Genes and Environment, Vol. 36, No. 3 pp. 99–102 (2014)

Review

Homo sapiens under Neutral Evolution
Naruya Saitou1
Division of Population Genetics, National Institute of Genetics, Mishima, Japan
Received March 3, 2014; Revised April 26, 2014; Accepted April 28, 2014
J-STAGE Advance published date: May 3, 2014

most important factor in organismal evolution.

People often would like to think themselves as special
existence. In studies on organismal evolution, unexpectedly many researchers believe in contribution of positive
selection for evolution of characters which made us
human. However, most of evolution at genomic level isneutral process, and this is also true for evolution at
protein level. There is no exception in evolution toward
human lineage. I would like to show various examples on
this point, including studies of my group, and would like toconˆrm natural phenomenon that most of evolution which
produced Homo sapiens was neutral. It should also be
noted that majority of this paper is from ``Introduction to
Evolutionary Genomics'' written by Saitou (Saitou N.
Berlin: Springer; 2014).

Our World is Finite
Randomness also comes in when abiotic phenomena
are involved in organismal evolution. Earthquakes, volcanic eruptions, continental drifts, meteorite hits, andmany other geological and astronomical events are notthe outcome of biotic evolution, and they can be considered to be stochastic from organismal point of view.
Before proposal of the neutral theory of evolution by
Kimura (3), randomness was not considered as the basic
process of evolution. Systematic pressure, particularly
natural selection, was believed to play the major role inevolution. This view is applicable if the population size,or the number of individuals in one population, is eŠectively inˆnite. However, the earth is ˆnite, and the number of individuals is always ˆnite. Even this whole
universe is ˆnite. This ˆniteness is the basis of therandom nature of organismal evolution.

Key words: evolutionary genomics, natural selection,
human evolution

Neutral Evolution as Default Process of the
Genome Changes

Basic Concept of Natural Selection

It is now established that the majority of mutations
ˆxed during evolution are selectively neutral, as amply
demonstrated by Kimura (1) and by Nei (2). Reports ofmany genome sequencing projects routinely mention
neutral evolution in the 21st Century. I thus discuss neutral evolution as one of the basic processes of genome
evolution in this paper.
Neutral evolution is characterized by the egalitarian
nature of the propagation of selectively neutral
mutants. Mutation is the ultimate source of diversity oforganisms. If a mutation occurring in some gene modiˆes gene function, there is a possibility of heterogeneity
in terms of number of oŠsprings. This is the start ofnatural selection. However, some mutations may notchange gene function, and although they are somewhat
diŠerent from parental type DNA sequences, mutants
and parental or wild types are equal in terms of oŠspring propagation. We meet the egalitarian characteristic of the selectively neutral mutants. If all members of
evolutionary units, such as DNA molecules, cells, individuals, or populations, are all equivallent, the frequency change of these types are dominated by random
events. It is therefore logical that randomness is the The Japanese Environmental Mutagen Society

The fundamental source of evolution is mutation, or
any change of genome sequences. Therefore, natural
selection is tightly connected with the eŠect of mutations. If mutations are highly deleterious, they will soon
disappear though natural selection. Before Darwin (4)proposed the possibility of natural selection as a creative
power of evolution, natural selection in modern term
has been considered as the mechanism to keep statusquo, as initially created by the divine power. Elimination of deleterious mutations is now called `negative'
selection after Kimura (1). When the conservative nature of this process is stressed, it is called `purifying'
selection (5). To keep the current genetic entity
thorough elimination of deleterious mutations is thecore of the ``struggle for existence''.
Most of mutations become extinct simply by chance,and only a small fraction exists for a long evolutionary
1Correspondence to: Naruya Saitou, Division of Population Genetics,
National Institute of Genetics, 1111 Yata, Mishima 411-8540, Japan.
Tel: ＋81-55-981-6790, Fax: ＋81-55-981-6789, E-mail: saitounr＠
nig.ac.jp
doi: org/10.3123/jemsge.2014.010

