Jessica Kerpez
April 6, 2015
BIO-356 Sec.004
Mitochondrial DNA Analysis Lab Report
Abstract
In this experiment, mitochondrial DNA (mtDNA) was used in order to estimate times of
evolutionary divergence. Two primary models of human evolution termed the multiregional and
displacement models were tested for accuracy by calculating pairwise divergence sequence
times. According to the multiregional model, modern humans developed concurrently from
several archaic populations in various parts of the world. The displacement model states that
modern Homo sapiens arose from a single founding population that emerged from Africa and
successfully migrated to Europe and Asia. The multiregional model predicts a divergence time
for the most recent common ancestor of humans to have occurred 1.5-3 million years ago, while
the displacement model predicts a time frame of 200,000-500,000 years. The time of divergence
between two classmates was calculated to be 3.39*104 years by using D-loop analysis, whereas
the divergence time between humans and Neanderthals was calculated to be 1.97*105 years. The
smaller time of divergence between two humans provided support for the displacement model.
Also, the divergence time for the most recent common ancestor to all living modern humans was
calculated at 5.03*105 years using mtDNA analysis. This finding provided further support for the
displacement model, which predicts a divergence time for the most recent common ancestor of
humans to be around 200,000 – 500,000 years ago.
Introduction
There is significant support in scientific literature that supports the endosymbiotic theory
of mitochondrial evolution, which is believed to have occurred when a primitive host cell
successively engulfed two forms of bacteria to obtain mitochondria and chloroplast. This theory
states that mitochondria originally existed as free-living bacteria that were taken up by primitive
ancestors of eukaryotic cells. The mitochondrion were developed from proteobacteria, whereas
chloroplast was derived from cyanobactiera. The primitive host cell containing a nucleus
provided the mitochondrion with a source of energy-rich nutrients, while the mitochondrion
provided the cell with a way to extract energy using oxygen. This symbiotic relationship allowed
for the atmosphere to accumulate oxygen, allowing for survival. Support for the endosymbiotic
theory is observed through several genomic features shared by both mitochondria and bacteria.
For example, they both have a circular mitochondrial genome that first evolved to provide
protection against exonucleases, which function to digest the free ends of linear DNA molecules.
Mitochondria also reproduce and multiply by pinching in half, which is the same method of
reproduction performed by bacteria.
The mitochondrion and its genome are inherited in a maternal fashion, meaning females
in a family all share identical mitochondrial chromosomes while male children share a common
mitochondrial genome with their mother and female siblings. Male mitochondria typically does
not enter the egg at the moment of conception, and are lost by dilution if the egg cytoplasm is
partitioned during the mitosis process. Ubiquitin also eliminates any male mitochondria from
being present in the egg by tagging the mitochondrial surface for destruction. Mitochondrial
inheritance is easier to study because the parental chromosomes cannot recombine so no new
crossovers occur. New mutations may still arise within a lineage, but are typically easy to discern
since they are few in number. The mitochondrial genome is called haploid, as it only has a
contribution from the mother while the mtDNA types are termed as haplotypes.
The mitochondrial genome is located close to the respiratory machinery of the cell, a
source of potent mutagens called oxygen free radicals that allows mtDNA to experience a high
mutation rate. Oxygen free radicals can evoke DNA damage that leads to a faster degradation of
mtDNA function while mutations in ribosomal and transfer RNA can lead to problems with
protein translation that is encoded by the mitochondrial genome. The mitochondrial genome has
helped recognize mtDNA disorders as a frequent cause of genetic disease. For instance, data on a
single-point mutation in the mtDNA genome in the British population found that approximately
1 in 3,500 people either have an mtDNA disease or at risk of developing it (Taylor & Turnbull,
2005). Mutations in mitochondrial genes have been implicated in degenerative disease that
requires a large ATP production like Alzheimer’s disease, Pearson syndrome, and diabetes. If
mutations accumulate at a constant rate, then the number of mutations present within a genome
should be proportional to the length of time since two groups have diverged. The number of
mutations that occur over time is called the molecular clock, which is useful for analysis of
divergence rates between species. According to this model, the genetic differences between two
species is proportional to the time since these species last shared a common ancestor. Divergence
rates previously calculated can be used as a baseline for future sequence divergence calculations.
