Understanding the Tree of Life: Bacteria, Archaea, and Eukarya, Study notes of Theory of Evolution

Download Understanding the Tree of Life: Bacteria, Archaea, and Eukarya and more Study notes Theory of Evolution in PDF only on Docsity! Biol 315 Evolution, Nason Lecture 37, 4/22/09. p.1 Take-home assignment announced in class today – Your assignment is to write a multiple-choice question (with five possible answers, a-e) suitable for use on the final exam. Your question may focus on any concepts or material addressed in this course during the semester. • Due Monday, April 27, at beginning of class, your question must be neatly printed on paper. Note: We began today’s lecture finishing up with material from Lecture 36. The Origins of Life (Freeman & Herron Ch. 17) What is the Shape of the Tree of Life? (F&H Ch. 17.3) One way to study the ancestry of all living things (excluding viruses) is to reconstruct their phylogeny. Morphology The first attempts to reconstruct the phlogeny of everything were based on morphology. • Useful for the tree of life that contains eukaryotes. • Not so useful for reconstructing the universal phylogeny containing prokaryotes, however, since they lack sufficient structural diversity to facilitate the reconstruction of morphology– based evolutionary trees. DNA sequence data The challenge to using sequence data to estimate the evolutionary tree for all living things is to find a gene that was present in the common ancestor and that still shows recognizable homology between all extant organisms. • Genes that meet these criteria are associated with the fundamental processes of DNA replication and protein translation. • One gene that has been particularly widely used for reconstruction the phylogeny of everything is the gene that codes for the small sub-unit ribosomal RNA (rRNA). - All extant organisms have ribosomes of similar composition (RNA and protein), tertiary structure, and function: the translation of mRNA transcripts into protein. - Translation is so vital that organisms are under strong stabilizing selection to maintain it. - As a result, organisms as widely divergent as humans and bacteria show recognizable similarities in ribosomal nucleotide sequence, even though they last shared a common ancestor billions of years ago (i.e., the sequence of the small sub-unit rRNA gene evolves very slowly). The Phylogeny of All Living Trees (F&H pp.663-666) An estimate of the universal phylogeny, based on sequences of the small sub-unit rRNA, appears in Figure 17.18. • The shape of this phylogeny has prompted a dramatic revision of our traditional view of the organization of life (illustrated in Figure 17.17). ⇒ It reveals that the five-kingdom classification (Monera [bacteria], Protista [single cell eukaryotes], Animals, Plants, and Fungi) bears only a limited resemblance to actual evolutionary relationships. The universal phylogeny estimated from small sub-unit rRNA (and more recently from other genes) indicates that the tree of life consists of three main branches or lineages. Biol 315 Evolution, Nason Lecture 37, 4/22/09. p.2 • Whereas prokaryotes were all grouped in the kingdom Monera in the traditional classification, they occupy two of the three main branches of the rRNA phlogeny. Eukaryotes, including protists, animals, plants and fungi, occupy the third branch ⇒ The three branches of the rRNA tree: Bacteria, Archaea, Eucarya (Figure 17.18). Bacteria - Includes virtually all of the well-known prokaryotes including gram positive bacteria, purple bacteria, and cyanobacteria. Archaea - Formerly known as the archaebacteria, these not-so-well-known prokaryotes live in physiologically, harsh environments, are difficult to grow in culture, and were discovered only recently. • Includes: - hyperthermophiles - live in hot springs up to 110˚C - anaerobic methane producers - extreme halophiles (highly salt dependent) Eucarya - Includes all eukaryotes, and thus the remaining four kingdoms of the traditional classification: Protista, Animals, Plants, and Fungi. • Animals, plants, and fungi each represent monophyletic groups (that is, each includes all the descendants of a single common ancestor). • The protists, in contrast, are scattered across several fundamental limbs on the eukaryotic branch of the tree of life. • If we want our kingdoms to be natural evolutionary groups, they should be monophyletic. ⇒ Unless we want the kingdom Protista to include animals, plants, and fungi, it will have to be disbanded and replaced by several new kingdoms. The universal rRNA phlogeny also demonstrates that, although Animals, Plants, and Fungi are the kingdoms that attract most of our attention, they are but mere twigs on the tip of one branch of the tree of life. • The remaining organisms account for over 90% of the small sub-unit rRNA gene sequence diversity on earth (a pattern found for other genes as well). Rooting the Tree of Life (F&H pp. 666-667) Figure 16.21 indicates the three branches to the tree of life that constitute the major lineages of all living organisms. Question: How was the relative relationship among these lineages determined? • As illustrated in Figure 17.20, and below, three phylogenetic relationships are possible between the Bacteria (B), Archaea (A), and Eucarya (E): • Distinguishing the actual relationships requires rooting the tree of life. - This is an enormous challenge because there is no out-group (surviving) to work with. A rooted tree of life The estimate of the universal phylogeny shown in Figure 17.18 is based on small sub-unit rRNA sequence data and shows the root placed between the Bacteria and Archaea + Eucarya.