genes, gene families, and genomes how does genome evolution relate to development and paleontology?...
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Genes, gene families, and genomes
• How does genome evolution relate to development and paleontology?
• Understanding how genomes evolve
• How do we use genomic data to infer phylogeny?
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Did the Cambrian Explosion actually happen?
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QuartetsTake fossils for AB and CD, plus molecular data, and
extrapolate the age of the ancestor of ABCD.
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Date estimates with 95% confidence intervals, given by quartets that passed the rate constancy test for the mitochondrial () and 18S rRNA () alignments, for two deep nodes: the split between vertebrates and echinoderms, and the split between deuterostomes (vertebrates and echinoderms) and protostomes
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“Phylogenetic Fuse”Molecular dating suggests origins prior to diversification.
Cambrian phylogenetic fuseCooper & Fortey 1998 TREE
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Can we reconcile fossil and molecular evidence?
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Marine lakes in Palau (Philippines): a modern day analogue of Vendian
conditions?
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Jelly fish with photosynthetic symbioints
Anemones that eat jellyfish
Algal mat on lake floor (45 ft)
Bacterial layer (90 ft)
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Is there a link between macroevolution and genomics?
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HOX genes
Regulate development of segmentation in animals
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Increasing complexity in vertebrates seems correlated with genome duplications
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Copy A Copy B
Gene duplication
• Two copies of original gene
• Copy B may be “lost” (e.g., lose function due to mutation)
• Copy B may evolve new function (A retains original function)
• Copy B may persist relatively unchanged (provides redundancy)
Original gene
Duplication event
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Orthology and Paralogy
A B C1 2 34 5 6
1 2 3 4 5 6
OrthologousOrthologous
Paralogous
Gene duplication
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Assumption: Gene tree = species tree
A B C1 2 3
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Duplication and loss
Duplication event
Lineage goes extinct (gene loss)
gene loss
gene loss
CBA1 2 3
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CBA1 2 3
CBA1 2 3
= incongruent gene and species trees
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Is paralogy common?
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Rhodopsin
• Gene duplication• Gene loss (and/or)• “missing genes”• Complex relationship
to species tree
0.1
mouse OPSD MOUSErat OPSD RAT
49
hamster OPSD CRIGR
58
human OPSD HUMANrabbit OPSD RABIT
7636
cow OPSD BOVINsheep OPSD SHEEP
98
26
dog OPSD CANFA
100
alligator OPSD ALLMIchicken OPSD CHICK66
63
bullfrog OPSD RANCAfrog OPSD RANPI
100
Xenopus OPSD XENLA
89
salamander OPSD AMBTI93
70
mosquito fish OPSD GAMAFguppy OPSD POERE
100
medeka fish OPSD ORYLA95
goby OPSD POMMI
88
Baikal omul OPSD CORAU
59
goldfish OPSD CARAUcarp OPSD CYPCA
100
zebrafish OPSU BRARE
100
cave fish OPSD ASTFA25
70
eel OPSD ANGAN
82
skate OPSD RAJER
62
29
anole OPSD ANOCA
81
Japanese lamprey OPSD LAMJAlamprey OPSD PETMA
100
93
anole OPSB ANOCAchicken OPSG CHICK
100
gecko OPSB GECGE
98
goldfish OPSG CARAUgoldfish OPSH CARAU
98
cave fish OPSI ASTFA100
99
100
cave fish OPSB ASTFAgoldfish OPSB CARAU
100
chicken OPSB CHICK
100
88
mouse OPSB MOUSErat OPSB RAT
100
cow OPSB BOVIN67
human OPSB HUMAN
97
chicken OPSV CHICK
88
Xenopus OPSV XENLA
100
goldfish OPSU CARAU
100
93
anole OPSR ANOCAchicken OPSR CHICK
100
cave fish OPSR ASTFAgoldfish OPSR CARAU
10060
cave fish OPSG ASTFAcave fish OPSH ASTFA
100
34
gecko OPSG GECGE
59
marmoset OPSL CALJAhuman OPSR HUMAN
52
human OPSG HUMAN
91
goat OPSR CAPHI
99
100
chicken OPSP CHICKpigeon OPSP COLLI
100
83
Drosophila DMRH3ADrosophila DPRH3OP
100
Drosophila DPRH2OPDrosophila DMOPSA
100
81
squid OPSD LOLFOoctopus OPSD OCTDO
100
100
amphibians
sharks
teleost fish
mammals
“reptiles”
birds
lampreys
outgroups
lungfish
Key
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Vertebrate gene families
Number of sequences against number of species for gene familiesfrom the Hovergen database
•From Slowinski & Page, 1999 (Syst Biol 48:814)
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Incongruent gene and species trees
a
b
c
d
a
b
c
d
organism gene
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dcba
bc d
a
1 duplication3 losses
Embedding gene tree inside species tree
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Gene tree parsimony
• We can identify duplications on gene trees, given a species tree
• Gene tree parsimony uses gene trees as characters, choosing the species tree that minimises duplications across a set of gene
family trees
• James Cotton (PhD student) assembled 118 gene family trees from the Hovergen database...
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GallusTrachemysAlligator
Sceloporus
Bos
HomoMusMonodelphisAmbystoma
Xenopus
NeoceratodusProtopterus
Latimeria
Danio
Oryzias
Oncorhynchus
Squalus
Heterodontus
TorpedoRaja
MyxineEptatretus
LampetraPetromyzon
StruthioGallus
ChrysemysAlligatorEumeces
BosHomoMus
DidelphisOrnithorhynchus
TyphlonectesXenopus
Protopterus
LatimeriaPolypterus
CarassiusCyprinus
CrossostomaDanio
OncorhynchusSalmoGadus
MustelusScyliorhinus
SqualusRaja
LampetraPetromyzon
Myxine
Mitochondrial genomes(16,000 bp DNA)
Nuclear genes(118 gene familes)
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Why so many duplications in vertebrates?
• Possibly entire genome duplicated twice (2R hypothesis)
Vertebrates
Vertebrates
Vertebrates
Vertebrates
Drosophila
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Have there been genome duplications in vertebrates?
Different hypotheses about the timing of genome duplication events (polyploidisation) during the evolution of vertebrates.
•Dark block indicates ‘explosion’ of independent dupl. events along a single lineage. Rectangles indicate uncertainty in timing of events. •Modified from Skrabenek & Wolfe, 1996 (Curr Op Genet Dev 8:694-).
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Distribution of duplications
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Summary
• Gene duplication and loss complicate interpretation of gene evolution
• Gene duplication very important in vertebrate evolution
• Genome duplication hypothesis still open (and controversial)