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CLADISTICS LAB Evolution G1F 7.5 ECtS (26/4/2019) Version 1

Authors School of Bioscienc University of Skövd BOX 40 541 28 Skövd

CLADISTIC ANALYSIS OF THE PHYLOGENY OF WHALES AND THEIR RELATIVES USING PAST (PALEONTOLOGICAL STATISTICS) Introduction For centuries, mankind has sought to classify organisms by degree of relatedness. In the 300s BCE Aristotle was beginning to note distinctions of plants and animals in a “Ladder of Nature,” which aimed to show organisms by hierarchy. Eventually, taxonomy was the main tool which grouped organisms by varying degrees. However, it was after Darwin's publication of On the Origin of Species by Natural Selection that the science community accepted species to only have similar features, but to have derived from a common ancestor. By understanding this and researching genetics, it is possible to find a single ‘tree’ of life and find where each organism branched off from another. Studying phylogeny gives the evolutionary history and relatedness between any and all species. Phylogeny describes the historic evolutionary relatedness between species (i.e where one species split on the evolutionary tree from another.) In practice, several methods are utilized. Synapomorphies are used as data to chart relation of species. This data is input into algorithmic software in order to see all possibilities, as some traits might be the result of convergent evolution and therefore be disregarded as analogous. In order to chart phylogeny as it happened historically, the statistical method of cladistics is used. This method will often result in several trees that call for further analysis. Software which uses cladistics such as PAST (paleontological statistics) will use synapomorphies to indicate the degree of similarity. The software will only give cladograms of the maximum parsimony due to the law of least resistance (i.e a tree of 12 steps will be disregarded if there is a tree with 11 or less.) More than one tree will be given if they match in number. The MPT (most parsimonious tree) will have the fewest evolutionary steps and is therefore more likely. In this exercise, we will explore the phylogenetic of several species using paleontological statistics software along with our own reasoning in order to narrow down a single cladogram and find the most parsimonious evolutionary tree. In studying aquatic mammals, we can observe the remnants of their time on land. Using PAST, we will find the closest living relative to the whale, before it split to adapt to their drastically different niche and environment. Phylogeny describes the historic evolutionary relatedness between species (i.e where one species split on the evolutionary tree from another.) In practice, several methods are utilized. Synapomorphies are used as data to chart relation of species. This data is input into algorithmic software in order to see all possibilities, as some traits might be the result of convergent evolution and therefore be disregarded as analogous. In order to chart phylogeny as it happened historically, the statistical method of cladistics is used. This method will often result in several trees that call for further analysis. Software which uses cladistics such as PAST (paleontological statistics) will use synapomorphies to indicate the degree of similarity. The software will only give cladograms of the maximum parsimony due to the law of least resistance (i.e a tree of 12 steps will be disregarded if there is a tree with 11 or less.) More than one tree will be given if they match in number. The MPT (most parsimonious tree) will have the fewest evolutionary steps and is therefore more likely. In this exercise, we will explore the phylogenetic of several species using paleontological statistics software along with our own reasoning in order to narrow down a single cladogram and find the most parsimonious evolutionary tree. In studying aquatic mammals, we can observe the remnants of their time on land. Using PAST, we will find the closest living relative to the whale, before it split to adapt to their drastically different niche and environment.

Methods The aim of this experiment was to (by the help of the PAST) identify the closest relatives to the whales. This experiment was carried has follows: Firstly, the data to be analyzed was uploaded in to the PAST program. The first data used (2a) showed the nucleotides which code for a milk protein in cows, camels, deer, pig, warthogs, hippos, whales, and an outgroup. The other data set (2b) gave us parasitic DNA, which can be more comprehensive as it is very specific and unlikely to evolve separately by chance. The same dataset was given, but without the outgroup identified so the next step was identifying the outgroup and placing it on the first row because PAST selects this row as the outgroup by default. The ideal outgroup is the selection with the largest zero inputs (i.e the organism with the minimum shared traits.) Through this, we found the camel to be the best fit for the outgroup. When this was done, a phylogenetic tree was created based on the data on the species characteristics. It was done by marking the data area to be analyzed and then choosing Cladistics, then selecting Parsimony analysis. In the Parsimony analysis, the algorithm selected by default was the Branch-and-Bound and the Optimization was set at Fitch. In order to test for the accuracy of the branching points in the phylogenetic trees, the bootstrap replicate was set at 100 and the program was run, and the most parsimonious trees were analyzed. Through bootstrapping, we can see the accuracy percentages for each branch in a given phylogenetic tree. The process was carried out several times, but each time excluding a specific characteristic and a parsimonious tree was then created. The tree was then visually analyzed to see if it had any patterns like the mother tree created. If any difference, the tree was then detailly analyzed and reported in the results section.

