Catherine Dong
Professor Bert Ely
Biology 303H
1 November 2012
Evolutionary Factors That Affect Amino Acid Substitution Rate
Molecular evolution has long been an accepted phenomenon, but what components of a
species specifically affect its rate of evolution? The primary focus for this paper is to discuss the
forces that affect the amino acid substitution rate of various species, notably the Tunicate Ciona
intestinalis and its close slow-evolving vertebrate sister group. Factors discussed that greatly
affect the amino acid substitution rate are mutation rate and natural selection. “Species body
size, population dynamics, lifestyle and location” (Bromham et al. 2008) influence mutation
rates. Natural selection then comes into play as genetic drift affects the fixation of the new trait.
Tunicates are largely used as subjects in research for protein variation because they evolve faster
than vertebrates due to shorter generation times, and are genetically similar (Bromham et al.
2008; Tsagkogeorga et al. 2012). Thus, tunicates can be used as rough models for the
implications of human evolution. In order to further one’s understanding of this theory, basic
relative genetic terms will be defined and applied.
Amino acids are the building blocks of proteins, macromolecules that perform a variety
of vital functions; for the purpose of this discussion, the function of proteins in DNA replication
will be largely examined. Occurring both naturally and experimentally, amino acid substitution
involves the replacement of one or more amino acids in a protein with another. The substitution
can be functionally equivalent, diminish, enhance, or completely eliminate protein function
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(Dorland’s Medical Dictionary of Health Consumers, 2007). Multiple evolutionary forces cause
these substitutions; Tsagkogeorga et al. (2012) discussed such factors, notably mutation and
prevalent adaptive evolution. They concluded that the increased amino acid substitution rate was
due to stronger adaptive evolution and a two to six times higher mutation rate per year than that
of vertebrates, depending on the species being compared. Adaptive evolution is more simply
defined as positive selection, a process in which an advantageous allele at one end of an extreme
increases in frequency due to its increased benefits to the survival of the species. (Dorland’s
Medical Dictionary for Health Consumers). In other words, if the mutation of the amino acid
substituted was beneficial for tunicate survival, selection increased the frequency of the allele
and that allele would become fixed in the population.
One of the evolutionary possibilities that Tsagkogeorga et al. (2012) discussed was that
the amino acid sequence evolution could have occurred due to less efficient natural selection,
which would be expected in smaller population sizes. The researchers considered negative
selection, or purifying selection, in which deleterious mutations are purged over time. One
hypothesis stated that the observed amino acid substitution rate was increased because the
species’ ability to purge deleterious mutations was weak. However, Tsagkogeorga et al. (2012
concluded that the increased amino acid substitution rate was “not due to a relaxing of purifying
selection, but rather reflects a stronger effect of adaptive evolution…” (Tsagkogeorga et al.
2012).
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This argument involves genetic drift, or fluctuations in the frequency of an allele due to random
chance in small populations, which would lead to an increase in the likelihood of fixation of the
new allele. Figure 1 shows a graphical representation of the πN/πS ratio, which, when below
0.05, indicates “a strong influence of purifying selection”.
Figure 1: Distribution of pS and pN/pS across
.
.
genes in three animal species In D simulans
.
,
the C. intestinalis genes analyzed in this study
were used here.
and H sapiens the subsets of orthologs to
When compared to H. sapiens, the “high πS of C. intestinalis and low average πN/πS indicates a
large population-sized species”. In other words, the population size of C. intestinalis is larger
than that of both D. simulans and H. sapiens. For these purposes, population size is described as
how widely spread the gene pool is for a species, as well as the overall quantity of the
population. The population size of C. intestinalis is large because it is a “widespread and
invasive broadcast spawner [external fertilization], occurring in large numbers of colonies in all
of the temperate areas along the Atlantic and Pacific coasts, and has a generation time of 1 year”
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(Tsagkogeorga et al. 2012). However, H. sapiens, in terms of behavioral differences, undergo
mate selection and a much lower frequency of migration, in regards to fertilization. Therefore,
the data indicates that the C. intestinalis has a lower rate of genetic drift and fixation from
relaxed negative selection due to its greater population size in comparison to humans. Thus, the
researchers concluded that the lower negative selection indicated higher positive selection, or
adaptive evolution.
The other factor that increased the amino acid substitution rate of tunicates was the
mutation rate. Specifically, mutations occur during DNA replication due to the 1 in 105 chance
that there will be an error in the copying of the base pairs. There is, however, a damage repair
process that exists and reduces the mutation rate to 1 in 109 (Cooper 2000). The figures below
are estimates for the error rates associated with chromosomal replication and base substitutions.
