lineage paper 3.18.15
TRANSCRIPT
LIST OF TABLES
TABLE 1: LIST OF SPECIMEN………………………………………………………………...6
TABLE 2: UNMODIFIED DATA IN ACCORDANCE WITH KAIFU ET AL. (2011) ON
EXCEL SPREADSHEET………………………………………………………………………..11
TABLE 3: MODIFIED DATA ON EXCEL SPREADSHEET…………………………………12
LIST OF FIGURES
FIGURE 1: UNMODIFIED ORDERED TREE…………………………………………………13
FIGURE 2: UNMODIFIED UNORDERED TREE………………………………......................13
FIGURE 3: MODIFIED UNORDERED TREE #1……………………………………...............15
FIGURE 4: MODIFIED UNORDERED TREE #2……………………………………...............15
FIGURE 5: MODIFIED ORDERED TREE……………………………………………………..16
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INTRODUCTION
In 2004, an almost completed skeleton (LB1) of Homo floresiensis was discovered on the
island of Liang Bua in a cave on Flores Island, in Indonesia. (Brown et al, 2004). This new
species lived around 17,000 years ago in the Pleistocene epoch (Dunsworth, 2010). As the most
well-preserved of the fossils, LB1 had an unusually small body and skull while still indicating
advanced Homo-like features. This created a question of whether Homo floresiensis was more
closely related to the genus Homo or Australophithecus (Brown and Maeda, 2009).
Multiple theories emerged in attempt to describe the evolutionary pathway of Homo
floresiensis. One theory is that it is a dwarf species of Homo erectus (Brown et al., 2004).
Another theory is that H. floresiensis is an entirely new species (Morwood et al., 2009).
Obviously, there is still much uncertainty in the evolutionary relationships among these species.
The phylogenetic relationships of H. floresiensis to other hominid species are still in
debate among researchers. Much research has been devoted in attempt to explain the
evolutionary path of this species. One article, Kaifu et al. (2011), describes a detailed report on
the external morphology of LB1, a well-known cranium of Homo floresiensis. In this article,
comparisons of LB1 were made with various taxa in the genus Homo to assess its evolutionary
relationships. Kaifu et al. (2011) assessed 67 characteristics and reported all their data in a chart.
However, the researchers did not did not complete a cladistic analysis of their data.
Phylogeny is central to understanding an organism. The phylogenetic relationship among
organisms helps organize the organisms’ history in order to understand their behavior and
relationships. It has been emphasized that the approaches to hominid phylogeny has changed
throughout history. As more species were being discovered, it became necessary to change the
way phylogenetic analyses were conducted (Strait et al., 2007). In the 1970s and 1980s, a new
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form of phylogenetic analysis, called cladistics, became used more often. This system was
developed by German entomologist Willi Hennig in 1950 (Hennig, 1996). Cladistics reconstructs
phylogenetic relationships based on the principle that not all morphological similarities indicate
phylogeny. Rather, only synapomorphies, similarities that are derived and inherited from a
common ancestor, should be indicative of evolutionary relationships. Yet, it can be difficult to
recognize which characters fall into this category. Therefore, cladistics relies on the principle of
parsimony to identify such characters in which parsimony is the idea that the simplest
explanation is the best one because it makes the fewest assumptions.
The purpose of this research is to undertake a cladistic analysis on the species within the
genus Homo to determine the phylogenetic relationships of Homo floresiensis. I reanalyzed all
the fossils that were used in Kaifu et al. (2011) and completed a cladistics analysis on my
data. I then took Kaifu et al. (2011)’s data and complete a cladistics analysis of their data.
Four hypotheses were tested, and they were the same as the ones tested in Kaifu et al. (2011).
The hypotheses are as follow.
1. “H. floresiensis originated from H. habilis with no direct relationship with Dmanisi
Homo or H. erectus.”
2. “H. floresiensis originated from Dmanisi Homo or its similar form with no direct
relationships with known Indonesian and Chinese H. erectus.”
3. “H. floresiensis originated from early Javanese H. erectus or a form similar to it with
dramatic dwarfism of body and brain sizes.”
4. “H. floresiensis is not related to any of the above three taxa.”
