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Molecular Phylogeny and Evolution Molecular Phylogeny and Evolution 10 – 14 February 2020 Juan I. MONTOYA BURGOS Lab of Molecular Phylogeny and Evolution in Vertebrates Title of the course: Molecular Phylogeny and Molecular Evolution Evolutionary relationships among organisms = tree topology A better understanding of molecular evolution improves: First phylogenetic methods did not - topology and branch length make use of models of molecular reconstruction (=phylogenetic tree) evolution (UPGMA, Maximum Parsimony) Better phylogenetic trees improve: - the understanding of evolutionary processes => Models of molecular evolution Lab of Molecular Phylogeny and Evolution in Vertebrates 1 Why should we care about phylogenies? Are you using phylogenetics ? Lab of Molecular Phylogeny and Evolution in Vertebrates Current phylogenetic methods allow: - reconstruction of evolutionary relationships But also the analysis of: Gene/genome duplication Recombination Evolutionary rates Divergence time among lineages Selective pressure Demography Biodiversity Genetic variability Conservation Biogeography Spread of contagious disease Discovery of biomedical compounds Adaptive evolution Biomonitoring Protein-protein co-evolution And more …. Lab of Molecular Phylogeny and Evolution in Vertebrates 2 Phylogenetic analyses: many uses Understanding evolutionary relationships Determining the closest extant relative to tetrapods Amemiya et al., 2013. The African coelacanth genome provides insights into tetrapod evolution. Nature 496. Lab of Molecular Phylogeny and Evolution in Vertebrates Phylogenetic analyses: many uses Understanding morphological evolution Using a species-level phylogeny of Aquilegia, Whittall and Hodges showed a significant evolutionary trend for longer nectar spur during directional shifts to pollinators with longer tongues (moths). Whittall and Hodges, 2007. Pollinator shifts drive increasingly long nectar spurs in columbine flowers. Nature 447, 706-709 Lab of Molecular Phylogeny and Evolution in Vertebrates 3 Phylogenetic analyses: many uses Understanding bio-diversification Calibrated phylogeny of Zosterops and relatives Moyle et al. 2009. Explosive Pleistocene diversification and hemispheric expansion of a "great speciator." PNAS Lab of Molecular Phylogeny and Evolution in Vertebrates Phylogenetic analyses: many uses Understanding bio-diversification Calibrated phylogeny of Zosterops and relatives Lineage-through-time plots (LTT) Moyle et al. 2009. Explosive Pleistocene diversification and hemispheric expansion of a "great speciator." PNAS Lab of Molecular Phylogeny and Evolution in Vertebrates 4 Phylogenetic analyses: many uses New biodiversity 1 Unexpected diversity in the catfish Pseudancistrus brevispinis 2 reveals dispersal routes in a Neotropical center of endemism: the 3 Guyanas Region 4 5 6 YAMILA P. CARDOSO1 and JUAN I. MONTOYA-BURGOS 1* 7 8 9 10 11 1 Department of Zoology and Animal Biology, University of Geneva, 30 quai Ernest 12 Ansermet, 1211 Geneva 4, Switzerland Lab of Molecular Phylogeny and Evolution in Vertebrates Phylogenetic analyses: many uses New biodiversity 1 species à 6 species Lab of Molecular Phylogeny and Evolution in Vertebrates 5 Phylogenetic analyses: many uses Biogeography Biogeography: four possible entrance scenarios Topological tests: -SH test -AU test Lab of Molecular Phylogeny and Evolution in Vertebrates Phylogenetic analyses: many uses DNA taxonomy of Animals: species identification Hebert et al. PNAS 101:14812 (2004) Lab of Molecular Phylogeny and Evolution in Vertebrates 6 Phylogenetic analyses: many uses Evolutionary rates and selective pressure acting on genes The evolutionary histories of genes bear the marks of the functional demands to which they have been subjected. A maximum likelihood phylogenetic tree of Hmr built by the free-ratio model in PAML FIG. 3.ﾑ A maximum likelihood phylogenetic tree of Hmr built by the free-ratio model in PAML. The likelihood of this model was significantly better than the one-ratio model (2l = 54.224, degrees of freedom = 11, P < 10ﾐ7). The tree length is defined as the number of nucleotide substitutions per codon. The number shown above each lineage is the estimated DN/ DS value of that lineage Maheshwari, S. et al. Mol Biol Evol 2008 25:2421-2430; doi:10.1093/molbev/msn190 Lab of Molecular Phylogeny and Evolution in Vertebrates Phylogenetic analyses: many uses Analysis of: - duplicated genes - gene families - genome duplication / polyploidisation Lab of Molecular Phylogeny and Evolution in Vertebrates 7 REVIEWS REVIEWS Phylogenetic analyses: many uses COMPUTATIONAL TOOLS COMPUTATIONAL TOOLS EmergingEvolution methods and selectionEmerging in protein on proteins, methods protein in protein co-evolutioninteractionsco-evolution and protein networks David de