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?

Did the Cambrian Explosion actually happen?

QuartetsTake fossils for AB and CD, plus molecular data, and

extrapolate the age of the ancestor of ABCD.

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

“Phylogenetic Fuse”Molecular dating suggests origins prior to diversification.

Cambrian phylogenetic fuseCooper & Fortey 1998 TREE

Can we reconcile fossil and molecular evidence?

Marine lakes in Palau (Philippines): a modern day analogue of Vendian

conditions?

Jelly fish with photosynthetic symbioints

Anemones that eat jellyfish

Algal mat on lake floor (45 ft)

Bacterial layer (90 ft)

Is there a link between macroevolution and genomics?

HOX genes

Regulate development of segmentation in animals

Increasing complexity in vertebrates seems correlated with genome duplications

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

Orthology and Paralogy

A B C1 2 34 5 6

1 2 3 4 5 6

OrthologousOrthologous

Paralogous

Gene duplication

Assumption: Gene tree = species tree

A B C1 2 3

Duplication and loss

Duplication event

Lineage goes extinct (gene loss)

gene loss

gene loss

CBA1 2 3

CBA1 2 3

CBA1 2 3

= incongruent gene and species trees

Is paralogy common?

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

Vertebrate gene families

Number of sequences against number of species for gene familiesfrom the Hovergen database

•From Slowinski & Page, 1999 (Syst Biol 48:814)

Incongruent gene and species trees

a

b

c

d

a

b

c

d

organism gene

dcba

bc d

a

1 duplication3 losses

Embedding gene tree inside species tree

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...

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)

Why so many duplications in vertebrates?

• Possibly entire genome duplicated twice (2R hypothesis)

Vertebrates

Vertebrates

Vertebrates

Vertebrates

Drosophila

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-).

Distribution of duplications

Summary

• Gene duplication and loss complicate interpretation of gene evolution

• Gene duplication very important in vertebrate evolution

• Genome duplication hypothesis still open (and controversial)