Throughout evolution, the human mitochondrial genome has been vastly reduced because
genes created for functions that could be provided by the host were lost over time. Also, the
genes needed for respiration were transferred to the nucleus. Over millions of years of evolution,
the reduction in the human mitochondrial genome that occurred resulted in the small
mitochondrial chromosome found in eukaryotes. In each mitochondria present within a living,
eukaryotic organism there are several copies of its own genome. Since there are several hundred
to several thousand mitochondria present within every cell, the mitochondrial (mt) genome in
highly amplified. Mitochondrial DNA (mtDNA) has provided genetics with a useful mechanism
for determining the source of DNA because each cell within an organism’s genome has
thousands of copies of a given mitochondrial gene per cell. The high copy number presents
makes it possible to obtain an mtDNA type from an equivalent single cell’s worth of mtDNA.
This makes mtDNA useful in genetic tests where tissue samples are degraded or there is a
limited amount of supply available. Furthermore, mtDNA is known for having acquired mutation
rates 10 times higher than that of nuclear genomic DNA. The high mutation rate and the
maternal inheritance pattern of mtDNA allow this method to track the ancestry of many species
back hundreds of generations.
The entire DNA sequence of the human mitochondrial genome contains 16,569
nucleotides and 37 genes, as determined by the Human Genome project. Thirteen of the genes
encode for proteins in oxidative phosphorylation, while the remaining genes consist of transfer
and ribosomal RNAs. Although genes take up the majority of the mitochondrial genome, there is
also a noncoding region which contains the D-loop. The D-loop is important because it marks the
early phase of replication, when the first newly-synthesized strand displaces one of the parental
stands thus forming a loop structure. This non-coding D-loop region acts as a promoter for both
the heavy and light strands of mtDNA and contains essential transcription and replication
elements while the hypervariable regions present serve as hot spots for mtDNA alterations and
resulting mutations (Crochet & Desmarais, 2000). Therefore, the D-loop is useful in studies
evaluating evolutionary relationships because the high mutation rate allows for variability to be
traced within species. The D-loop is relatively tolerant of a high mutation rate because the
binding sites for DNA and RNA polymerase are provided by short nucleotide sequences.
Neanderthals were first discovered in Neander Valley in Germy in 1856, and were
discovered to be an archaic member of the genus Homo who lived in Europe approximately
300,000 years ago. There has been a longstanding controversy regarding if Neanderthals are the
direct ancestors of modern humans. Even if Neanderthals and Homo sapiens were separate
species, scientists have also debated whether there was any gene exchange that affected the
genomes between the two populations. Two primary models that were tested in this laboratory
experiment through mtDNA testing are the multiregional and displacement model. According to
the multiregional model, modern humans developed concurrently from several archaic
populations in various parts of the world. In some versions of the model, Neanderthals were
considered to be ancestors of modern Europeans.
The displacement model, also known as the “Out of Africa” model, predicts that modern
Homo sapiens arose from a single founding population that emerged from Africa and migrated to
Europe and Asia. Divergence times for the most recent common ancestor (MRCA) of modern
humans that are based on the multiregional model are on the order of 1.5 – 3 million years,
whereas the displacement model predicts a divergence time of 200,000 – 500,000 years. If the
multiregional model is supported, then some human sequences should be more similar to
Neanderthal DNA than other humans. However, if the displacement model is supported by the
data then the divergence time between modern humans and Neanderthals should exceed that
observed between any two modern humans. The mtDNA sequence data in this experiment was
used in order to distinguish between the displacement and multiregional model.
