Transcript monkey pig
What is positive selection? dN = rate of nonsynonymous substitution dS = rate of synonymous substitution Let ratio = ratio of dN/dS Positive selection occurs when the ratio exceeds unity __________________________________ Type of Selection Outcome __________________________________ Purifying selection dN/dS < 1 No selection Positive selection dN/dS = 1 dN/dS > 1 __________________________________ How do we test for positive selection? 1. Estimate means and variances of dN and dS for all pair-wise species comparisons. 2. Use t-test to determine if dN and dS differ significantly. Some problems… 1. Averages over all amino acid positions in a protein. Some problems… 1. Averages over all amino acid positions in a protein. 2. Averages over all lineages. Some problems… 1. Averages over all amino acid positions in a protein. 2. Averages over all lineages. 3. Can detect positive selection only when it is very strong and consistent through evolutionary time. Some more problems… 4. Ignores the phylogenetic framework in which adaptive molecular evolution occurs! Suppose a significant ratio is detected between cow and pig 1. Cow 2. Deer 3. Whale 4. Hippo 5. Pig 6. Camel 1 --- 2 ns --- ns = non significant 3 ns ns --- 4 ns ns ns --- 5 3.45 ns ns ns --- 6 ns ns ns ns ns --- A phylogenetic perspective > 1? > 1? > 1? > 1? Cow Deer Whale Hippo Pig Camel Outgroup An example: lysozyme evolution in colobine monkeys • Colobine monkeys are leaf-eaters that have evolved a complex foregut (like ruminants). • Stomach expresses a high level of the bacteriolytic enzyme, lysozyme. Phylogeny of Colobines and Cercopithecines Foregut fermentation evolved Hanuman langur Purple-faced langur Dusky Langur Francois’ Langur Proboscis monkey Guereza colobus Angolan colobus Patas monkey Vervet Talapoin Rhesus macaque Allen’s monkey Olive baboon Sooty mangabey Chimpanzee from Messier & Stewart (1997) Colobines Cercopithecines Phylogeny of Colobines and Cercopithecines = 4.7 Hanuman langur Purple-faced langur Dusky Langur Francois’ Langur Proboscis monkey Guereza colobus Angolan colobus Patas monkey Vervet Talapoin Rhesus macaque Allen’s monkey Olive baboon Sooty mangabey Chimpanzee from Messier & Stewart (1997) Colobines Cercopithecines A Maximum-Likelihood (ML) approach to the detection of positive selection A Maximum-Likelihood (ML) approach to the detection of positive selection ML methods evaluate the probability (i.e., likelihood) of obtaining a set of DNA sequences given: 1. a specific phylogenetic tree 2. an explicit model of nucleotide substitution. Some details of the model… Implemented in the PAML package of Yang (1997) Uses a Markov process to describe substitutions between sense codons Parameters include: transition/transversion ratio () codon frequencies () branch lengths scaled for time (t) Testing for positive selection involves comparing two models: Model M7: Assumes ratios follow a beta distribution (i.e., constrained in the interval 0-1). Testing for positive selection involves comparing two models: Model M7: Assumes ratios follow a beta distribution (i.e., constrained in the interval 0-1). Model M8: Adds a second class of sites to M7 at which ratios can exceed unity (i.e., positive selection). Statistical testing can be done by likelihood ratio tests (LRTs) 1. Obtain log likelihood score from model M7, ℓM7 (null model). Statistical testing can be done by likelihood ratio tests (LRTs) 1. Obtain log likelihood score from model M7, ℓM7 (null model). 2. Obtain log likelihood score from model M8, ℓM8 (positive selection). Statistical testing can be done by likelihood ratio tests (LRTs) 1. Obtain log likelihood score from model M7, ℓM7 (null model). 2. Obtain log likelihood score from model M8, ℓM8 (positive selection). 3. Test for significance: X 2 = 2 (ℓM8 – ℓM7 ) with 1 d.f. Advantages of ML approach 1. Allows for formal statistical testing by likelihood ratio tests. Advantages of ML approach 1. Allows for formal statistical testing by likelihood ratio tests. 