Sec$on 9. Evolu$onary Rela$onships

Sec$on 9 Evolu$onary Rela$onships

Sec$on 9 Learning Goals Explain why the ribosomal 16S gene is a good marker for molecular phylogene$c comparisons. Be able to interpret a phylogene$c tree. Explain the origins of mitochondria and chloroplasts and the evidence that supports this theory.

Evolu$on is the thread that connects all biology. What is useful is retained. What is not is subject to elimina$on While DNA muta$ons can cause harm, without them popula$ons would not evolve.

Taxonomy places organisms into groups with shared features

Phylogene$c trees can be constructed to represent a hypothesis about the evolu$onary rela$onships between taxonomic groups Branches link groups according to their presumed ancestry Groups for which less distance separates them share more features than groups that are separated by greater distance

All life can be divided into three domains Certain features are shared across all life. For example: Core set of macromolecules DNA as the gene$c code ATP as an energy source Transfer of electrons to acquire energy Yet, random muta$on leads to differences in individuals; selec$ve pressure leads to reten$on of those differences within a popula$on. For example: Structural difference of conserved features (e.g. ribosome, RNA polymerase) Gain of features that are advantageous (or loss of those that are costly) (e.g. wings, gills, pep$doglycan, nucleus,tail, etc.)

Classifica$on systems allow us to group organisms These grouping allow us to make hypotheses regarding the extent of their shared evolu$onary history Group by anatomical features Group by biochemical pathways (bacteria) Group by molecular traits (mainly DNA sequence) - Scien$sts now rely heavily on comparison of molecular traits, but tradi$onal evolu$onary trees were built by comparing anatomical features. - Trait used for comparison must be heritable

With limited anatomical features, clinicians tradi$onally relied on biochemical tests for bacterial iden$fica$on Gram Posi$ve? Yes No Gram Nega$ve Coccus? Bacillus? Catalase nega$ve? Yes Alpha hemoly$c? Yes Sensi$ve to optochin? Yes No Beta hemoly$c? Yes Catalase posi$ve? Does it produce endospores? Yes Yes No Clusters of cocci? Lactobacillus Tetrads of cocci? Bacillus species species Yes Staphylococcus species Yes Micrococcus species S. pneumoniae Staphylococcus pyogenes

The advent of molecular techniques has allowed comparison using markers present in all organisms Gold standard is ribosomal small subunit rrna gene, but others are also used

Nucleo$de sequence within the conserved or variable region can be compared with that from another species 0 100 200 300 400 500 600 700 800 900 1000 1100 1200 1300 1400 1500 0 V1 V2 V3 V4 V5 V6 V7 V8 V9 Conserved regions Variable regions

Why is the 16S gene a good phylogene$c marker The gene is universally conserved (all living organisms contain this gene). The sequence has both highly conserved (unchanging) regions and variable regions. The length (~1500 nucleo$des) provides a good amount of material for comparison but is small enough for easy sequencing.

Isolate DNA from pure culture* SSU LSU 5S Amplify 16S using PCR Popula$on of iden$cal PCR products Sequence and compare to known 16S sequences in database *culture does not need to be pure if PCR is followed by cloning step (see metagenomics lecture)

Sec$on 9 Learning Goals ü Explain why the ribosomal 16S gene is a good marker for molecular phylogene$c comparisons. Be able to interpret a phylogene$c tree. Explain the origins of mitochondria and chloroplasts and the evidence that supports this theory.

Oversimplified view of molecular comparison to build phylogenetic trees The two sequences must be aligned to produce the most matches - Some$mes gaps need to be introduced - Whether and where to introduce gaps is subjective The number of matches is counted Organism 1: ACTGCATACCG - AGGCTCT Organism 2: ACTGCTTACGGTAGGCTCT Adapted from Salyers and Whitt (2001) Microbiology: Diversity, Disease and the Environment

Oversimplified view of molecular comparison to build phylogenetic trees X is a common ancestor A and B share the most nucleo$des (10), so they diverged from each other more recently than from C B and C share 6 nucleo$des; A and C share 6 nucleo$des; we can t tell which is more closely related to C, thus their distance of separa$on from C is the same. Adapted from Salyers and Whitt (2001) Microbiology: Diversity, Disease and the Environment

