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Journal of Phylogenetics & Evolutionary Biology
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Estimation of Genome Evolution Time by Mutation Rate

Ahmed M El-Shehawi1,2* and Mona M Elseehy2

1Department of Biotechnology, Faculty of Science, Taif University, Taif, Saudi Arabia

2Department of Genetics, Faculty of Agriculture, University of Alexandria, Alexandria, Egypt

*Corresponding Author:
Ahmed Mohamed El-Shehawi
Department of Biotechnology,
Taif University, Taif 21974,
Saudi Arabia.
Tel: +966554904625
E-mail: [email protected]
 

Received Date: April 29, 2016; Accepted Date: July 25, 2016; Published Date: August 03, 2016

Citation: El-Shehawi AM, Elseehy MM (2016) Estimation of Genome Evolution Time by Mutation Rate. J Phylogenetics Evol Biol 4:172. doi: 10.4172/2329- 9002.1000172

Copyright: © 2016 El-Shehawi AM, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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Abstract

Mutations, transposable elements, and recombination are the main mechanisms for genome size evolution. The quantitative impact of mutations, excluding polyploidy, on genome size is well studied in some genomes while the impact of other factors has not been investigated. Mutation rate was used to estimate the evolution time of origin genome to form a higher size genome and test if the estimated age of earth fits for these evolution events. Results indicated that the evolution time of the smallest detected genome through mutation rate to the largest detected genome is much higher than the estimated age of earth. The cumulative evolution time of the studied origin genomes was estimated at 5300 folds of earth's age and the average evolution time is 2.7 × 1012 years per genome. The relationship among genome size, mutation rate, and evolution time indicated that evolution time is positively correlated with genome size suggesting that larger genomes take longer time to evolve in size. Estimation of evolution time would lead to establishment of genome evolution timeline to replace or support the fossil evolution timeline.

Keywords

Mutation rate; Evolution time; Genome size; Cumulative evolution time

Introduction

Genome is the unique string of nucleotide sequence tailored and organized in a very unique architecture to reproduce unique specific features of a species. It is determined by the amount of DNA in the cell "C-value" distributed on a certain number of chromosomes. When mutated to a critical level, this string will not be able to define the species' unique characteristics. The detailed unique organization of a genome is very significant because two distinct species could have the same genome size. For example, Homo sapiens (human) [1] and the grass Festuca tatrae [2] have the same genome size (3.5 pg) and they have completely different structural features and development. Charles Darwin introduced his evolution theory of common ancestor [3] based on series of continuous phenotypic and structural similarities in the absence of principles of genetics and genomics, yet he was not able to explain how the original cell had formed. In the view of evolution theory and the uniqueness of genomes and species, the common ancestor genome had to contain a specific amount of DNA (genome). Based on our current knowledge in genomics, this common ancestor genome (original genome) had to gain more DNA and arrange it in a new unique format to generate new genome and then new species with distinct features. This way the original genome can change and evolve to other genomes to define new species.

Mechanisms of genome evolution

Various mechanisms contribute to genome evolution (change in genome size) including recombination [4,5], transposition [6,7], and mutations [8,9]. Recombination affects the genome architecture and evolutionary rate. Its effect on genome evolution is not well understood because its impact on genomes requires whole genome sequencing and global recombination rate [4]. Previous studies indicated that high recombination rate is negatively correlated with genome size [10], positively correlated with Long Terminal Repeats (LTR) content [11], and positively correlated with GC% content and CpG density [5].

Transposable elements (TEs) are highly represented in nearly all genomes. They make up about 45% of the human genome and most of plant genomes [6]. For example, about 85% of maize genome is TEs [12]. Their integration in host genomes leads to various types of rearrangements including insertions, deletions, duplications, inversions, and loss or change in gene expression [6].

Polyploidy is one type of mutations that involves the most drastic change in genome size, yet it is limited to the polyploid genomes. After polyplodization, rapid genome rearrangements and gene silencing occur [13] indicating that polyploidy is not a dead end in genome evolution. Several studies also reported that polyplodization occurred early during plant evolution [14].

The distinct role of recombination, TEs, and mutation is not clear because their impact on genome size evolution is extensively intermingled. It is believed that TEs increase genome reconstruction in polyploids [15] and they are suspected to be involved in evolution of gene silencing mechanisms including methylation and heterochromatin formation in eukaryotes [16]. Also, recombination is positively correlated with LTR content because removal of LTRs involves recombination processes [11]. These overlapping roles make it extremely difficult to estimate their distinct impact on genome size evolution in a quantitative way. On the other hand, there have been clear estimates of mutation rates, excluding polyploidy, in many different genomes [9,17-22].