Results Parsimonious tree of task 2a.

Deer

Cow

Hippo

Whale

Warthog

Pig

Camel

OUT

Figure 1.1. Phylogenetic tree of the animals based on the all characteristics.

The figure above shows the parsimonious tree of the animals when all the characteristic was selected.

55

23

D eer

C ow

H ippo

W hale

Warthog

Pig

C am el

O UT

Figure 1.2. Phylogenetic tree bootstrapped

49

41

98

100

The figure above is a phylogenetic tree based on the characteristics of the various animals with bootstrap.

31

Deer

Cow

Warthog

Pig

Hippo

Whale

Camel

OUT

Figure 1.3 the figure below shows the phylogenetic tree with bootstrap of the various animals when the characteristics in column 162 where omitted.

65

59

22

96

100

98

11

D eer

C ow

H ippo

W hale

W arthog

P ig

C am el

O UT

Figure 1.4a the figure below shows the phylogenetic tree with bootstrap of the various animals when the characteristics in column 166 where omitted.

100

85

99

100

The figure shows the phylogenetic tree with bootstrap of the various animals when the characteristics in column 166 where omitted. The tree had parsimonious trees.

98

Hippo

Deer

Cow

Whale

Warthog

Pig

Camel

OUT

Figure1.4a

100

2

85

99

100

85

28

Deer

Cow

Hippo

Whale

Warthog

Pig

Camel

Figure 2.0 the phylogenetic tree with bootstrapping and stating the camel group at first as the outgroup.

29

16

100

The figure above shows the polygenetic tree using bootstrapping while the camel group was put at first as the outgroup.

100

Warthog

Pig

Camel

Deer

Cow

Whale

Hippo

OUT

Figure 2.1. The most likely parasiminous phylogenetic tree of whales and their closest relatives using bootstrapping.

100

73

73

73

100

The figure shows the most likely parsimonious polygenetic tree of whales and their closest relatives.

Discussions

Interpreting the data from Figures 1.1,1.2,1.3 and 1.4 that were constructed using PAST to produce the most likely parsimonious tree using bootstrapping to analyze the data from different base pairs and their variables by the phylogenetic tree and variable characteristics. In figure 2.0 the phylogenetic tree started with the camel group as the outgroup in order to trace a base pair of DNA which contained a parasitic DNA which existed long time ago. While in figure 2.1, using the data in PAST the most likely parsimonious tree was constructed in order to analyze the phylogeny of whales and their closest relatives. It has been shown from the results above that the Hippo’s are the closest relatives to whales based on the phylogenetic trees. A science news research organization stated that in 2001, the university of Michigan reviewed the origin of whales and they confirmed that they evolved from early ancestors of deer, sheep and hippopotami and stating that the hippos are the closest living relatives to whales based on fossil studies (ScienceDaily, 2019). Moreover, Japanese researchers suggested that the hippopotami are the closest living relatives to whales by tracking DNA sequences from ancient animal cells (Abc.net.au, 2019).

Reference

Abc.net.au. (2019). Hippos - the closest living relatives of whales? › News in Science (ABC Science). [online] Available at: https://www.abc.net.au/science/articles/1999/08/31/48122.htm [Accessed 26 Apr. 2019].

ScienceDaily. (2019). New Fossils Suggest Whales And Hippos Are Close Kin. [online] Available at: https://www.sciencedaily.com/releases/2001/09/010920072245.htm [Accessed 26 Apr. 2019]....