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Evolution and Diversity of Fishes

B. Venkatesh

Institute of Molecular and Cell Biology, A*STAR

Singapore

Lobe-finned fishes

and Tetrapods

Teleost fishesSpotted garSturgeon

Bichir

Bony Fishes (Osteichthyes)

https://commons.wikimedia.org/w/index.php?curid=24336974

Devonian – The Age of Fishes

Tetrapods

Teleost fishesSpotted garSturgeon

Bichir

Bony Fishes (Osteichthyes)

Lungfish

Coelacanth

Lobe-finned

fishes

Water to Land Transition

Tetrapods

Teleost fishesSpotted garSturgeon

Bichir

Bony Fishes (Osteichthyes)

Lungfish

Coelacanth

Lobe-finned

fishes

Which Living Fish is the Closest to Humans?

Coelacanth

Lungfish Coelacanth

Lungfish

Coelacanth

Lungfish

Genome size

3.0 Gb

2.9 Gb

40 - 130 Gb

1.0 GbSpotted gar

Coelacanth – A Living Fossil

Coelacanth genome sequenced in 2013

Closest fish to human

Amemiya et al., Nature 2013

Lungfish is the closest to land animals

Bayesian tree (251 genes)

Mammals

Birds

Amphibians

Ray-fin

fishes

Non-avian

reptiles

Cartilaginous

fishes

Lobe-fin

fishes

100200300400500 Myr

Tetrapods

Jawless

vertebrates

Transition from Aquatic to Terrestrial life

Fin-to-limb transition

zebrafish

fin raysdistal radials

mouse

stylopod

zeugopodautopod

Dogfish shark

“distal radials”ceratotrichia

HoxD cluster and long-range autopod enhancers

800 kb

Island1 Island2 Island3 Island4

Montavon T. et al. Cell 2011

Early phase HoxD gene expression: patterns the stylopod and zeugopod

Late phase HoxD gene expression: development of digits

HoxD cluster and long-range autopod enhancers

800 kb

Island1 Island2 Island3 Island4

Montavon T. et al. Cell 2011

Transgenic mouse embryos (E12.5)

Human

ChickenFrog

CoelacanthFugu

MedakaStickleback

Zebrafish

E shark

Atf2 Atp5g3 Lnp Evx2 Mtx2HoxdIs1 Is2 Is3 Is4 GCR ProxMouse

Amemiya et al., Nature 2013

Coelacanth Is1 expression in transgenic mouse (E12.5)

Limb budLimb buds

Conserved noncoding elements in HoxD locus

Teleost fishesSpotted garSturgeon

Bichir

Bony Fishes (Osteichthyes)

Lobe-finned fishes

and Tetrapods

https://commons.wikimedia.org/w/index.php?curid=24375559

Evolution of ray-finned fishes

Bony Fishes (Osteichthyes)

14 species27 species 8 species

33,200

species

30,500

species

Non-avian reptiles14.9%

Birds16.3%

Mammals9.2%

Amphibians11.6%

Teleosts: the largest group of vertebrates

Teleost fishes47.8%

What is the genetic basis of phenotypic variation?

Most diverse group of vertebrates

~30,500 species

Teleost fishesSpotted garSturgeon

Bichir

Bony fishes (Osteichthyes)

Lobe-finned fishes

and Tetrapods

Whole Genome

Duplication

WGD

Clarke JT et al. PNAS 2016

Phenotypic variation in Holosteans and Teleosts

Fossil+extant holosteans

(only 8 extant species)

Stem-group teleosts

Crown-group teleosts

(a) Teleosts do not show enhanced phenotypic evolution relative to holosteans

WGD

(b) Uneven diversification rate

Near et al. PNAS 2012; Santini et al. BMC Evol Biol 2009

WGD

8,900 species(Ostariophysi)

15,640 species(Percomorpha)

(c) Time lag between WGD

and major diversifications

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Cichlid Fishes(>2,200 species)

Tarang Mehta

No Whole-Genome Duplication in cichlid lineage

Colour patterns

Lake Tanganyika species Lake Malawi species

Julidochromis ornatus

Tropheus brichardi

Cyphotilapia frontosa

Melanochromis auratus

Pseudotropheus microstoma

Cyrtocara moorii

Lake Victoria Lake Malawi Lake Tanganyika Lake Nicaragua

H. chilotes M. labrosus L. labiatus A. labiatus

EV

OLU

TIO

NA

RY

PA

RA

LL

ELIS

M

Thick-lipped phenotype

Salzburger, W. (2009)

EAST AFRICAN CICHLIDSVictoria

Tanganyika

Malawi

Brawand et al. Nature 2014

15,000-100,000 years

10-12 million years

<5 million years

Lake Victoria (~500 species)

Lake Tanganyika (~250 species)

Lake Malawi (~500 species)