The experiment performed recreated a study by Svante Pääbo in 1997, in which DNA
was extracted from the humerus of an original Neanderthal specimen, amplified by PCR, and
cloned the products in E. coli. The cloned fragments were then used to reconstruct a 379-bp
stretch of the mtDNA control region. In the experiment performed, genomic DNA was isolated
via DNA extraction and DNA amplification by PCR was performed. DNA amplification by use
of PCR was performed using specific mtDNA control region primers and the genomic DNA
previously isolated. Successful amplification were then tested by using agarose gel
electrophoresis analysis. The next section of this experiment involved estimating rates of
evolution with mtDNA analysis on the NCBI database, in order to infer other mitochondrial
sequences or “Haplotypes” that were identical or similar. The average proportional divergence
and number of substitutions per site for humans vs. Neanderthal’s, humans vs. chimps, and
humans vs. humans was evaluated. Control region mutations used a molecular clock by
implementing an estimated divergence rate of 5 million years ago for humans and chimpanzees
and 200,000 years for modern human divergence. These divergence rates allowed for the rate of
substitution to be calculated, which then could be used to estimate the divergence time for the
most recent common ancestor. The divergence times were then compared to the multiregional
and displacement models.
In order to search for nucleotide sequences in the NCBI database, the assigned D-loop
DNA sequence was copied into the “nucleotide blast” section of the BLAST database. This
allowed for the D-loop nucleotide sequence to be compared against other nucleotide sequences
in the database. A blastn search allowed for nucleotide sequences (nr) in the database that were
similar to the query sequence inputted to be analyzed, and hitting the BLAST button allowed the
search to be submitted. The “Graphic Summary” region on NCBI indicated the size of the region
and degree of homology shared between the query sequence and database entries. A table
containing a list of the top 100 DNA sequences similar to the query sequence were accessible on
the page, each with an Accession number and a corresponding Max score (S). The larger the
alignment score S, the more significant the match observed and conversely the closer the E value
is to 0, the more significant the match. An E score larger than 0.05 means the match is a result of
random chance, whereas an E score less than 0.01 meant the match was a result of homology.
The pairwise alignment between the query and database entry was observed by clicking on the
sequence description hypertext. In this experiment performed, the two highest matches were
analyzed in terms of the accession number numbers, E-scores, max scores, and lengths.
Materials and Methods
In the first section of this experiment, DNA extraction was performed. Two empty 1.5 ml
tubes were obtained and 10 ml of the saline solution (0.9% NaCl) was poured inside the mouth
and swished vigorously for 30 seconds. The saline solution was expelled back into the 50mL
tube, and the cells were swirled for mixing. About 1.5 ml (1500 µl) of the liquid was transferred
to a 1.5 ml tube using a transfer pipet. The sample tube was placed along the other student’s
samples in a balanced configuration in the microcentrifuge and spun for 5 minutes at maximum
speed. The supernatant was carefully removed, making sure not to disturb the cell pellet at the
bottom of the tube. The cells were resuspended in the remaining saline by pipetting and out of
the solution. Then, the resuspended cells were transferred to the 1.5 mL microcentrifuge tube
containing 100 µl of 10% Chelex solution. The solution was vortexed to ensure the cells were
completed suspended in the Chelex solution. The tube was then heated for 10 minutes with a
heat block set at 100°C by the cell instructor. After the heating process was performed, the tube
was shook and placed in a balanced configuration in a microcentrifuge and spun for one minute.
Using a micropipette, 50 µl of supernatant containing the DNA was transferred to the clean
labeled 1.5 ml tube and stored for future PCR amplification.
