"Nothing in biology makes sense except in the light of evolution"

1. "Nothing in biology makes senseexcept in the light of evolution" Theodosius Dobzhansky (1900-1975)

2. Genomes of living organisms sequencedbetween 1995 and 2002 eubacteria eukaryote Archaea

3. Molecular search for the Last Universal Common Ancestor (LUCA) "All the organic beings that have ever lived on this Earth maybe descended from some single primordial form" Charles Darwin: "Origin of Species" Life appeared on the Earth 3.5 to 3.8 x 109 years ago, soon after the planet was formed (Archean sedimentary rocks).The first phyla that emerge in the tree of life based on rRNA sequences are hyper-thermophylic. This led to the hypothesis that the last universal common ancestor (LUCA) and possibly the original living organism was hyperthermophylic.What was the nature of such a primordial form? How did the transition from this first form of life of all extant biological species take place? What was the LUCA gene content? The computationally- and experimentally-derived (random gene-knockouts) minimal gene-set might be as low as 250-300 genes. The present estimate suggest that LUCA genome could have only 500-600 genes.

4. Late-Archaean biosphere acc. Nisbet i Sleep (2001) Hyperthermophile biofilms and mats Mesophiles Mid-early Archaean Water Mid-early Archaean Hyperthermophiles CO2 SO4 Salt-loving archaea Sulphate reducers Fermenters Methanogens A R C H A E A B A C T E R I A Methanogens (lower T) CH4 H2S Cyanobacteria (oxybenic photosynthesizers) Holdfast Earliest Archaean Earliest Archaean H2 Anoxygenic S photosynthesizers and other purple bacteria Methanogens (hyperthermophile) LUCA S-processing archaea Anoxygenic green photosynthesizers High-T fermenters and hydrogen users Hadean

5. Tree and timescale of life acc. S. B. Hedges, 2002 Eubacteria(Bacteria) Eukaryotes(Eukarya) Archaebacteria(Archaea) Eubacteria(Bacteria) Eukaryotes(Eukarya) Archaebacteria(Archaea) 0 0 Cy Ap Pl An Fu Cy Ap Pl An,Fu 1 1 Ps Am Ps Am? Mi Billion years ago Billion years ago 2 2 Eu? Mi 3 3 Eu Last common ancestor 4 4 Last common ancestor Origin of life Origin of life 1.0 – D. melanogaster 1.15 – C. elegans1.55 – A. thaliana, S. cerevisiae 2.6 – E. coli,3.8 – Methanobacterium thermoautotrophicum An early 1990s view The 2002 view

6. Understanding basic mechanisms of genetic diversity It is estimated that there are now recognized at least 1.5 million living species of all organisms on the Earth. There were many more from the beginning of timescaleof life.The basic mechanisms shaping the evolution of living species are: exon-shuffling,polyploidy,segmental duplication of eukaryotic chromosomes,horizontal gene transfer (HGT),symbiotic and mutualistic associations.

7. Millions of years ago 1000 500 1500 Exon shuffling:An example of ancestral triosephosphate isomerase (2) acc. W. Gilbert et al. (1986) Human (6) Rabbit Chicken (6) Fish Maize (8) Budding yeast (0) Aspergillus (5) Progenote E. coli (0) B. stearothermophilus (0) C. An evolutionary tree from AA sequence

8. Exon shuffling: An example of ancestral triosephosphate isomerase (1) acc. W. Gilbert et al. (1986) A. Three dimentional structureof the enzyme with:coils – α-helices,arrows – β-sheets COOH NH2 14asn 38glu 78ser 108phe 152glu 184val 210gly 238pro 13cys 107glu 183glu 237lys NH2 COOH leu 108 ala181 glu 107 gln 180 ser78 asp152 gly210 glu38 met13 glu 133 trp169 phe 108 glu 132 glu 107 phe240 B. Comparison of proteins sequences of maize, chicken and the fungus Aspergillus

9. Segmentally duplicated regions in the Arabidopsis genome Individual chromosomes are presented as horizontal grey bars. Coloured bands connect corresponding duplicated segments. Duplicated segments in reversed orientation are connected with twisted coloured bands.

