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The Role of Mutation Bias in Adaptive Molecular Evolution: Insights from 2 Convergent Changes in Protein Function 3

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The Role of Mutation Bias in Adaptive Molecular Evolution: Insights from 2 Convergent Changes in Protein Function 3 bioRxiv preprint doi: https://doi.org/10.1101/580175; this version posted March 17, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. 1 1 The role of mutation bias in adaptive molecular evolution: insights from 2 convergent changes in protein function 3 4 5 Jay F. Storz1*, Chandrasekhar Natarajan1, Anthony V. Signore1, Christopher C. Witt2,3, David M. 6 McCandlish4, Arlin Stoltzfus5* 7 8 1School of Biological Sciences, University of Nebraska, Lincoln, NE 68588 9 2Department of Biology, University of New Mexico, Albuquerque, NM 87131 10 3Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131 11 4Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724 12 5Office of Data and Informatics, Material Measurement Laboratory, NIST, and Institute for Bioscience 13 and Biotechnology Research, Rockville, MD 20850 14 15 *Corresponding authors: Jay F. Storz ([email protected]), Arlin Stoltzfus ([email protected]) 16 17 18 Abstract 19 An underexplored question in evolutionary genetics concerns the extent to which mutational bias in the 20 production of genetic variation influences outcomes and pathways of adaptive molecular evolution. In the 21 genomes of at least some vertebrate taxa, an important form of mutation bias involves changes at CpG 22 dinucleotides: If the DNA nucleotide cytosine (C) is immediately 5’ to guanine (G) on the same coding 23 strand, then – depending on methylation status – point mutations at both sites occur at an elevated rate 24 relative to mutations at non-CpG sites. Here we examine experimental data from case studies in which it 25 has been possible to identify the causative substitutions that are responsible for adaptive changes in the 26 functional properties of vertebrate hemoglobin (Hb). Specifically, we examine the molecular basis of 27 convergent increases in Hb-O2 affinity in high-altitude birds. Using a data set of experimentally verified, 28 affinity-enhancing mutations in the Hbs of highland avian taxa, we tested whether causative changes are 29 enriched for mutations at CpG dinucleotides relative to the frequency of CpG mutations among all 30 possible missense mutations. The tests revealed that a disproportionate number of causative amino acid 31 replacements were attributable to CpG mutations, suggesting that mutation bias can influence outcomes 32 of molecular adaptation. 33 34 Keywords 35 Adaptation; CpG; hemoglobin; high altitude; mutation bias; protein evolution 36 bioRxiv preprint doi: https://doi.org/10.1101/580175; this version posted March 17, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. 2 37 1. Introduction 38 39 A question of enduring interest in EvoDevo research concerns the extent to which the biased 40 production of variation during development influences directional trends and patterns of 41 convergence in morphological evolution [1-4]. At the molecular sequence level, an analogous 42 question concerns the extent to which mutational bias in the production of genetic variation 43 influences pathways of molecular evolution [5, 6]. Mutation bias is known to exert an important 44 influence on patterns of neutral molecular evolution [7], but an emerging understanding of the 45 implications of mutation as an introduction process suggest that it may be an important orienting 46 factor in adaptive evolution as well [8, 9]. The Modern Synthesis originally included a strong 47 position on the importance of recombination, and did not attach much importance to the role of 48 mutation bias [10-13]. When the process of evolution is defined in terms of shifts in the 49 frequencies of pre-existing alleles, recombination serves as the main source of new genetic 50 variation and mutation rates must be on the order of selection coefficients to exert an appreciable 51 influence on the direction of adaptive change [14]. 52 An alternative view is that outcomes and pathways of evolution may be influenced by the 53 rate of mutation even in the presence of selection [5]. For instance, in the simple case of origin- 54 fixation models [8], the substitution rate is given as K = 2Nμλ, where N is the size of a diploid 55 population, μ is the per-copy rate of mutation, and λ is the probability of fixation [15]. This 56 model specifies the substitution rate as the product of the rate at which new alleles originate via 57 mutation (2Nμ) and the probability that they become fixed once they arise (λ). In this type of 58 model, mutation bias in the introduction of variation can produce a bias in substitution rates even 59 when the substitutions are beneficial [8]. Results of several experimental evolution studies 60 suggest that mutation bias can influence trajectories of adaptive protein evolution [9, 16-20], and 61 Stoltzfus and McCandlish [9] also provide evidence for transition-transversion bias among 62 adaptive substitutions that contributed to natural protein evolution. 