Once DNA extraction was completed, DNA amplification by PCR was performed. A
200µl tube containing the Read-to-Go PCR bead was obtained. A 200 µl micropipettor with a
fresh tip was used to add 22.5 µl of the primer/ddH2O mix to the PCR tube with the Ready-ToGo PCR Bead. A 20 µl micropipettor with fresh tip was used to transfer 2.5 µl of genomic DNA
to a reaction tube, and then tapped to mix. Using a microcentrifuge, the reagents were mixed
together. All samples were placed on ice until ready to amplify. The cycling program included
an initial denaturing stage at 94°C for 2 minutes, a denature stage 94°C for 30 minutes, an
annealing stage at 58°C for 30 seconds, and the extend phase at 72°C for 30 seconds. Then, the
denature phase was repeated 30 times so the final extension phase could occur at 72°C for 6
minutes and then held indefinitely at 4°C. Successful amplification was then tested by using
agarose gel electrophoresis analysis and observing the banding patterns present on the agarose
gel.
In next laboratory performed for this experiment, the data provided in the Excel file for
the pairwise divergences was analyzed by determining the average proportional nucleotide
sequence divergence in the mtDNA control region between the Neanderthal sequence and
modern humans. The average pairwise sequences between humans and chimpanzees was also
calculated in the experiment. DNA sequencing had been performed in order to determine the
precise order of nucleotides within the mitochondrial DNA molecule. In order to calculate the
average proportional divergence (pa) between humans versus Neanderthals, the average number
of the nucleotide sequence variation between these two species was solved for. Then, each
proportional divergence was converted into the number of substitutions per site using the
formula Kn (=–ln [1 – pd]). The same process of solving for average proportional divergence and
average number of substitutions per site was then repeated for humans versus Chimps. It was
noted which comparison, humans vs. Chimps or humans versus Neanderthals, resulted in greater
values and how this could be properly explained. Then, the average proportional nucleotide
sequence divergence between modern humans was calculated by taking the average of all
numbers above the line in the pairwise divergence table.
The average proportional divergence and the average number of substitutions per site for
a human vs. a human were calculated using the same formulas described previously for the
human vs. Chimp and human vs. Neanderthal calculations. The rate of nucleotide substitution
was calculated by dividing the average number of substitutions per site for the human-chimp
comparison (KHC) by the human-chimp divergence time (5,000,000 years). Once the rate of
substitution was calculated, the divergence time for the most recent common ancestor to all
living modern humans (TMRCA) was calculated by dividing the average number of substitutions
per site (KHH) by the rate of nucleotide substitution. The resulting estimate for the divergence
time of modern humans was then compared to the calculation made by population geneticists of
about 200,000 years. Next, the divergence time between Neanderthals and modern humans was
calculated by using the established date of modern human divergence of 200,000 years as a
reference. To perform this calculation, the average amount of substitutions per site (KHH) was
divided by 200,000 years. The divergence time in years was calculated by dividing KHN, the
average number of substitutions per site between modern humans and Neanderthals, by the rate
of substitution previously calculated. Using the same methodology and series of calculations, the
time since a lab partner and I last shared a common ancestor was then calculated.
In the next section of this experiment, nucleotide sequences were searched on the NCBI
database. By observing the assigned student number that appeared above the D-loop sequence,
the proper nucleotide sequence was copied and selected from a file on Blackboard. The retrieved
D-loop sequence was copied into the “nucleotide blast” section of the NCBI database found
under the “Basic BLAST” section in order to search for the D-loop nucleotide sequence against
all the other nucleotide sequences in the database. The default settings were altered so the
database was changed to Nucleotide collection (nr/nt), the organism selected was Homo sapiens,
and the sequence was optimized for somewhat similar sequences (blastn). The sequence was
pasted within the large yellow box under the “Enter Query Sequence” section and a blastn search
allowed for the identification of nucleotide sequences (nr) in the database similar to the pasted
sequence. The blue BLAST button as pressed to submit the search. The two sequences with the
greatest similar to the query sequence were identified as having the largest “Max score” (S)
value. The GenBank accession number of the two sequences with the largest alignment score (S)
were recorded. Then, the nucleotide positions associated with each region of similarity shared
between the query and database sequences for the two highest matches were recorded. The
number of nucleotide positions in the query sequence identical to the database entry for each of
the two matches was recorded so the % identity could be calculated (= 100* #identical/total #bp
in query) for each match. To identify which haplotype the mtDNA was most similar to, “source”
under the FEATURES header was observed.