Building phylogene$c trees A phylogene$c tree is a structure in which species are arranged on branches that link them according to their rela$onship and/or evolu$onary descent. Gene$c distance is the number of muta$on/evolu$onary events between species since their divergence (but not all muta$on events are revealed in the current sequences). There are many methods that can be used to build trees, each resul$ng in differences in the final outcome. Computers can do much of the work, but human input is needed in much of the decision making. All methods group more similar sequences together. One must be careful not to over- interpret taxonomic informa$on gained through less sophis$cated tree- building methods.

Of the choices listed, which group is the most divergent from its closest rela$ve? B C DEF G A A) Group G B) Group F C) Group C D) Group B

Of the choices listed, which group is the most divergent from its closest rela$ve? B C DEF G A A) Group G B) Group F C) Group C D) Group B The branch length between groups is indica$ve of relatedness

Of the choices listed, which two groups share the most evolu$onary history? B C DEF G A A) Group C and D B) Group B and A C) Group D and E D) Cannot determine

Of the choices listed, which two groups share the most evolu$onary history? B C DEF G A A) Group C and D B) Group B and A C) Group D and E D) Cannot determine The distance between D and E is the same as between E and F; therefore, we cannot determine the answer from these data

Sec$on 9 Learning Goals ü Explain why the ribosomal 16S gene is a good marker for molecular phylogene$c comparisons. ü Be able to interpret a phylogene$c tree. Explain the origins of mitochondria and chloroplasts and the evidence that supports this theory.

Comparison of DNA sequences allows us to compare across all life But the eukaryotes were originally grouped based on phylogene$c traits

What are the differences that dis$nguish the prokaryotes from the eukaryotes?

What are the differences that dis$nguish the prokaryotes from the eukaryotes? Some possible answers: Prokaryotes do not have membrane- bound organelles; eukaryotes do. Prokaryotes reproduce asexually, eukaryotes undergo sexual reproduc$on The prokaryotes are evolu$onarily more ancient and diverse

What are the differences that dis$nguish the prokaryotes from the eukaryotes? Some possible answers: Prokaryotes do not have membrane- bound organelles; eukaryotes do. Prokaryotes reproduce asexually, eukaryotes undergo sexual reproduc$on The prokaryotes are evolu$onarily more ancient and diverse e.g. mitochondria

The evolu$on of mitochondria allowed cells to take advantage of oxygen in cellular respira$on Earth s crust cools First cellular life (prokaryotes) Oldest cyanobacteria fossils (photosynthesis) Oxygen accumula$on First eukaryotes Mul$cellular eukaryotes Early animals oxygena$on 4 3 2 1 0 Billion years from present Using oxygen as a terminal electron acceptor allows extrac$on of much more energy from the input molecule (e.g. glucose)

Models for the origin of the eukaryotic cell Bacteria Eukarya animals plants Ancestor of chloroplast Archaea Nucleus formed Eukarya Ancestor of mitochondrion Bacteria animals plants Archaea Ancestor of chloroplast Nucleus formed Ancestor of mitochondrion Adapted from Brock Biology of Organisms Fig. 14.10 (12 th ed.)

Strong evidence indicates that mitochondria originated as a bacterium that was engulfed by or invaded another cell Mitochondria are the same size and shape of bacteria. Both have small, circular DNA genomes. Mitochondrial replica$on is autonomous from that of the host cell. Both have ribosomes of the eukaryo$c type. The electron transport chain is located in the cell membrane of bacteria (inner membrane of gram- nega$ves) and the inner membrane of mitochondria.

Whole genome analysis supports the hypothesis that the mitochondrial ancestor was most closely related to the Alphaproteobacteria Thrash et al. (2011) Sci Rep. 1:13

Sec$on 9 Learning Goals ü Explain why the ribosomal 16S gene is a good marker for molecular phylogene$c comparisons. ü Be able to interpret a phylogene$c tree. ü Explain the origins of mitochondria and chloroplasts and the evidence that supports this theory.