10. Horizontal gene transfer (HGT) and the origin of species:lessons from bacteria In bacteria, HGT is widely recognized as the mechanism responsible for the widespread distribution of antibiotic resistance genes, gene clusters encoding biodegradative pathways, pathogenicity and symbiosis determinants. Massive HGT events occurred ~2 billion years ago, when the Earth changed from reducing to oxidizing atmosphere.Bacterial and viral DNA are constantly integrating in the chromosomes of plantsand animals today by conjugation, transformation (T-DNA of A. tumefaciens), retroviruses and integrative viruses.

11. Why are the genomes of endosymbiotic bacteria so stable? Bacterial genomes are continuously modified by the gain and loss of genes. HGT is one of the most important mechanisms of bacterial evolution.The comparative analysis of endosymbiotic bacterium Buchnera aphidicola (640 kb) has revealed high genome stability associated with the absence of chromosomal rearrangements and HGT events during the past 150 million years. The loss of genes involved in DNA uptake and recombination in the initial stages of endosymbiosis underlies this stability. By contrast, two strains of E. coli: K-12 and OH 157:H7 with only 4.5 Myr of divergence, exhibit genomes whose homology is interrupted by hundreds of DNA segments.Extensive loss of genes is a general attribute of the evolution of endosymbiotic bacteria. Genome stability of microsymbionts is responsible for its co-evolution with the eukaryotic hosts. This is not the case for facultative symbionts whose genomes are much larger (e.g. rhizobial species symbiotising with legume plants; 4.5 – 7.5 Mb).

12. Symbiotic interaction between legume and nodule-forming rhizobia Root hair cell Sucrose Rhizobia HOST CELL Infection thread Malate (invagination of root hair cell membrane) BACTEROID N N Fixation Nod gene activation 2 2 Infected cell + NH Symbiosome 4 membrane Glutamine Asparagine Rhizobia enter the root cortex Matabolism of infected cells in a root cell through the infection thread nodule. Glutamine and asparagine are the main products of N2 -fixation

13. Yellow lupine root nodule morphology Cross – section of lupine nodule (42 dpi) nodule cortex bacteroid tissue meristematic zone vascular bundle Mature lupine root nodules (42 dpi)

14. Primate phylogenetic relationship based on molecular and fossil record analyses Haplorhini Simiiformes Catarrhini Cercopithecoidea Hominoidea PlatyrrhiniCebus LemuriformesLorisiformesGalago CercopithecinaeColobinaeMacaca TarsiiformesTarsilus HylobatidaeHylobatesSymphalangus PongidaePongo HominidaeGorilla Pan 0 Homo 4-6 7-9 Mya 14 18 25 35-45 50-60 65-85 Modern humans (Homo sapiens) and chimpanzees (Pan paniscus and Pan troglodytes) are located in the same genus (Homo) with a common ancestor living 4-6 Mya. A divergence 7-9 Mya is accepted for separation of gorilla (Gorilla) and Homo clade. An estimate of 14 Mya for the divergence of orangutan (Pongo) and African Apes. Gibbon lineage divergence took place about 18 Mya. The Old World monkeys (Cercopithecoidea) include many primate species with baboons (Papio), mandrills (Mandrillus) and Cercopitheques (Cercopithecus) mainly found in Africa as well as macaques (Macaca) predominant in Asia. Divergence for Hominoidea and Cerco-pithecoidea was estimed to 25 Mya.

15. Birth of "human-specific" genes importantfor primate evolution Humans and the Great African Apes share very similar chromosome structure and genomic sequence at the DNA level with 98.5-99% homology (chimpanzee).What makes us different at the genetic level from the closest relatives - Antropoids? A recent major breakthrough was identification of "human-specific" genes. Also, specific chromosomal regions have been mapped that display all the features of "gene nurseries" and could have played a major role in gene innovation and speciation during primate evolution.Two highly conserved human genes were identified (PRM2, histon-like protein essential to spermatogenesis and FOXP2-transcription factor involved in speechand language development) which were probably the selection targets in recent human evolution.