Algal phylogeny - content Chapters 5 and 7

Transcription

1 Algal phylogeny - content Chapters 5 and 7 Some principles and expressions in phylogeny Molecular phylgeny - methods Algal phylogeny The origin of plastids

2 What is phylogeny? Phylogeny expresses relationships between organisms (or genes) Which species that share a common close ancestor (nær felles stamform) Phylogenies are hypotheses The tree of life, from Baldauf 2004.

3 Phylogenetic trees - expressions Trees with 4 taxa (e.g. species) internal nodes = ancestors root = common ancestors Terminal and internal branches = changes terminal taxa (monophyletic taxonomic groups) A diagram with branches showing which taxa that share a close common ancestor = sister groups Shows in which order they share a common ancestor with each other a=b and d=e

4 Fylogenetiske trær (in Norwegian) trær med 4 arter interne noder = stamformer rot = felles stamform terminale og interne greiner = forandringer terminale taksa (monofyletisk taksonomisk gruppe) Et diagram med forgreninger som viser hvilke taksa som deler en nær felles stamform= søstergrupper viser i hvilken rekkefølge de deler felles stamform med hverandre a=b og d=e

5 Phylogenetic reconstruction In a set of 4 species there are 15 possible trees. How can we determine which is the best? We cannot observe evolution directly or by experiments We try to reconstruct the evolution based (or inferred/avledet) from common characters by deduction (deduksjon) A. Phylogeny inferred from morphological characters in living organisms and the use of cladistic methods and parsimony B. Molecular phylogeny from molecular evidence (DNA or proteins) and statistical methods It is an advantage to use all available evidence (molecular and morphological) at phylogenetic reconstruction

6 Cladogram and phylogram Bakterie 1 Bakterie 2 Bakterie 3 Eukaryot 1 Eukaryot 2 Eukaryot 3 Eukaryot 4 Bakterie 1 Bakterie 2 Bakterie 3 Eukaryot 1 Cladograms show the order for divergence (branching order), branch length has no meaning Phylograms show the branching order, and branch length indicate the number of evolutionary events or genetic distance Eukaryot 2 Eukaryot 3 Eukaryot 4

7 Characters Only inheritable/arvelige (genetically based) characters can be used in phylogeny (are informative). Characters with different discrete states can be used, morphological and genetical. Characters should be independent Often will a set of characters point towards different phylogenies (incongruence) and then at least one character is misleading. How can we know which characters to trust?

8 Homology inherited similarity Homology: Similarity in two or more taxa in a character that was present in their common ancestor.

9 Homoplasy- not inherited similarity Homoplasy: Similarity that is not a result of inheritance from a common ancestor. The similarity has evolved independently in different lines. Ridley 2003 Homoplasies may appear by convergence or parallell evolution when the selection pressure is the same in different lines.

10 Primitiv or derived (avledet) homology A primitive homology was present in the ancestor of all species. A derived homology evolved later than a common ancestor for all species. Ridley 2003 A is primitiv or derived depending on the species composition

11 Derived homology Common derived homologies = synapomorphy (Felles avledet homologi = synapomorfi) Primitiv homologies = symplesiomorpy (Primitiv homologi = symplesiomorfi) Only derived homologies are reliable evidence for a common ancestry

12 Incongruence If we assume that only one tree is correct: When the characters support different phylogenies (incongruence) we know that at least one character is misleading (e.g. due to homoplasy or primitiv homology) Congruence = two or more characters suggest the same phylogeny

13 Only similarity in synapomorphies (shared derived homology) is evidence for a common ancestor but not symplesiomorphies (primitive homology)

14 Homoplasies (similar traits that independently have developed in different lines) are not evidence for common ancestry (opphav)

15 Molecular phylogeny and out group Based on protein or DNA sequences The unrooted tree is without an order for the branching. We root a tree with an outgroup (if the outgroup is most similar to A the root will be on the branch to A). Ridley 2003

16 Molecular phylogeny possible problems Which sequence to use? Does the region contain the information we look for (it can be to variable or too conserved)? Are there misleading characters?