Results
In this experiment, a nucleotide BLAST search was performed on the D-loop Sequence
listed as Section 4-9. As seen in Table I, the first and second highest matches resulting from the
BLAST search were analyzed in terms of the length of match, percent identity, e-score, and
accession number. The query sequence can be located under Blackboard under Section 4-9. In
Table II, pairwise comparisons on the humans vs. chimps, humans vs. Neanderthals, and humans
vs. humans were analyzed in terms of the average proportional divergence and the average
number of substitutions per site. The results indicated that humans and Neanderthals share a
more common ancestry when compared to humans and chimps, because they resulted in a lower
average substitution and divergence rate. Table III lists the results from the divergence time
sequence calculations solving for divergence rates between species. The time of human’s most
recent common ancestor was analyzed in terms of whether the value represented the
multiregional or displacement out of Africa model. Using the rate of nucleotide substitution
calculated, it was found that the time of humans most recent common ancestor occurred 5.03*105
years ago. This value supported to displacement model, which predicts human divergence
occurred ~200,000-500,000 years ago. The divergence time between Neanderthals and modern
humans was calculated to be 1.97*105 years, whereas the divergence time between humans was
calculated at 3.39*104 years.
Table I: Nucleotide BLAST D-loop Sequence
Length of
Percent
E-score
Accession
Match
Identity
1st Match
16570
96%
8*10173
JX120762.1
2nd Match
16569
96%
8*10173
JX120730.1
Number
Table I lists the two sequences bearing the largest similarity to the query sequence having
the largest “Max score.” The larger the max score (S) value, the closer the (E) score should be to
0. An E-score larger than 0.05 indicates the match is due to random chance, whereas E score
smaller than 0.01 represent the match is a result of common ancestry. The two highest matches
found from the query sequence with the highest percent identity of 96% had accession number
JX120762.1 and JX120730.1, respectively. The E-score for both the matches was the same, at a
value of 8*10173. This large E-score means that the match is most likely due to random chance.
The length of the matches was also recorded, with the first match having a length of 16570 and
the second match having a length of 16569.
Table II: Pairwise Comparison Results with Chimp & Neanderthal and Student Sequences
Species Compared
Average Proportional
Average # of Substitutions
Divergence
per Site
Human-Chimp
0.156
0.169
Human-Neanderthal
0.047
0.049
Human-Human
0.017
0.017
Table II lists the pairwise comparisons with humans vs. chimps, humans vs.
Neanderthals, and humans vs. humans. The average proportional divergence (pd) was calculated
for each pairwise comparison by taking the average of the relevant numbers in each column on
the Excel file. Each proportional divergence was calculated to the number of substitutions per
site by using the formula Kn (= –ln [1 – pd]). For instance, to get the number of substitutions per
site for humans vs. Neanderthals, the calculation performed was KHN (= –ln [1 – 0.047])= 0.049
average substitutions per site. It was found that the average proportional divergence was larger
for humans vs. chimps compared to humans vs. Neanderthals, yielding values of 0.156 and
0.047. Similarly, the amount of substitutions per site was larger for humans versus chimps at a
value of 0.169 whereas the average amount of substitutions per site for humans versus
Neanderthals was 0.049. These differences can be interpreted as meaning that there are more
differences between humans and chimps than humans and Neanderthals. Humans and
Neanderthals and more closely related based upon this data when compared to the human and
chimp relationship. The average proportional nucleotide sequence divergence between modern
humans was derived by taking the average of all pairwise sequence comparisons between
modern humans and converting the proportional difference to KHH with the Kn (= –ln [1 – pd])
formula. The average proportional divergence and average number of substitutions per site for
humans versus humans was .017.