The far left indicates the total error rate. The center figure shows the baseline misincorporation
rate without proofreading corrections, and the final figure displays the error rates after
proofreading (Lynch 2008). The units are the error rate per site per replication. The three figures
allow one to visualize the major impact that proofreading has on DNA replication.
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[Figure 2; Lynch 2008]
Therefore, the generation time of C. intestinalis has a large influence on its mutation rate,
because “species with shorter generation times have faster rates of molecular evolution,
presumably because they copy their germline DNA more often per year” (Bromham L. 2009). In
other words, more copies of germline DNA results in higher mutation rates because the more
DNA that is replicated, the higher the chance that the processes will make a mistake (Lynch
2009). This factor explains how the tunicate mutation rate can be 2-6 times higher than that of
vertebrates. The comparative range is so large because, even among vertebrates, generation
times fluctuate greatly, i.e. human vs. mouse.
Why were the tunicates chosen as a comparative species in the first place? The factors of
evolution discussed (adaptive selection, genetic drift, population size, and mutation rate) all
affected the amino acid substitution rate of the tunicates with varying intensities. In order to
unscramble these factors, a within-species collection of data on a genome-wide scale was
needed. Most of the published genomic data sets consisted of slow-evolving vertebrates and one
genus of insect (i.e. Drosophila, Bierne and Eyre-Walker 2004; Tsagkogeorga et al. 2012).
Therefore, researchers determined that data from a fast-evolving animal was essential in order to
further advance the current knowledge of evolutionary factors. Tunicates have been identified as
the “closest living relatives of vertebrates and with their higher rates of genomic evolution, and
offered promising comparative perspective with respect to [vertebrates]” (Tsagkogeorga et al.
2012). Therefore, they became promising subjects for research.
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The need for understanding mutations and their effects on amino acid substitution rates
arise from their possible benefits for the human race. From A.R. Boyko’s 2008 paper, becoming
empirically informed about the mutation rate for humans and its implications for evolution can
settle debates including those over the advantages of sexual reproduction and recombination, and
population genetic theories involving human complex disease. Interestingly, he found that
although a large number of harmful mutations enter into the human genome, the majority are
neutral (Boyko, et al. 2008). The same situation occurs in the tunicate, Ciona intestinalis, and
the effects of the mutations on evolution can be further understood by utilizing data from this
fast-evolving sister group of vertebrates.
In conclusion, molecular evolution studies have been conducted through various taxa, but
it is difficult to compare them across groups. There are many factors that affect the evolutionary
rate such as mutation and adaptive selection, as discussed previously. These factors contribute to
the amino acid substitution rate and the fixation of the new traits in such varying quantities that it
is currently difficult to make a conclusion about the details of the evolutionary rate of one
species based on data from another. In order to better define the inner workings of evolution for
slow-evolving animals, such as humans, the sequencing of entire genomes of faster-evolving
vertebrates than H. sapiens would be useful and be a more ideal comparison. This would also aid
in the research if the species had more similar behavioral patterns, rates of genetic drift, and
population dynamics as well.
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Literature Cited
Bierne N., Eyre-Walker A. 2004. The genomic rate of adaptive amino acid substitution in Drosophila.
Mol Biol Evol. 21:1350–1360. Web. 30 Oct. 2012.
http://mbe.oxfordjournals.org/content/21/7/1350.abstract
Boyko A.R., et al. 2008. Assessing the evolutionary impact of amino acid mutations in the human
genome. PLoS Genet. 4:e1000083. Web. 30 Oct. 2012.
<http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000083>
Bromham L. 2009. Why do species vary in their rate of molecular evolution? Biol Lett. 5:401–404.
Web. 30 Oct. 2012. <http://rsbl.royalsocietypublishing.org/content/5/3/401.abstract>
Cooper G.M. The Cell: A Molecular Approach. 2nd edition. Sunderland (MA): Sinauer Associates;
2000. DNA Replication. Web. 30 Oct. 2012. <http://www.ncbi.nlm.nih.gov/books/NBK9940/>
Dorland's Medical Dictionary for Health Consumers. Saunders, Elsevier, Inc. 2007. Web. 30 Oct.
2012. <http://www.nlm.nih.gov/pubs/factsheets/mesh.html>
Tsagkogeorga G., Cahais V., and Galtier N. 2012. The population genomics of a fast evolver: high
levels of diversity, functional constraint and molecular adaptation in the tunicate Ciona
intestinalis. Genome Biol Evol. 10:740-749. Web. 30 Oct. 2012.
Lynch M. 2008. The cellular, developmental and population- genetic determinants of mutation-rate
evolution. Genetics 180: 933–943. Web. 30 Oct. 2012.
<http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2567392/>