Mutation rate (μg)

Two main approaches have been used to estimate mutation rates in living organisms quantitatively. The first is based on using function analysis (FA) of one locus [17,18] and the second is the recently introduced whole genome sequencing (WGS) for accurate estimation of mutation rate after high number of generations [9,19- 22]. Many types of mutations contribute to genome evolution including insertion, deletion (indel), and base substitution. Various studies give estimation of total mutation rate because sometimes it is not practically possible to give separate estimates for different types of mutations, but generally, excluding polyploids, the change in genome size via mutations comes from the net difference between insertion and deletion mutations [9,17-22].

The estimated value of mutation rate differs depending on the estimation approach and the organism (Table 1). For example, the average mutation rate of E. coli determined by FA was 0.0025 base per genome per generation (bgg) [17,18] (Table 1), whereas it was 8.9 × 10-11 base per site per generation (bsg) (0.00045 bgg) when it was estimated using WGS [20]. This is much lower than the previous reported rate (0.0025 bgg) or the average microbial mutation rate (0.0034 bgg) [18]. Generally, the WGS approach gave more accurate but lower estimates of spontaneous mutations than the FA (Table 1). Base substitution represents the major percentage of mutations, whereas indel mutations are rare and sometimes are not estimated distinctly. This was reported in yeast [9], C. reinhardtii [21], and D. melanogaster [22-24] raising the question about the effectiveness of mutation to change genomes size enough to the level of genome evolution. In this study, we assumed that total mutation rate is insertion mutations for simplified calculations.

Organism, locus EM# Gb µb µg Reference
E. coli, lacI FA 4.6 × 106 6.93 × 10-10 0.0033 17
E. coli, lacI FA 4.6 × 106 4.08 × 10-10 0.0019 17
E. coli, hisGDCBHAFE FA 4.6 x 106 5.06 x 10-10 0.0024 17
E. coli, average FA 4.6 × 106 - 0.0025 18
E. coli, B REL606 WGS 4.6 × 106 8.9 × 10-11 0.00041 20
E. coli WGS 4.6 × 106 - 0.001 23
E. coli, average FA 4.6 × 106 - 0.0016 -
S. cerevisiae, URA3 FA 12.1 × 106 2.76 × 10-10 0.00381 17
S. cerevisiae, CAN1 FA 12.1 × 106 1.73 × 10-10 0.00238 17
S. cerevisiae, average FA 12.1 × 106 2.2 × 10-10 0.0027 18
S. cerevisiae WGS 12.1 × 106 - 0.004 24
S. cerevisiae WGS 12.1 × 106 1.67 × 10-10 0.002 9
N. crassa, ad-3AB FA 43 × 106 4.47 × 10-11 0.00187 17
N. crassa, mtr FA 43 × 106 9.96 ×10-11 0.00417 17
N. crassa, average FA 43 × 106 - 0.003 18
Microbes, average FA - - 0.0034 18
C. reinhardi WGS 111 × 106 3.23 × 10-10 0.036 21
A. thaliana WGS 157 × 106 7 × 10-9 1* 19
C. elegans FA 97 × 106 - 0.036* 18
D. melanogaster FA 130 × 106 - 0.14* 18
D. melanogaster WGS 130 × 109 2.8 × 10-9 0.57* 22
M. musculus FA 2.7 × 109 - 0.9* 18
H. sapiens FA 3.2 x 109 - 1.6* 18

Table 1: Mutation rate of some studied genomes.

Previous studies have focused on getting estimations of mutation rates (Table 1), whereas the impact of mutations on genome size has not been investigated quantitatively. In this study, mutation rate, excluding polyploidy, of different genomes was used to estimate the evolution time of origin diploid genomes to higher size target diploid genomes and test the possibility of genome evolution via mutation rate during the estimated age of earth. The impact of recombination, transposition, and polyploidy mutations were excluded because their accurate quantitative rates have been not determined.

Materials and Methods

Estimation of genome evolution time

Estimated mutation rates in Table 1 were used to calculate evolution time (Et) from nine well studied origin genomes to target genomes of higher size. The smallest detected bacterial genome of Buchnera sp. (25) was used to represent the anonymous controversial common ancestral genome. Because its mutation rate has not been detected the average microbial mutation rate (0.0034 bgg, Table 1) was used. The human (H. sapiens) and the lung fish Protopterus aethiopicus (P. aethiopicus) genomes were used as target genomes because human is the most recent organism on earth [25,26] and P. aethiopicus has the largest detected genome (130000 Mb). When there is more than one estimate for mutation rate for an origin genome (Table 1), the highest rate was used in calculations of evolution time. Mutation rate (bsg, μs) was multiplied by genome size in base pairs (Gb) to give mutation rate per genome per generation (bgg, μg). This was multiplied by the number of generation per year to give mutation rate per year (bgy, μy). To calculate the Et of an origin genome to a target genome the genome difference in bp was divided by μy. The estimated age of earth is 4.5 billion years [27] and the estimated age of life on earth is 4 billion years [28]. The calculated Et was divided by the age of earth (A) to give the Et in folds of the earth's age (NA), Et/A. Calculation details are summarized in Supplementary Material S1.