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Naruya Saitou

Positive Selection for Ape and Human Genes

time. If we focus on these mutations that contribute toevolution for a certain period, say 1000 generations, themajority is selectively neutral, and only a small fraction
is kept through natural selection that favors advantageous mutations. Charles Darwin, together with
Alfred Russel Wallace, proposed this type of natural
selection as the mechanism of evolution in 1858. This
process is therefore sometimes called `Darwinian' selection, but nowadays `positive' selection, after Kimura(1), is commonly used. Negative and positive selection
sandwich the selective neutrality, the dominant situationin evolution.
Natural selection is tightly connected with two concepts: adaptation and ˆtness. Although `adaptation' iswidely used in many books on evolution, it is often not
quantitatively deˆned, and we should be careful for using this word in the context of natural selection unlessclearly deˆned. This word is also used to describe various characters of many organisms without testingwhether those characters were products of positive
selection. For example, `adaptive radiation' has often
been used on the evolution of many mammalian lineages as if adaptation caused by positive selection is themain factor for radiation. Recent studies, however, suggest that the geographical isolation caused by the continental drift seems to be the main cause of mammalianradiation. Any evolutionary biologist should have a
discreet attitude on the usage of `adaptation'.
In contrast, `ˆtness' is quantitatively deˆned in population genetics theory. There are two kinds of ˆtness;absolute and relative. Because the basis of evolution isthe change of genetic constituents of organisms, natural
selection should be discussed in terms of diŠerential
rates of reproduction among genotypes. The absoluteˆtness is the mean number of oŠsprings for one particular genotype. If this is larger than 1, the genotype is
expected to increase its oŠspring if the eŠect of random
genetic drift is negligible. Consideration of the absoluteˆtness is important, for we can directly discuss the temporal change of population size. It should be noted thatthe absolute ˆtness may change without mutations, if
the environmental condition changes.
We are often interested in the relative success of one
genotype to other ones, and consider the relative ˆtness.
The relative ˆtness of one particular genotype is usually
set to be 1, and that of other genotypes are expressedusing selection coe‹cients. Genotypes are identical withalleles in haploid organisms, and the relative ˆtness forallele i may be written as 1＋si, where si is selectioncoe‹cient for allele i. Let us assume that the relative
ˆtness of allele 0 is 1 (s0＝0). If si (iÀ0) is positive, allele
i is advantageous compared to allele 0 and is positively
selected, while allele i is deleterious compared to allele 0
and is negatively selected when si is negative. Allele i isselectively neutral with allele 0 when si＝0.

We now move to discuss positive selection. Because
the author is familiar with studies on primates, lest usˆrst consider positive selection in primates. Hughes andNei (6,7) showed that both MHC class I and class II
genes experienced positive selection, probably of theoverdominant type, through the comparison of synonymous and non-synonymous nucleotide substitutions(Dn/Ds test). This test is quite powerful to detect positive selection based on the neutral theory, and many studies were conducted to detect such selection. However,
one drawback of this test is that it can detect only alimited type of genes under positive selection, and toobtain a statistically signiˆcant result, we need to have
many substitutions. Therefore, a protein gene musthave many variable amino acids, a pre-condition that
may be satisˆed in protein-coding genes that are involved in the immune system, such as MHC. If a singleamino acid change was responsible in enhancing ˆtness,
however, it would be di‹cult to detect it though theDn/Ds test.
The majority of protein-coding genes have lower nonsynonymous substitutions than synonymous ones, andonly a small proportion is under positive selection.
Although most of the genes were found to have experienced positive selection thorough the Dn/Ds test,
the FOXP2 gene studied by Enard et al. (8) and Zhang
et al. (9) did not show signiˆcantly higher Dn than Ds.
The FOXP2 gene was initially found in mouse (10),and its highly homologous human ortholog was shown
to be responsible for hereditary orofacial dyspraxia associated with dysphasia (11). Interestingly, two nonsynonymous nucleotide substitutions at codon 304(ACC:Thr⇒AAC:Asn) and at codon 326 (AAT:Asn⇒
AGT:Ser) occurred after the human and chimpanzee
divergence, and the DNA polymorphism study ofmodern human populations suggested that the FOXP2
gene region experienced a selective sweep after mutations occurred within modern humans (8,9). However,
one of the two amino acid substitutions occurred in thehuman lineage after the divergence of the human-chimpanzee common ancestor also occurred in the carnivores(9). It is therefore not clear if these amino acid changes
were truly responsible for the emergence of language.
There was a report that FOXP2 of Neandelthals also
had these two amino acid substitutions (12). If this ˆnding is true, two nonsynonymous substitutions occurredin the common ancestor of modern humans and Neandelthals. Coop et al. (13) suggested two alternative
scenarios for this; low rates of gene ‰ow between
modern humans and Neanderthals or contamination ofmodern human DNA in the putative Neanderthal genome. Mouse FOXP2 gene knockin experiment by Fujita et al. (14) and Enard et al. (15) both showed somephenotypic diŠerences in vocalization. Konopka et al.
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Homo sapiens under Neutral Evolution

