The Root of the Tree
Fig. 5. A modern phylogeny of life. Wikipedia commons
Linnaeus divided all life into two kingdoms: plants and animals. When microorganisms were discovered in the 19th century, a third taxon was created by Haeckel to include them: the kingdom Protista. As more was learned about the biochemistry and microscopic structure of cells, it became clear that certain groups of microorganisms should be grouped separately or placed in the plant and animal kingdoms. Single-celled organisms that lacked nuclei (prokaryotes) were spun off into the kingdom Monera and the other microorganisms were left in Protista. Fungi, which didn't fit in as either plants or animals were put into their own kingdom. This "five kingdom" system prevailed for decades.
When creation of molecular phylogenies became possible in the 1990's, systematists sought to reorganize taxa into groups that better reflected the phylogenetic patterns they inferred from their data. Fig. 5 shows an idealized modern phylogeny that includes major taxa of living organisms. The center of the figure represents the moment in time when the first evolutionary split occurred after the last universal ancestor of all extant organisms. The radial distance from the center of the diagram represents time that elapsed since then, with the present time at the branch tips on the outside of the diagram. The length of a particular branch radiating from the center represents the time that elapsed between the split that formed the taxonomic group represented by the branch and a later split that separated that group into two daughter taxonomic groups (i.e. this diagram assumes a molecular clock).
The branching pattern near the "root" (starting point) of the tree was determined by Woese et al. (1990) based on molecular data. (See also Brown and Doolittle 1995 for a clever strategy involving gene duplication for rooting the Tree of Life in the absence of an outgroup.) They showed that several groups of unusual prokaryotes that had previously been considered bacteria were actually more closely related to eukaryotes than bacteria. Based on this pattern, they proposed dividing all life into three groups at a taxonomic level higher than kingdom which is now called domain (or superkingdom). The domain Archaea (those unusual prokaryotes) is shown at the lower left in Fig. 5 (groups ending in "archaerota"). Eukaryote groups are shown in the upper left and Bacteria are shown at the right. The organization of the domains Archaea and Bacteria at the kingdom levels is somewhat unclear - they are not usually divided into kingdoms, although taxa within the domains are organized into definite phyla. The organization of the domain Eukaryota is more clearcut. Eukaryotes are divided into the traditional Plantae, Fungi, and Animalia (or Metazoa) kingdoms as well as two or more kingdoms of what have traditionally been called protists. Each of those kingdoms is then subdivided into phyla and lower taxonomic groups as in the traditional Linnaean system.
Many systematists have assumed that the phylogeny of all life could be traced back using a simple tree pattern back to a single "last universal ancestor" as shown in Fig. 1. The simply branching "tree" phylogeny works quite well for the part of the tree of life representing eukaryotes. However, it appears that lateral transfer of genetic material (transfer of genes from one branch of the tree to another) may have been relatively common among early prokaryotes. Each prokaryotic gene might have a different evolutionary history, making it difficult or impossible to place prokaryotes on clearly defined branches of a single phylogenetic tree. Thus some systematists believe that the "tree of life" for prokaryotes might be better represented as a pattern of reticulated vines that cross and merge over time.
Molecular phylogeny of the Great Apes
Note: to provide additional background for today's experiment, we will be watching the 2011 Howard Hughes Medical Institute Holiday Lecture by Sarah Tishkoff entitled "Genetics of Human Origins and Adaptation". It integrates much of the material covered in this experiment as well as other topics we will study over the course of the semester. This lecture can be viewed online at http://www.hhmi.org/biointeractive/genetics-human-origins-and-adaptation
The relationship among the great apes (family Hominidae): human, chimpanzee, bonobo (or pygmy chimpanzee), gorilla, and orangutan has been of interest to biologists since the time of Darwin. However, the precise relationship among humans, gorillas, and the two types of chimpanzees has been unclear because they apparently diverged at approximately the same time (Fig. 6).
Fig. 6 Evolutionary relationships among homonoids and their nearest relatives. CC=chimpanzee, PC=bonobo, GO=gorilla, HO=human, OR=orangutan, GB=gibbon, OWM=old world monkeys. Hixson and Brown 1986 Fig. 1
Hixson and Brown (1986) used the small (12S) subunit ribosomal RNA (rRNA) gene from mitochondrial DNA (mtDNA) from the great apes to address this question. In their study, they did not find a significant difference between the tree showing humans clustering with the chimp/bonobo clade and the tree showing humans clustering with gorilla. However, since that time, analyses based on more sequence data (e.g. Fig. 7) from a broader range of genes show humans consistently forming a clade with chimpanzees and bonobos (rather than with gorillas).
Fig. 7. Maximum likelihood phylogenetic tree for mammals, based on third codon-position nucleotide data from mitochondrial genes. Yoder and Yang (2000) Fig 2.A.
Yoder and Yang (2000) used mammalian evolutionary divergences having known dates to calibrate a molecular clock, then applied that clock to estimate the divergence times of apes. Depending on the assumptions and the sequence data used in the analysis, they arrived at Homo-Pan (human-chimpanzee) divergence times ranging from 4 to 6 million years which is consistent with the primate fossil record.
