazonian Chocolate Tree (Theobroma cacao L)

PLoS ONE ◽  
2008 ◽  
Vol 3 (10) ◽  
pp. e3311 ◽  
Author(s):  
Juan C. Motamayor ◽  
Philippe Lachenaud ◽  
Jay Wallace da Silva e Mota ◽  
Rey Loor ◽  
David N. Kuhn ◽  
...  
Keyword(s):  
Population Differentiation ◽  
Theobroma Cacao ◽  
Genetic Population ◽  
Genetic Population Differentiation ◽  
Theobroma Cacao L

scholarly journals Characterizing Y-STRs in the Evaluation of Population Differentiation Using the Mean of Allele Frequency Difference between Populations

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 566
Author(s):  
Yuxiang Zhou ◽  
Yining Yao ◽  
Baonian Liu ◽  
Qinrui Yang ◽  
Zhihan Zhou ◽  
...  
Keyword(s):  
Allele Frequency ◽  
Population Differentiation ◽  
Tandem Repeats ◽  
Single Copy ◽  
Genetic Distances ◽  
Frequency Difference ◽  
Population Substructure ◽  
Allele Frequency Difference ◽  
The Mean ◽  
Short Tandem

Y-chromosomal short tandem repeats (Y-STRs) are widely used in human research for the evaluation of population substructure or population differentiation. Previous studies show that several haplotype sets can be used for the evaluation of population differentiation. However, little is known about whether each Y-STR in these sets performs well during this procedure. In this study, a total of 20,927 haplotypes of a Yfiler Plus set were collected from 41 global populations. Different configurations were observed in multidimensional scaling (MDS) plots based on pairwise genetic distances evaluated using a Yfiler set and a Yfiler Plus set, respectively. Subsequently, 23 single-copy Y-STRs were characterized in the evaluation of population differentiation using the mean of allele frequency difference (mAFD) between populations. Our results indicated that DYS392 had the largest mAFD value (0.3802) and YGATAH4 had the smallest value (0.1845). On the whole, larger pairwise genetic distances could be obtained using the set with the top fifteen markers from these 23 single-copy Y-STRs, and clear clustering or separation of populations could be observed in the MDS plot in comparison with those using the set with the minimum fifteen markers. In conclusion, the mAFD value is reliable to characterize Y-STRs for efficiency in the evaluation of population differentiation.

Adaptation and Natural Selection

2021 ◽  
pp. 125-154
Author(s):  
Áki J. Láruson ◽  
Floyd A. Reed
Keyword(s):  
Natural Selection ◽  
Allele Frequency ◽  
Levels Of Selection ◽  
Frequency Data ◽  
Selection Coefficient ◽  
Frequency Distributions ◽  
Single Allele ◽  
Selection Strength ◽  
The Difference ◽  
Over Time

Here non-random shifts in allele frequencies over time are introduced, as well as how to incorporate varying levels of selection into a model of a single population through time. This chapter highlights the difference between weak and strong selection, the dynamics of single allele versus genotype-level selection, and how selection strength and population size affect allele frequency distributions over time. Finally the inference of the selection coefficient from allele frequency data is discussed, alongside the concepts of overdominance and underdominance.

Sign in / Sign up

Export Citation Format

Share Document