Cumulative evolution time

The cumulative genome evolution time for the nine origin genomes was calculated to estimate the total time needed for the smallest genome (Buchnera sp.) to reach the largest genome of P. aethiopicus passing by the other 8 genomes. The calculation details of evolution time of origin genomes to target genomes are summarized in Supplementary Material S1. The cumulative evolution time was divided by the number of genomes [9] to give the average evolution time per genome. This was used to predict the total evolution time for the current characterized or predicted number of genomes on earth.

Results

Genome evolution time

Estimated evolution time (Et) from the nine genomes (Table 1) is summarized in Table 2. Estimation of Et from the eight genomes to human genome or nine genomes to P. aethiopicus genome revealed some interesting features. Et from the 8 studied genomes to the human genome ranged from 3.58 × 107 to 3.6 × 108 years (0.008-0.08 NA), whereas it ranged from 9.9 × 108 to 2.4 × 1013 years (0.22-5300 NA) for the 9 genomes to the P. aethiopicus genome (Table 2). The smallest detected genome Buchnera sp would take 3.58 × 107 years (0.008 NA) to reach human genome or 1.45 × 109 years (0.32 NA) to reach P. aethiopicus genome. The Et differed among the 9 origin genomes used in this study depending on the mutation rate of the origin genome and the difference (bp) between the origin and the target genome. For example, human genome would take 2.4 × 1013 years (5.3 × 103 NA) to reach P. aethiopicus genome (Table 2). Also, in one evolution leap, S. cerevisiae genome would take as twice as the earth's age and C. elegans genome would take as 9 folds as the earth's age to reach P. aethiopicus genome (Table 2). Total evolution time for the 8 origin genomes to reach human genome is 1.88 × 109 years (0.42 NA) and for the 9 genomes to reach P. aethiopicus genome is 2.4 × 1013 years (5300 NA) (Table 2).

Origin genome Gm µg µy Target genome
Homo sapiens P. aethiopicus
Et NA Et NA
Buchnera sp. 0.449 0.0034 89.35 3.58 × 107 0.008 1.45 × 109 0.32
E. coli 4.6 0.0025 65.7 48.64 × 106 0.01 1.98 × 109 0.44
S. cerevisiae 12.1 0.004 14.6 2.18 × 108 0.048 8.9 × 109 1.98
C. elegans 97 0.036 3.2 9.7 × 108 0.22 4 × 1010 8.9
C. reinhardtii 111 0.036 131 2.36 × 107 0.005 9.9 × 108 0.22
D. melanogaster 130 0.57 24 1.3 × 108 0.03 5.4 × 109 1.2
A. thaliana 157 1* 8.5 3.6 × 108 0.08 1.5 × 1010 3.3
M. musculus 2700 0.9* 5.4 9.3 × 107 0.02 2.4 × 1010 5.3
H. sapiens 3200 1.6* 5.3 × 10-3 - - 2.4 × 1013 5.3 × 103
Total - - - 1.88 × 109 0.42 2.4 × 1013 5.3×103

Table 2: Estimated evolution time of origin genomes to target genomes.

Cumulative evolution time

To estimate the average genome evolution time of the 8 genomes used in this study based on their mutation rates, the cumulative Et was calculated. This gives indication about the time during which the smallest detected genome took to reach the largest detected genome passing by other origin genomes. This was done by estimation of Et of the smallest detected genome to the next genome in size then estimation of the second genome to the third and so on. These independent Ets of origin genomes were added to give the cumulative Et for the 9 genomes. The cumulative Et for the nine origin genomes used in this study to develop P. aethiopicus genome was 2.4 × 1013 years (5.3 × 103 NA). Based on this estimation, the average Et of the 9 genomes can be estimated as 2.7 × 1013 years per genome (5.9 × 102 NA) (Table 3). Although the average Et per genome comes from a quiet few number of genomes compared to the number of characterized genomes (1.2 × 106)29 it could give an approximate estimation because the studied genomes represent a wide range of genome size. They include the smallest detected genome of Buchnera sp. (0.449 Mb), the largest detected genome of P. aethiopicus (130000 Mb), and other small and average size genomes (Table 2). Therefore, it could represent the average evolution time based on mutation rate without recombination, TEs, and polyploidy.

