Gene Families part 2. Review: Gene Families /727 Lecture 8. Protein family. (Multi)gene family

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Virgil Jennings
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1 Review: Gene Families Gene Families part /727 Lecture 8 What is a Case study: ian globin genes Gene trees and how they differ from species trees Homology, orthology, and paralogy Last tuesday 1 2 (Multi)gene family The set of genes that descended from a common ancestral gene. Gene families expand through gene duplication and speciation and contract through gene loss. Typically, genes in the same family encode similar functions, but this is a side effect. Conserved function is neither a necessary nor a sufficient condition for family membership. Protein family The set of proteins encoded by genes that descended from a common ancestral gene. In an evolutionary context, a protein family is a set of proteins encoded by a gene family. Typically, proteins in the same family have similar structures, but this is a side effect. Conserved structure is neither a necessary nor a sufficient condition for family membership

2 Today ian beta globin family Time Gene trees evolve within species trees 5 A A 1 A 2 A 1 A 1 A 2 6 A tree interpretation exercise A tree interpretation exercise Mamma l What does the gene tree look like? FA CA 1 MA 1 HA 1 CA 2 HA 2 A A 1 A 2 A 1 A 1 A 2 7 A A 1 A 2 A 1 A 1 A 2 8 2

3 Reconstructing the evolution of a gene family and its coevolution If we could observe evolution in progress, we would know the rooted tree topology and branch lengths the cause of each divergence (duplication, speciation, HGT ) Reconstructing the evolution of a gene family and its coevolution If you know the species tree and the number of genes in each species what can you say about the history of the the association between ancestral genes and ancestral species how many gene family members were present in each ancestral species A A 1 A 2 A 1 A 1 A 2 9 A A 1 A 2 A A 1 A 2 10 Some plausible hypotheses H1: Lineage specific duplications occurred in birds and primates H2: A duplication occurred in the amniote ancestor and one copy was lost in rodents. Reconstructing the evolution of a gene family and its coevolution What we actually know present day gene sequences the associated species H3: A duplication occurred in the tetrapod ancestor. One copy was lost in amphibians. One copy was lost in rodents. FA CA 1 MA 1 HA 1 CA 2 HA 2 A A 1 A 2 A A 1 A

4 Reconstructing the evolution of a gene family and its coevolution What we can infer from sequences Reconstructing the evolution of a gene family and its coevolution What we can infer the (un)rooted tree topology and branch lengths ttaacatccctcg acatcgtccttaa ttaacatccttag acaacgcccttaa ataacgacctttg ataatgtcctttg We might be able to root the tree in post processing using midpoint rooting minization of dupliations and losses. the (un)rooted tree topology and branch lengths What about. the cause of each divergence (duplication, speciation, HGT )? the association between ancestral genes and ancestral species? how many gene family members were present in each ancestral species? FA CA 1 MA 1 HA 1 CA 2 HA Reconstructing the evolution of a gene family and its coevolution Outline What we can infer the (un)rooted tree topology and branch lengths What about. the cause of each divergence (duplication, speciation, HGT )? the association between ancestral genes and ancestral species? how many gene family members were present in each ancestral species? This information can be inferred by gene tree species tree reconciliation: the topological comparison of a gene tree with a species tree ian beta globin family

5 Reconciling a gene tree with a species tree Outline FA A A 1 A 2 A 1 A 1 A 2 CA 1 D MA 1 HA 1 CA 2 HA 2 17 ian beta globin family 19 Species trees versus gene family trees Species trees versus gene family trees Species trees represent the evolutionary history of a group of species and may be constructed with molecular sequences. Use sequences that are coevolving with the species tree One gene per species No duplication, horizontal transfer or loss. Gene trees represent the evolutionary history of a gene family and must be constructed with molecular sequences. Zero, one or many genes per species Evolve by gene duplication and loss (and horizontal transfer). 5

6 Outline ian beta globin family Terminology review. Homology: the relationship of two characters that have descended from a common ancestral character. FA CA 1 MA 1 HA 1 CA 2 HA Orthologs: characters that have descended from a common ancestral character via speciation. Paralogs: characters that have descended from a common ancestral character via Duplication. FA CA 1 MA 1 HA 1 CA 2 HA 2 FA CA 1 MA 1 HA 1 CA 2 HA

Beta globin evolution in vertebrates Case study: Hemoglobin Time ε/β ε/γ When did the duplications that gave rise to new globin genes occur?

7 Outline alpha beta But fetal β globin (γ) can partially compensate for the sickle cell mutation in adult fetal β globin! ian beta globin family 27 beta alpha, 0 wks 8 wks birth Embryo Fetus Adult In some individuals, fetal globin continues to be expressed into adulthood Beta globin evolution in vertebrates Case study: Hemoglobin Time ε/β ε/γ When did the duplications that gave rise to new globin genes occur? Which globins are most closely related? How is the appearance of new genes related to Frog Wallaby Human β ε β β γ ε new physiology? human disease? Globin expression, embryonic foetal adult 30 7

8 Case study: Long wave opsins Species with two long wave sensitive opsin genes have tri color vision Full 3 color vision Human Baboon Full 3 color vision 2 color 2 color Marmoset 3 color 2 color Howler 2 color Spider Tarsier 31 Hypothesis 1: The ancestor had 2 opsin genes and tri color vision Hypothesis 2: The ancestor had 1 opsin genes and bi color vision One opsin gene was lost in Tarsiers and most new world monkeys Full 3 color vision One opsin gene and tri color vision was gained in Howlers and most old world primates Full 3 color vision 8

9 We can test these hypotheses using evolutionary trees for the long wave opsin gene family Hypothesis 1 Hypothesis 2 Case study: Long wave opsins Was the ancestral primate di chromatic or tri chromatic? Is the current taxonomic distribution of color vision in primates due to parallel gains? Parallel losses? Does tri chromatic vision confer a particular fitness advantage in specific niches? For example, is tri chromatic vision in Howler monkeys linked to their food foraging patterns? (Exercise: Which gene pairs are orthologous? Which gene pairs are paralogous?) 37 9

Classification and Phylogeny

Classification and Phylogeny The diversity of life is great. To communicate about it, there must be a scheme for organization. There are many species that would be difficult to organize without a scheme