Convergent evolution of the genomes of marine mammals - PowerPoint Presentation

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Convergent evolution of the genomes of marine mammals - PPT Presentation

Gregg Thomas Indiana University SMBE 2014 Convergent evolution is observed at the phenotypic level Porcupine Rodentia Echidna Monotremata Hedgehog Erinaceomorpha 2 Predictable Evolution ID: 930876

mammals convergence molecular convergent convergence mammals convergent molecular marine elephant dolphin killer whale walrus manatee dog cow land alpaca

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Slide1

Convergent evolution of the genomes of marine mammals

Gregg Thomas

Indiana University

SMBE 2014

Slide2

Convergent evolution is observed at the phenotypic level

Porcupine

(

Rodentia

)

Echidna

(Monotremata)

Hedgehog

(Erinaceomorpha)

Slide3

Predictable Evolution

If phenotypic convergence can be attributed to specific molecular changes, it would suggest that evolution is to some extent predictable

We have very few examples…

Slide4

Phenotypic convergence can be attributed to molecular convergence

Lysozyme

(

Kornegay

et al, 1994)

Prestin

(Parker et al 2013, Li et al 2010, Liu et al 2010)

COCH

(Parker et al

2013)

Foregut fermenters

Echolocation

Slide5

Marine mammals provide a chance to study molecular convergence

Slide6

Convergent phenotypes of marine mammals

Hydrodynamic body structure with reduced neck length

Sensory adaptations

ight in low light environments

Changes in ear structure to accommodate hearing in high pressure

Changes in respiratory and cardiac patterns depending on how long and deep the animal dives

Variations in bone density based on dive depth

Insulating blubber layer

Slide7

Marine mammal genome sequencing

16,878 orthologous protein coding genes between the four marine mammals and

ten

other

mammals

5,900

orthologs

which

are present in all 4 marine mammals and their sister land mammals (cow, dog, elephant)

Slide8

Detecting molecular convergence

Ancestral reconstruction implemented

PAML v4.7

Controlled for

CpG

sitesVarious cutoffs for confidence in ancestral sites

Slide9

Convergent substitutions

Slide10

Simulations suggest excess convergence

Alpaca

Cow

Dolphin

Killer Whale

Dog

Walrus

Elephant

Manatee

44 convergent substitutions

Slide11

Positively selected genes are also convergent

Slide12

Adaptive convergent genes are related to convergent phenotypes

Gene

Function

Associated phenotype

GCLC

Glutathione metabolism

Antioxidation during long dives

S100a9

Calcium binding

Bone formation

Mgp

Calcium binding

Bone formation

Smpx

Inner ear formation

Separation of the auditory bulla from the skull in the inner ear

Myh7b

Cardiac muscle formation

Cardiovascular regulation during diving

Serpinc1

Blood coagulation

Low flow rate of viscous blood particularly during diving

Slide13

Molecular convergence has been demonstrated

Phenotypic convergence can be inferred on a genome wide scale at the molecular level

But another comparison can be made…

Slide14

Marine mammal convergence

Alpaca

Cow

Dolphin

Killer Whale

Dog

Walrus

Elephant

Manatee

Slide15

Land mammal convergence

Alpaca

Cow

Dolphin

Killer Whale

Dog

Walrus

Elephant

Manatee

Slide16

Expectations for molecular convergence in land mammals

Any molecular convergence observed should be due to chance

There should be less convergence than we found for marine mammals

Slide17

Convergent substitutions in land mammals

Alpaca

Cow

Dolphin

Killer Whale

Dog

Walrus

Elephant

Manatee

93 convergent substitutions

Slide18

Simulations suggest excess

convergence even among land mammals

93 convergent substitutions

Alpaca

Cow

Dolphin

Killer Whale

Dog

Walrus

Elephant

Manatee

Slide19

Land mammals have more convergence than marine mammals

Alpaca

Cow

Dolphin

Killer Whale

Dog

Walrus

Elephant

Manatee

Slide20

Positive selection comparable between marine and land mammals

Marine Mammals

Land Mammals

Slide21

Genes can have more than one convergent site

= convergent substitution

Slide22

Genes with multiple convergent sites are more prevalent in land mammals

Slide23

What we have learned from marine mammals

Some intriguing genes linking molecular and phenotypic convergence

Surprisingly, just as much molecular convergence among land mammals

Simulations do not fully account for background convergence

Slide24

What we have learned from marine mammals

Some intriguing genes linking molecular and phenotypic convergence

Surprisingly, just as much molecular convergence among land mammals

Simulations do not fully account for background convergence

Slide25

Simulations do not provide an adequate null model

Difference between observed and simulated numbers of convergent substitutions

Value =

(% observed - % simulated)

Manatee

Elephant

Walrus

Dog

Cow

Killer Whale

Dolphin

Alpaca

Rat

Mouse

Marmoset

Baboon

Macaque

Human

Manatee

Elephant

Walrus

Dog

Cow

Killer Whale

Dolphin

Alpaca

Rat

Mouse

Marmoset

Baboon

Macaque

Human

Slide26

Simulations do not provide an adequate null model

Manatee

Elephant

Walrus

Dog

Cow

Killer Whale

Dolphin

Alpaca

Rat

Mouse

Marmoset

Baboon

Macaque

Human

Manatee

Elephant

Walrus

Dog

Cow

Killer Whale

Dolphin

Alpaca

Rat

Mouse

Marmoset

Baboon

Macaque

Human

Slide27

Molecular convergence of echolocation

Echolocatin

Slide28

Molecular convergence of echolocation

Echolocatin

Non-

echolocating

Slide29

Convergence and echolocation genes

2525

Slide30

Convergence and echolocation genes

2525

Prestin

OTOF COCH

Slide31

Convergence and echolocation genes

Prestin

OTOF COCH

Slide32

Conclusions

Phenotypic convergence can be attributed to molecular convergence, but this is rare

Simulations do not provide an adequate null model for convergence

Our results suggest that evolution is not easily predictable

Slide33

Acknowledgements

Matt Hahn

Collaborators:

Andy Foote

Kim WorleyTomas Vinar

Colleagues:James PeaseSimo

ZhangFabio MendesRafael GuerreroMelissa ToupsJeff Adrion

Genome Assembly

Yue Liu

Jixin

Deng

Carson

Sequencing

Project Managers

Vandita

Joshi

Shannon Dugan

Sequencing

Ziad

Khan

Christie Kovar

Sandra Lee

Donna

Muzny

RNAseq

analysis

Xiang Qin

Tissue Samples for Dolphin

Annalaura

Mancia

Manatee Sequencing

Kerstin

Lindblad-Toh

Jessica

Alföldi

Tissue samples for walrus and killer whale

Nils van Elk

Multi-genome alignment

Brian J. Raney

Bioinformatics and statistical support

Rasmus

Nielsen

Nagarjun

Vijay

Jochen

Wolf

Principal Investigators

Richard Gibbs

Thomas Gilbert

Images:

P:Yellowstone

Digital Slide

File, E: australiazoo.com,

H: instagram.com/

biddythehedgehog

H: amazonwiki.org, E:

asu.edu,

jlhweb.net/BOSS/AKCstandard.html,

B: John Gould from The Zoology of the Voyage of H.M.S. Beagle

Convergent evolution of the genomes of marine mammals - PowerPoint Presentation

Convergent evolution of the genomes of marine mammals - PPT Presentation

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