Table III: Computation and Presentation of Divergence Time Sequences
Rate of Nucleotide Substitution
3.38*10-8 substitutions per site/per year
TMRCA
5.03*105 years
Supported Model
Displacement Model
Recalibrated Rate of Nucleotide
2.39*10-7 substitutions per site/year
Substitution
Divergence Time from Neanderthal
1.97*105 years
Divergence Time from Classmate
3.39*104 years
Table III lists the results from the divergence time sequence calculations that solved for
the rate of nucleotide substitution and the time of human’s most recent common ancestor. Using
a reference rate of 5 million years for the estimated divergence time between chimpanzees and
humans, the rate of nucleotide substitution was calculated by using the KHC value for the average
number of substitutions per site for the human-chimp comparison. As shown in Table II, the KHC
value was previously calculated to be 0.169. The formula for determining the rate of nucleotide
substitution was (0.169 substitutions per site/5,000,000 years) which resulted in a value of
3.38*10-8 substitutions per site/per year. Once the rate of substitution was calculated, the
divergence time for the most recent common ancestor to all living modern humans represented
by TMRCA was calculated by dividing the average number of substitutions per site, KHH, by the
rate of nucleotide substitution just calculated. The formula for this was (0.017 substitutions per
site/ 3.38*10-8 substitutions per site/per year) which resulted in a TMRCA value of 5.03*105 years.
The multiregional model estimates human divergence occurred ~1.5-3 million years ago, while
the displacement model predicts human divergence happened ~200,000-500,000 years ago.
Therefore, the calculated estimate of modern human divergence of 5.03*105 years is closer to the
displacement model’s estimates on human divergence.
Population geneticists have used mitochondrial and chromosomal DNA mutations in
order to calculate a divergence time of about 200,000 years for modern humans. The divergence
time between Neanderthals and modern humans was calculated using this value as a calibration
point. The calculation was (average KHH value, 0.017/ 200,000 years) which resulted in a value
of 2.39*10-7 substitutions per site/year. The divergence time in years for humans versus
Neanderthals was calculated by dividing KHN, the average number of substitutions per site
between modern humans and Neanderthals, by the rate of substitution 2.39*10-7 substitutions per
site/year. The formula (0.049 substitutions per site /2.39*10-7 substitution per site per year)
which resulted in a value of 1.97*105 years. This value represents the divergence time between
humans and Neanderthals, and can be indicative of how closely they are related to one another.
The same approach to determine the divergence time was then conducted with two classmates
from the Excel document, student’s number 9 and 10. Student number 9 had a divergence rate of
7.93*104 while student 10 had a divergence rate of 4.0*104. Using these values and the same
methodology for calculating the Neanderthal divergence rate, the divergence time for the
classmates was calculated at 3.39*104 years. As expected, the divergence time between two
humans is smaller than the divergence between a human and a Neanderthal, indicating a closer
common ancestry.
Discussion
From this series of labs, the concept of human evolution was investigated by analyzing
mtDNA in order to evaluate the displacement model in comparison to the multiregional model. I
learned that the displacement model predicts that modern Homo sapiens arose from a single
founding population that emerged from Africa, and then migrated to Europe and Asia. According
to this model, the divergence time for the most recent common ancestor of humans should have
occurred around 200,000-500,000 years ago. On the other hand, the multiregional model claims
that our ancestors evolved continually in separate groups, but interbreeding between the groups
created a single, continuous human species. This model predicts a divergence time for the most
recent common ancestors of humans that is significantly longer, at 1.5-3 million years ago.
In terms of human evolution, I also learned how useful mtDNA and the D-loop sequence are
for studying divergence times. Mitochondria have their own genome of about 16,500 bp that
exists outside the cell nucleus, each containing 13 coding genes, 22 tRNAs, and 2 rRNAs. The
mitochondrial DNA is particularly useful for constructing evolutionary analyzes because they are
present in large numbers in every cell and have a higher rate of substitutions than nuclear DNA.