Origin genome Et
Buchnerasp 4.65 × 104
E. coli 1.1 × 105
 S. cerevisiae 5.8 × 106
C. elegans 4.4 × 106
C. reinhardi 1.45 × 105
D. melanogaster 1.13 × 106
A. thaliana 3 × 108
M. musculus 9.3 × 107
H. sapiens 2.4 × 1013
P. aethiopicus -
Total 2.4 × 1013
NA 5.3 × 103
Average of Et 2.7 × 1012
Average of NA 5.9 × 102
Et for characterized species 3.2 × 1018
NA for characterized species 7.2 × 108
Et for predicted species 2.3 × 1019
NA for predicted species 5.2 × 109

Table 3: Cumulative Et and eEt of origin genomes used in this study. Value opposite to a genome indicates its Et to the following genome in the Table. For calculation details see Supplementary materials S1.

Mutation rate, genome size, and evolution time

Using genome size (Gm), mutation rate per year (μy), and estimated evolution time (Et) of the 9 genomes (Table 2), a relationship was drawn to investigate how these three genomic factors are interrelated. Mutation rate per generation (bgg) of microorganisms is lower than that of higher organisms [18]. On the other hand, mutation rate per year (μy) is higher in microorganisms because of the high number of generation per year (Table 2). Data obtained showed that Et was found to be positively correlated with genome size, whereas μy was found to be negatively correlated with Gm (Figure 1). This introduces a very interesting conclusion that larger genomes would take longer time to evolve to higher size genomes because of their low mutation rate per year.

Evolutionary-Biology-Relationship-between-log10-genome-size

Figure 1: Relationship between log10 genome size (Gb), mutation rate per year (µy), and evolution time (Et).

Discussion

The WGS approach gives more accurate estimates of spontaneous mutations but generally it showed lower estimates of mutation rate (Table 1). This could be due to the correction of mutations by repair systems during high number of generations or successive mutations in the same site [10,29]. The high number of generation before calculation of mutation rate in the WGS approach gives the repair system to correct mutations so that they are not detectable. Also, in some origin genomes of this study the deletion mutation rate was higher than the insertion mutation rate. For example, in C. reinhardtii, spontaneous mutation rate was estimated using WGS after mutation accumulation experiment for 350 generations. Only 7% of detected mutations were insertions, whereas 29% were deletions [21]. These observations suggest that the estimated impact of mutations on genome evolution might be slower than expected. This is supported by the long estimations of Et in Table 2.

Based on the principle of evolution from common ancestor, all living organisms should have been evolved from one common ancestor genome in a number of evolution steps equal to the number of living species. Currently, there are 1.2 × 106 characterized and 8.7 × 106 predicted species [30]. Therefore, the smallest genome had to take 1.2 million evolution leaps to form the largest known genome among the characterized species or 8.7 million evolution leaps to develop the expected number of genomes. Moreover, each evolution leap includes unlimited processes of genome evolution mechanisms (mutations, transposition, recombination) to make up the new genome. When the average Et and number of characterized or predicted genomes are put together in this context some estimations can be laid down. The average Et of genome is estimated as 2.7 × 1012 years per genome (Table 3). Therefore, the cumulative Et of characterized species would be 3.2 × 1018 years (7.2 × 108 NA). Similarly, the cumulative Et of predicted species would be 2.3 × 1019 years (5.2 × 109 NA) (Table 3). These estimates give indication that it is impractical for the characterized or predicted number of genomes to have been evolved from common ancestral genome through mutations during the estimated age of earth [27].

In addition, the devolution is a continuous process working against the evolution mechanisms to repair and tune the genome and keep it functional. Recombination is corrected by the repair systems and it is involved in the efficient elimination of transposons after their integration in the genomes. Also, Long Terminal Repeats retrotransposons (LTRRTs), one major type of TEs, can be eliminated from the genome via different mechanisms including deletions and recombinations [7]. It was suggested that genome size is maintained by retrotranspositon (addition of DNA) and elimination of TE sequences through deletions and recombination [7]. In addition, after polyploidization, genome rearrangement and gene silencing can lead to diploidization which can remove the polyploid feature of the genome. This phenomenon was found in maize, sorghum, polyploid species of sugarcane, and Brassica sp. [13]. This gives evidence that, the impact of genome evolution mechanisms is counteracted by devolution processes which slow down genome evolution process than have been estimated in this study.

This study represents the first report about the quantitative impact of mutation rate on genome size evolution. In this study investigated the impact of mutations only on genome size evolution time while other genome evolution mechanisms (recombination and transposition) were excluded because their independent impact on genome size has not been determined quantitatively. It shows the need for more extensive studies to estimate the impact of recombination and transposition. Results also show that the estimated genome evolution time can be used in establishing genome evolution timeline based on changes in genome size evolution which provide another novel quantitative tool for evolution of living species. This can be used in parallel or alternative to the fossil evolution timeline, the principle of Darwinian evolution. Genome evolution timeline is expected to be more accurate and reliable than fossil evolution timeline because the first is based on changes in genome size, common to all living species, not on gradual phenotypic and anatomical similarities.

Conflict of Interest

Authors have nothing to disclose.

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