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Sachdeva V, Husain K, Sheng J, Wang S, Murugan A. Tuning environmental timescales to evolve and maintain generalists. Proc Natl Acad Sci U S A 2020; 117:12693-12699. [PMID: 32457160 PMCID: PMC7293598 DOI: 10.1073/pnas.1914586117] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Natural environments can present diverse challenges, but some genotypes remain fit across many environments. Such "generalists" can be hard to evolve, outcompeted by specialists fitter in any particular environment. Here, inspired by the search for broadly neutralizing antibodies during B cell affinity maturation, we demonstrate that environmental changes on an intermediate timescale can reliably evolve generalists, even when faster or slower environmental changes are unable to do so. We find that changing environments on timescales comparable with evolutionary transients in a population enhance the rate of evolving generalists from specialists, without enhancing the reverse process. The yield of generalists is further increased in more complex dynamic environments, such as a "chirp" of increasing frequency. Our work offers design principles for how nonequilibrium fitness "seascapes" can dynamically funnel populations to genotypes unobtainable in static environments.
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Affiliation(s)
- Vedant Sachdeva
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL 60627
| | - Kabir Husain
- Department of Physics, The University of Chicago, Chicago, IL 60627
| | - Jiming Sheng
- Department of Physics and Astronomy, The University of California, Los Angeles, CA 90095
| | - Shenshen Wang
- Department of Physics and Astronomy, The University of California, Los Angeles, CA 90095
| | - Arvind Murugan
- Department of Physics, The University of Chicago, Chicago, IL 60627;
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2
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Donath A, Stadler PF. Split-inducing indels in phylogenomic analysis. Algorithms Mol Biol 2018; 13:12. [PMID: 30026791 PMCID: PMC6047143 DOI: 10.1186/s13015-018-0130-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 06/16/2018] [Indexed: 11/13/2022] Open
Abstract
Background Most phylogenetic studies using molecular data treat gaps in multiple sequence alignments as missing data or even completely exclude alignment columns that contain gaps. Results Here we show that gap patterns in large-scale, genome-wide alignments are themselves phylogenetically informative and can be used to infer reliable phylogenies provided the gap data are properly filtered to reduce noise introduced by the alignment method. We introduce here the notion of split-inducing indels (splids) that define an approximate bipartition of the taxon set. We show both in simulated data and in case studies on real-life data that splids can be efficiently extracted from phylogenomic data sets. Conclusions Suitably processed gap patterns extracted from genome-wide alignment provide a surprisingly clear phylogenetic signal and an allow the inference of accurate phylogenetic trees. Electronic supplementary material The online version of this article (10.1186/s13015-018-0130-7) contains supplementary material, which is available to authorized users.
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3
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Schaibley VM, Zawistowski M, Wegmann D, Ehm MG, Nelson MR, St. Jean PL, Abecasis GR, Novembre J, Zöllner S, Li JZ. The influence of genomic context on mutation patterns in the human genome inferred from rare variants. Genome Res 2013; 23:1974-84. [PMID: 23990608 PMCID: PMC3847768 DOI: 10.1101/gr.154971.113] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 08/19/2013] [Indexed: 01/22/2023]
Abstract
Understanding patterns of spontaneous mutations is of fundamental interest in studies of human genome evolution and genetic disease. Here, we used extremely rare variants in humans to model the molecular spectrum of single-nucleotide mutations. Compared to common variants in humans and human-chimpanzee fixed differences (substitutions), rare variants, on average, arose more recently in the human lineage and are less affected by the potentially confounding effects of natural selection, population demographic history, and biased gene conversion. We analyzed variants obtained from a population-based sequencing study of 202 genes in >14,000 individuals. We observed considerable variability in the per-gene mutation rate, which was correlated with local GC content, but not recombination rate. Using >20,000 variants with a derived allele frequency ≤ 10(-4), we examined the effect of local GC content and recombination rate on individual variant subtypes and performed comparisons with common variants and substitutions. The influence of local GC content on rare variants differed from that on common variants or substitutions, and the differences varied by variant subtype. Furthermore, recombination rate and recombination hotspots have little effect on rare variants of any subtype, yet both have a relatively strong impact on multiple variant subtypes in common variants and substitutions. This observation is consistent with the effect of biased gene conversion or selection-dependent processes. Our results highlight the distinct biases inherent in the initial mutation patterns and subsequent evolutionary processes that affect segregating variants.
