The African coelacanth genome provides insights into tetrapod

evolution Amemiya, C. T. et al. Nature

(2013)

Presented by: Noam Perry

Zina Deretsky, National Science Foundation

Today I will talk about…

• Tetrapods & evolution

• The coelacanth – a living fossil

• Methods & results

• Conclusions

Ted Daeschler, National Science Foundation

Tetrapods• The superclass of Tetrapods has four classes:

amphibians, reptiles, birds, and mammals.

• The tetrapods evolved from the lobe-finned fishes about 395 million years ago in the Devonian period.

• The specific aquatic ancestors of the tetrapods, and the process by which land colonization occurred, remain unclear.

Tetrapod evolutionlobe-finned fish, like Eusthenopteron, exhibited a

sequence of adaptations. The Tiktaalik had limb-like fins

that could take it onto land. Early tetrapods in weed-

filled swamps, such as Ichthyostega had real limbs.

Living on land has its perks

• More oxygen

• More food

• No predators

• No competition

"coelacanth" comes from the Greek for "hollow spine“—a reference to the hollow spines that are part of its fin structure.

These nocturnal animals hide in underwater caves by day (100m), then venture out at night, feeding on small fish, squid, and octopus.

The coelacanth's slow, graceful stroke is like no other fish's. It moves left pectoral and right pelvic fins, then right pectoral and left pelvic fins—akin to the cross-step of tetrapods.

©Laurent ballesta

An extra tail lobe, unique to coelacanths, can be seen today and in fossils from millions of years ago.

the coelacanth – a living

fossil

© Laurent ballesta

the coelacanth – a living

fossil

Kingdom: Animalia

Phylum: Chordata

Class: Sarcopterygii

Subclass: Actinistia

Order: Coelacanthiformes

Two living species were discovered :

1938 – African coelacanth

1997 - Indonesian coelacanth (Latimeria menadoensis).

(Latimeria chalumnae)

wikipedia

http://animals.nationalgeographic.com/animals/fish/coelacanth/

In the past 15 years, targeted sequencing efforts have produced the sequences of the coelacanth mitochondrial genomes, HOX clusters and a few gene families. Yet, more data was needed.This article describes the sequencing and comparative analysis of the genome of Latmeria chalumnae, the African coelacanth. Named after Marjorie Courtenay Latimer, who found the unusual fish in 1938.

the coelacanth – a living

fossil

• Genome Assembly & Annotation

• The closest living fish relative of the tetrapod ancestor

• The slowly evolving coelacanth

• Vertebrates adapting to land: - lost genes

- CNE’s - Globin types - Urea cycle - IgM vs. IgW

Methods & Results

Genome Assembly & Annotation

• The coelacanth's genome is approx. 2.86 Gb.

• 19,033 protein coding genes containing 21,817 transcripts.

RNA Genomic DNA

Muscle sample (>20 years)

Blood sample (2004) Source

Illumina Illumina Sequencing

Trinity ALLPATHS-LG Assembly

The closest living fish relative of the tetrapod ancestor

Scientists believe the closest living fish related to ‘the fish that first crawled on to land’ is either the lungfish or the coelacanth. To find out which one is closest, a comparison was made between the lungfish and selected tetrapods.

251 genes, with a 1:1 orthology ratio, were chosen to create a phylogenic tree.

http://photos.zoochat.com

Amemiya, C. T. et al. (2013)

Tetrapods are more closely related to lungfish than to the coelacanth.

The slowly evolving coelacanth

Some gene families, like Hox and protocadherins, have slower protein-coding evolution in coelacanth than in other vertebrate lineages. The substitution rate in coelacanth is approximately half that in tetrapods since the two lineages diverged.

the coelacanth genome contains a wide variety of transposable element s and has a relatively high transposable-element content (25%).

slow protein evolution vs. a lot of transposons!

Vertebrates adapting to land

Critical characters in the morphological transition from water to land are reflected in the loss of specific genes along the phylogenetic branch leading to tetrapods.

Homebox genes which are responsible for the development of an organism’s basic body plan, have remained largely conserved during the vertebrate land transition.

Other genes were not so lucky...

Some of the lost genes:

Blue – fin development

And1 & And2 – code for actinotrichia – which stiffens fin folds.

Acvlr1 – codes BMP receptor for fin tail

Red – ear development

Otomp gene is essential for otolith formation in the zebrafish ear.

M. Courtenay-Latimer

Amemiya, C. T. et al. (2013)

• Changes occurred not only in gene content but also in the regulation of existing genes.

• Conserved non-coding elements (CNEs) that changed in tetrapods are involved with smell perception, morphogenesis, cell differentiation, and immunoglobulin recombination.

Vertebrates adapting to land

Amemiya, C. T. et al. (2013)

Regulatory elements near in the hoxD gene:

• The coelacanth is the only known vertebrate that includes all eight globin types.

• the coelacanth is a globin "fossil", providing the toolbox for tetrapod globin evolution.

• This suggests an early divergence of distinct globin types in the vertebrate evolution before the emergence of tetrapods.

Amemiya, C. T. et al. (2013)

Vertebrates adapting to land

• The use of urea as the main nitrogenous waste product was a key innovation in the vertebrate transition from water to land.

• For the rate-limiting enzyme of the hepatic urea cycle, carbamoyl phosphate synthase I (CPS1), only two branchs of the tree shows a strong signature of selection: tetrapods and amniotes.

• This proves that adaptive evolution occurred in the hepatic urea cycle during the vertebrate land transition.

Vertebrates adapting to land

The coelacanth lacks immunoglobulin-M

IgM is a class of antibodies that takes part in adaptive immunity and is present in all vertebrates (so far…)

IgM genes cannot be found in coelacanth!

Instead, two IgW genes were found

How do coelacanth B cells respond to microbial pathogens ?

The IgW molecules can serve a compensatory function?

There is no indication that the coelacanth IgW was derived from vertebrate IgM genes.

Conclusions

• The coelacanth evolves slowly, even though it has all the tools needed for quick genetic changes.

•Living in a stable environment for millions of years may have made the ability to evolve quickly unnecessary, unlike tetrapods who needed to adjust to many changes fast, in order to survive.

• The closest living fish to the tetrapod ancestor is the lungfish, not the coelacanth.

• And yet, the coelacanth is critical to our understanding of this transition, because it is hard to work with the the lungfish’s genome size (estimated at 50–100 Gb).

• 309 recorded individuals

• Conservation

• Further reasearch: immunology, DNA damage control

My Conclusions

So close…

and yet, so far!

©Laurent Ballesta

Thank you!