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MATERIALS AND METHODS
Ingroup Taxa
The ingroup was composed of eight different taxa and includes all taxa whose
phylogenetic relationships are to be resolved in the experiment. This consisted of 11 taxa which
were H. habilis, H. ergaster from Dmanisi, H. ergaster from Africa, H. erectus from
Zhoukoudian, H. erectus from Sangiran/Trinil, H. erectus from Ngangdong, H. erectus from
Sambungmacan, H. heidelbergensis from Kabwe, H. heidelbergensis from Dali, H.
heidelbergensis from Maba, and H. floresiensis.
Homo habilis existed 2.3 to 1.4 million years ago and is widely accepted as the common
ancestor of all later Homo species (Dunsworth, 2010). This species forms the bond between
Australopithecus and Homo in morphology (Cartmill, M. et al, 2009).
The Dmanisi skull was found in Dmanisi, Georgia. It was categorized into Homo
ergaster. It existed around 1.7 million years ago in the early Pleistocene epoch and may
represent the first species that migrated out of Africa (Gabunia, 2000). However, some now
suggest that the skull Dmanisi should be placed into its own category of Homo georgicus
(Gabounia, 2002).
Homo ergaster from Africa lived around 1.8 – 1.5 million years ago in the Middle
Pleistocene. This species was discovered and named by C. Groves and V. Mazak in 1975; it
previously was placed into the taxa Homo erectus (Cartmill & Smith, 2009).
Homo erectus from Zhoukoudian existed around 700 thousand years ago (Hyodo et al.
2002). It exhibited some sophisticated behavior such as collecting plants, hunting certain
animals, control of fire, and cannibalism (Wu and Li, 1983).
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H. erectus from Sangiran/Trinil were found in Java (Indonesia). These skulls date back to
1.8 million years ago (Cartmill & Smith, 2009). They are part of the more primitive Indonesian
taxa.
H. erectus from Ngangdong in Indonesia is known from the late Pleistocene, about 200
thousand years ago. The Ngangdong fossils lead to some problems in taxonomy and phylogeny,
and it is the center of some discussion (Cartmill & Smith, 2009).
H. erectus from Sambungmacan was found in the central part of Java. The most complete
skull of this is Sangiran 17 (Cartmill & Smith, 2009), which was used in this study.
The Kabwe skull was discovered in Kabwe, Zambia. Its nickname is the Rhodesian Man
and belongs to the species Homo heidelbergensis. It lived 700,000 to 200,000 years ago and is
thought to be the descendant of H. ergaster (Klein, 1989).
H. heidlebergensis from Dali in China is characterized by an impressive supraorbital
torus with a flat face. It has a moderate degree of facial prognathism (Cartmill & Smith, 2009).
H. heidelbergensis from Maba in China was the first post-Erectine archaic skull from
China (Woo & Peng 1959). It seems to be more recent than Dali (Cartmill & Smith, 2007).
Outgroup
One outgroup taxon was used in this study. The outgroup taxon consists of species whose
phylogenetic position relative to the ingroup taxon is known, and it is used to “polarize” the
characters in the study in order to determine which character states are primitive and which states
are derived. Australophitecus africanus was the only outgroup taxon used in this study.
Australophithecus africanus was found in Sterkfontein in southern Africa (Broom 1936).
The most complete skull of A. africanus is STS 5, which was used in this study. This skull looks
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very primitive. It has apelike features with a small brain and a face that sticks out (Hooton 1946).
Nevertheless, it has a bigger brain relative to its size than any other animal during its time
(Cartmill & Smith, 2007).
A. africanus was placed into the outgroup because its relationship to the others are
already known. The genus Australophitecus is the predecessor to humans, and this was the only
Australophitecus taxa included in this study. It can be accurately stated that A. aficanus is
distantly related to all the other taxa in this study.
Selection of Skulls
These species were chosen based on Kaifu et al. (2011). However, direct observations could not
be made on the original fossil specimen, so observations were made on casts instead. The list of
specimen used in Kaifu et al (2011) is listed in Table 1 below.