17 Mutations Molecular evolution is inferred from differneces in the DNA or protein sequences caused by mutations. 1. substitutions 2. deletions 3. insertions 4. inversions

18 DNA and mutations T and C are pyrimidines A and G are purines Transversion: from purin to pyrimidin and the opposite Transition: From purin to purin and pyrimidin to pyrimidin

19 Mutations a= original sequence b= transition from C to T c= transversion from G to C d= deletion e= insertion f= inversion

20 Substitutions Substitutions in protein coding genes can be: a. synonym b. missense: change to a different AA c. nonsense: change to a stopcodon

21 Multiple hits and saturation When two species develop over time DNA will be more and more different. More than one substitutions can be behind a change. Ridley 2003 It is possible to correct for multiple hits in I and II by evolutionary models III: phylogenetic inference impossible Divergence rate decreases when the substitutions start to take place in the same positions At 75% difference thet do not become more different saturation.

22 Molecular phylogeny in the lab. PCR

23 PCR- exponential amplification of DNA

24 Sequencing

25 PCR DNAsequencing

26 An alignment (flersekvenssammenstilling) is a hypothesis on homology of bases (homologi hos baser) Thermus ruber UCCGAUGC-UAAAGA-CCGAAG=CUCAA=CUUCGG=GGGU=GCGUUGGA Th. thermophilus UCCCAUGU-GAAAGA-CCACGG=CUCAA=CCGUGG=GGGA=GCGUGGGA E.coli UCAGAUGU-GAAAUC-CCCGGG=CUCAA=CCUGGG=AACU=GCAUCUGA Ancyst.nidulans UCUGUUGU-CAAAGC-GUGGGG=CUCAA=CCUCAU=ACAG=GCAAUGGA B.subtilis UCUGAUGU-GAAAGC-CCCCGG=CUCAA=CCGGGG=AGGG=UCAUUGGA Chl.aurantiacus UCGGCGCU-GAAAGC-GCCCCG=CUUAA=CGGGGC=GAGG=CGCGCCGA match ** *** * ** ** * ** 16S (SSU) rrna sekvenser fra ulike bakterier U= uracil

27 Ribosomale RNA gener rrna has been shown to be a valuable marker in phylogeny because it is present in all organisms (some differences in prokarytes and eukaryotes), and is present in both the nucleus, chloroplasts and mitochondria. The level of variation varies within the molecule (conserved and variable regions) and between the different organelles. The selection pressure is considered to be rather similar among different orgsnisms since the function of the molecule is the same. It has been used to produce a molecular clock (best when calibrated to fossils)

28 Ribosomal DNA operon in eukaryotes

29 Molecular phylogeny Distance methods group after base similarity Parsimony chose the tree with lowest number of evolutionary events (changes) Maximum likelihood chose the most probable tre when using a model for sequence evolution. Problems may be: an uncertain alignment, a large number of possible trees, large distance and multiple hits, different substitution rates, paraloge genes, horizontal gene transfer etc. Phylogenetic trees are hypotheses! It is advised to compare independent phylogenies from different datasets (use more than one gene)

30 Monophyletic, paraphyletic, and polyphyletic groups Monophyletic= has a common ancestor that no one else shares Paraphyletic=includes monophyletic taxa, but some members in this clade are placed in other systematic groups Polyfyletisk=includes species that are more closely related to other taxa outside the group than in the group.

31 Tree of eukaryotic life by Keeling et al supergroups

32 Phylogeny of plastids

33 Chloroplasts in 7 eukaryotic algal divisions

34 Chloroplasts in 7 eukaryotic algal divisions

35 Chromalveolate hypothesis Cavalier-Smith analysis of six nuclearencoded genes for cytoplasmic proteins strong support for heterokonts + alveolates weak support for haptophytes + cryptophytes chromalveolates paraphyletic..due to horisontal gene transfer (HGT)? or not one common secondary evolutionary event? Harper et al. 2005: J. Syst. Evol. Microbiol. 55:

36 Primary and secondary endosymbiosis

37 Tertiary symbiosis in dinoflagellates

38 Endosymbiotic origin of plastids

39

40 Summary Phylogeny is a hypothesis on the relationships between organisms based on similarities in derived homologous characters Molecular phylogeny uses nucleotide or amino acid sequences or gene organisation as characters Algae are not monophyletic, but are found in all but one of the supergroups. Protists is a polyphyletic group as well.