A. burtoniO. niloticus

Summary

‣ Accelerated evolution of protein-coding sequence

‣ Transposable element insertions altering gene

expression

‣ Increased gene duplication with new expression

patterns

‣ Regulatory sequence evolution

Genome sequence

Lake representatives

N. brichardiP. nyererei M. zebra

Lake Victoria Lake Tanganyika Lake Malawi

Riverine

Regulatory Sequence Evolution

Medaka

Medaka

Medaka

Alvin Ng, Zhi Wei Lim and Venkatesh

O. niloticus (Nile tilapia) CNE

P. nyererei (Lake Victoria) CNE

Phenotype:

Sexual dimorphism

Ecotype:

Ecological opportunities

Genotype:

Genome plasticity

Adapted from Seehausen, O. (2015)

MAJOR DRIVERS OF ADAPTIVE RADIATION OF AFRICAN CICHLIDS

seahorses

seadragons

pipefish

pipefish

Seahorses, pipefish and seadragon

Hamilton et al. 2016

‘Extreme phenotypes’

Dorsal fin

Pectoral finPelvic fin

Anal fin

Caudal fin

Specialized Morphology of Seahorse

Brood pouch

Male seahorse

Salmon

No pelvic fin

No teeth

Fused jawsTube-like mouth

No caudal fin

Prehensile tail

No scales

Bony plates

Mating seahorses

Photograph: George Grall/Getty Images/National Geographic

Birthing Father

Credit: Rudie Kuiter

Tiger tail seahorse (Hippocampus comes)

IUCN List of Threatened Species: “Vulnerable”

Seahorse Genome

Seahorse

Nile tilapia

Platyfish

Medaka

Stickleback

Fugu

Mudskipper

Zebrafish

Spotted gar

0.04

0.463

0.415

0.443

0.460

0.437

0.454

0.450

0.422

Seahorse protein sequences evolving faster

4,122 protein sequences; ML treeLin et al. Nature 2016

Seahorse

Nile tilapia

Platyfish

Medaka

Stickleback

Fugu

Zebrafish

Spotted gar

1.924

1.693

1.919

1.868

1.8885

1.748

1.818

1.622

0.2

Mudskipper

Seahorse nucleotide sequences evolving faster

Neutral tree based on four-fold degenerate (4D) sites)

• SCPP genes critical for skeletal mineralization

• Present in all bony vertebrates

• Two groups – Acidic SCPP and P/Q-rich SCPP

mineralization of bone

and dentin

Enamel or enameloid

formation

Secretory calcium-binding phosphoprotein

(SCPP) gene family

Secretory Calcium-binding Phosphoprotein (SCPP)

genes

Chr4ChrX

Human genome

Acidic SCPP genes – bone and dentine

Proline/Glutamine-rich SCPP genes – enamel

milk, saliva, tears

17 Mb

Fugu Chr17

Seahorse scaf51 scaf_232

Zebrafish Chr1 Chr10 Chr5

Chr4ChrXHuman

Seahorse has lost P/Q-rich SCPP genes

Acidic SCPP genes

P/Q-rich SCPP genes

Toothless vertebrates (‘edentulism’)

All turtles Baleen whaleAll birds Pangolin

Loss of all enamel-related and dentin-related genes

Seahorse

Mutations in some or all of enamel-related and dentin-related genes

Meredith et al. Science 2014

Pitx1/Pitx2, Tbx4/Tbx5

Tanaka et al. Dev Biol 2005

Pitx2

Forelimb (Pectoral fin)

Hindlimb (Pelvic fin)

Loss of pelvic fins

Marcil et al. Development 2003

tbx2 tbx4 brip1

Seahorse

Fugu

Stickleback

Zebrafish

Tbx4 gene is missing in seahorse

Lin et al. Nature 2016

Lin et al. Nature 2016

CRISPR-Cas9 mediated knockout of Tbx4 in zebrafish

Loss of pelvic fins

Wild type

ventral ventral

WT tbx4- / -

Tbx4 knockout

Loss of Tbx4

IntactTbx4

IntactTbx4

IntactTbx4

Loss of pelvic fins

Freshwater stickleback

Near et al. 2012

Male pregnancy

Astacin metalloprotease subfamily (C6AST)

High choriolytic enzyme (HCE)

Low choriolytic enzyme (LCE)

Hatching enzymes

Patristacin (pipefish)

Expansion of a gene family

Expansion of patristacin gene family

Patristacin genes express in male brood pouch

Lin et al. Nature 2016

Expansion of patristacin gene family

Platyfish – ovoviviparous (‘female pregnancy’)

Genetic basis for the specialized phenotype of seahorse

Higher molecular evolutionary rate

Loss of some crucial genes

Expansion of some gene families with novel expression pattern

High turnover of regulatory elements

‘Nature’s gift to Science’