Table 1: List of Specimen
Group SpecimenH. hailis KNM-ER *1470, 1590, 1805, *1813, 3732, 3735, 7330; *OH
24Early African H. erectus KNM-ER 730, 1808, *3733, *3883, 3891; SK 847 KNM-WT
15000 Late African H. erectus *OH 9, 12; Daka
c. .5 Ma African Homo Bodo *Kabwe, Saldanha, Ndutu, Sale
Dmanisi D 2280, 2282, 3444, *2700
Early Javanese H. erectus *Trinil: T 2 Sangiran: S2, 4, 10, 12, *17, 38, IX; Bukuran 1(not in article
Late Javanese H. erecuts Sambungmacan: Sm 1,3,4Ngangdong: Ng *1, 3, 6, 7, 100, 11, 12
Chinese H. erecuts Zhoukoudian: ZKD 2, 5, 10 ,11, 12Nganjing: Nangjing 1
.2 Ma Chinese Homo Dali; Maba; Jinniushan
A. africanus **STS5
H. floresiensis LB1
6
KEY*Indicates that the specimen was used in this study**Indicates that Kaifu et al (2011) did not use this specimen, but it was used in this research.No asterisk indicates that the specimen was used in Kaifu et al. (2011), but not in this study.
Character Analysis
After the skulls were gathered, the casts were independently assessed for certain
characteristics. These characteristics were determined was based on the features of H.
floresiensis and how the species portrayed that specific characteristic. Overall, 67 characteristics
were examined. After observation, the data was transferred to Microsoft Excel with a number
system with codes 0, 1, 2, 3. 0 was for the value H. floresisensis showed; all the other specimens
were compared to this assessment. If only two states were present in the species, then the state
present in H. floresiensis was assigned a code of 0, and the other states was assigned a code of 1.
If some taxa were variable in the character (i.e., exhibiting both states), then an intermediate
code of 1 was assigned to the variable taxa and a code of 2 was assigned to the taxa exhibiting
that other state. If multiple states were present, then codes of 0, 1, 2, etc. were assigned as
necessary. One spreadsheet was made for all the data assessed by Kaifu et al. (2011) and another
was made with character states in which there were disagreements with the morphological
assessment of Kaifu et al. (2011)
Characteristics with Disagreements
There were some disagreements with the assessments made in Kaifu et al. (2011). Modifications
were made and a second Excel spreadsheet was created to record these. A separate phylogenetic
analysis was done with the modified data. The following lists all the disagreements and the
reasoning.
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S2: Facial Skeleton (small v large)
H. habilis specimens KNM ER 1813 and OH24 appear to have small skeletons instead of large
ones as indicated by Kaifu et al (2011). Therefore, this was changed to variable.
C8: Temporal Line Extension towards Lamboid Suture Presence
The value of H. floresiensis was changed because it does not extend to the lamboid suture. H.
habilis also looks like it extends more to the end, so that was changed to variable. Ngangdong
was changed to variable because specimen XI had the character state while VI did not.
C10: Strength of Medial Incursion of the Temporal Lines
For KNM ER 3733 of H. ergaster, I found the temporal lines as well defined and marked.
Therefore, that was changed to variable.
C12: Temporal Line Relative Strength on the Anterior Frontal
The article suggested that Dmanisi’s temporal line was marked; however, it was evident that it
was not developed.
C16: Temporal Squama Length and Parietomastoid Suture Length
Zhoukoudian was changed to a short temporal squama and long parietomastoid suture from a
long temporal squama and short parietomastoid suture.
C17. Occipital Plane Shape
Ngangdong’s occipital plane shape was changed from straight to curved forward.
C21: Frontal Squama Curve Strength
H. habilis was changed to variable because KNM-ER 1813 curved quite a bit. Based on this
analysis, A. africanus should also be changed to having a strong curve.
C23. Height and Width of Occipital Squama
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Dmanisi and H. ergaster were changed to a low height and a large width for the occipital squama
instead of high and narrow as indicated by the article.
C24: Parietal Sagittal Curvature Strength
H. habilis should be changed to variable because KNM-ER 1813 has a curve. This also changed
the decision made on A. africanus from having a small curve to having a large curve.
C31: Condition of the Extension of Midcranial Base
H. ergaster should be changed to variable from short because KNM-ER 3883 has a long
midcranial base, not short.
C39: Size and Shape of Mastoid Process
Zhoukoudian was changed from having a small mastoid process to having a large and bulbous
one.
F2: Shape of Supratoral Plane
H. habilis was changed from not grooved to grooved supratoral plane.
F10: Shape of the Lateral End of the Supraorbital Plane
KNM-ER 1813 protrudes laterally. The classification of H. habilis was changed to variable from
the Kaifu et al. (2011) analysis, which states that it does not protrude laterally.