This means that fewer samples are required, and differences between closely related individuals
are easier to track. Furthermore, since mtDNA is only inherited from the mother a direct genetic
line can be traced. They are also useful because the process of recombination does not occur as it
does in nuclear DNA, which makes a genetic history harder to trace and sections of DNA from
the mother and father are mixed. The D-loop in the mitochondrial genome proved particularly
useful in this experiment because of the high mutation rate it undergoes, making the differences
between this relatively short sequences clear between closely related sequences. However,
studies have implied potential error in studying the D-loop region, as it only constitutes 7% of
the mitochondrial genome and a high rate of parallel and back-state mutations make it difficult to
properly estimate genetic distance relationships (Ingman et. al, 2000).
By performing a nucleotide blast on the assigned D-loop DNA sequence under Section 4-9, a
comparison between the query search and identification of homology with other sequences was
performed. Table I lists the two sequences bearing the largest similarity to the query sequence
obtained from the D-loop data. The first and second highest matches resulting from the BLAST
search on the D-loop were identified as having a 96% identity match and an E-score value of
8*10173. An E-score larger than 0.05 means the match is a result of random chance, while an E
score less than 0.01 means the match is due to common ancestry. Therefore, this large E-score
value means that the high sequence matches were most likely the result of random chance.
In this experiment, the average proportional divergence and average number of substitution
per site calculations for humans vs. Neanderthals and humans vs. chimps demonstrated that
humans are more closely related to Neanderthals than chimps. The average proportional
divergence for humans vs. Neanderthals was .047, a lower value than the average proportional
divergence value of .156 for humans vs. chimps. Furthermore, the average number of
substitutions per site was lower for humans vs. Neanderthals when compared to humans vs.
chimps, yielding value of .049 and .169, respectively. These differences can be interpreted as
meaning that more differences exist between humans and chimps vs humans and Neanderthals.
Therefore, it is likely based upon the data that humans and Neanderthals share a closer
evolutionary relationship.
As observed in Table III, the divergence time for the most recent common ancestor to all
living modern humans was calculated at 5.03*105 years. The multiregional model predicts the
divergence time for the most recent common ancestor of humans to have occurred 1.5–3 million
years ago, whereas the displacement model predicts a divergence time of 200,000–500,000
years. Therefore, the displacement model was supported by the TMRCA results calculated in this
experiment. Population geneticists have used mitochondrial and chromosomal DNA to calculate
a divergence time for humans of about 200,000 years. The estimate of at 5.03*105 years derived
in this experiment is off by approximately 300,000 years. The discrepancy between these results
could be the result of mutational variation in the mtDNA control region being analyzed that
could affect the calculated rate of substitution.
It can also be observed from Table III that the divergence time between humans and
Neanderthals was calculated to be 1.97*105 years. The divergence time between two modern
humans was calculated to be 3.39*104 years. Since the divergence time between two modern
humans resulted in a smaller divergence time in years than the divergence time between modern
humans and Neanderthal’s, the data supported the divergence model. If the human sequences
were more similar to Neanderthal DNA than to other humans, the multiregional model would
have been supported.
The data generated in this experiment is in support of the displacement model of human
evolution, also known as the “Out of Africa” model. This model supports the idea that modern
Homo Sapiens arose from a single founding population that emerged from Africa in the last
200,000 to 500,000 years and then migrated successfully to Europe and Asia. This idea was
supported by the TMRCA estimated value of 5.03*105 years. It was also supported by the lower
divergence time between modern humans of 3.39*104 years compared to the divergence time
between Neanderthals and humans.
Works Cited
Crochet A. C., & Desmarais, E. D. (2000). Slow Rate of Evolution in the Mitochondrial Control
Region. Oxford Journal. Mol Bio Evol, 17(12), 1797-1806
Ingman, M., & Kaessmann, H. (2000.) Mitochondrial Genome Variation and the Origin of
Modern Humans. Nature Reviews. Genetics, 4(3), 708-713
Taylor, R. W., & Turnbull, D. M. (2005). Mitochondrial DNA Mutations in Human Disease.
Nature Reviews. Genetics, 6(5), 389–402