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Affiliation(s)
- Valerie M. Schaibley
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Matthew Zawistowski
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48019, USA
| | - Daniel Wegmann
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Switzerland
| | - Margaret G. Ehm
- Department of Quantitative Sciences, GlaxoSmithKline (GSK), Research Triangle Park, North Carolina 27709, USA
| | - Matthew R. Nelson
- Department of Quantitative Sciences, GlaxoSmithKline (GSK), Research Triangle Park, North Carolina 27709, USA
| | - Pamela L. St. Jean
- Department of Quantitative Sciences, GlaxoSmithKline (GSK), Research Triangle Park, North Carolina 27709, USA
| | - Gonçalo R. Abecasis
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48019, USA
| | - John Novembre
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Sebastian Zöllner
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48019, USA
- Department of Psychiatry, University of Michigan, Ann Arbor, Michigan 48019, USA
| | - Jun Z. Li
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
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4
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Kvikstad EM, Duret L. Strong heterogeneity in mutation rate causes misleading hallmarks of natural selection on indel mutations in the human genome. Mol Biol Evol 2013; 31:23-36. [PMID: 24113537 PMCID: PMC3879449 DOI: 10.1093/molbev/mst185] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Elucidating the mechanisms of mutation accumulation and fixation is critical to understand the nature of genetic variation and its contribution to genome evolution. Of particular interest is the effect of insertions and deletions (indels) on the evolution of genome landscapes. Recent population-scaled sequencing efforts provide unprecedented data for analyzing the relative impact of selection versus nonadaptive forces operating on indels. Here, we combined McDonald-Kreitman tests with the analysis of derived allele frequency spectra to investigate the dynamics of allele fixation of short (1-50 bp) indels in the human genome. Our analyses revealed apparently higher fixation probabilities for insertions than deletions. However, this fixation bias is not consistent with either selection or biased gene conversion and varies with local mutation rate, being particularly pronounced at indel hotspots. Furthermore, we identified an unprecedented number of loci with evidence for multiple indel events in the primate phylogeny. Even in nonrepetitive sequence contexts (a priori not prone to indel mutations), such loci are 60-fold more frequent than expected according to a model of uniform indel mutation rate. This provides evidence of as yet unidentified cryptic indel hotspots. We propose that indel homoplasy, at known and cryptic hotspots, produces systematic errors in determination of ancestral alleles via parsimony and advise caution interpreting classic selection tests given the strong heterogeneity in indel rates across the genome. These results will have great impact on studies seeking to infer evolutionary forces operating on indels observed in closely related species, because such mutations are traditionally presumed homoplasy-free.
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Affiliation(s)
- Erika M Kvikstad
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, CNRS, Université Lyon 1, Villeurbanne, France
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Babbitt GA, Cotter CR. Functional conservation of nucleosome formation selectively biases presumably neutral molecular variation in yeast genomes. Genome Biol Evol 2010; 3:15-22. [PMID: 21135411 PMCID: PMC3014273 DOI: 10.1093/gbe/evq081] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
One prominent pattern of mutational frequency, long appreciated in comparative genomics, is the bias of purine/pyrimidine conserving substitutions (transitions) over purine/pyrimidine altering substitutions (transversions). Traditionally, this transitional bias has been thought to be driven by the underlying rates of DNA mutation and/or repair. However, recent sequencing studies of mutation accumulation lines in model organisms demonstrate that substitutions generally do not accumulate at rates that would indicate a transitional bias. These observations have called into question a very basic assumption of molecular evolution; that naturally occurring patterns of molecular variation in noncoding regions accurately reflect the underlying processes of randomly accumulating neutral mutation in nuclear genomes. Here, in Saccharomyces yeasts, we report a very strong inverse association (r = −0.951, P < 0.004) between the genome-wide frequency of substitutions and their average energetic effect on nucleosome formation, as predicted by a structurally based energy model of DNA deformation around the nucleosome core. We find that transitions occurring at sites positioned nearest the nucleosome surface, which are believed to function most importantly in nucleosome formation, alter the deformation energy of DNA to the nucleosome core by only a fraction of the energy changes typical of most transversions. When we examined the same substitutions set against random background sequences as well as an existing study reporting substitutions arising in mutation accumulation lines of Saccharomyces cerevisiae, we failed to find a similar relationship. These results support the idea that natural selection acting to functionally conserve chromatin organization may contribute significantly to genome-wide transitional bias, even in noncoding regions. Because nucleosome core structure is highly conserved across eukaryotes, our observations may also help to further explain locally elevated transition bias at CpG islands, which are known to destabilize nucleosomes at vertebrate promoters.
