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Detecting Signatures of Positive Selection along Defined Branches of a Population Tree Using LSD

Librado, Pablo, Orlando, Ludovic·2018·Molecular Biology and Evolution
DOI 10.1093/molbev/msy053PMC PMC5967574
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Fig. 1. Overview of methods for identifying lineage-specific adaptations. (A) PBS calculations for population A, applying the Gromov product on pairs of FST indexes. (B) The time spanned from the MRCA to the split of populations A and B determines the total branch length on which mutations could have been accumulated in the ancestral population, and thus its diversity. (C) Five population tree, with popA-popE representing external populations, AB and CD internal balanced branches, and ABCD an internal unbalanced branch. (D) Collection of gene trees, each summarizing local evolutionary forces operating on particular genomic regions, potentially including lineage-specific selection. (E) Local gene tree highlighting the footprint of selection on the individuals belonging to population A. The right panel provides a zoom into the population A undergoing selection at a particular locus, and its sister population B, altogether with the equations underlying the calculation of LSD(A). Note this local gene tree exemplifies strong selection signatures, characterized by low intrapopulation diversity and high interpopulation divergence. LSD can also be calculated from sister clades that are not reciprocally monophyletic.
Fig. 1. Overview of methods for identifying lineage-specific adaptations. (A) PBS calculations for population A, applying the Gromov product on pairs of FST indexes. (B) The time spanned from the MRCA to the split of populations A and B determines the total branch length on which mutations could have been accumulated in the ancestral population, and thus its diversity. (C) Five population tree, with popA-popE representing external populations, AB and CD internal balanced branches, and ABCD an internal unbalanced branch. (D) Collection of gene trees, each summarizing local evolutionary forces operating on particular genomic regions, potentially including lineage-specific selection. (E) Local gene tree highlighting the footprint of selection on the individuals belonging to population A. The right panel provides a zoom into the population A undergoing selection at a particular locus, and its sister population B, altogether with the equations underlying the calculation of LSD(A). Note this local gene tree exemplifies strong selection signatures, characterized by low intrapopulation diversity and high interpopulation divergence. LSD can also be calculated from sister clades that are not reciprocally monophyletic.CC BY-NC · PubMed Central
Fig. 2. Performance of LSDnorm in trifurcating population trees. Fifty chromosomes (25 diploid individuals) were sampled for populations A and B. The initial frequency and dominance coefficient of beneficial mutations were assumed to be 0.05 and 0.5, respectively. (A) The left panel shows the simulated scenario, where beneficial alleles were introduced in population A. The x–y scatterplot shows that only LSDnorm(A) scales with increasing selection coefficients. (B) The same adaptive mutations appeared, independently, in populations A and B. LSDnorm(A) reached lower values than in (A). (C) Convergent evolution from variants that were already segregating in the ancestral population, and became beneficial after the split of populations A and B.
Fig. 2. Performance of LSDnorm in trifurcating population trees. Fifty chromosomes (25 diploid individuals) were sampled for populations A and B. The initial frequency and dominance coefficient of beneficial mutations were assumed to be 0.05 and 0.5, respectively. (A) The left panel shows the simulated scenario, where beneficial alleles were introduced in population A. The x–y scatterplot shows that only LSDnorm(A) scales with increasing selection coefficients. (B) The same adaptive mutations appeared, independently, in populations A and B. LSDnorm(A) reached lower values than in (A). (C) Convergent evolution from variants that were already segregating in the ancestral population, and became beneficial after the split of populations A and B.CC BY-NC · PubMed Central
Fig. 3. Comparing LSDnorm.phased, LSDnorm.unphased, and PBS, across a wide range of initial allele frequencies (iAFs) and sample sizes. Intermediate dominance was assumed. The y-axis measures the difference between the scores estimated at s = 0.03 and s = 0.00, as proxies for the discriminatory power of LSDnorm.phased, LSDnorm.unphased, and PBS. LSDnorm.phased was generally associated with increased accuracy, compared with LSDnorm.unphased, and this, in turn, to PBS. Wider confidence intervals for LSDnorm than for PBS were partly due to different sample sizes from the outgroup population.