Juan1, Florencio Pazos2 and AlfonsoDavid Valencia de Juan11, Florencio Pazos2 and Alfonso Valencia1 Abstract | Co-evolution is a fundamental componentAbstract of| Co-evolution the theory of is evolution a fundamental and is component of the theory of evolution and is essential for understanding the relationshipsessential between for species understanding in complex the ecological relationships between species in complex ecological networks. A wide range of co-evolution-inspirednetworks. computational A wide range methods of co-evolution has been -inspired computational methods has been designed to predict molecular interactions, butdesigned it is only to recentlypredict molecular that important interactions, advances but it is only recently that important advances have been made. Breakthroughs in the handlinghave of been phylogenetic made. Breakthroughs information inand the in handling of phylogenetic information and in disentangling indirect relationships have resulteddisentangling in an improved indirect capacity relationships to predict have resulted in an improved capacity to predict interactions between proteins and contacts interactionsbetween different between protein proteins residues. and contacts Here, we between different protein residues. Here, we review the main co-evolution-based computationalreview the approaches, main co-evolution their theoretical-based computational basis, approaches, their theoretical basis, potential applications and foreseeable developments.potential applications and foreseeable developments. As a part of evolutionary theory, co-evolution is essential Tools at the residue level were inspired by the existence Molecular phylogenetics As a part of evolutionary theory,Molecular co-evolution phylogenetics is essential Tools at the residue level were inspired by the existence The study of evolutionary for understanding living systems.The study In itsof evolutionarysimplest definition, for understandingof interdependent living changes systems. inIn groupsits simplest of variable definition, amino of interdependent changes in groups of variable amino phenomena using biomolecular co-evolution refers to the coordinatedphenomena using changes biomolecular that occur co-evolution acids, as refersformulated to the coordinated for the first changes time by that the occur covarion acids, as formulated for the first time by the covarion data, generally in the form of in pairs of organisms or biomolecules,data, generally typically in the form to of mainin- pairsmodel of 6organisms, and they or typically biomolecules, use the typically multiple to mainsequence- model 6, and they typically use the multiple sequence Lab of Molecular Phylogenysequences and of Evolution nucleic acids in Vertebrates sequences of nucleic acids tain or to refine functional interactions between thosetain alignmentor to refine (MSA) functional for ainteractions protein family between of homologues those alignment (MSA) for a protein family of homologues or proteins. or proteins. pairs. Darwin himself initiated the study of co-evolution,pairs. to Darwin search forhimself correlated initiated mutations the study. Such of co-evolution,correlated muta -to search for correlated mutations. Such correlated muta- Covarion model and his observation on the Covarionrelationship model between the sizeand tionshis observation are suggestive on the of compensatory relationship between changes the that size occur tions are suggestive of compensatory changes that occur A phylogenetic model in of orchids’ corollae and the lengthA phylogenetic of the modelproboscis in of polof- orchids’between corollae entangled and theresidues length (for of the example, proboscis those of inpol prox- -between entangled residues (for example, those in prox- which the evolutionary linators led him to predict successfullywhich the evolutionary the existence of alinators imity, led direct him to contact predict or successfully acting together the existence in catalytic of a orimity, direct contact or acting together in catalytic or rate of different codons rate of different codons new species that was able to suck from the large spur of binding sites) to maintain protein stability, function are interdependent. new species that was able toare suck interdependent. from the large spur of binding sites) to maintain protein stability, function Darwin’s orchid. The studies of Dobzhansky1 and othersDarwin’s2 or folding orchid.7–10 The. Furthermore, studies of Dobzhansky extending1 andthese others methods2 or folding7–10. Furthermore, extending these methods Phylogenetic analyses: many uses Protein family contributed to the establishmentProtein of family this concept in geneticcontributed to search to the for establishment correlated ofmutations this concept between in genetic
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