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Polak P, Querfurth R, Arndt PF. The evolution of transcription-associated biases of mutations across vertebrates. BMC Evol Biol 2010; 10:187. [PMID: 20565875 PMCID: PMC2927911 DOI: 10.1186/1471-2148-10-187] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Accepted: 06/18/2010] [Indexed: 02/03/2024] Open
Abstract
Background The interplay between transcription and mutational processes can lead to particular mutation patterns in transcribed regions of the genome. Transcription introduces several biases in mutational patterns; in particular it invokes strand specific mutations. In order to understand the forces that have shaped transcripts during evolution, one has to study mutation patterns associated with transcription across animals. Results Using multiple alignments of related species we estimated the regional single-nucleotide substitution patterns along genes in four vertebrate taxa: primates, rodents, laurasiatheria and bony fishes. Our analysis is focused on intronic and intergenic regions and reveals differences in the patterns of substitution asymmetries between mammals and fishes. In mammals, the levels of asymmetries are stronger for genes starting within CpG islands than in genes lacking this property. In contrast to all other species analyzed, we found a mutational pressure in dog and stickleback, promoting an increase of GC-contents in the proximity to transcriptional start sites. Conclusions We propose that the asymmetric patterns in transcribed regions are results of transcription associated mutagenic processes and transcription coupled repair, which both seem to evolve in a taxon related manner. We also discuss alternative mechanisms that can generate strand biases and involves error prone DNA polymerases and reverse transcription. A localized increase of the GC content near the transcription start site is a signature of biased gene conversion (BGC) that occurs during recombination and heteroduplex formation. Since dog and stickleback are known to be subject to rapid adaptations due to population bottlenecks and breeding, we further hypothesize that an increase in recombination rates near gene starts has been part of an adaptive process.
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Affiliation(s)
- Paz Polak
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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7
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Abstract
Many methods exist for reconstructing phylogenies from molecular sequence data, but few phylogenies are known and can be used to check their efficacy. Simulation remains the most important approach to testing the accuracy and robustness of phylogenetic inference methods. However, current simulation programs are limited, especially concerning realistic models for simulating insertions and deletions. We implement a portable and flexible application, named INDELible, for generating nucleotide, amino acid and codon sequence data by simulating insertions and deletions (indels) as well as substitutions. Indels are simulated under several models of indel-length distribution. The program implements a rich repertoire of substitution models, including the general unrestricted model and nonstationary nonhomogeneous models of nucleotide substitution, mixture, and partition models that account for heterogeneity among sites, and codon models that allow the nonsynonymous/synonymous substitution rate ratio to vary among sites and branches. With its many unique features, INDELible should be useful for evaluating the performance of many inference methods, including those for multiple sequence alignment, phylogenetic tree inference, and ancestral sequence, or genome reconstruction.
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Affiliation(s)
- William Fletcher
- Department of Genetics, Evolution and Environment and Centre for Mathematics and Physics in the Life Sciences and Experimental Biology, University College London, London, UK
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8
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Imamura H, Karro JE, Chuang JH. Weak preservation of local neutral substitution rates across mammalian genomes. BMC Evol Biol 2009; 9:89. [PMID: 19416516 PMCID: PMC2689173 DOI: 10.1186/1471-2148-9-89] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2008] [Accepted: 05/05/2009] [Indexed: 01/06/2023] Open
Abstract
Background The rate at which neutral (non-functional) bases undergo substitution is highly dependent on their location within a genome. However, it is not clear how fast these location-dependent rates change, or to what extent the substitution rate patterns are conserved between lineages. To address this question, which is critical not only for understanding the substitution process but also for evaluating phylogenetic footprinting algorithms, we examine ancestral repeats: a predominantly neutral dataset with a significantly higher genomic density than other datasets commonly used to study substitution rate variation. Using this repeat data, we measure the extent to which orthologous ancestral repeat sequences exhibit similar substitution patterns in separate mammalian lineages, allowing us to ascertain how well local substitution rates have been preserved across species. Results We calculated substitution rates for each ancestral repeat in each of three independent mammalian lineages (primate – from human/macaque alignments, rodent – from mouse/rat alignments, and laurasiatheria – from dog/cow alignments). We then measured the correlation of local substitution rates among these lineages. Overall we found the correlations between lineages to be statistically significant, but too weak to have much predictive power (r2 <5%). These correlations were found to be primarily driven by regional effects at the scale of several hundred kb or larger. A few repeat classes (e.g. 7SK, Charlie8, and MER121) also exhibited stronger conservation of rate patterns, likely due to the effect of repeat-specific purifying selection. These classes should be excluded when estimating local neutral substitution rates. Conclusion Although local neutral substitution rates have some correlations among mammalian species, these correlations have little predictive power on the scale of individual repeats. This indicates that local substitution rates have changed significantly among the lineages we have studied, and are likely to have changed even more for more diverged lineages. The correlations that do persist are too weak to be responsible for many of the highly conserved elements found by phylogenetic footprinting algorithms, leading us to conclude that such elements must be conserved due to selective forces.
