Anne-Lise Nilsen and Jenny Gardner

Honors 369 B
Research Paper
Speciation of Humans and Chimpanzees: The Debates
INTRODUCTION
It has been established that humans and chimpanzees are separate species but
share the most recent common ancestor of the great ape monophyletic group. But the
type of speciation, time of speciation and some specific genes contributing to the
speciation are under debate in the field.
There are two dominant hypotheses about the type of speciation that occurred
between chimpanzees and humans: complex and simple speciation. The complex
speciation hypothesis was developed to explain the differences in divergence time
found between autosomal chromosomes and the X chromosome. It states that human
and chimpanzee lineages diverged, then later exchanged genes and then finally
separated permanently [7,8]. Simple speciation on the other hand states that humans
and chimpanzees diverged only once but at a more recent time [10]. The cause to the
debate between these two hypotheses is rooted in the X-chromosome.
The X-chromosome is also the cause of the large range of suggested times of
speciation. Based on comparisons of the chimpanzee and human genomes there is a
wide range of time that speciation could have occurred based on what parts of the
genome one looks at [2,3]. Most experts agree that speciation occurred about 4-6
million years ago [2,3,4,6]. Certain studies have now put that estimate closer to the 4
million mark but there is evidence that speciation began occurring much earlier than that
[3,7]. The timing of speciation debate is linked to the debate over type of speciation; the
central question of each being whether speciation was occurring during the entire period
or if it occurred at separate points when the diverging species were separated then
converged. Even though there is still debate about the exact timing of speciation one
thing that experts agree on is the fact that no matter which end of the time range
speciation occurred on, it was still a very recent speciation in terms of evolutionary time
scale.
The final controversial matter that this paper will focus on is the search for the
genes that make us human. While humans have obvious phenotypic differences from
chimpanzees, their genomes are actually shockingly similar [6]. A search for the specific
genes that make us human has not turned up many promising results during the many
decades it has been going on. Now, geneticists are turning instead to a theory that
changes in regulation of gene products and rearrangements of chromosomal segments
are what make us human rather than specific novel genes in our chromosomes [4,5,6].
METHODS
Our first step in this process was researching the broad topic of speciation in
evolution. There was a wealth of information on this topic so we decided to narrow it
down and just investigate the speciation of humans and chimpanzees. Biologist have
been investigating the origins of humans and which species we are the most related to
for many years but there were many limitations in the field. One of the largest factors
that have greatly increased our knowledge in this field is due to rapid boom in the
amount and quality of the technology to analyze the genomes. This improvement in
technology has led to a new wealth of information but at the same time many debates
have arose. Although we have found out many crucial pieces of evidence leading to the
answers about the speciation of humans, there are still many controversial areas and
the results are certainly not black and white. We decided to focus this paper on three
prominent debates currently found in the field, including the evidence for both sides.
Most of these debates are in a standstill because more studies need to be done to
confirm or deny the given hypotheses and the current technology does not answer all
the questions present. We are also not experts in the field and found it difficult to
choose a side without fully understanding the all the methods and statistics behind the
different opposing results.
FIGURES
FIGURE 1
Fig 1 Three basic theories of human-chimpanzee speciation, showing simple and
complex speciation along with differences in timing for all. State HC1 shows the
youngest timing estimate [3]. State HC2 shows the oldest timing estimate [7]. State HG
shows one possible example of complex speciation with times [7]. Figure modified from
Hobolth et al. [3].
FIGURE 2

Fig 2- Basic phylogenetic trees with approximate speciation times calculated from
comparison of human, chimpanzee, gorilla, and orangutan genome using a speciation
time of 16.0 MYA for orangutans to calibrate the molecular clock used to obtain
speciation times [2]. The tree titled Autosomal was constructed from comparisons of
only autosomal chromosomes while the tree titled X-Chromosome was constructed from
comparisons of only the X chromosome. Figure adapted from Ebersberger et al. [2].