F11: Shape of the Supraorbital Arch
H. habilis should be changed to variable because KNM-ER 1813 has an arch. Kabwe should be
changed to having an arch. Lastly, Zhoukoudian should be changed to variable because the
Zhoukoudian Skull I (650) appears to have an arch.
F13: Position of the Infraorbital Surface
KMN-WT 1500 appears to face superiorly instead of inferiorly and should be changed to
variable.
9
F16: Width of Upper Facial Breadth
H. habilis was changed to variable because KNM-ER-1813 has a narrow facial breadth. Dmanisi
was changed to narrow, H. ergaster was changed to narrow and Sagiran/Trinil was changed to
variable because Sangiran 17 was wide.
F18: Midfacial Breadth Width
H. habilis should be changed to variable because of KMN-ER-1813 and H. ergaster should be
changed to variable because of KMN-WT-1500.
Phylogeny
The information from the Excel spreadsheet was then used to create a phylogenetic tree. First,
the data from Microsoft Excel was transferred to the MacClade program in order to format the
data for the cladistics analysis. The software used for the analysis was called Phylogenetic
Analysis Using Parsimony (PAUP). This is a program used to infer or determine evolutionary
trees. It implements principles such as parsimony and other useful techniques that can be
changed manually. Parsimony states that the simplest tree (the one with the least amount of
branches) is the most accurate because it makes the least amount of assumptions. Cladistics
relies on the principle of parsimony to identify synapomorphies and reconstruct human
phylogeny. Synapmorphies are traits shared by taxa, which are the opposites of homoplasy.
Homoplasies are characters that are shared, but do not represent a common ancestor.
Homoplasies are to be avoided because they are unnecessary to understanding the phylogeny.
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Table 3: Modified Data on Excel Spreadsheet
RESULTS
After running the cladistics analysis on PAUP, two cladograms were created for the results
according to Kaifu et al (2011). One cladogram was found in which the characters were treated
as being ordered (i.e., assuming that characters had to change in sequence from state 0 to state 1
to state 2, etc.) and the other cladogram was found in which characters were treated as being
unordered (i.e., characters could change from state 0 to state 2 in a single step). Then, two
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equally parsimonious unordered trees and one ordered tree were created with the modified data.
In this research, there were two different analyses. For each of the two analyses, unordered and
ordered trees were generated. The purpose of having these types is because each makes an
assumption about how characters are related. The unordered analysis allows characters to change
from a certain state into any other state in one step. The ordered analysis allows character states
to change throughout all steps. The different assumptions shape the number of steps in a tree and
can possibly affect the shape of the most parsimonious tree. However, in this research, there
were not any major differences between the ordered and unordered trees.
Results for Unmodified Data
Figure 1: Unmodified Ordered Tree Figure 2: Unmodified Unordered Tree
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Unmodified Ordered Cladogram
In the above ordered cladogram in figure 1, A. africanus is in the outgroup because its
relationship to the other taxa is known. Maba and H. floresiensis are sister taxa that have a
common ancestor at 8. They share a common ancestor with the group consisting of Ngangdong,
San Bungmacan, and Zhoukoudian. Dali shares a common ancestor with all of these. Next,
Sangiran/Trinil shares a common ancestor with all of the above listed taxa at 5. H. ergaster and
Kabwe are sister taxa that share a common ancestor at 9. They also share a common ancestor
with the rest of the taxa listed above at 4. At 3, Dmanisi shares a common ancestor with the
previously stated taxa. Lastly, H. habilis shares a common ancestor with the taxa previously
stated. A. africanus is the oldest and shares a common ancestor to all the taxa presented.
Unmodified Unordered Cladogram
A. africanus is the outgroup, which shares a common ancestor with all the other taxa. At 11, H.
habilis and Dmanisi share a common ancestor. They are sister taxa, so they are closely related.
H. floresiensis and Maba share a common ancestor at 5. They are sister taxa as well. Ngangdong,
Sam Bungmacan, Dali, Zhoukoudian, and Sangiran/Trinil are a group. Zhoukoudian and
Sangiran/Trinil are sister taxa. They share a common ancestor with Ngangdong, Sam
Bungmacan and Dali at point 9. These all share a common ancestor with H. floresiensis and
Maba at 4. This whole clade shares a common ancestor with H ergaster and Kabwe, which is a
sister taxon at point 3.