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Affiliation(s)
- Hideo Imamura
- Boston College, Department of Biology, Chestnut Hill, MA 02467, USA.
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9
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Peifer M, Karro JE, von Grünberg HH. Is there an acceleration of the CpG transition rate during the mammalian radiation? Bioinformatics 2008; 24:2157-64. [PMID: 18662928 PMCID: PMC2553435 DOI: 10.1093/bioinformatics/btn391] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2008] [Revised: 07/27/2008] [Accepted: 07/27/2008] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION In this article we build a model of the CpG dinucleotide substitution rate and use it to challenge the claim that, that rate underwent a sudden mammalian-specific increase approximately 90 million years ago. The evidence supporting this hypothesis comes from the application of a model of neutral substitution rates able to account for elevated CpG dinucleotide substitution rates. With the initial goal of improving that model's accuracy, we introduced a modification enabling us to account for boundary effects arising by the truncation of the Markov field, as well as improving the optimization procedure required for estimating the substitution rates. RESULTS When using this modified method to reproduce the supporting analysis, the evidence of the rate shift vanished. Our analysis suggests that the CpG-specific rate has been constant over the relevant time period and that the asserted acceleration of the CpG rate is likely an artifact of the original model.
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Affiliation(s)
- M Peifer
- Institute of Chemistry, Karl-Franzens University Graz, Graz, Austria.
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10
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Mustonen V, Lässig M. Molecular evolution under fitness fluctuations. PHYSICAL REVIEW LETTERS 2008; 100:108101. [PMID: 18352233 DOI: 10.1103/physrevlett.100.108101] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2006] [Revised: 11/20/2007] [Indexed: 05/26/2023]
Abstract
Molecular evolution is a stochastic process governed by fitness, mutations, and reproductive fluctuations in a population. Here, we study evolution where fitness itself is stochastic, with random switches in the direction of selection at individual genomic loci. As the correlation time of these fluctuations becomes larger than the diffusion time of mutations within the population, fitness changes from an annealed to a quenched random variable. We show that the rate of evolution has its maximum in the crossover regime, where both time scales are comparable. Adaptive evolution emerges in the quenched fitness regime (evidence for such fitness fluctuations has recently been found in genomic data). The joint statistical theory of reproductive and fitness fluctuations establishes a conceptual connection between evolutionary genetics and statistical physics of disordered systems.
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Affiliation(s)
- Ville Mustonen
- Institut für Theoretische Physik, Universität zu Köln, Zülpicher Str. 77, 50937 Köln, Germany
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11
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Karro JE, Peifer M, Hardison RC, Kollmann M, von Grünberg HH. Exponential decay of GC content detected by strand-symmetric substitution rates influences the evolution of isochore structure. Mol Biol Evol 2007; 25:362-74. [PMID: 18042807 DOI: 10.1093/molbev/msm261] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The distribution of guanine and cytosine nucleotides throughout a genome, or the GC content, is associated with numerous features in mammals; understanding the pattern and evolutionary history of GC content is crucial to our efforts to annotate the genome. The local GC content is decaying toward an equilibrium point, but the causes and rates of this decay, as well as the value of the equilibrium point, remain topics of debate. By comparing the results of 2 methods for estimating local substitution rates, we identify 620 Mb of the human genome in which the rates of the various types of nucleotide substitutions are the same on both strands. These strand-symmetric regions show an exponential decay of local GC content at a pace determined by local substitution rates. DNA segments subjected to higher rates experience disproportionately accelerated decay and are AT rich, whereas segments subjected to lower rates decay more slowly and are GC rich. Although we are unable to draw any conclusions about causal factors, the results support the hypothesis proposed by Khelifi A, Meunier J, Duret L, and Mouchiroud D (2006. GC content evolution of the human and mouse genomes: insights from the study of processed pseudogenes in regions of different recombination rates. J Mol Evol. 62:745-752.) that the isochore structure has been reshaped over time. If rate variation were a determining factor, then the current isochore structure of mammalian genomes could result from the local differences in substitution rates. We predict that under current conditions strand-symmetric portions of the human genome will stabilize at an average GC content of 30% (considerably less than the current 42%), thus confirming that the human genome has not yet reached equilibrium.