Detection of Positive
Genome-wide Searches(16) reported that the FoxP2 gene is responsible for thehuman-speciˆc transcriptional regulation of the central
nervous system.
Pollard et al. (17,18) found a series of short DNA sequences which are highly conserved in vertebrates but
show accelerated evolution only in human, and named
them HARs (human accelerated regions). Prabhakar etal. (19) and Bird et al. (20) also conducted similar
genome-wide studies. Prabhakar et al. (21) found one
such sequence from the human genome, HACNS1
which includes 119-bp HAR2, and showed it to act as alimb bud enhancer with enhanced limb enhancer activity
speciˆcally in human. This change was caused by 13
human-speciˆc substitutions within that region, andthey interpreted that accumulation of these positively
selected substitutions created multiple novel transcription factor binding sites (gain-of-function) and that thedeposition of those facilitated the human-speciˆc enhanced activity (21).
However, a GC-biased gene conversion may be an alternative explanation for ˆxation of such mutations
causing loss-of-function in a repressor element within
HACNS1 (22–24). GC-biased gene conversion is a consequence of DNA double strand break repair between
homologous chromosomal regions, and the alleles fromone chromosome are converted to the other with a biasof A or T to G or C (25). Neutral or even deleterious alleles could be ˆxed by GC-biased gene conversions (26).
It is possible that the 13 human-speciˆc substitutions
were caused by a GC-biased gene conversion and resulted in a disruption of repressor function of the 81 bp
region (loss-of-function), which may eventually enhance
the activity of human HACNS1.
To evaluate the function of HACNS1, Sumiyama andSaitou (27) performed transgenic mouse assay by using
the HACNS1 construct lacking the 13 human-speciˆcsubstitutions. The deleted construct showed similar enhancer activity to the intact human HACNS1. This
result suggests that the function of HACNS1 is not an
activating enhancer, but rather a disrupted repressor. If
so, loss-of-function in the HACNS1, possibly via a GCbiased gene conversion, not via positive selection,
played an important role in human-speciˆc evolution.
Kryukov et al. (28) reported that the selective pressure
aŠecting the evolution of regulatory elements in thehominid lineage was signiˆcantly relaxed compared withthat of the rodent lineage. Keightley et al. (29) suggested
that regulatory elements in hominids may be diverging
at a neutral evolutionary rate. All these studies discussed in this section revealed the di‹culty in detecting
evidence of positive selection in one lineage. We therefore should be careful for any study which jumped to aconclusion of accelerated evolution without carefully
examining an alternative neutral evolution scenario.

Selection

through

Let us now discuss on positive selection on modern
humans. Adaptation to a high altitude environment haslong been an interesting subject in human genetics. Recently, three independent genome-wide studies (30–32)
found that the EPAS1 gene showed the highest diŠerentiation between Han Chinese and Tibetans who are believed to adapted to high altitude. This gene codes atranscription factor HIF–2a involved in the induction ofgenes regulated by oxygen. The EGLN1 gene, which
encodes HIF-prolyl hydroxylase 2, was the second-bestdiŠerentiated gene. EGLN1 catalyzes the post-translational formation of 4-hydroxyproline in HIF-a proteins.
Moreno-Estrada et al. (33) compared ¿11,000 human genes with their orthologs in chimpanzee, mouse,rat, and dog, and found 11 genes as showing the signatures of positive selection on the human lineage througha branch-site likelihood method (34). These genes werethen analyzed for signatures of recent positive selection
using SNP data in modern humans. One SNP every
5–10 kb inside each candidate gene and up to around 30
kb in both upstream and downstream ‰anking regions,plus additional SNPs around 200 kb in both ‰anking
regions were selected, and a total of 223 SNPs weretyped for 39 worldwide populations from the HGDPCEPH diversity panel (35). They also analyzed 4,814
SNP data distributed along 2 Mb centered on each genefrom the HGDP-CEPH panel. Through examination ofallele frequency spectrum, population diŠerentiation,and the maintenance of long unbroken haplotypes, theyfound signals of recent adaptive phenomena in only one
gene region. The signal of recent positive selection camefrom a neighboring gene CD5, which codes a transmembrane receptor expressed in the T-cell surface (33). This
careful study suggests that most of positively selected
genes in modern humans are involved in the immune
system. It is not surprising, for our ancestors have
suŠered many sorts of infectious diseases, and the human immune system-related genes confronted the battle
against bacteria, virus, or parasitic eukaryotes. When
we discuss positive selection on modern humans, weshould consider natural selection on the interaction withother organisms, before attempting to apply other typesof natural selection such as sexual selection.

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