lineage paper 3.18.15

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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 1

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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

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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.

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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 2: Unmodified Data in Accordance with Kaifu et al. (2011) on Excel Spreadsheet

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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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