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Affiliation(s)
- J E Karro
- Department of Computer Science and Systems Analysis, Miami University, Ohio, USA.
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12
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Saxonov S, Berg P, Brutlag DL. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci U S A 2006; 103:1412-7. [PMID: 16432200 PMCID: PMC1345710 DOI: 10.1073/pnas.0510310103] [Citation(s) in RCA: 904] [Impact Index Per Article: 50.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A striking feature of the human genome is the dearth of CpG dinucleotides (CpGs) interrupted occasionally by CpG islands (CGIs), regions with relatively high content of the dinucleotide. CGIs are generally associated with promoters; genes, whose promoters are especially rich in CpG sequences, tend to be expressed in most tissues. However, all working definitions of what constitutes a CGI rely on ad hoc thresholds. Here we adopt a direct and comprehensive survey to identify the locations of all CpGs in the human genome and find that promoters segregate naturally into two classes by CpG content. Seventy-two percent of promoters belong to the class with high CpG content (HCG), and 28% are in the class whose CpG content is characteristic of the overall genome (low CpG content). The enrichment of CpGs in the HCG class is symmetric and peaks around the core promoter. The broad-based expression of the HCG promoters is not a consequence of a correlation with CpG content because within the HCG class the breadth of expression is independent of the CpG content. The overall depletion of CpGs throughout the genome is thought to be a consequence of the methylation of some germ-line CpGs and their susceptibility to mutation. A comparison of the frequencies of inferred deamination mutations at CpG and GpC dinucleotides in the two classes of promoters using SNPs in human-chimpanzee sequence alignments shows that CpGs mutate at a lower frequency in the HCG promoters, suggesting that CpGs in the HCG class are hypomethylated in the germ line.
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Affiliation(s)
- Serge Saxonov
- BioMedical Informatics Program, Stanford University, Stanford, CA 94305, USA
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13
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Messer PW, Arndt PF, Lässig M. Solvable sequence evolution models and genomic correlations. PHYSICAL REVIEW LETTERS 2005; 94:138103. [PMID: 15904043 DOI: 10.1103/physrevlett.94.138103] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2004] [Indexed: 05/02/2023]
Abstract
We study a minimal model for genome evolution whose elementary processes are single site mutation, duplication and deletion of sequence regions, and insertion of random segments. These processes are found to generate long-range correlations in the composition of letters as long as the sequence length is growing; i.e., the combined rates of duplications and insertions are higher than the deletion rate. For constant sequence length, on the other hand, all initial correlations decay exponentially. These results are obtained analytically and by simulations. They are compared with the long-range correlations observed in genomic DNA, and the implications for genome evolution are discussed.
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Affiliation(s)
- Philipp W Messer
- Institute for Theoretical Physics, University of Cologne, Köln, Germany
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14
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Yi S, Li WH. Molecular evolution of recombination hotspots and highly recombining pseudoautosomal regions in hominoids. Mol Biol Evol 2005; 22:1223-30. [PMID: 15703241 DOI: 10.1093/molbev/msi106] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We examined the effects of recombination on the molecular evolution of noncoding regions in pseudoautosomal regions (PARs) and recombination hotspots in hominoids. The PAR-linked regions analyzed had on average longer branch lengths than those of the recombination hotspots. Moreover, contrary to previous observations, we found no correlation between recombination rate and silent site divergence in our data set and little change in the GC content during recent hominoid evolution. This suggests that the current rate of recombination is not a good indicator of the past rates of recombination for these highly recombining regions. Furthermore, human recombination hotspots show increased AT to GC substitutions in the human lineage, while no such pattern is detected for PAR-linked regions. Together, these observations suggest that recombination hotspots in hominoids are transient in the evolutionary time-scale. Interestingly, the 16p13.3 recombination hotspot locus violates a local molecular clock, though the locus appears to be noncoding and should evolve neutrally. We hypothesize that sudden changes in recombination rate have caused the changes in substitution rate at this locus.
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Affiliation(s)
- Soojin Yi
- Department of Ecology and Evolution, University of Chicago, USA.
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15
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2005. [PMCID: PMC2448604 DOI: 10.1002/cfg.419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
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