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Results for the Modified Data
Figure 3: Modified Unordered Tree #1 Figure 4: Modified Unordered Tree #2
Modified Unordered Trees
Two equally parsimonious unordered trees were generated based on the modified data. All
characteristics were unordered and had equal weight. In both these trees, the sister taxa of Maba
and H. floresiensis share a common ancestor at 6. They share a common ancestor with the group
consisting of Ngangdong, Sam Bungmacan, Sangiran/Trinil, and Zhoukoudian at 5. This group is
different in tree #1 and tree #2. In tree #1, Ngangdong and Sam Bungmacan are sister taxa while
Zhoukoudian shares a common ancestor with these at 8 and Sangiran/Trinil shares a common
ancestor with them at 7. In tree #2, Ngangdong and Sam Bungmacan still are sister taxa, but
Sangiran/Trinil and Zhoukoudian are as well. These sister taxa share a common ancestor at 7.
This is the only difference between the two trees. At 4, the sister taxa Dali and Kabwe share a
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common ancestor with the polyphyletic group and the sister taxa H. floresiensis and Maba. At 3,
Dmanisi shares a common ancestor with the previously stated taxa. At 11, H. ergaster and H.
habilis are sister taxa, sharing a common ancestor with the previously stated taxa at 2. At 1, the
outgroup, A. africanus, shares a common ancestor with all of the other taxa.
Figure 5: Modified Ordered Tree
Modified Ordered Tree
One parsimonious tree was generated. 67 characters were examined. At 8, H. floresiensis and
Maba share a common ancestor. Ngangdong and Sam Bungmacan are sister taxa at 10, sharing a
common ancestor with Zhoukoudian at 9. At 7, this group shares a common ancestor with H.
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floresiensis and Maba. At 6, Dali shares a common ancestor with the previously mentioned taxa.
At 5, Sangiran/Trinil share a common ancestor with the previously stated taxa. Kabwe and H.
ergaster are sister taxa at 11 and share a common ancestor with the previously mentioned taxa at
4. Then, at 3, Dmanisi share a common ancestor with all the taxa below it. At 2, H. habilis shares
a common ancestor with all the taxa below it. Then, at 1, A. africanus shares a common ancestor
with all of the taxa.
DISCUSSION AND CONCLUSION
There were some similarities that existed between all phylogenetic trees. In every tree,
Homo floresiensis was the sister taxon of Maba, indicating a close relationship to the Chinese
fossil. Homo floresiensis and Maba are always related to a group of Chinese taxa consisting of
Zhoukoudian and sometimes Dali. The taxa are also closely related to the Indonesia taxa of
Ngangdong, Sangiran/Trinil, and Sam Bungmacan. In none of the cladograms are they related to
H. habilis, A. africanus, Dmanisi, Kabwe, or H. ergaster. Given all this data, we were able to
evaluate whether each hypothesis was true or not.
Hypothesis one states that “H. floresiensis originated from H. habilis with no direct
relationships with Dmanisis Homo or H. erectus.” In none of the trees did Homo floresiensis
share a close relationship with H. habilis. This is inconsistent with hypothesis 1, suggesting that
it can be rejected.
Hypothesis two states “Homo floresiensis originated from Dmanisi Homo or its similar
form with no direct relationships with known Indonesian and Chinese H. erectus.” As indicated
in each cladogram, there not a close relationship between these taxa. Again the results are
inconsistent with the hypothesis, allowing it to be rejected.
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Hypothesis three states “Homo floresiensis originated from early Javanese H. erectus or a
form similar to it with dramatic dwarfism of body and brain size.” H. floresiensis is closely
related to the taxa Maba, which is a Chinese fossil, not Javanese. The results are not consistent
with a strict reading of the hypothesis; however, the clade including both H. floresiensisi and
Maba was closely related to Indonesian taxa, so there is at least some support for the general idea
expressed in the hypothesis.
Hypothesis four states “Homo floresiensis is not related to any of the above three taxa.”
H. floresiensis is closely related to Maba, which is a Chinese taxon. Maba was not included in
any of the above hypothesis. Therefore, results are consistent with this hypothesis.
In conclusion, a phylogenetic analysis of the species within the genus Homo was
undertaken. H. floresiensis was most closely related to Maba. Results were most consistent with
hypothesis four, which states “Homo floresiensis is not related to any of the above three taxa.”
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