DISSCUSSION
The debate between the type of speciation between chimps and humans is all
rooted on the discrepancies between the timing of autosomes and the X-chromosome.
Through their analysis of the genomes Patterson et al. found that there were conflicting
times of divergence between the autosome chromosomes and the X-chromosome.
Their explanation for these results is that humans and chimpanzees initially diverged
around 6.3 MYA and then exchanged genes and then finally splitting permanently about
1.2 MYA later [7]. On the other hand, Wakeley pointed out that Patterson et al, did not
statistically test their null model and do not consider alternative explanation other than
their complex speciation hypothesis. A reply from Patterson et al. was included in the
same journal, which they defended their initial point, restating their main pieces of
evidence. Presgraves et al. also shared Wakeleys opinion and had doubts about the
complex speciation and proposed that it was simple speciation at a slightly later date
that led to the divergence between chimpanzees and humans. He explained the
differences in the divergence time between the autosome and X-chromosome to be due
to a difference in population size, and a sperm competition hypothesis which led to a
difference in [10]. The mating systems of chimpanzees lead to a more intense effect
of sperm competition which has an effect on the speed of evolution in the genes [9].
One of the problems we had with this debate was that there were relatively few papers
published that addressed these claims. Patterson et al. published their first paper in
2006, which was quite controversial and led to a debate two years later in the same
journal. A year later another author published a hypothesis with some more research,
going against Patterson et al.s original paper trying to disprove the complex species
hypothesis. Patterson et al. was cited a few times in other papers we found but none of
the authors citing it took a stance, rather just acknowledged the hypothesis. Because
this debate is so recent, we believe it contributes to the lack of new data on these
hypotheses that could lead to more conclusive results. Therefore we cannot come to a
decisive conclusion about the type of speciation that had occurred and will just have to
look forward to more research to come because both arguments have valid points that
are worth investigating.
The timing debate originates from multiple points. First off, there is the matter of
the X-chromosome diverging later than the rest of the genome. Secondly, there is the
matter of methods used to calculate the speciation times. As seen in Figure 2, the
speciation times using the exactly same methods [2] can differ greatly when based
either on the autosomes or the X-chromosome. While most researchers recognize the
difficulty presented by the different times given by the autosomes and X-chromosome,
there is still a wide range of times given for the actual speciation of humans and
chimpanzees. The more recent estimates put final speciation around 4 million years ago
(MYA) [3], while other studies have found an earlier start of speciation starting as far
back as 7 MYA [4]. Most commonly seen is a range of 4-6 MYA as the speciation time,
the range accounting both for uncertainty as well as the difference between autosomal
and X-chromosome speciation [2,3,5,6].
The second point that could be a root cause of the differences found in times of
speciation is the methods used to calculate these times. Several papers I read used the
method of comparing the entire genome of humans, chimpanzees, gorillas, and
orangutans and by using a molecular clock to analyze the time it would take for
differences within the genomes to accrue [2,3,5,11]. The major problem with this is that
the molecular clock requires calibration based off the speciation time of an outgroup. All
the studies, while using the same method, used different calibration times without
explaining their reasoning for using the date. Each paper used orangutan speciation
time to calibrate, but while some used 16 MYA [2], others used 18 MYA [3], while others
proposed a range of 12-16 MYA [11] or 14-16 MYA [5]. The differences in these
calibration times could maybe account for the differences in found times of speciation.
While there is no heated debate over the specific speciation time there certainly is a
lack of consensus, which seems to arise from the fact that different studies are using
different calibration times without taking into account other recent studies that have
used different calibration times.
The last major controversy surrounding the study of human-chimpanzee
speciation is the search for the specific genes that make us human. For most of human
history, we have believed that we are perfect organisms, be it under the theory of
special creation, that God made us in his own image, or under the theory of evolution,
that throughout history organisms have been evolving to the point of perfection that is
human beings. However, Charles Darwin came along to throw a monkey wrench in the
works. Ever since, the thought that we evolved from monkeys has led us on a frantic
search to find out what makes us so different from them. Much of the search has
resulted in the knowledge that humans and chimpanzees arent all that different, being
98.5% similar in genomes, and 99% similar in coding regions alone [6]. This knowledge
has now led the search for the specific genes that make us human.
Thus far, the search hasnt yielded any home-runs. There havent been any
genes that jump out and say This is why humans look different from chimps. While a
few select regions of the genome have been identified as different, there is still more
research that need to be done to identify the specific phenotypic expressions of these
regions [6]. The prevailing explanation now for the differences between humans and
other apes is not the existence of novel genes but rather differences in gene expression
and regulation among the different species [4,5,6]. This theory is now widely supported
and researched but is highly involved and complex to look at in the genome [5].
Differences in regulation and expression can take place at many different levels of
expression and it can be very difficult to track these differences [5]. In addition to
differences in gene expression, there are small differences in the chromosomes
themselves that while not called novel genes can also be considered differences that
could separate humans from chimpanzees [4].
Another important note is the common misconception that these changes are
only happening on the human side of lineage split. It is important to remember that while
humans have been evolving one way, chimpanzees have also been evolving away from
our common ancestor. A recent study has found that more genes have undergone
positive selection in chimpanzees than in humans [1]. While this doesnt necessarily get
us any closer to identifying the specific reasons were human, it is valuable to note that
both humans and chimpanzees have been evolving and in different ways ever since the
split.
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