Fig. 3. Comparing LSDnorm.phased, LSDnorm.unphased, and PBS, across a wide range of initial allele frequencies (iAFs) and sample sizes. Intermediate dominance was assumed. The y-axis measures the difference between the scores estimated at s = 0.03 and s = 0.00, as proxies for the discriminatory power of LSDnorm.phased, LSDnorm.unphased, and PBS. LSDnorm.phased was generally associated with increased accuracy, compared with LSDnorm.unphased, and this, in turn, to PBS. Wider confidence intervals for LSDnorm than for PBS were partly due to different sample sizes from the outgroup population.CC BY-NC · PubMed Central
Fig. 4. Performance of LSDnorm in five-population trees. Fifty chromosomes (25 diploid individuals) were sampled for all populations. The initial frequency and dominance coefficient of beneficial mutations were assumed to be 0.05 and 0.5, respectively. (A) The left panel shows the simulated scenario, where beneficial alleles are introduced in the unbalanced lineage ABCD. The x–y scatterplot shows that only LSDnorm(ABCD) scales with increasing selection coefficients. (B) Beneficial alleles, associated with a range of selection coefficients, are introduced in population A, increasing LSDnorm(A) scores. (C) The unbalanced lineage ABCD experiences introgression from its sister lineage, leading to population E. As the proportion of migrants increases towards one, LSDnorm(ABCD) approaches to zero, which is indicative of the absence of genetic differentiation from its sister lineage. (D) Population A experiences introgression from the distant population population E. LSDnorm(ABCD) values can eventually become negative.
Fig. 4. Performance of LSDnorm in five-population trees. Fifty chromosomes (25 diploid individuals) were sampled for all populations. The initial frequency and dominance coefficient of beneficial mutations were assumed to be 0.05 and 0.5, respectively. (A) The left panel shows the simulated scenario, where beneficial alleles are introduced in the unbalanced lineage ABCD. The x–y scatterplot shows that only LSDnorm(ABCD) scales with increasing selection coefficients. (B) Beneficial alleles, associated with a range of selection coefficients, are introduced in population A, increasing LSDnorm(A) scores. (C) The unbalanced lineage ABCD experiences introgression from its sister lineage, leading to population E. As the proportion of migrants increases towards one, LSDnorm(ABCD) approaches to zero, which is indicative of the absence of genetic differentiation from its sister lineage. (D) Population A experiences introgression from the distant population population E. LSDnorm(ABCD) values can eventually become negative.CC BY-NC · PubMed Central
Fig. 5. LSDnorm applied to the 1000 human genome project (phase III). (A) Human population tree assumed to investigate selection along the lineage ancestral to Europeans (CEU) and Asians (PJB and CHB) (red arrow), and the European population (green arrow). (B) Histogram showing the empirical LSDnorm distribution for the CEU population. The black arrow highlights the excess of 10-kb windows with a maximum score of one. (C) LSDnorm scores along the SH2B3-ATXN2 locus, altogether with the local gene tree at chr12: 111,440,001–111,450,000, which shows widely spread derived alleles amongst CEU (green), PJL (dark yellow) and CHB (dark brown) populations.
Fig. 5. LSDnorm applied to the 1000 human genome project (phase III). (A) Human population tree assumed to investigate selection along the lineage ancestral to Europeans (CEU) and Asians (PJB and CHB) (red arrow), and the European population (green arrow). (B) Histogram showing the empirical LSDnorm distribution for the CEU population. The black arrow highlights the excess of 10-kb windows with a maximum score of one. (C) LSDnorm scores along the SH2B3-ATXN2 locus, altogether with the local gene tree at chr12: 111,440,001–111,450,000, which shows widely spread derived alleles amongst CEU (green), PJL (dark yellow) and CHB (dark brown) populations.CC BY-NC · PubMed Central

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  • Ancient DNA analysis

    Orlando, L., Allaby, R., Skoglund, P., Der Sarkissian, C., Stockhammer, P. W., Ávila-Arcos, M. C., Fu, Q., Krause, J., Willerslev, E., Stone, A. C., et al. (2021) · Nature Reviews Methods Primers · doi:10.1038/s43586-020-00011-0 · Cited by 411

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Metadata

Authors
Librado, P., & Orlando, L.
Affiliations
Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
Venue
Molecular Biology and Evolution
Publisher
Oxford University Press (OUP)
Published
2018-03-29
Volume
35
Issue
6
Pages
1520-1535
ISSN
  • 0737-4038
  • 1537-1719
DOI
10.1093/molbev/msy053
PMC
PMC5967574
Cited by
28
References
15
Language
en
Licence
creativecommons.org/licenses/by-nc/4.0/ (vor, 1 d)

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