63 One especially powerful means of addressing questions about the role of mutation bias in 64 molecular adaptation is to examine convergent changes in protein function that can be traced to 65 specific amino acid substitutions. The experimental identification of causative substitutions 66 provides a means of testing whether such changes are random with respect to different classes of 67 site or different classes of mutational change. In vertebrate genomes, transition:transversion bias 68 results in especially high rates of change from one pyrimidine to another (C↔T) or from one 69 purine to another (G↔A). In the genomes of mammals and birds, the dinucleotide CG – often 70 designated “CpG” – is a hotspot of nucleotide point mutations due to the effect of methylation on 71 damage and repair. In mammals, the mutation rate at CpG sites is elevated 10-fold for transition 72 mutations and several-fold for transversions [21, 22]. A recent mutation-accumulation study in 73 birds confirmed a similar increase in mutation rate at CpG sites [23]. Mammalian and avian 74 genomes both exhibit roughly five-fold depletions of CpG dinucleotides, consistent with elevated 75 rates of mutation at such sites [24]. 76 In studies of hemoglobin (Hb) evolution in high-altitude birds, site-directed mutagenesis 77 experiments have documented three cases in which missense mutations at CpG dinucleotides A 78 contributed to derived increases in Hb-O2 affinity: 55Ile→Val (I55V) in the β -globin gene of 79 Andean house wrens (Troglodytes aedon)[25] and parallel 34Ala→Thr substitutions (A34T) in 80 the αA-globin genes of two different passerine species that are native to the Tibetan Plateau, the 81 ground tit (Parus humilis [= Pseudopodoces humilis]) and the grey crested tit (Lophophanes 82 dichrous)[26]. The patterns documented in these three high-altitude taxa are consistent with a bioRxiv preprint doi: https://doi.org/10.1101/580175; this version posted March 17, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. 3 83 broader pattern of convergence in Hb function in highland birds [26-30], and the direction of 84 character-state change is consistent with theoretical and experimental results which suggest that 85 it is generally beneficial to have an increased Hb-O2 affinity under conditions of severe 86 environmental hypoxia [30-32]. Moreover, in the case of the high-altitude house wrens, an 87 analysis of genome-wide patterns of nucleotide polymorphism revealed evidence for altitude- 88 related selection on the missense CpG variant [25], providing additional support for the inferred 89 adaptive significance of the affinity-altering amino acid change. 90 The documented cases in which CpG mutations have contributed to altitude-related 91 changes in Hb function suggest that mutation bias may influence which mutations are most likely 92 to contribute to molecular adaptation. However, a far more comprehensive and systematic 93 analysis is required to draw firm conclusions. Here we examine existing data from a larger set of 94 case-studies in which it has been possible to identify the causative substitutions that are 95 responsible for convergent increases in Hb-O2 affinity in high-altitude birds. Using a data set of 96 experimentally verified, affinity-enhancing mutations in the Hbs of highland avian taxa, we test 97 whether a disproportionate number involve mutations at CpG sites. The results suggest that 98 mutation bias has influenced outcomes of molecular adaptation. 99 100 2. Methods 101 102 (a) Sampling design 103 To test for convergent changes in Hb-O2 affinity, we conducted phylogenetically independent 104 comparisons involving 70 avian taxa representing 35 matched pairs of high- versus low-altitude 105 species or subspecies (Fig. 1). These taxa include ground doves, nightjars, hummingbirds, 106 passerines, and waterfowl [25-29, 33-36]. All pairwise comparisons involved dramatic 107 elevational contrasts; high-altitude taxa native to very high elevations in the Andes, Ethiopian 108 highlands, or Tibetan Plateau (with upper range limits of 3,500 to 5,000 m above sea level) were 109 paired with close relatives that typically occur at or near sea level. Thus, the highland members 110 of each taxon pair have upper elevational range limits that likely exceed the threshold at which 111 an increased Hb-O2 affinity becomes physiologically beneficial. 112 113 (b) Experimental measurement of Hb function 114 For each taxon, we used our previously measured O2 affinities of purified Hbs in the presence of 115 allosteric cofactors: Cl- ions (added as KCl) and inositol hexaphosphate (IHP).
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