2. Allows for individual codons subject to positive selection to be identified. Advantages of ML approach 1. Allows for formal statistical testing by likelihood ratio tests. 2. Allows for individual codons subject to positive selection to be identified. 3. Allows for positive selection to be inferred along individual branches of a phylogeny. Application to the pantophysin gene in marine gadid fishes Pantophysin is an integral membrane protein localized to small (<100 nm) cytoplasmic microvesicles Believed to function in a variety of intracellular shuttling pathways Exact function remains unknown Transmembrane structure of pantophysin T S I V A L V N E E I F A S F N Y P F R L M Q P P G T P V Q Y K C Q K N G V T T E S N F I L S Y N G I T T T S S G A S E P S Y S S C T A G L G L N S V S I V A L F L S G W F F L S L F Y L L G V V I Y F G G Q A V L Q N V V D M-NH2 F I P Y G K R H P R W V G E L C D V F K N L L L S F L P W T R E L A S S L T Y K R Microvesicle membrane I A A P N A L T E F L F S V A S G L G R S V L M A S I H K I I P V G T F S T W T F N D V A G V F A R D S K F S Lumen of microvesicle D V C T T A W E Q P E D A P T N E P T-COOH P A A G F H K S R Cytoplasm Transmembrane structure of pantophysin Intravesicular domains T S I V A L V N E E I F A S F N Y P F R L M Q P P G T P V Q Y K C Q K N G V T T E S N F I L S Y N G I T T T S S G A S E S IV1 Y D G L N S V S I L F L S G W F F L S L Y L L G V V I Y F G G Q A V L Q N V V D M-NH2 F I P Y G K R H P R W V G E L C D V F K N L L L S F L P W T R E L A S S L T Y K R Microvesicle membrane I A A P N A L T E F L F S V A S V A L G R S G L M A F S H K V I A G P V L S I C T T I F IV2 V N G T F G W T A R D S K V Lumen of microvesicle D V C T T A W F A Cytoplasmic (Cyt) domains S S F S TransMembrane (TM) domains P E Q P E D A P T N E P T-COOH P A A G F H K S R Cytoplasm BA105A BS39A BA107A BA108A Genealogy of PanI alleles in the 100 Atlantic cod BA112A BA143A BS21A BS29A IC70A IC74A BS71A BS72A BA126A BA115A BA128A BS49A BS53A BA132A BS81A BS87A NS1A NS12A NS28A NS73A NS79A NS91A NS34A NS41A NS58A NS74A IC2A IC30A NF24A NF42A NF88A NF94A NF142A NF158A NF162A BA138A BA140A BA149A BS20A NS83A NF17A NF73A BS31A BS64A NS68A NS70A IC6A IC8A IC9A IC41A IC80A IC42A IC61A IC78A NF6A NF56A NF11A NF36A PanIA alleles (N = 64) BA105B BA107B BA108B BA112B BA128B NS1B NF88B BA115B BA126B BA132B BA138B BA140B BA143B BA149B BS20B BS21B BS29B BS31B BS39B BS49B BS53B BS64B BS71B BS72B BS81B BS87B NS12B NS28B NS41B NS68B NS70B NS74B NS91B IC2B IC6B IC8B IC25B IC30B IC41B IC42B IC61B IC70B IC74B IC78B IC80B NF11B NF24B NF36B NF56B NF73B NF94B NF158B 100 1 change PanIB alleles (N = 64) NS34B NF6B NF17B NF162B NS58B NS73B NS79B NS83B NF42B NF142B Gadus ogac Amino acid differences between PanIA and PanIB alleles E • T Q • • IV1 SV N P GK P V C K N G Q V T S I V A L E I F A S F N Y P F R L MQ P P T T E S N S • TS G N C T V A G D Y N G I T T G S R D S K F L I D V C T T A W Y S T F L W N A T S T G V S I V A L F L S I S S V F G W F F L S L F L L T A L G V V Y P P R F I Y G R S L T Y K R F G G Q A V L Q N V V D M-NH2 W P H L V G E K C D V F E N L L L S F L P W T R I F L A S V Microvesicle membrane I A E L N A S L L F Y I A S I F G R G V A M K F A H G A E S P V L S Y Lumen of microvesicle S S Cytoplasm K E Q P E D A P T N E P T-COOH P A A G F H K S R Amino acid substitutions within PanI allelic classes _____________________________________________________ ______ Allele Codon Position Amino Acid Change Location Classificationa Distribution in sample _____________________________________________________ ______ PanIA PanIB 61 64 79 43 61 64 Lys to Gln Asn to Thr Ser to Thr Glu to Val Lys to Asn Asn to Asp IV1 IV1 IV1 IV1 IV1 IV1 Radical Radical Radical Radical Radical Radical Fixed Fixed Fixed Fixed Fixed Fixed _____________________________________________________ ______ a following Taylor (1986)